Text Mining Genotype-Phenotype Relationships from Biomedical Literature for Database Curation and Precision Medicine.

Science.gov (United States)

Singhal, Ayush; Simmons, Michael; Lu, Zhiyong

2016-11-01

The practice of precision medicine will ultimately require databases of genes and mutations for healthcare providers to reference in order to understand the clinical implications of each patient's genetic makeup. Although the highest quality databases require manual curation, text mining tools can facilitate the curation process, increasing accuracy, coverage, and productivity. However, to date there are no available text mining tools that offer high-accuracy performance for extracting such triplets from biomedical literature. In this paper we propose a high-performance machine learning approach to automate the extraction of disease-gene-variant triplets from biomedical literature. Our approach is unique because we identify the genes and protein products associated with each mutation from not just the local text content, but from a global context as well (from the Internet and from all literature in PubMed). Our approach also incorporates protein sequence validation and disease association using a novel text-mining-based machine learning approach. We extract disease-gene-variant triplets from all abstracts in PubMed related to a set of ten important diseases (breast cancer, prostate cancer, pancreatic cancer, lung cancer, acute myeloid leukemia, Alzheimer's disease, hemochromatosis, age-related macular degeneration (AMD), diabetes mellitus, and cystic fibrosis). We then evaluate our approach in two ways: (1) a direct comparison with the state of the art using benchmark datasets; (2) a validation study comparing the results of our approach with entries in a popular human-curated database (UniProt) for each of the previously mentioned diseases. In the benchmark comparison, our full approach achieves a 28% improvement in F1-measure (from 0.62 to 0.79) over the state-of-the-art results. For the validation study with UniProt Knowledgebase (KB), we present a thorough analysis of the results and errors. Across all diseases, our approach returned 272 triplets (disease

Integration of curated databases to identify genotype-phenotype associations

Directory of Open Access Journals (Sweden)

Li Jianrong

2006-10-01

Full Text Available Abstract Background The ability to rapidly characterize an unknown microorganism is critical in both responding to infectious disease and biodefense. To do this, we need some way of anticipating an organism's phenotype based on the molecules encoded by its genome. However, the link between molecular composition (i.e. genotype and phenotype for microbes is not obvious. While there have been several studies that address this challenge, none have yet proposed a large-scale method integrating curated biological information. Here we utilize a systematic approach to discover genotype-phenotype associations that combines phenotypic information from a biomedical informatics database, GIDEON, with the molecular information contained in National Center for Biotechnology Information's Clusters of Orthologous Groups database (NCBI COGs. Results Integrating the information in the two databases, we are able to correlate the presence or absence of a given protein in a microbe with its phenotype as measured by certain morphological characteristics or survival in a particular growth media. With a 0.8 correlation score threshold, 66% of the associations found were confirmed by the literature and at a 0.9 correlation threshold, 86% were positively verified. Conclusion Our results suggest possible phenotypic manifestations for proteins biochemically associated with sugar metabolism and electron transport. Moreover, we believe our approach can be extended to linking pathogenic phenotypes with functionally related proteins.

NSDNA: a manually curated database of experimentally supported ncRNAs associated with nervous system diseases.

Science.gov (United States)

Wang, Jianjian; Cao, Yuze; Zhang, Huixue; Wang, Tianfeng; Tian, Qinghua; Lu, Xiaoyu; Lu, Xiaoyan; Kong, Xiaotong; Liu, Zhaojun; Wang, Ning; Zhang, Shuai; Ma, Heping; Ning, Shangwei; Wang, Lihua

2017-01-04

The Nervous System Disease NcRNAome Atlas (NSDNA) (http://www.bio-bigdata.net/nsdna/) is a manually curated database that provides comprehensive experimentally supported associations about nervous system diseases (NSDs) and noncoding RNAs (ncRNAs). NSDs represent a common group of disorders, some of which are characterized by high morbidity and disabilities. The pathogenesis of NSDs at the molecular level remains poorly understood. ncRNAs are a large family of functionally important RNA molecules. Increasing evidence shows that diverse ncRNAs play a critical role in various NSDs. Mining and summarizing NSD-ncRNA association data can help researchers discover useful information. Hence, we developed an NSDNA database that documents 24 713 associations between 142 NSDs and 8593 ncRNAs in 11 species, curated from more than 1300 articles. This database provides a user-friendly interface for browsing and searching and allows for data downloading flexibility. In addition, NSDNA offers a submission page for researchers to submit novel NSD-ncRNA associations. It represents an extremely useful and valuable resource for researchers who seek to understand the functions and molecular mechanisms of ncRNA involved in NSDs. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Text Mining Genotype-Phenotype Relationships from Biomedical Literature for Database Curation and Precision Medicine.

Directory of Open Access Journals (Sweden)

Ayush Singhal

2016-11-01

Full Text Available The practice of precision medicine will ultimately require databases of genes and mutations for healthcare providers to reference in order to understand the clinical implications of each patient's genetic makeup. Although the highest quality databases require manual curation, text mining tools can facilitate the curation process, increasing accuracy, coverage, and productivity. However, to date there are no available text mining tools that offer high-accuracy performance for extracting such triplets from biomedical literature. In this paper we propose a high-performance machine learning approach to automate the extraction of disease-gene-variant triplets from biomedical literature. Our approach is unique because we identify the genes and protein products associated with each mutation from not just the local text content, but from a global context as well (from the Internet and from all literature in PubMed. Our approach also incorporates protein sequence validation and disease association using a novel text-mining-based machine learning approach. We extract disease-gene-variant triplets from all abstracts in PubMed related to a set of ten important diseases (breast cancer, prostate cancer, pancreatic cancer, lung cancer, acute myeloid leukemia, Alzheimer's disease, hemochromatosis, age-related macular degeneration (AMD, diabetes mellitus, and cystic fibrosis. We then evaluate our approach in two ways: (1 a direct comparison with the state of the art using benchmark datasets; (2 a validation study comparing the results of our approach with entries in a popular human-curated database (UniProt for each of the previously mentioned diseases. In the benchmark comparison, our full approach achieves a 28% improvement in F1-measure (from 0.62 to 0.79 over the state-of-the-art results. For the validation study with UniProt Knowledgebase (KB, we present a thorough analysis of the results and errors. Across all diseases, our approach returned 272 triplets

A curated database of cyanobacterial strains relevant for modern taxonomy and phylogenetic studies.

Science.gov (United States)

Ramos, Vitor; Morais, João; Vasconcelos, Vitor M

2017-04-25

The dataset herein described lays the groundwork for an online database of relevant cyanobacterial strains, named CyanoType (http://lege.ciimar.up.pt/cyanotype). It is a database that includes categorized cyanobacterial strains useful for taxonomic, phylogenetic or genomic purposes, with associated information obtained by means of a literature-based curation. The dataset lists 371 strains and represents the first version of the database (CyanoType v.1). Information for each strain includes strain synonymy and/or co-identity, strain categorization, habitat, accession numbers for molecular data, taxonomy and nomenclature notes according to three different classification schemes, hierarchical automatic classification, phylogenetic placement according to a selection of relevant studies (including this), and important bibliographic references. The database will be updated periodically, namely by adding new strains meeting the criteria for inclusion and by revising and adding up-to-date metadata for strains already listed. A global 16S rDNA-based phylogeny is provided in order to assist users when choosing the appropriate strains for their studies.

Can we replace curation with information extraction software?

Science.gov (United States)

Karp, Peter D

2016-01-01

Can we use programs for automated or semi-automated information extraction from scientific texts as practical alternatives to professional curation? I show that error rates of current information extraction programs are too high to replace professional curation today. Furthermore, current IEP programs extract single narrow slivers of information, such as individual protein interactions; they cannot extract the large breadth of information extracted by professional curators for databases such as EcoCyc. They also cannot arbitrate among conflicting statements in the literature as curators can. Therefore, funding agencies should not hobble the curation efforts of existing databases on the assumption that a problem that has stymied Artificial Intelligence researchers for more than 60 years will be solved tomorrow. Semi-automated extraction techniques appear to have significantly more potential based on a review of recent tools that enhance curator productivity. But a full cost-benefit analysis for these tools is lacking. Without such analysis it is possible to expend significant effort developing information-extraction tools that automate small parts of the overall curation workflow without achieving a significant decrease in curation costs.Database URL. © The Author(s) 2016. Published by Oxford University Press.

Qrator: A web-based curation tool for glycan structures

Science.gov (United States)

Eavenson, Matthew; Kochut, Krys J; Miller, John A; Ranzinger, René; Tiemeyer, Michael; Aoki, Kazuhiro; York, William S

2015-01-01

Most currently available glycan structure databases use their own proprietary structure representation schema and contain numerous annotation errors. These cause problems when glycan databases are used for the annotation or mining of data generated in the laboratory. Due to the complexity of glycan structures, curating these databases is often a tedious and labor-intensive process. However, rigorously validating glycan structures can be made easier with a curation workflow that incorporates a structure-matching algorithm that compares candidate glycans to a canonical tree that embodies structural features consistent with established mechanisms for the biosynthesis of a particular class of glycans. To this end, we have implemented Qrator, a web-based application that uses a combination of external literature and database references, user annotations and canonical trees to assist and guide researchers in making informed decisions while curating glycans. Using this application, we have started the curation of large numbers of N-glycans, O-glycans and glycosphingolipids. Our curation workflow allows creating and extending canonical trees for these classes of glycans, which have subsequently been used to improve the curation workflow. PMID:25165068

MSDD: a manually curated database of experimentally supported associations among miRNAs, SNPs and human diseases

OpenAIRE

Yue, Ming; Zhou, Dianshuang; Zhi, Hui; Wang, Peng; Zhang, Yan; Gao, Yue; Guo, Maoni; Li, Xin; Wang, Yanxia; Zhang, Yunpeng; Ning, Shangwei; Li, Xia

2017-01-01

Abstract The MiRNA SNP Disease Database (MSDD, http://www.bio-bigdata.com/msdd/) is a manually curated database that provides comprehensive experimentally supported associations among microRNAs (miRNAs), single nucleotide polymorphisms (SNPs) and human diseases. SNPs in miRNA-related functional regions such as mature miRNAs, promoter regions, pri-miRNAs, pre-miRNAs and target gene 3′-UTRs, collectively called ‘miRSNPs’, represent a novel category of functional molecules. miRSNPs can lead to m...

Improving the Acquisition and Management of Sample Curation Data

Science.gov (United States)

Todd, Nancy S.; Evans, Cindy A.; Labasse, Dan

2011-01-01

This paper discusses the current sample documentation processes used during and after a mission, examines the challenges and special considerations needed for designing effective sample curation data systems, and looks at the results of a simulated sample result mission and the lessons learned from this simulation. In addition, it introduces a new data architecture for an integrated sample Curation data system being implemented at the NASA Astromaterials Acquisition and Curation department and discusses how it improves on existing data management systems.

Lnc2Cancer: a manually curated database of experimentally supported lncRNAs associated with various human cancers.

Science.gov (United States)

Ning, Shangwei; Zhang, Jizhou; Wang, Peng; Zhi, Hui; Wang, Jianjian; Liu, Yue; Gao, Yue; Guo, Maoni; Yue, Ming; Wang, Lihua; Li, Xia

2016-01-04

Lnc2Cancer (http://www.bio-bigdata.net/lnc2cancer) is a manually curated database of cancer-associated long non-coding RNAs (lncRNAs) with experimental support that aims to provide a high-quality and integrated resource for exploring lncRNA deregulation in various human cancers. LncRNAs represent a large category of functional RNA molecules that play a significant role in human cancers. A curated collection and summary of deregulated lncRNAs in cancer is essential to thoroughly understand the mechanisms and functions of lncRNAs. Here, we developed the Lnc2Cancer database, which contains 1057 manually curated associations between 531 lncRNAs and 86 human cancers. Each association includes lncRNA and cancer name, the lncRNA expression pattern, experimental techniques, a brief functional description, the original reference and additional annotation information. Lnc2Cancer provides a user-friendly interface to conveniently browse, retrieve and download data. Lnc2Cancer also offers a submission page for researchers to submit newly validated lncRNA-cancer associations. With the rapidly increasing interest in lncRNAs, Lnc2Cancer will significantly improve our understanding of lncRNA deregulation in cancer and has the potential to be a timely and valuable resource. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

A curated gluten protein sequence database to support development of proteomics methods for determination of gluten in gluten-free foods.

Science.gov (United States)

Bromilow, Sophie; Gethings, Lee A; Buckley, Mike; Bromley, Mike; Shewry, Peter R; Langridge, James I; Clare Mills, E N

2017-06-23

The unique physiochemical properties of wheat gluten enable a diverse range of food products to be manufactured. However, gluten triggers coeliac disease, a condition which is treated using a gluten-free diet. Analytical methods are required to confirm if foods are gluten-free, but current immunoassay-based methods can unreliable and proteomic methods offer an alternative but require comprehensive and well annotated sequence databases which are lacking for gluten. A manually a curated database (GluPro V1.0) of gluten proteins, comprising 630 discrete unique full length protein sequences has been compiled. It is representative of the different types of gliadin and glutenin components found in gluten. An in silico comparison of their coeliac toxicity was undertaken by analysing the distribution of coeliac toxic motifs. This demonstrated that whilst the α-gliadin proteins contained more toxic motifs, these were distributed across all gluten protein sub-types. Comparison of annotations observed using a discovery proteomics dataset acquired using ion mobility MS/MS showed that more reliable identifications were obtained using the GluPro V1.0 database compared to the complete reviewed Viridiplantae database. This highlights the value of a curated sequence database specifically designed to support the proteomic workflows and the development of methods to detect and quantify gluten. We have constructed the first manually curated open-source wheat gluten protein sequence database (GluPro V1.0) in a FASTA format to support the application of proteomic methods for gluten protein detection and quantification. We have also analysed the manually verified sequences to give the first comprehensive overview of the distribution of sequences able to elicit a reaction in coeliac disease, the prevalent form of gluten intolerance. Provision of this database will improve the reliability of gluten protein identification by proteomic analysis, and aid the development of targeted mass

Using random forests for assistance in the curation of G-protein coupled receptor databases.

Science.gov (United States)

Shkurin, Aleksei; Vellido, Alfredo

2017-08-18

Biology is experiencing a gradual but fast transformation from a laboratory-centred science towards a data-centred one. As such, it requires robust data engineering and the use of quantitative data analysis methods as part of database curation. This paper focuses on G protein-coupled receptors, a large and heterogeneous super-family of cell membrane proteins of interest to biology in general. One of its families, Class C, is of particular interest to pharmacology and drug design. This family is quite heterogeneous on its own, and the discrimination of its several sub-families is a challenging problem. In the absence of known crystal structure, such discrimination must rely on their primary amino acid sequences. We are interested not as much in achieving maximum sub-family discrimination accuracy using quantitative methods, but in exploring sequence misclassification behavior. Specifically, we are interested in isolating those sequences showing consistent misclassification, that is, sequences that are very often misclassified and almost always to the same wrong sub-family. Random forests are used for this analysis due to their ensemble nature, which makes them naturally suited to gauge the consistency of misclassification. This consistency is here defined through the voting scheme of their base tree classifiers. Detailed consistency results for the random forest ensemble classification were obtained for all receptors and for all data transformations of their unaligned primary sequences. Shortlists of the most consistently misclassified receptors for each subfamily and transformation, as well as an overall shortlist including those cases that were consistently misclassified across transformations, were obtained. The latter should be referred to experts for further investigation as a data curation task. The automatic discrimination of the Class C sub-families of G protein-coupled receptors from their unaligned primary sequences shows clear limits. This study has

Text mining effectively scores and ranks the literature for improving chemical-gene-disease curation at the comparative toxicogenomics database.

Directory of Open Access Journals (Sweden)

Allan Peter Davis

Full Text Available The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/ is a public resource that curates interactions between environmental chemicals and gene products, and their relationships to diseases, as a means of understanding the effects of environmental chemicals on human health. CTD provides a triad of core information in the form of chemical-gene, chemical-disease, and gene-disease interactions that are manually curated from scientific articles. To increase the efficiency, productivity, and data coverage of manual curation, we have leveraged text mining to help rank and prioritize the triaged literature. Here, we describe our text-mining process that computes and assigns each article a document relevancy score (DRS, wherein a high DRS suggests that an article is more likely to be relevant for curation at CTD. We evaluated our process by first text mining a corpus of 14,904 articles triaged for seven heavy metals (cadmium, cobalt, copper, lead, manganese, mercury, and nickel. Based upon initial analysis, a representative subset corpus of 3,583 articles was then selected from the 14,094 articles and sent to five CTD biocurators for review. The resulting curation of these 3,583 articles was analyzed for a variety of parameters, including article relevancy, novel data content, interaction yield rate, mean average precision, and biological and toxicological interpretability. We show that for all measured parameters, the DRS is an effective indicator for scoring and improving the ranking of literature for the curation of chemical-gene-disease information at CTD. Here, we demonstrate how fully incorporating text mining-based DRS scoring into our curation pipeline enhances manual curation by prioritizing more relevant articles, thereby increasing data content, productivity, and efficiency.

Text Mining Effectively Scores and Ranks the Literature for Improving Chemical-Gene-Disease Curation at the Comparative Toxicogenomics Database

Science.gov (United States)

Johnson, Robin J.; Lay, Jean M.; Lennon-Hopkins, Kelley; Saraceni-Richards, Cynthia; Sciaky, Daniela; Murphy, Cynthia Grondin; Mattingly, Carolyn J.

2013-01-01

The Comparative Toxicogenomics Database (CTD; http://ctdbase.org/) is a public resource that curates interactions between environmental chemicals and gene products, and their relationships to diseases, as a means of understanding the effects of environmental chemicals on human health. CTD provides a triad of core information in the form of chemical-gene, chemical-disease, and gene-disease interactions that are manually curated from scientific articles. To increase the efficiency, productivity, and data coverage of manual curation, we have leveraged text mining to help rank and prioritize the triaged literature. Here, we describe our text-mining process that computes and assigns each article a document relevancy score (DRS), wherein a high DRS suggests that an article is more likely to be relevant for curation at CTD. We evaluated our process by first text mining a corpus of 14,904 articles triaged for seven heavy metals (cadmium, cobalt, copper, lead, manganese, mercury, and nickel). Based upon initial analysis, a representative subset corpus of 3,583 articles was then selected from the 14,094 articles and sent to five CTD biocurators for review. The resulting curation of these 3,583 articles was analyzed for a variety of parameters, including article relevancy, novel data content, interaction yield rate, mean average precision, and biological and toxicological interpretability. We show that for all measured parameters, the DRS is an effective indicator for scoring and improving the ranking of literature for the curation of chemical-gene-disease information at CTD. Here, we demonstrate how fully incorporating text mining-based DRS scoring into our curation pipeline enhances manual curation by prioritizing more relevant articles, thereby increasing data content, productivity, and efficiency. PMID:23613709

The Neotoma Paleoecology Database: An International Community-Curated Resource for Paleoecological and Paleoenvironmental Data

Science.gov (United States)

Williams, J. W.; Grimm, E. C.; Ashworth, A. C.; Blois, J.; Charles, D. F.; Crawford, S.; Davis, E.; Goring, S. J.; Graham, R. W.; Miller, D. A.; Smith, A. J.; Stryker, M.; Uhen, M. D.

2017-12-01

The Neotoma Paleoecology Database supports global change research at the intersection of geology and ecology by providing a high-quality, community-curated data repository for paleoecological data. These data are widely used to study biological responses and feedbacks to past environmental change at local to global scales. The Neotoma data model is flexible and can store multiple kinds of fossil, biogeochemical, or physical variables measured from sedimentary archives. Data additions to Neotoma are growing and include >3.5 million observations, >16,000 datasets, and >8,500 sites. Dataset types include fossil pollen, vertebrates, diatoms, ostracodes, macroinvertebrates, plant macrofossils, insects, testate amoebae, geochronological data, and the recently added organic biomarkers, stable isotopes, and specimen-level data. Neotoma data can be found and retrieved in multiple ways, including the Explorer map-based interface, a RESTful Application Programming Interface, the neotoma R package, and digital object identifiers. Neotoma has partnered with the Paleobiology Database to produce a common data portal for paleobiological data, called the Earth Life Consortium. A new embargo management is designed to allow investigators to put their data into Neotoma and then make use of Neotoma's value-added services. Neotoma's distributed scientific governance model is flexible and scalable, with many open pathways for welcoming new members, data contributors, stewards, and research communities. As the volume and variety of scientific data grow, community-curated data resources such as Neotoma have become foundational infrastructure for big data science.

Designing a database for performance assessment: Lessons learned from WIPP

International Nuclear Information System (INIS)

Martell, M.A.; Schenker, A.

1997-01-01

The Waste Isolation Pilot Plant (WIPP) Compliance Certification Application (CCA) Performance Assessment (PA) used a relational database that was originally designed only to supply the input parameters required for implementation of the PA codes. Reviewers used the database as a point of entry to audit quality assurance measures for control, traceability, and retrievability of input information used for analysis, and output/work products. During these audits it became apparent that modifications to the architecture and scope of the database would benefit the EPA regulator and other stakeholders when reviewing the recertification application. This paper contains a discussion of the WPP PA CCA database and lessons learned for designing a database

CORE: a phylogenetically-curated 16S rDNA database of the core oral microbiome.

Directory of Open Access Journals (Sweden)

Ann L Griffen

2011-04-01

Full Text Available Comparing bacterial 16S rDNA sequences to GenBank and other large public databases via BLAST often provides results of little use for identification and taxonomic assignment of the organisms of interest. The human microbiome, and in particular the oral microbiome, includes many taxa, and accurate identification of sequence data is essential for studies of these communities. For this purpose, a phylogenetically curated 16S rDNA database of the core oral microbiome, CORE, was developed. The goal was to include a comprehensive and minimally redundant representation of the bacteria that regularly reside in the human oral cavity with computationally robust classification at the level of species and genus. Clades of cultivated and uncultivated taxa were formed based on sequence analyses using multiple criteria, including maximum-likelihood-based topology and bootstrap support, genetic distance, and previous naming. A number of classification inconsistencies for previously named species, especially at the level of genus, were resolved. The performance of the CORE database for identifying clinical sequences was compared to that of three publicly available databases, GenBank nr/nt, RDP and HOMD, using a set of sequencing reads that had not been used in creation of the database. CORE offered improved performance compared to other public databases for identification of human oral bacterial 16S sequences by a number of criteria. In addition, the CORE database and phylogenetic tree provide a framework for measures of community divergence, and the focused size of the database offers advantages of efficiency for BLAST searching of large datasets. The CORE database is available as a searchable interface and for download at http://microbiome.osu.edu.

Improving the Discoverability and Availability of Sample Data and Imagery in NASA's Astromaterials Curation Digital Repository Using a New Common Architecture for Sample Databases

Science.gov (United States)

Todd, N. S.; Evans, C.

2015-01-01

The Astromaterials Acquisition and Curation Office at NASA's Johnson Space Center (JSC) is the designated facility for curating all of NASA's extraterrestrial samples. The suite of collections includes the lunar samples from the Apollo missions, cosmic dust particles falling into the Earth's atmosphere, meteorites collected in Antarctica, comet and interstellar dust particles from the Stardust mission, asteroid particles from the Japanese Hayabusa mission, and solar wind atoms collected during the Genesis mission. To support planetary science research on these samples, NASA's Astromaterials Curation Office hosts the Astromaterials Curation Digital Repository, which provides descriptions of the missions and collections, and critical information about each individual sample. Our office is implementing several informatics initiatives with the goal of better serving the planetary research community. One of these initiatives aims to increase the availability and discoverability of sample data and images through the use of a newly designed common architecture for Astromaterials Curation databases.

Lessons Learned From Developing Reactor Pressure Vessel Steel Embrittlement Database

Energy Technology Data Exchange (ETDEWEB)

Wang, Jy-An John [ORNL

2010-08-01

Materials behaviors caused by neutron irradiation under fission and/or fusion environments can be little understood without practical examination. Easily accessible material information system with large material database using effective computers is necessary for design of nuclear materials and analyses or simulations of the phenomena. The developed Embrittlement Data Base (EDB) at ORNL is this comprehensive collection of data. EDB database contains power reactor pressure vessel surveillance data, the material test reactor data, foreign reactor data (through bilateral agreements authorized by NRC), and the fracture toughness data. The lessons learned from building EDB program and the associated database management activity regarding Material Database Design Methodology, Architecture and the Embedded QA Protocol are described in this report. The development of IAEA International Database on Reactor Pressure Vessel Materials (IDRPVM) and the comparison of EDB database and IAEA IDRPVM database are provided in the report. The recommended database QA protocol and database infrastructure are also stated in the report.

The curation of genetic variants: difficulties and possible solutions.

Science.gov (United States)

Pandey, Kapil Raj; Maden, Narendra; Poudel, Barsha; Pradhananga, Sailendra; Sharma, Amit Kumar

2012-12-01

The curation of genetic variants from biomedical articles is required for various clinical and research purposes. Nowadays, establishment of variant databases that include overall information about variants is becoming quite popular. These databases have immense utility, serving as a user-friendly information storehouse of variants for information seekers. While manual curation is the gold standard method for curation of variants, it can turn out to be time-consuming on a large scale thus necessitating the need for automation. Curation of variants described in biomedical literature may not be straightforward mainly due to various nomenclature and expression issues. Though current trends in paper writing on variants is inclined to the standard nomenclature such that variants can easily be retrieved, we have a massive store of variants in the literature that are present as non-standard names and the online search engines that are predominantly used may not be capable of finding them. For effective curation of variants, knowledge about the overall process of curation, nature and types of difficulties in curation, and ways to tackle the difficulties during the task are crucial. Only by effective curation, can variants be correctly interpreted. This paper presents the process and difficulties of curation of genetic variants with possible solutions and suggestions from our work experience in the field including literature support. The paper also highlights aspects of interpretation of genetic variants and the importance of writing papers on variants following standard and retrievable methods. Copyright © 2012. Published by Elsevier Ltd.

MSDD: a manually curated database of experimentally supported associations among miRNAs, SNPs and human diseases.

Science.gov (United States)

Yue, Ming; Zhou, Dianshuang; Zhi, Hui; Wang, Peng; Zhang, Yan; Gao, Yue; Guo, Maoni; Li, Xin; Wang, Yanxia; Zhang, Yunpeng; Ning, Shangwei; Li, Xia

2018-01-04

The MiRNA SNP Disease Database (MSDD, http://www.bio-bigdata.com/msdd/) is a manually curated database that provides comprehensive experimentally supported associations among microRNAs (miRNAs), single nucleotide polymorphisms (SNPs) and human diseases. SNPs in miRNA-related functional regions such as mature miRNAs, promoter regions, pri-miRNAs, pre-miRNAs and target gene 3'-UTRs, collectively called 'miRSNPs', represent a novel category of functional molecules. miRSNPs can lead to miRNA and its target gene dysregulation, and resulting in susceptibility to or onset of human diseases. A curated collection and summary of miRSNP-associated diseases is essential for a thorough understanding of the mechanisms and functions of miRSNPs. Here, we describe MSDD, which currently documents 525 associations among 182 human miRNAs, 197 SNPs, 153 genes and 164 human diseases through a review of more than 2000 published papers. Each association incorporates information on the miRNAs, SNPs, miRNA target genes and disease names, SNP locations and alleles, the miRNA dysfunctional pattern, experimental techniques, a brief functional description, the original reference and additional annotation. MSDD provides a user-friendly interface to conveniently browse, retrieve, download and submit novel data. MSDD will significantly improve our understanding of miRNA dysfunction in disease, and thus, MSDD has the potential to serve as a timely and valuable resource. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Learning lessons from Natech accidents - the eNATECH accident database

Science.gov (United States)

Krausmann, Elisabeth; Girgin, Serkan

2016-04-01

When natural hazards impact industrial facilities that house or process hazardous materials, fires, explosions and toxic releases can occur. This type of accident is commonly referred to as Natech accident. In order to prevent the recurrence of accidents or to better mitigate their consequences, lessons-learned type studies using available accident data are usually carried out. Through post-accident analysis, conclusions can be drawn on the most common damage and failure modes and hazmat release paths, particularly vulnerable storage and process equipment, and the hazardous materials most commonly involved in these types of accidents. These analyses also lend themselves to identifying technical and organisational risk-reduction measures that require improvement or are missing. Industrial accident databases are commonly used for retrieving sets of Natech accident case histories for further analysis. These databases contain accident data from the open literature, government authorities or in-company sources. The quality of reported information is not uniform and exhibits different levels of detail and accuracy. This is due to the difficulty of finding qualified information sources, especially in situations where accident reporting by the industry or by authorities is not compulsory, e.g. when spill quantities are below the reporting threshold. Data collection has then to rely on voluntary record keeping often by non-experts. The level of detail is particularly non-uniform for Natech accident data depending on whether the consequences of the Natech event were major or minor, and whether comprehensive information was available for reporting. In addition to the reporting bias towards high-consequence events, industrial accident databases frequently lack information on the severity of the triggering natural hazard, as well as on failure modes that led to the hazmat release. This makes it difficult to reconstruct the dynamics of the accident and renders the development of

submitter BioSharing: curated and crowd-sourced metadata standards, databases and data policies in the life sciences

CERN Document Server

McQuilton, Peter; Rocca-Serra, Philippe; Thurston, Milo; Lister, Allyson; Maguire, Eamonn; Sansone, Susanna-Assunta

2016-01-01

BioSharing (http://www.biosharing.org) is a manually curated, searchable portal of three linked registries. These resources cover standards (terminologies, formats and models, and reporting guidelines), databases, and data policies in the life sciences, broadly encompassing the biological, environmental and biomedical sciences. Launched in 2011 and built by the same core team as the successful MIBBI portal, BioSharing harnesses community curation to collate and cross-reference resources across the life sciences from around the world. BioSharing makes these resources findable and accessible (the core of the FAIR principle). Every record is designed to be interlinked, providing a detailed description not only on the resource itself, but also on its relations with other life science infrastructures. Serving a variety of stakeholders, BioSharing cultivates a growing community, to which it offers diverse benefits. It is a resource for funding bodies and journal publishers to navigate the metadata landscape of the ...

CPAD, Curated Protein Aggregation Database: A Repository of Manually Curated Experimental Data on Protein and Peptide Aggregation.

Science.gov (United States)

Thangakani, A Mary; Nagarajan, R; Kumar, Sandeep; Sakthivel, R; Velmurugan, D; Gromiha, M Michael

2016-01-01

Accurate distinction between peptide sequences that can form amyloid-fibrils or amorphous β-aggregates, identification of potential aggregation prone regions in proteins, and prediction of change in aggregation rate of a protein upon mutation(s) are critical to research on protein misfolding diseases, such as Alzheimer's and Parkinson's, as well as biotechnological production of protein based therapeutics. We have developed a Curated Protein Aggregation Database (CPAD), which has collected results from experimental studies performed by scientific community aimed at understanding protein/peptide aggregation. CPAD contains more than 2300 experimentally observed aggregation rates upon mutations in known amyloidogenic proteins. Each entry includes numerical values for the following parameters: change in rate of aggregation as measured by fluorescence intensity or turbidity, name and source of the protein, Uniprot and Protein Data Bank codes, single point as well as multiple mutations, and literature citation. The data in CPAD has been supplemented with five different types of additional information: (i) Amyloid fibril forming hexa-peptides, (ii) Amorphous β-aggregating hexa-peptides, (iii) Amyloid fibril forming peptides of different lengths, (iv) Amyloid fibril forming hexa-peptides whose crystal structures are available in the Protein Data Bank (PDB) and (v) Experimentally validated aggregation prone regions found in amyloidogenic proteins. Furthermore, CPAD is linked to other related databases and resources, such as Uniprot, Protein Data Bank, PUBMED, GAP, TANGO, WALTZ etc. We have set up a web interface with different search and display options so that users have the ability to get the data in multiple ways. CPAD is freely available at http://www.iitm.ac.in/bioinfo/CPAD/. The potential applications of CPAD have also been discussed.

EVLncRNAs: a manually curated database for long non-coding RNAs validated by low-throughput experiments

Science.gov (United States)

Zhao, Huiying; Yu, Jiafeng; Guo, Chengang; Dou, Xianghua; Song, Feng; Hu, Guodong; Cao, Zanxia; Qu, Yuanxu

2018-01-01

Abstract Long non-coding RNAs (lncRNAs) play important functional roles in various biological processes. Early databases were utilized to deposit all lncRNA candidates produced by high-throughput experimental and/or computational techniques to facilitate classification, assessment and validation. As more lncRNAs are validated by low-throughput experiments, several databases were established for experimentally validated lncRNAs. However, these databases are small in scale (with a few hundreds of lncRNAs only) and specific in their focuses (plants, diseases or interactions). Thus, it is highly desirable to have a comprehensive dataset for experimentally validated lncRNAs as a central repository for all of their structures, functions and phenotypes. Here, we established EVLncRNAs by curating lncRNAs validated by low-throughput experiments (up to 1 May 2016) and integrating specific databases (lncRNAdb, LncRANDisease, Lnc2Cancer and PLNIncRBase) with additional functional and disease-specific information not covered previously. The current version of EVLncRNAs contains 1543 lncRNAs from 77 species that is 2.9 times larger than the current largest database for experimentally validated lncRNAs. Seventy-four percent lncRNA entries are partially or completely new, comparing to all existing experimentally validated databases. The established database allows users to browse, search and download as well as to submit experimentally validated lncRNAs. The database is available at http://biophy.dzu.edu.cn/EVLncRNAs. PMID:28985416

Curation of complex, context-dependent immunological data

Directory of Open Access Journals (Sweden)

Sidney John

2006-07-01

Full Text Available Abstract Background The Immune Epitope Database and Analysis Resource (IEDB is dedicated to capturing, housing and analyzing complex immune epitope related data http://www.immuneepitope.org. Description To identify and extract relevant data from the scientific literature in an efficient and accurate manner, novel processes were developed for manual and semi-automated annotation. Conclusion Formalized curation strategies enable the processing of a large volume of context-dependent data, which are now available to the scientific community in an accessible and transparent format. The experiences described herein are applicable to other databases housing complex biological data and requiring a high level of curation expertise.

EMU Lessons Learned Database

Science.gov (United States)

Matthews, Kevin M., Jr.; Crocker, Lori; Cupples, J. Scott

2011-01-01

As manned space exploration takes on the task of traveling beyond low Earth orbit, many problems arise that must be solved in order to make the journey possible. One major task is protecting humans from the harsh space environment. The current method of protecting astronauts during Extravehicular Activity (EVA) is through use of the specially designed Extravehicular Mobility Unit (EMU). As more rigorous EVA conditions need to be endured at new destinations, the suit will need to be tailored and improved in order to accommodate the astronaut. The Objective behind the EMU Lessons Learned Database(LLD) is to be able to create a tool which will assist in the development of next-generation EMUs, along with maintenance and improvement of the current EMU, by compiling data from Failure Investigation and Analysis Reports (FIARs) which have information on past suit failures. FIARs use a system of codes that give more information on the aspects of the failure, but if one is unfamiliar with the EMU they will be unable to decipher the information. A goal of the EMU LLD is to not only compile the information, but to present it in a user-friendly, organized, searchable database accessible to all familiarity levels with the EMU; both newcomers and veterans alike. The EMU LLD originally started as an Excel database, which allowed easy navigation and analysis of the data through pivot charts. Creating an entry requires access to the Problem Reporting And Corrective Action database (PRACA), which contains the original FIAR data for all hardware. FIAR data are then transferred to, defined, and formatted in the LLD. Work is being done to create a web-based version of the LLD in order to increase accessibility to all of Johnson Space Center (JSC), which includes converting entries from Excel to the HTML format. FIARs related to the EMU have been completed in the Excel version, and now focus has shifted to expanding FIAR data in the LLD to include EVA tools and support hardware such as

Integration of data: the Nanomaterial Registry project and data curation

International Nuclear Information System (INIS)

Guzan, K A; Mills, K C; Gupta, V; Murry, D; Ostraat, M L; Scheier, C N; Willis, D A

2013-01-01

Due to the use of nanomaterials in multiple fields of applied science and technology, there is a need for accelerated understanding of any potential implications of using these unique and promising materials. There is a multitude of research data that, if integrated, can be leveraged to drive toward a better understanding. Integration can be achieved by applying nanoinformatics concepts. The Nanomaterial Registry is using applied minimal information about nanomaterials to support a robust data curation process in order to promote integration across a diverse data set. This paper describes the evolution of the curation methodology used in the Nanomaterial Registry project as well as the current procedure that is used. Some of the lessons learned about curation of nanomaterial data are also discussed. (paper)

The art of curation at a biological database: Principles and application

Directory of Open Access Journals (Sweden)

Sarah G. Odell

2017-09-01

Full Text Available The variety and quantity of data being produced by biological research has grown dramatically in recent years, resulting in an expansion of our understanding of biological systems. However, this abundance of data has brought new challenges, especially in curation. The role of biocurators is in part to filter research outcomes as they are generated, not only so that information is formatted and consolidated into locations that can provide long-term data sustainability, but also to ensure that the relevant data that was captured is reliable, reusable, and accessible. In many ways, biocuration lies somewhere between an art and a science. At GrainGenes (https://wheat.pw.usda.gov;https://graingenes.org, a long-time, stably-funded centralized repository for data about wheat, barley, rye, oat, and other small grains, curators have implemented a workflow for locating, parsing, and uploading new data so that the most important, peer-reviewed, high-quality research is available to users as quickly as possible with rich links to past research outcomes. In this report, we illustrate the principles and practical considerations of curation that we follow at GrainGenes with three case studies for curating a gene, a quantitative trait locus (QTL, and genomic elements. These examples demonstrate how our work allows users, i.e., small grains geneticists and breeders, to harness high-quality small grains data at GrainGenes to help them develop plants with enhanced agronomic traits.

Text Mining to Support Gene Ontology Curation and Vice Versa.

Science.gov (United States)

Ruch, Patrick

2017-01-01

In this chapter, we explain how text mining can support the curation of molecular biology databases dealing with protein functions. We also show how curated data can play a disruptive role in the developments of text mining methods. We review a decade of efforts to improve the automatic assignment of Gene Ontology (GO) descriptors, the reference ontology for the characterization of genes and gene products. To illustrate the high potential of this approach, we compare the performances of an automatic text categorizer and show a large improvement of +225 % in both precision and recall on benchmarked data. We argue that automatic text categorization functions can ultimately be embedded into a Question-Answering (QA) system to answer questions related to protein functions. Because GO descriptors can be relatively long and specific, traditional QA systems cannot answer such questions. A new type of QA system, so-called Deep QA which uses machine learning methods trained with curated contents, is thus emerging. Finally, future advances of text mining instruments are directly dependent on the availability of high-quality annotated contents at every curation step. Databases workflows must start recording explicitly all the data they curate and ideally also some of the data they do not curate.

Meeting Curation Challenges in a Neuroimaging Group

Directory of Open Access Journals (Sweden)

Angus Whyte

2008-08-01

Full Text Available The SCARP project is a series of short studies with two aims; firstly to discover more about disciplinary approaches and attitudes to digital curation through ‘immersion’ in selected cases; secondly to apply known good practice, and where possible, identify new lessons from practice in the selected discipline areas. The study summarised here is of the Neuroimaging Group in the University of Edinburgh’s Division of Psychiatry, which plays a leading role in eScience collaborations to improve the infrastructure for neuroimaging data integration and reuse. The Group also aims to address growing data storage and curation needs, given the capabilities afforded by new infrastructure. The study briefly reviews the policy context and current challenges to data integration and sharing in the neuroimaging field. It then describes how curation and preservation risks and opportunities for change were identified throughout the curation lifecycle; and their context appreciated through field study in the research site. The results are consistent with studies of neuroimaging eInfrastructure that emphasise the role of local data sharing and reuse practices. These sustain mutual awareness of datasets and experimental protocols through sharing peer to peer, and among senior researchers and students, enabling continuity in research and flexibility in project work. This “human infrastructure” is taken into account in considering next steps for curation and preservation of the Group’s datasets and a phased approach to supporting data documentation.

Directly e-mailing authors of newly published papers encourages community curation

Science.gov (United States)

Bunt, Stephanie M.; Grumbling, Gary B.; Field, Helen I.; Marygold, Steven J.; Brown, Nicholas H.; Millburn, Gillian H.

2012-01-01

Much of the data within Model Organism Databases (MODs) comes from manual curation of the primary research literature. Given limited funding and an increasing density of published material, a significant challenge facing all MODs is how to efficiently and effectively prioritize the most relevant research papers for detailed curation. Here, we report recent improvements to the triaging process used by FlyBase. We describe an automated method to directly e-mail corresponding authors of new papers, requesting that they list the genes studied and indicate (‘flag’) the types of data described in the paper using an online tool. Based on the author-assigned flags, papers are then prioritized for detailed curation and channelled to appropriate curator teams for full data extraction. The overall response rate has been 44% and the flagging of data types by authors is sufficiently accurate for effective prioritization of papers. In summary, we have established a sustainable community curation program, with the result that FlyBase curators now spend less time triaging and can devote more effort to the specialized task of detailed data extraction. Database URL: http://flybase.org/ PMID:22554788

Database Description - Arabidopsis Phenome Database | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available List Contact us Arabidopsis Phenome Database Database Description General information of database Database n... BioResource Center Hiroshi Masuya Database classification Plant databases - Arabidopsis thaliana Organism T...axonomy Name: Arabidopsis thaliana Taxonomy ID: 3702 Database description The Arabidopsis thaliana phenome i...heir effective application. We developed the new Arabidopsis Phenome Database integrating two novel database...seful materials for their experimental research. The other, the “Database of Curated Plant Phenome” focusing

AtlasT4SS: a curated database for type IV secretion systems.

Science.gov (United States)

Souza, Rangel C; del Rosario Quispe Saji, Guadalupe; Costa, Maiana O C; Netto, Diogo S; Lima, Nicholas C B; Klein, Cecília C; Vasconcelos, Ana Tereza R; Nicolás, Marisa F

2012-08-09

The type IV secretion system (T4SS) can be classified as a large family of macromolecule transporter systems, divided into three recognized sub-families, according to the well-known functions. The major sub-family is the conjugation system, which allows transfer of genetic material, such as a nucleoprotein, via cell contact among bacteria. Also, the conjugation system can transfer genetic material from bacteria to eukaryotic cells; such is the case with the T-DNA transfer of Agrobacterium tumefaciens to host plant cells. The system of effector protein transport constitutes the second sub-family, and the third one corresponds to the DNA uptake/release system. Genome analyses have revealed numerous T4SS in Bacteria and Archaea. The purpose of this work was to organize, classify, and integrate the T4SS data into a single database, called AtlasT4SS - the first public database devoted exclusively to this prokaryotic secretion system. The AtlasT4SS is a manual curated database that describes a large number of proteins related to the type IV secretion system reported so far in Gram-negative and Gram-positive bacteria, as well as in Archaea. The database was created using the RDBMS MySQL and the Catalyst Framework based in the Perl programming language and using the Model-View-Controller (MVC) design pattern for Web. The current version holds a comprehensive collection of 1,617 T4SS proteins from 58 Bacteria (49 Gram-negative and 9 Gram-Positive), one Archaea and 11 plasmids. By applying the bi-directional best hit (BBH) relationship in pairwise genome comparison, it was possible to obtain a core set of 134 clusters of orthologous genes encoding T4SS proteins. In our database we present one way of classifying orthologous groups of T4SSs in a hierarchical classification scheme with three levels. The first level comprises four classes that are based on the organization of genetic determinants, shared homologies, and evolutionary relationships: (i) F-T4SS, (ii) P-T4SS, (iii

Geroprotectors.org: a new, structured and curated database of current therapeutic interventions in aging and age-related disease

Science.gov (United States)

Moskalev, Alexey; Chernyagina, Elizaveta; de Magalhães, João Pedro; Barardo, Diogo; Thoppil, Harikrishnan; Shaposhnikov, Mikhail; Budovsky, Arie; Fraifeld, Vadim E.; Garazha, Andrew; Tsvetkov, Vasily; Bronovitsky, Evgeny; Bogomolov, Vladislav; Scerbacov, Alexei; Kuryan, Oleg; Gurinovich, Roman; Jellen, Leslie C.; Kennedy, Brian; Mamoshina, Polina; Dobrovolskaya, Evgeniya; Aliper, Alex; Kaminsky, Dmitry; Zhavoronkov, Alex

2015-01-01

As the level of interest in aging research increases, there is a growing number of geroprotectors, or therapeutic interventions that aim to extend the healthy lifespan and repair or reduce aging-related damage in model organisms and, eventually, in humans. There is a clear need for a manually-curated database of geroprotectors to compile and index their effects on aging and age-related diseases and link these effects to relevant studies and multiple biochemical and drug databases. Here, we introduce the first such resource, Geroprotectors (http://geroprotectors.org). Geroprotectors is a public, rapidly explorable database that catalogs over 250 experiments involving over 200 known or candidate geroprotectors that extend lifespan in model organisms. Each compound has a comprehensive profile complete with biochemistry, mechanisms, and lifespan effects in various model organisms, along with information ranging from chemical structure, side effects, and toxicity to FDA drug status. These are presented in a visually intuitive, efficient framework fit for casual browsing or in-depth research alike. Data are linked to the source studies or databases, providing quick and convenient access to original data. The Geroprotectors database facilitates cross-study, cross-organism, and cross-discipline analysis and saves countless hours of inefficient literature and web searching. Geroprotectors is a one-stop, knowledge-sharing, time-saving resource for researchers seeking healthy aging solutions. PMID:26342919

dinoref: A curated dinoflagellate (Dinophyceae) reference database for the 18S rRNA gene.

Science.gov (United States)

Mordret, Solenn; Piredda, Roberta; Vaulot, Daniel; Montresor, Marina; Kooistra, Wiebe H C F; Sarno, Diana

2018-03-30

Dinoflagellates are a heterogeneous group of protists present in all aquatic ecosystems where they occupy various ecological niches. They play a major role as primary producers, but many species are mixotrophic or heterotrophic. Environmental metabarcoding based on high-throughput sequencing is increasingly applied to assess diversity and abundance of planktonic organisms, and reference databases are definitely needed to taxonomically assign the huge number of sequences. We provide an updated 18S rRNA reference database of dinoflagellates: dinoref. Sequences were downloaded from genbank and filtered based on stringent quality criteria. All sequences were taxonomically curated, classified taking into account classical morphotaxonomic studies and molecular phylogenies, and linked to a series of metadata. dinoref includes 1,671 sequences representing 149 genera and 422 species. The taxonomic assignation of 468 sequences was revised. The largest number of sequences belongs to Gonyaulacales and Suessiales that include toxic and symbiotic species. dinoref provides an opportunity to test the level of taxonomic resolution of different 18S barcode markers based on a large number of sequences and species. As an example, when only the V4 region is considered, 374 of the 422 species included in dinoref can still be unambiguously identified. Clustering the V4 sequences at 98% similarity, a threshold that is commonly applied in metabarcoding studies, resulted in a considerable underestimation of species diversity. © 2018 John Wiley & Sons Ltd.

Lessons from an enterprise-wide technical and administrative database using CASE and GUI front-ends

International Nuclear Information System (INIS)

Chan, A.; Crane, G.; MacGregor, I.; Meyer, S.

1995-07-01

An enterprise-wide database built via Oracle*CASE is a hot topic. The authors describe the PEP-II/BABAR Project-Wide Database, and the lessons learned in delivering and developing this system with a small team averaging two and one half people. They also give some details of providing World Wide Web (WWW) access to the information, and using Oracle*CASE and Oracle Forms4. The B Factory at the Stanford Linear Accelerator Center (SLAC) is a project built to study the physics of matter and anti-matter. It consists of two accelerator storage rings (PEP-II) and a detector (BABAR)--a project of approximately $250 million with collaboration by many labs worldwide. Foremost among these lessons is that the support and vision of management are key to the successful design and implementation of an enterprise-wide database. The authors faced the challenge of integrating both administrative and technical data into one CASE enterprise design. The goal, defined at the project's inception in late 1992, was to use a central database as a tool for the collaborating labs to: (1) track quality assurance during construction of the accelerator storage rings and detectors; (2) track down problems faster when they develop; and (3) facilitate the construction process. The focus of the project database, therefore, is on technical data which is less well-defined than administrative data

LncRNAWiki: harnessing community knowledge in collaborative curation of human long non-coding RNAs

KAUST Repository

Ma, L.

2014-11-15

Long non-coding RNAs (lncRNAs) perform a diversity of functions in numerous important biological processes and are implicated in many human diseases. In this report we present lncRNAWiki (http://lncrna.big.ac.cn), a wiki-based platform that is open-content and publicly editable and aimed at community-based curation and collection of information on human lncRNAs. Current related databases are dependent primarily on curation by experts, making it laborious to annotate the exponentially accumulated information on lncRNAs, which inevitably requires collective efforts in community-based curation of lncRNAs. Unlike existing databases, lncRNAWiki features comprehensive integration of information on human lncRNAs obtained from multiple different resources and allows not only existing lncRNAs to be edited, updated and curated by different users but also the addition of newly identified lncRNAs by any user. It harnesses community collective knowledge in collecting, editing and annotating human lncRNAs and rewards community-curated efforts by providing explicit authorship based on quantified contributions. LncRNAWiki relies on the underling knowledge of scientific community for collective and collaborative curation of human lncRNAs and thus has the potential to serve as an up-to-date and comprehensive knowledgebase for human lncRNAs.

miRandola 2017: a curated knowledge base of non-invasive biomarkers

DEFF Research Database (Denmark)

Russo, Francesco; Di Bella, Sebastiano; Vannini, Federica

2018-01-01

databases. Data are manually curated from 314 articles that describe miRNAs, long non-coding RNAs and circular RNAs. Fourteen organisms are now included in the database, and associations of ncRNAs with 25 drugs, 47 sample types and 197 diseases. miRandola also classifies extracellular RNAs based...

PFR²: a curated database of planktonic foraminifera 18S ribosomal DNA as a resource for studies of plankton ecology, biogeography and evolution.

Science.gov (United States)

Morard, Raphaël; Darling, Kate F; Mahé, Frédéric; Audic, Stéphane; Ujiié, Yurika; Weiner, Agnes K M; André, Aurore; Seears, Heidi A; Wade, Christopher M; Quillévéré, Frédéric; Douady, Christophe J; Escarguel, Gilles; de Garidel-Thoron, Thibault; Siccha, Michael; Kucera, Michal; de Vargas, Colomban

2015-11-01

Planktonic foraminifera (Rhizaria) are ubiquitous marine pelagic protists producing calcareous shells with conspicuous morphology. They play an important role in the marine carbon cycle, and their exceptional fossil record serves as the basis for biochronostratigraphy and past climate reconstructions. A major worldwide sampling effort over the last two decades has resulted in the establishment of multiple large collections of cryopreserved individual planktonic foraminifera samples. Thousands of 18S rDNA partial sequences have been generated, representing all major known morphological taxa across their worldwide oceanic range. This comprehensive data coverage provides an opportunity to assess patterns of molecular ecology and evolution in a holistic way for an entire group of planktonic protists. We combined all available published and unpublished genetic data to build PFR(2), the Planktonic foraminifera Ribosomal Reference database. The first version of the database includes 3322 reference 18S rDNA sequences belonging to 32 of the 47 known morphospecies of extant planktonic foraminifera, collected from 460 oceanic stations. All sequences have been rigorously taxonomically curated using a six-rank annotation system fully resolved to the morphological species level and linked to a series of metadata. The PFR(2) website, available at http://pfr2.sb-roscoff.fr, allows downloading the entire database or specific sections, as well as the identification of new planktonic foraminiferal sequences. Its novel, fully documented curation process integrates advances in morphological and molecular taxonomy. It allows for an increase in its taxonomic resolution and assures that integrity is maintained by including a complete contingency tracking of annotations and assuring that the annotations remain internally consistent. © 2015 John Wiley & Sons Ltd.

The Developmental Brain Disorders Database (DBDB): a curated neurogenetics knowledge base with clinical and research applications.

Science.gov (United States)

Mirzaa, Ghayda M; Millen, Kathleen J; Barkovich, A James; Dobyns, William B; Paciorkowski, Alex R

2014-06-01

The number of single genes associated with neurodevelopmental disorders has increased dramatically over the past decade. The identification of causative genes for these disorders is important to clinical outcome as it allows for accurate assessment of prognosis, genetic counseling, delineation of natural history, inclusion in clinical trials, and in some cases determines therapy. Clinicians face the challenge of correctly identifying neurodevelopmental phenotypes, recognizing syndromes, and prioritizing the best candidate genes for testing. However, there is no central repository of definitions for many phenotypes, leading to errors of diagnosis. Additionally, there is no system of levels of evidence linking genes to phenotypes, making it difficult for clinicians to know which genes are most strongly associated with a given condition. We have developed the Developmental Brain Disorders Database (DBDB: https://www.dbdb.urmc.rochester.edu/home), a publicly available, online-curated repository of genes, phenotypes, and syndromes associated with neurodevelopmental disorders. DBDB contains the first referenced ontology of developmental brain phenotypes, and uses a novel system of levels of evidence for gene-phenotype associations. It is intended to assist clinicians in arriving at the correct diagnosis, select the most appropriate genetic test for that phenotype, and improve the care of patients with developmental brain disorders. For researchers interested in the discovery of novel genes for developmental brain disorders, DBDB provides a well-curated source of important genes against which research sequencing results can be compared. Finally, DBDB allows novel observations about the landscape of the neurogenetics knowledge base. © 2014 Wiley Periodicals, Inc.

Curating NASA's Past, Present, and Future Astromaterial Sample Collections

Science.gov (United States)

Zeigler, R. A.; Allton, J. H.; Evans, C. A.; Fries, M. D.; McCubbin, F. M.; Nakamura-Messenger, K.; Righter, K.; Zolensky, M.; Stansbery, E. K.

2016-01-01

The Astromaterials Acquisition and Curation Office at NASA Johnson Space Center (hereafter JSC curation) is responsible for curating all of NASA's extraterrestrial samples. JSC presently curates 9 different astromaterials collections in seven different clean-room suites: (1) Apollo Samples (ISO (International Standards Organization) class 6 + 7); (2) Antarctic Meteorites (ISO 6 + 7); (3) Cosmic Dust Particles (ISO 5); (4) Microparticle Impact Collection (ISO 7; formerly called Space-Exposed Hardware); (5) Genesis Solar Wind Atoms (ISO 4); (6) Stardust Comet Particles (ISO 5); (7) Stardust Interstellar Particles (ISO 5); (8) Hayabusa Asteroid Particles (ISO 5); (9) OSIRIS-REx Spacecraft Coupons and Witness Plates (ISO 7). Additional cleanrooms are currently being planned to house samples from two new collections, Hayabusa 2 (2021) and OSIRIS-REx (2023). In addition to the labs that house the samples, we maintain a wide variety of infra-structure facilities required to support the clean rooms: HEPA-filtered air-handling systems, ultrapure dry gaseous nitrogen systems, an ultrapure water system, and cleaning facilities to provide clean tools and equipment for the labs. We also have sample preparation facilities for making thin sections, microtome sections, and even focused ion-beam sections. We routinely monitor the cleanliness of our clean rooms and infrastructure systems, including measurements of inorganic or organic contamination, weekly airborne particle counts, compositional and isotopic monitoring of liquid N2 deliveries, and daily UPW system monitoring. In addition to the physical maintenance of the samples, we track within our databases the current and ever changing characteristics (weight, location, etc.) of more than 250,000 individually numbered samples across our various collections, as well as more than 100,000 images, and countless "analog" records that record the sample processing records of each individual sample. JSC Curation is co-located with JSC

Data Curation Education in Research Centers (DCERC)

Science.gov (United States)

Marlino, M. R.; Mayernik, M. S.; Kelly, K.; Allard, S.; Tenopir, C.; Palmer, C.; Varvel, V. E., Jr.

2012-12-01

Digital data both enable and constrain scientific research. Scientists are enabled by digital data to develop new research methods, utilize new data sources, and investigate new topics, but they also face new data collection, management, and preservation burdens. The current data workforce consists primarily of scientists who receive little formal training in data management and data managers who are typically educated through on-the-job training. The Data Curation Education in Research Centers (DCERC) program is investigating a new model for educating data professionals to contribute to scientific research. DCERC is a collaboration between the University of Illinois at Urbana-Champaign Graduate School of Library and Information Science, the University of Tennessee School of Information Sciences, and the National Center for Atmospheric Research. The program is organized around a foundations course in data curation and provides field experiences in research and data centers for both master's and doctoral students. This presentation will outline the aims and the structure of the DCERC program and discuss results and lessons learned from the first set of summer internships in 2012. Four masters students participated and worked with both data mentors and science mentors, gaining first hand experiences in the issues, methods, and challenges of scientific data curation. They engaged in a diverse set of topics, including climate model metadata, observational data management workflows, and data cleaning, documentation, and ingest processes within a data archive. The students learned current data management practices and challenges while developing expertise and conducting research. They also made important contributions to NCAR data and science teams by evaluating data management workflows and processes, preparing data sets to be archived, and developing recommendations for particular data management activities. The master's student interns will return in summer of 2013

Research resources: curating the new eagle-i discovery system

Science.gov (United States)

Vasilevsky, Nicole; Johnson, Tenille; Corday, Karen; Torniai, Carlo; Brush, Matthew; Segerdell, Erik; Wilson, Melanie; Shaffer, Chris; Robinson, David; Haendel, Melissa

2012-01-01

Development of biocuration processes and guidelines for new data types or projects is a challenging task. Each project finds its way toward defining annotation standards and ensuring data consistency with varying degrees of planning and different tools to support and/or report on consistency. Further, this process may be data type specific even within the context of a single project. This article describes our experiences with eagle-i, a 2-year pilot project to develop a federated network of data repositories in which unpublished, unshared or otherwise ‘invisible’ scientific resources could be inventoried and made accessible to the scientific community. During the course of eagle-i development, the main challenges we experienced related to the difficulty of collecting and curating data while the system and the data model were simultaneously built, and a deficiency and diversity of data management strategies in the laboratories from which the source data was obtained. We discuss our approach to biocuration and the importance of improving information management strategies to the research process, specifically with regard to the inventorying and usage of research resources. Finally, we highlight the commonalities and differences between eagle-i and similar efforts with the hope that our lessons learned will assist other biocuration endeavors. Database URL: www.eagle-i.net PMID:22434835

PhytoREF: a reference database of the plastidial 16S rRNA gene of photosynthetic eukaryotes with curated taxonomy.

Science.gov (United States)

Decelle, Johan; Romac, Sarah; Stern, Rowena F; Bendif, El Mahdi; Zingone, Adriana; Audic, Stéphane; Guiry, Michael D; Guillou, Laure; Tessier, Désiré; Le Gall, Florence; Gourvil, Priscillia; Dos Santos, Adriana L; Probert, Ian; Vaulot, Daniel; de Vargas, Colomban; Christen, Richard

2015-11-01

Photosynthetic eukaryotes have a critical role as the main producers in most ecosystems of the biosphere. The ongoing environmental metabarcoding revolution opens the perspective for holistic ecosystems biological studies of these organisms, in particular the unicellular microalgae that often lack distinctive morphological characters and have complex life cycles. To interpret environmental sequences, metabarcoding necessarily relies on taxonomically curated databases containing reference sequences of the targeted gene (or barcode) from identified organisms. To date, no such reference framework exists for photosynthetic eukaryotes. In this study, we built the PhytoREF database that contains 6490 plastidial 16S rDNA reference sequences that originate from a large diversity of eukaryotes representing all known major photosynthetic lineages. We compiled 3333 amplicon sequences available from public databases and 879 sequences extracted from plastidial genomes, and generated 411 novel sequences from cultured marine microalgal strains belonging to different eukaryotic lineages. A total of 1867 environmental Sanger 16S rDNA sequences were also included in the database. Stringent quality filtering and a phylogeny-based taxonomic classification were applied for each 16S rDNA sequence. The database mainly focuses on marine microalgae, but sequences from land plants (representing half of the PhytoREF sequences) and freshwater taxa were also included to broaden the applicability of PhytoREF to different aquatic and terrestrial habitats. PhytoREF, accessible via a web interface (http://phytoref.fr), is a new resource in molecular ecology to foster the discovery, assessment and monitoring of the diversity of photosynthetic eukaryotes using high-throughput sequencing. © 2015 John Wiley & Sons Ltd.

Advances in Astromaterials Curation: Supporting Future Sample Return Missions

Science.gov (United States)

Evans, C. A.; Zeigler, R. A.; Fries, M. D..; Righter, K.; Allton, J. H.; Zolensky, M. E.; Calaway, M. J.; Bell, M. S.

2015-01-01

NASA's Astromaterials, curated at the Johnson Space Center in Houston, are the most extensive, best-documented, and leastcontaminated extraterrestrial samples that are provided to the worldwide research community. These samples include lunar samples from the Apollo missions, meteorites collected over nearly 40 years of expeditions to Antarctica (providing samples of dozens of asteroid bodies, the Moon, and Mars), Genesis solar wind samples, cosmic dust collected by NASA's high altitude airplanes, Comet Wild 2 and interstellar dust samples from the Stardust mission, and asteroid samples from JAXA's Hayabusa mission. A full account of NASA's curation efforts for these collections is provided by Allen, et al [1]. On average, we annually allocate about 1500 individual samples from NASA's astromaterials collections to hundreds of researchers from around the world, including graduate students and post-doctoral scientists; our allocation rate has roughly doubled over the past 10 years. The curation protocols developed for the lunar samples returned from the Apollo missions remain relevant and are adapted to new and future missions. Several lessons from the Apollo missions, including the need for early involvement of curation scientists in mission planning [1], have been applied to all subsequent sample return campaigns. From the 2013 National Academy of Sciences report [2]: "Curation is the critical interface between sample return missions and laboratory research. Proper curation has maintained the scientific integrity and utility of the Apollo, Antarctic meteorite, and cosmic dust collections for decades. Each of these collections continues to yield important new science. In the past decade, new state-of-the-art curatorial facilities for the Genesis and Stardust missions were key to the scientific breakthroughs provided by these missions." The results speak for themselves: research on NASA's astromaterials result in hundreds of papers annually, yield fundamental

Lessons learned bulletin

International Nuclear Information System (INIS)

1994-05-01

During the past four years, the Department of Energy -- Savannah River Operations Office and the Westinghouse Savannah River Company (WSRC) Environmental Restoration (ER) Program completed various activities ranging from waste site investigations to closure and post closure projects. Critiques for lessons learned regarding project activities are performed at the completion of each project milestone, and this critique interval allows for frequent recognition of lessons learned. In addition to project related lessons learned, ER also performs lessons learned critiques. T'he Savannah River Site (SRS) also obtains lessons learned information from general industry, commercial nuclear industry, naval nuclear programs, and other DOE sites within the complex. Procedures are approved to administer the lessons learned program, and a database is available to catalog applicable lessons learned regarding environmental remediation, restoration, and administrative activities. ER will continue to use this database as a source of information available to SRS personnel

Argo: an integrative, interactive, text mining-based workbench supporting curation

Science.gov (United States)

Rak, Rafal; Rowley, Andrew; Black, William; Ananiadou, Sophia

2012-01-01

Curation of biomedical literature is often supported by the automatic analysis of textual content that generally involves a sequence of individual processing components. Text mining (TM) has been used to enhance the process of manual biocuration, but has been focused on specific databases and tasks rather than an environment integrating TM tools into the curation pipeline, catering for a variety of tasks, types of information and applications. Processing components usually come from different sources and often lack interoperability. The well established Unstructured Information Management Architecture is a framework that addresses interoperability by defining common data structures and interfaces. However, most of the efforts are targeted towards software developers and are not suitable for curators, or are otherwise inconvenient to use on a higher level of abstraction. To overcome these issues we introduce Argo, an interoperable, integrative, interactive and collaborative system for text analysis with a convenient graphic user interface to ease the development of processing workflows and boost productivity in labour-intensive manual curation. Robust, scalable text analytics follow a modular approach, adopting component modules for distinct levels of text analysis. The user interface is available entirely through a web browser that saves the user from going through often complicated and platform-dependent installation procedures. Argo comes with a predefined set of processing components commonly used in text analysis, while giving the users the ability to deposit their own components. The system accommodates various areas and levels of user expertise, from TM and computational linguistics to ontology-based curation. One of the key functionalities of Argo is its ability to seamlessly incorporate user-interactive components, such as manual annotation editors, into otherwise completely automatic pipelines. As a use case, we demonstrate the functionality of an in

Database Description - tRNADB-CE | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us tRNAD...B-CE Database Description General information of database Database name tRNADB-CE Alter...CC BY-SA Detail Background and funding Name: MEXT Integrated Database Project Reference(s) Article title: tRNAD... 2009 Jan;37(Database issue):D163-8. External Links: Article title: tRNADB-CE 2011: tRNA gene database curat...n Download License Update History of This Database Site Policy | Contact Us Database Description - tRNADB-CE | LSDB Archive ...

Curating Big Data Made Simple: Perspectives from Scientific Communities.

Science.gov (United States)

Sowe, Sulayman K; Zettsu, Koji

2014-03-01

The digital universe is exponentially producing an unprecedented volume of data that has brought benefits as well as fundamental challenges for enterprises and scientific communities alike. This trend is inherently exciting for the development and deployment of cloud platforms to support scientific communities curating big data. The excitement stems from the fact that scientists can now access and extract value from the big data corpus, establish relationships between bits and pieces of information from many types of data, and collaborate with a diverse community of researchers from various domains. However, despite these perceived benefits, to date, little attention is focused on the people or communities who are both beneficiaries and, at the same time, producers of big data. The technical challenges posed by big data are as big as understanding the dynamics of communities working with big data, whether scientific or otherwise. Furthermore, the big data era also means that big data platforms for data-intensive research must be designed in such a way that research scientists can easily search and find data for their research, upload and download datasets for onsite/offsite use, perform computations and analysis, share their findings and research experience, and seamlessly collaborate with their colleagues. In this article, we present the architecture and design of a cloud platform that meets some of these requirements, and a big data curation model that describes how a community of earth and environmental scientists is using the platform to curate data. Motivation for developing the platform, lessons learnt in overcoming some challenges associated with supporting scientists to curate big data, and future research directions are also presented.

Correcting Inconsistencies and Errors in Bacterial Genome Metadata Using an Automated Curation Tool in Excel (AutoCurE).

Science.gov (United States)

Schmedes, Sarah E; King, Jonathan L; Budowle, Bruce

2015-01-01

Whole-genome data are invaluable for large-scale comparative genomic studies. Current sequencing technologies have made it feasible to sequence entire bacterial genomes with relative ease and time with a substantially reduced cost per nucleotide, hence cost per genome. More than 3,000 bacterial genomes have been sequenced and are available at the finished status. Publically available genomes can be readily downloaded; however, there are challenges to verify the specific supporting data contained within the download and to identify errors and inconsistencies that may be present within the organizational data content and metadata. AutoCurE, an automated tool for bacterial genome database curation in Excel, was developed to facilitate local database curation of supporting data that accompany downloaded genomes from the National Center for Biotechnology Information. AutoCurE provides an automated approach to curate local genomic databases by flagging inconsistencies or errors by comparing the downloaded supporting data to the genome reports to verify genome name, RefSeq accession numbers, the presence of archaea, BioProject/UIDs, and sequence file descriptions. Flags are generated for nine metadata fields if there are inconsistencies between the downloaded genomes and genomes reports and if erroneous or missing data are evident. AutoCurE is an easy-to-use tool for local database curation for large-scale genome data prior to downstream analyses.

A computational platform to maintain and migrate manual functional annotations for BioCyc databases.

Science.gov (United States)

Walsh, Jesse R; Sen, Taner Z; Dickerson, Julie A

2014-10-12

BioCyc databases are an important resource for information on biological pathways and genomic data. Such databases represent the accumulation of biological data, some of which has been manually curated from literature. An essential feature of these databases is the continuing data integration as new knowledge is discovered. As functional annotations are improved, scalable methods are needed for curators to manage annotations without detailed knowledge of the specific design of the BioCyc database. We have developed CycTools, a software tool which allows curators to maintain functional annotations in a model organism database. This tool builds on existing software to improve and simplify annotation data imports of user provided data into BioCyc databases. Additionally, CycTools automatically resolves synonyms and alternate identifiers contained within the database into the appropriate internal identifiers. Automating steps in the manual data entry process can improve curation efforts for major biological databases. The functionality of CycTools is demonstrated by transferring GO term annotations from MaizeCyc to matching proteins in CornCyc, both maize metabolic pathway databases available at MaizeGDB, and by creating strain specific databases for metabolic engineering.

Scaling drug indication curation through crowdsourcing.

Science.gov (United States)

Khare, Ritu; Burger, John D; Aberdeen, John S; Tresner-Kirsch, David W; Corrales, Theodore J; Hirchman, Lynette; Lu, Zhiyong

2015-01-01

Motivated by the high cost of human curation of biological databases, there is an increasing interest in using computational approaches to assist human curators and accelerate the manual curation process. Towards the goal of cataloging drug indications from FDA drug labels, we recently developed LabeledIn, a human-curated drug indication resource for 250 clinical drugs. Its development required over 40 h of human effort across 20 weeks, despite using well-defined annotation guidelines. In this study, we aim to investigate the feasibility of scaling drug indication annotation through a crowdsourcing technique where an unknown network of workers can be recruited through the technical environment of Amazon Mechanical Turk (MTurk). To translate the expert-curation task of cataloging indications into human intelligence tasks (HITs) suitable for the average workers on MTurk, we first simplify the complex task such that each HIT only involves a worker making a binary judgment of whether a highlighted disease, in context of a given drug label, is an indication. In addition, this study is novel in the crowdsourcing interface design where the annotation guidelines are encoded into user options. For evaluation, we assess the ability of our proposed method to achieve high-quality annotations in a time-efficient and cost-effective manner. We posted over 3000 HITs drawn from 706 drug labels on MTurk. Within 8 h of posting, we collected 18 775 judgments from 74 workers, and achieved an aggregated accuracy of 96% on 450 control HITs (where gold-standard answers are known), at a cost of $1.75 per drug label. On the basis of these results, we conclude that our crowdsourcing approach not only results in significant cost and time saving, but also leads to accuracy comparable to that of domain experts. Published by Oxford University Press 2015. This work is written by US Government employees and is in the public domain in the US.

A hybrid human and machine resource curation pipeline for the Neuroscience Information Framework.

Science.gov (United States)

Bandrowski, A E; Cachat, J; Li, Y; Müller, H M; Sternberg, P W; Ciccarese, P; Clark, T; Marenco, L; Wang, R; Astakhov, V; Grethe, J S; Martone, M E

2012-01-01

The breadth of information resources available to researchers on the Internet continues to expand, particularly in light of recently implemented data-sharing policies required by funding agencies. However, the nature of dense, multifaceted neuroscience data and the design of contemporary search engine systems makes efficient, reliable and relevant discovery of such information a significant challenge. This challenge is specifically pertinent for online databases, whose dynamic content is 'hidden' from search engines. The Neuroscience Information Framework (NIF; http://www.neuinfo.org) was funded by the NIH Blueprint for Neuroscience Research to address the problem of finding and utilizing neuroscience-relevant resources such as software tools, data sets, experimental animals and antibodies across the Internet. From the outset, NIF sought to provide an accounting of available resources, whereas developing technical solutions to finding, accessing and utilizing them. The curators therefore, are tasked with identifying and registering resources, examining data, writing configuration files to index and display data and keeping the contents current. In the initial phases of the project, all aspects of the registration and curation processes were manual. However, as the number of resources grew, manual curation became impractical. This report describes our experiences and successes with developing automated resource discovery and semiautomated type characterization with text-mining scripts that facilitate curation team efforts to discover, integrate and display new content. We also describe the DISCO framework, a suite of automated web services that significantly reduce manual curation efforts to periodically check for resource updates. Lastly, we discuss DOMEO, a semi-automated annotation tool that improves the discovery and curation of resources that are not necessarily website-based (i.e. reagents, software tools). Although the ultimate goal of automation was to

SABIO-RK: an updated resource for manually curated biochemical reaction kinetics

Science.gov (United States)

Rey, Maja; Weidemann, Andreas; Kania, Renate; Müller, Wolfgang

2018-01-01

Abstract SABIO-RK (http://sabiork.h-its.org/) is a manually curated database containing data about biochemical reactions and their reaction kinetics. The data are primarily extracted from scientific literature and stored in a relational database. The content comprises both naturally occurring and alternatively measured biochemical reactions and is not restricted to any organism class. The data are made available to the public by a web-based search interface and by web services for programmatic access. In this update we describe major improvements and extensions of SABIO-RK since our last publication in the database issue of Nucleic Acid Research (2012). (i) The website has been completely revised and (ii) allows now also free text search for kinetics data. (iii) Additional interlinkages with other databases in our field have been established; this enables users to gain directly comprehensive knowledge about the properties of enzymes and kinetics beyond SABIO-RK. (iv) Vice versa, direct access to SABIO-RK data has been implemented in several systems biology tools and workflows. (v) On request of our experimental users, the data can be exported now additionally in spreadsheet formats. (vi) The newly established SABIO-RK Curation Service allows to respond to specific data requirements. PMID:29092055

From field to database : a user-oriented approche to promote cyber-curating of scientific drilling cores

Science.gov (United States)

Pignol, C.; Arnaud, F.; Godinho, E.; Galabertier, B.; Caillo, A.; Billy, I.; Augustin, L.; Calzas, M.; Rousseau, D. D.; Crosta, X.

2016-12-01

Managing scientific data is probably one the most challenging issues in modern science. In plaeosciences the question is made even more sensitive with the need of preserving and managing high value fragile geological samples: cores. Large international scientific programs, such as IODP or ICDP led intense effort to solve this problem and proposed detailed high standard work- and dataflows thorough core handling and curating. However many paleoscience results derived from small-scale research programs in which data and sample management is too often managed only locally - when it is… In this paper we present a national effort leads in France to develop an integrated system to curate ice and sediment cores. Under the umbrella of the national excellence equipment program CLIMCOR, we launched a reflexion about core curating and the management of associated fieldwork data. Our aim was then to conserve all data from fieldwork in an integrated cyber-environment which will evolve toward laboratory-acquired data storage in a near future. To do so, our demarche was conducted through an intimate relationship with field operators as well laboratory core curators in order to propose user-oriented solutions. The national core curating initiative proposes a single web portal in which all teams can store their fieldwork data. This portal is used as a national hub to attribute IGSNs. For legacy samples, this requires the establishment of a dedicated core list with associated metadata. However, for forthcoming core data, we developed a mobile application to capture technical and scientific data directly on the field. This application is linked with a unique coring-tools library and is adapted to most coring devices (gravity, drilling, percussion etc.) including multiple sections and holes coring operations. Those field data can be uploaded automatically to the national portal, but also referenced through international standards (IGSN and INSPIRE) and displayed in international

MET network in PubMed: a text-mined network visualization and curation system.

Science.gov (United States)

Dai, Hong-Jie; Su, Chu-Hsien; Lai, Po-Ting; Huang, Ming-Siang; Jonnagaddala, Jitendra; Rose Jue, Toni; Rao, Shruti; Chou, Hui-Jou; Milacic, Marija; Singh, Onkar; Syed-Abdul, Shabbir; Hsu, Wen-Lian

2016-01-01

Metastasis is the dissemination of a cancer/tumor from one organ to another, and it is the most dangerous stage during cancer progression, causing more than 90% of cancer deaths. Improving the understanding of the complicated cellular mechanisms underlying metastasis requires investigations of the signaling pathways. To this end, we developed a METastasis (MET) network visualization and curation tool to assist metastasis researchers retrieve network information of interest while browsing through the large volume of studies in PubMed. MET can recognize relations among genes, cancers, tissues and organs of metastasis mentioned in the literature through text-mining techniques, and then produce a visualization of all mined relations in a metastasis network. To facilitate the curation process, MET is developed as a browser extension that allows curators to review and edit concepts and relations related to metastasis directly in PubMed. PubMed users can also view the metastatic networks integrated from the large collection of research papers directly through MET. For the BioCreative 2015 interactive track (IAT), a curation task was proposed to curate metastatic networks among PubMed abstracts. Six curators participated in the proposed task and a post-IAT task, curating 963 unique metastatic relations from 174 PubMed abstracts using MET.Database URL: http://btm.tmu.edu.tw/metastasisway. © The Author(s) 2016. Published by Oxford University Press.

MS_HistoneDB, a manually curated resource for proteomic analysis of human and mouse histones.

Science.gov (United States)

El Kennani, Sara; Adrait, Annie; Shaytan, Alexey K; Khochbin, Saadi; Bruley, Christophe; Panchenko, Anna R; Landsman, David; Pflieger, Delphine; Govin, Jérôme

2017-01-01

Histones and histone variants are essential components of the nuclear chromatin. While mass spectrometry has opened a large window to their characterization and functional studies, their identification from proteomic data remains challenging. Indeed, the current interpretation of mass spectrometry data relies on public databases which are either not exhaustive (Swiss-Prot) or contain many redundant entries (UniProtKB or NCBI). Currently, no protein database is ideally suited for the analysis of histones and the complex array of mammalian histone variants. We propose two proteomics-oriented manually curated databases for mouse and human histone variants. We manually curated >1700 gene, transcript and protein entries to produce a non-redundant list of 83 mouse and 85 human histones. These entries were annotated in accordance with the current nomenclature and unified with the "HistoneDB2.0 with Variants" database. This resource is provided in a format that can be directly read by programs used for mass spectrometry data interpretation. In addition, it was used to interpret mass spectrometry data acquired on histones extracted from mouse testis. Several histone variants, which had so far only been inferred by homology or detected at the RNA level, were detected by mass spectrometry, confirming the existence of their protein form. Mouse and human histone entries were collected from different databases and subsequently curated to produce a non-redundant protein-centric resource, MS_HistoneDB. It is dedicated to the proteomic study of histones in mouse and human and will hopefully facilitate the identification and functional study of histone variants.

Data Curation

Science.gov (United States)

Mallon, Melissa, Ed.

2012-01-01

In their Top Trends of 2012, the Association of College and Research Libraries (ACRL) named data curation as one of the issues to watch in academic libraries in the near future (ACRL, 2012, p. 312). Data curation can be summarized as "the active and ongoing management of data through its life cycle of interest and usefulness to scholarship,…

Annotation of phenotypic diversity: decoupling data curation and ontology curation using Phenex.

Science.gov (United States)

Balhoff, James P; Dahdul, Wasila M; Dececchi, T Alexander; Lapp, Hilmar; Mabee, Paula M; Vision, Todd J

2014-01-01

Phenex (http://phenex.phenoscape.org/) is a desktop application for semantically annotating the phenotypic character matrix datasets common in evolutionary biology. Since its initial publication, we have added new features that address several major bottlenecks in the efficiency of the phenotype curation process: allowing curators during the data curation phase to provisionally request terms that are not yet available from a relevant ontology; supporting quality control against annotation guidelines to reduce later manual review and revision; and enabling the sharing of files for collaboration among curators. We decoupled data annotation from ontology development by creating an Ontology Request Broker (ORB) within Phenex. Curators can use the ORB to request a provisional term for use in data annotation; the provisional term can be automatically replaced with a permanent identifier once the term is added to an ontology. We added a set of annotation consistency checks to prevent common curation errors, reducing the need for later correction. We facilitated collaborative editing by improving the reliability of Phenex when used with online folder sharing services, via file change monitoring and continual autosave. With the addition of these new features, and in particular the Ontology Request Broker, Phenex users have been able to focus more effectively on data annotation. Phenoscape curators using Phenex have reported a smoother annotation workflow, with much reduced interruptions from ontology maintenance and file management issues.

The DCC Curation Lifecycle Model

Directory of Open Access Journals (Sweden)

Sarah Higgins

2008-08-01

Full Text Available Lifecycle management of digital materials is necessary to ensure their continuity. The DCC Curation Lifecycle Model has been developed as a generic, curation-specific, tool which can be used, in conjunction with relevant standards, to plan curation and preservation activities to different levels of granularity. The DCC will use the model: as a training tool for data creators, data curators and data users; to organise and plan their resources; and to help organisations identify risks to their digital assets and plan management strategies for their successful curation.

METHODS OF CONTENTS CURATOR

Directory of Open Access Journals (Sweden)

V. Kukharenko

2013-03-01

Full Text Available Content curated - a new activity (started in 2008 qualified network users with process large amounts of information to represent her social network users. To prepare content curators developed 7 weeks distance course, which examines the functions, methods and tools curator. Courses showed a significant relationship success learning on the availability of advanced personal learning environment and the ability to process and analyze information.

Textpresso Central: a customizable platform for searching, text mining, viewing, and curating biomedical literature.

Science.gov (United States)

Müller, H-M; Van Auken, K M; Li, Y; Sternberg, P W

2018-03-09

The biomedical literature continues to grow at a rapid pace, making the challenge of knowledge retrieval and extraction ever greater. Tools that provide a means to search and mine the full text of literature thus represent an important way by which the efficiency of these processes can be improved. We describe the next generation of the Textpresso information retrieval system, Textpresso Central (TPC). TPC builds on the strengths of the original system by expanding the full text corpus to include the PubMed Central Open Access Subset (PMC OA), as well as the WormBase C. elegans bibliography. In addition, TPC allows users to create a customized corpus by uploading and processing documents of their choosing. TPC is UIMA compliant, to facilitate compatibility with external processing modules, and takes advantage of Lucene indexing and search technology for efficient handling of millions of full text documents. Like Textpresso, TPC searches can be performed using keywords and/or categories (semantically related groups of terms), but to provide better context for interpreting and validating queries, search results may now be viewed as highlighted passages in the context of full text. To facilitate biocuration efforts, TPC also allows users to select text spans from the full text and annotate them, create customized curation forms for any data type, and send resulting annotations to external curation databases. As an example of such a curation form, we describe integration of TPC with the Noctua curation tool developed by the Gene Ontology (GO) Consortium. Textpresso Central is an online literature search and curation platform that enables biocurators and biomedical researchers to search and mine the full text of literature by integrating keyword and category searches with viewing search results in the context of the full text. It also allows users to create customized curation interfaces, use those interfaces to make annotations linked to supporting evidence statements

ALFRED: An Allele Frequency Database for Microevolutionary Studies

Directory of Open Access Journals (Sweden)

Kenneth K Kidd

2005-01-01

Full Text Available Many kinds of microevolutionary studies require data on multiple polymorphisms in multiple populations. Increasingly, and especially for human populations, multiple research groups collect relevant data and those data are dispersed widely in the literature. ALFRED has been designed to hold data from many sources and make them available over the web. Data are assembled from multiple sources, curated, and entered into the database. Multiple links to other resources are also established by the curators. A variety of search options are available and additional geographic based interfaces are being developed. The database can serve the human anthropologic genetic community by identifying what loci are already typed on many populations thereby helping to focus efforts on a common set of markers. The database can also serve as a model for databases handling similar DNA polymorphism data for other species.

Protein-Protein Interaction Databases

DEFF Research Database (Denmark)

Szklarczyk, Damian; Jensen, Lars Juhl

2015-01-01

Years of meticulous curation of scientific literature and increasingly reliable computational predictions have resulted in creation of vast databases of protein interaction data. Over the years, these repositories have become a basic framework in which experiments are analyzed and new directions...

Mycobacteriophage genome database.

Science.gov (United States)

Joseph, Jerrine; Rajendran, Vasanthi; Hassan, Sameer; Kumar, Vanaja

2011-01-01

Mycobacteriophage genome database (MGDB) is an exclusive repository of the 64 completely sequenced mycobacteriophages with annotated information. It is a comprehensive compilation of the various gene parameters captured from several databases pooled together to empower mycobacteriophage researchers. The MGDB (Version No.1.0) comprises of 6086 genes from 64 mycobacteriophages classified into 72 families based on ACLAME database. Manual curation was aided by information available from public databases which was enriched further by analysis. Its web interface allows browsing as well as querying the classification. The main objective is to collect and organize the complexity inherent to mycobacteriophage protein classification in a rational way. The other objective is to browse the existing and new genomes and describe their functional annotation. The database is available for free at http://mpgdb.ibioinformatics.org/mpgdb.php.

Gene Name Thesaurus - Gene Name Thesaurus | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available 08/lsdba.nbdc00966-001 Description of data contents Curators who have expertize in biological research edit ...onym information fields in various gene/genome databases. 2. The curators who have expertise in biological research

Data Curation for the Exploitation of Large Earth Observation Products Databases - The MEA system

Science.gov (United States)

Mantovani, Simone; Natali, Stefano; Barboni, Damiano; Cavicchi, Mario; Della Vecchia, Andrea

2014-05-01

National Space Agencies under the umbrella of the European Space Agency are performing a strong activity to handle and provide solutions to Big Data and related knowledge (metadata, software tools and services) management and exploitation. The continuously increasing amount of long-term and of historic data in EO facilities in the form of online datasets and archives, the incoming satellite observation platforms that will generate an impressive amount of new data and the new EU approach on the data distribution policy make necessary to address technologies for the long-term management of these data sets, including their consolidation, preservation, distribution, continuation and curation across multiple missions. The management of long EO data time series of continuing or historic missions - with more than 20 years of data available already today - requires technical solutions and technologies which differ considerably from the ones exploited by existing systems. Several tools, both open source and commercial, are already providing technologies to handle data and metadata preparation, access and visualization via OGC standard interfaces. This study aims at describing the Multi-sensor Evolution Analysis (MEA) system and the Data Curation concept as approached and implemented within the ASIM and EarthServer projects, funded by the European Space Agency and the European Commission, respectively.

Sharing and community curation of mass spectrometry data with GNPS

Science.gov (United States)

Nguyen, Don Duy; Watrous, Jeramie; Kapono, Clifford A; Luzzatto-Knaan, Tal; Porto, Carla; Bouslimani, Amina; Melnik, Alexey V; Meehan, Michael J; Liu, Wei-Ting; Crüsemann, Max; Boudreau, Paul D; Esquenazi, Eduardo; Sandoval-Calderón, Mario; Kersten, Roland D; Pace, Laura A; Quinn, Robert A; Duncan, Katherine R; Hsu, Cheng-Chih; Floros, Dimitrios J; Gavilan, Ronnie G; Kleigrewe, Karin; Northen, Trent; Dutton, Rachel J; Parrot, Delphine; Carlson, Erin E; Aigle, Bertrand; Michelsen, Charlotte F; Jelsbak, Lars; Sohlenkamp, Christian; Pevzner, Pavel; Edlund, Anna; McLean, Jeffrey; Piel, Jörn; Murphy, Brian T; Gerwick, Lena; Liaw, Chih-Chuang; Yang, Yu-Liang; Humpf, Hans-Ulrich; Maansson, Maria; Keyzers, Robert A; Sims, Amy C; Johnson, Andrew R.; Sidebottom, Ashley M; Sedio, Brian E; Klitgaard, Andreas; Larson, Charles B; P., Cristopher A Boya; Torres-Mendoza, Daniel; Gonzalez, David J; Silva, Denise B; Marques, Lucas M; Demarque, Daniel P; Pociute, Egle; O'Neill, Ellis C; Briand, Enora; Helfrich, Eric J. N.; Granatosky, Eve A; Glukhov, Evgenia; Ryffel, Florian; Houson, Hailey; Mohimani, Hosein; Kharbush, Jenan J; Zeng, Yi; Vorholt, Julia A; Kurita, Kenji L; Charusanti, Pep; McPhail, Kerry L; Nielsen, Kristian Fog; Vuong, Lisa; Elfeki, Maryam; Traxler, Matthew F; Engene, Niclas; Koyama, Nobuhiro; Vining, Oliver B; Baric, Ralph; Silva, Ricardo R; Mascuch, Samantha J; Tomasi, Sophie; Jenkins, Stefan; Macherla, Venkat; Hoffman, Thomas; Agarwal, Vinayak; Williams, Philip G; Dai, Jingqui; Neupane, Ram; Gurr, Joshua; Rodríguez, Andrés M. C.; Lamsa, Anne; Zhang, Chen; Dorrestein, Kathleen; Duggan, Brendan M; Almaliti, Jehad; Allard, Pierre-Marie; Phapale, Prasad; Nothias, Louis-Felix; Alexandrov, Theodore; Litaudon, Marc; Wolfender, Jean-Luc; Kyle, Jennifer E; Metz, Thomas O; Peryea, Tyler; Nguyen, Dac-Trung; VanLeer, Danielle; Shinn, Paul; Jadhav, Ajit; Müller, Rolf; Waters, Katrina M; Shi, Wenyuan; Liu, Xueting; Zhang, Lixin; Knight, Rob; Jensen, Paul R; Palsson, Bernhard O; Pogliano, Kit; Linington, Roger G; Gutiérrez, Marcelino; Lopes, Norberto P; Gerwick, William H; Moore, Bradley S; Dorrestein, Pieter C; Bandeira, Nuno

2017-01-01

The potential of the diverse chemistries present in natural products (NP) for biotechnology and medicine remains untapped because NP databases are not searchable with raw data and the NP community has no way to share data other than in published papers. Although mass spectrometry techniques are well-suited to high-throughput characterization of natural products, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social molecular networking (GNPS, http://gnps.ucsd.edu), an open-access knowledge base for community wide organization and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations. We also introduce the concept of ‘living data’ through continuous reanalysis of deposited data. PMID:27504778

The BioC-BioGRID corpus: full text articles annotated for curation of protein–protein and genetic interactions

Science.gov (United States)

Kim, Sun; Chatr-aryamontri, Andrew; Chang, Christie S.; Oughtred, Rose; Rust, Jennifer; Wilbur, W. John; Comeau, Donald C.; Dolinski, Kara; Tyers, Mike

2017-01-01

A great deal of information on the molecular genetics and biochemistry of model organisms has been reported in the scientific literature. However, this data is typically described in free text form and is not readily amenable to computational analyses. To this end, the BioGRID database systematically curates the biomedical literature for genetic and protein interaction data. This data is provided in a standardized computationally tractable format and includes structured annotation of experimental evidence. BioGRID curation necessarily involves substantial human effort by expert curators who must read each publication to extract the relevant information. Computational text-mining methods offer the potential to augment and accelerate manual curation. To facilitate the development of practical text-mining strategies, a new challenge was organized in BioCreative V for the BioC task, the collaborative Biocurator Assistant Task. This was a non-competitive, cooperative task in which the participants worked together to build BioC-compatible modules into an integrated pipeline to assist BioGRID curators. As an integral part of this task, a test collection of full text articles was developed that contained both biological entity annotations (gene/protein and organism/species) and molecular interaction annotations (protein–protein and genetic interactions (PPIs and GIs)). This collection, which we call the BioC-BioGRID corpus, was annotated by four BioGRID curators over three rounds of annotation and contains 120 full text articles curated in a dataset representing two major model organisms, namely budding yeast and human. The BioC-BioGRID corpus contains annotations for 6409 mentions of genes and their Entrez Gene IDs, 186 mentions of organism names and their NCBI Taxonomy IDs, 1867 mentions of PPIs and 701 annotations of PPI experimental evidence statements, 856 mentions of GIs and 399 annotations of GI evidence statements. The purpose, characteristics and possible future

BioM2MetDisease: a manually curated database for associations between microRNAs, metabolites, small molecules and metabolic diseases.

Science.gov (United States)

Xu, Yanjun; Yang, Haixiu; Wu, Tan; Dong, Qun; Sun, Zeguo; Shang, Desi; Li, Feng; Xu, Yingqi; Su, Fei; Liu, Siyao; Zhang, Yunpeng; Li, Xia

2017-01-01

BioM2MetDisease is a manually curated database that aims to provide a comprehensive and experimentally supported resource of associations between metabolic diseases and various biomolecules. Recently, metabolic diseases such as diabetes have become one of the leading threats to people’s health. Metabolic disease associated with alterations of multiple types of biomolecules such as miRNAs and metabolites. An integrated and high-quality data source that collection of metabolic disease associated biomolecules is essential for exploring the underlying molecular mechanisms and discovering novel therapeutics. Here, we developed the BioM2MetDisease database, which currently documents 2681 entries of relationships between 1147 biomolecules (miRNAs, metabolites and small molecules/drugs) and 78 metabolic diseases across 14 species. Each entry includes biomolecule category, species, biomolecule name, disease name, dysregulation pattern, experimental technique, a brief description of metabolic disease-biomolecule relationships, the reference, additional annotation information etc. BioM2MetDisease provides a user-friendly interface to explore and retrieve all data conveniently. A submission page was also offered for researchers to submit new associations between biomolecules and metabolic diseases. BioM2MetDisease provides a comprehensive resource for studying biology molecules act in metabolic diseases, and it is helpful for understanding the molecular mechanisms and developing novel therapeutics for metabolic diseases. http://www.bio-bigdata.com/BioM2MetDisease/. © The Author(s) 2017. Published by Oxford University Press.

Constructing Data Curation Profiles

Directory of Open Access Journals (Sweden)

Michael Witt

2009-12-01

Full Text Available This paper presents a brief literature review and then introduces the methods, design, and construction of the Data Curation Profile, an instrument that can be used to provide detailed information on particular data forms that might be curated by an academic library. These data forms are presented in the context of the related sub-disciplinary research area, and they provide the flow of the research process from which these data are generated. The profiles also represent the needs for data curation from the perspective of the data producers, using their own language. As such, they support the exploration of data curation across different research domains in real and practical terms. With the sponsorship of the Institute of Museum and Library Services, investigators from Purdue University and the University of Illinois interviewed 19 faculty subjects to identify needs for discovery, access, preservation, and reuse of their research data. For each subject, a profile was constructed that includes information about his or her general research, data forms and stages, value of data, data ingest, intellectual property, organization and description of data, tools, interoperability, impact and prestige, data management, and preservation. Each profile also presents a specific dataset supplied by the subject to serve as a concrete example. The Data Curation Profiles are being published to a public wiki for questions and discussion, and a blank template will be disseminated with guidelines for others to create and share their own profiles. This study was conducted primarily from the viewpoint of librarians interacting with faculty researchers; however, it is expected that these findings will complement a wide variety of data curation research and practice outside of librarianship and the university environment.

Affiliation to the work market after curative treatment of head-and-neck cancer: a population-based study from the DAHANCA database.

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Kjær, Trille; Bøje, Charlotte Rotbøl; Olsen, Maja Halgren; Overgaard, Jens; Johansen, Jørgen; Ibfelt, Else; Steding-Jessen, Marianne; Johansen, Christoffer; Dalton, Susanne O

2013-02-01

Survivors of squamous cell carcinoma of the head and neck (HNSCC) are more severely affected in regard to affiliation to the work market than other cancer survivors. Few studies have investigated associations between socioeconomic and disease-related factors and work market affiliation after curative treatment of HNSCC. We investigated the factors for early retirement pension due to disability and unemployment in patients who had been available for work one year before diagnosis. In a nationwide, population-based cohort study, data on 2436 HNSCC patients treated curatively in 1992-2008 were obtained from the Danish Head and Neck Cancer Group database and linked to Danish administrative population-based registries to obtain demographic and socioeconomic variables. We used multivariate logistic regression models to assess associations between socioeconomic factors (education, income and cohabitating status), cancer-specific variables such as tumour site and stage, comorbidity, early retirement pension and unemployment, with adjustment for age, gender and year of diagnosis. Short education [odds ratio (OR) 4.8; 95% confidence interval (CI) 2.2-10.4], low income (OR 3.2; 95% CI 1.8-5.8), living alone (OR 3.0; 95% CI 2.1-4.4) and having a Charlson comorbidity index score of 3 or more (OR 5.9; 95% CI 3.1-11) were significantly associated with early retirement overall and in all site groups. For the subgroup of patients who were employed before diagnosis, the risk pattern was similar. Tumour stage was not associated with early retirement or unemployment. Cancer-related factors were less strongly associated with early retirement and unemployment than socioeconomic factors and comorbidity. Clinicians treating HNSCC patients should be aware of the socioeconomic factors related to work market affiliation in order to provide more intensive social support or targeted rehabilitation for this patient group.

Morbidity of curative cancer surgery and suicide risk.

Science.gov (United States)

Jayakrishnan, Thejus T; Sekigami, Yurie; Rajeev, Rahul; Gamblin, T Clark; Turaga, Kiran K

2017-11-01

Curative cancer operations lead to debility and loss of autonomy in a population vulnerable to suicide death. The extent to which operative intervention impacts suicide risk is not well studied. To examine the effects of morbidity of curative cancer surgeries and prognosis of disease on the risk of suicide in patients with solid tumors. Retrospective cohort study using Surveillance, Epidemiology, and End Results data from 2004 to 2011; multilevel systematic review. General US population. Participants were 482 781 patients diagnosed with malignant neoplasm between 2004 and 2011 who underwent curative cancer surgeries. Death by suicide or self-inflicted injury. Among 482 781 patients that underwent curative cancer surgery, 231 committed suicide (16.58/100 000 person-years [95% confidence interval, CI, 14.54-18.82]). Factors significantly associated with suicide risk included male sex (incidence rate [IR], 27.62; 95% CI, 23.82-31.86) and age >65 years (IR, 22.54; 95% CI, 18.84-26.76). When stratified by 30-day overall postoperative morbidity, a significantly higher incidence of suicide was found for high-morbidity surgeries (IR, 33.30; 95% CI, 26.50-41.33) vs moderate morbidity (IR, 24.27; 95% CI, 18.92-30.69) and low morbidity (IR, 9.81; 95% CI, 7.90-12.04). Unit increase in morbidity was significantly associated with death by suicide (odds ratio, 1.01; 95% CI, 1.00-1.03; P = .02) and decreased suicide-specific survival (hazards ratio, 1.02; 95% CI, 1.00-1.03, P = .01) in prognosis-adjusted models. In this sample of cancer patients in the Surveillance, Epidemiology, and End Results database, patients that undergo high-morbidity surgeries appear most vulnerable to death by suicide. The identification of this high-risk cohort should motivate health care providers and particularly surgeons to adopt screening measures during the postoperative follow-up period for these patients. Copyright © 2016 John Wiley & Sons, Ltd.

Curative effects of small incision cataract surgery versus phacoemulsification: a Meta-analysis

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Chang-Jian Yang

2013-08-01

Full Text Available AIM: To evaluate the curative efficacy of small incision cataract surgery(SICSversus phacoemulsification(Phaco.METHODS: A computerized literature search was carried out in Chinese Biomedical Database(CBM, Wanfang Data, VIP and Chinese National Knowledge Infrastructure(CNKIto collect articles published between 1989-2013 concerning the curative efficacy of SICS versus Phaco. The studies were assessed in terms of clinical case-control criteria. Meta-analysis were performed to assess the visual acuity, the complications rates between SICS and Phaco 90 days after surgery. Treatment effects were measured as risk difference(RDbetween SICS and Phaco. Fixed and random effect models were employed to combine results after a heterogeneity test. RESULTS:A total of 8 studies were included in our Meta-analysis. At 90 days postoperative time, there were no significant differences between the two groups at the visual acuity >0.5(P=0.14; and no significant differences on the complications rates of corneal astigmatism, corneal edema, posterior capsular rupture and anterior iris reaction(P>0.05.CONCLUSION: These results suggest that there is no different on the curative effects of SICS and Phaco for cataract.

Digital Management and Curation of the National Rock and Ore Collections at NMNH, Smithsonian

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Cottrell, E.; Andrews, B.; Sorensen, S. S.; Hale, L. J.

2011-12-01

The National Museum of Natural History, Smithsonian Institution, is home to the world's largest curated rock collection. The collection houses 160,680 physical rock and ore specimen lots ("samples"), all of which already have a digital record that can be accessed by the public through a searchable web interface (http://collections.mnh.si.edu/search/ms/). In addition, there are 66 accessions pending that when catalogued will add approximately 60,000 specimen lots. NMNH's collections are digitally managed on the KE EMu° platform which has emerged as the premier system for managing collections in natural history museums worldwide. In 2010 the Smithsonian released an ambitious 5 year Digitization Strategic Plan. In Mineral Sciences, new digitization efforts in the next five years will focus on integrating various digital resources for volcanic specimens. EMu sample records will link to the corresponding records for physical eruption information housed within the database of Smithsonian's Global Volcanism Program (GVP). Linkages are also planned between our digital records and geochemical databases (like EarthChem or PetDB) maintained by third parties. We anticipate that these linkages will increase the use of NMNH collections as well as engender new scholarly directions for research. Another large project the museum is currently undertaking involves the integration of the functionality of in-house designed Transaction Management software with the EMu database. This will allow access to the details (borrower, quantity, date, and purpose) of all loans of a given specimen through its catalogue record. We hope this will enable cross-referencing and fertilization of research ideas while avoiding duplicate efforts. While these digitization efforts are critical, we propose that the greatest challenge to sample curation is not posed by digitization and that a global sample registry alone will not ensure that samples are available for reuse. We suggest instead that the ability

Curation Micro-Services: A Pipeline Metaphor for Repositories

OpenAIRE

Abrams, Stephen; Cruse, Patricia; Kunze, John; Minor, David

2010-01-01

The effective long-term curation of digital content requires expert analysis, policy setting, and decision making, and a robust technical infrastructure that can effect and enforce curation policies and implement appropriate curation activities. Since the number, size, and diversity of content under curation management will undoubtedly continue to grow over time, and the state of curation understanding and best practices relative to that content will undergo a similar constant evolution, one ...

Earth System Model Development and Analysis using FRE-Curator and Live Access Servers: On-demand analysis of climate model output with data provenance.

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Radhakrishnan, A.; Balaji, V.; Schweitzer, R.; Nikonov, S.; O'Brien, K.; Vahlenkamp, H.; Burger, E. F.

2016-12-01

There are distinct phases in the development cycle of an Earth system model. During the model development phase, scientists make changes to code and parameters and require rapid access to results for evaluation. During the production phase, scientists may make an ensemble of runs with different settings, and produce large quantities of output, that must be further analyzed and quality controlled for scientific papers and submission to international projects such as the Climate Model Intercomparison Project (CMIP). During this phase, provenance is a key concern:being able to track back from outputs to inputs. We will discuss one of the paths taken at GFDL in delivering tools across this lifecycle, offering on-demand analysis of data by integrating the use of GFDL's in-house FRE-Curator, Unidata's THREDDS and NOAA PMEL's Live Access Servers (LAS).Experience over this lifecycle suggests that a major difficulty in developing analysis capabilities is only partially the scientific content, but often devoted to answering the questions "where is the data?" and "how do I get to it?". "FRE-Curator" is the name of a database-centric paradigm used at NOAA GFDL to ingest information about the model runs into an RDBMS (Curator database). The components of FRE-Curator are integrated into Flexible Runtime Environment workflow and can be invoked during climate model simulation. The front end to FRE-Curator, known as the Model Development Database Interface (MDBI) provides an in-house web-based access to GFDL experiments: metadata, analysis output and more. In order to provide on-demand visualization, MDBI uses Live Access Servers which is a highly configurable web server designed to provide flexible access to geo-referenced scientific data, that makes use of OPeNDAP. Model output saved in GFDL's tape archive, the size of the database and experiments, continuous model development initiatives with more dynamic configurations add complexity and challenges in providing an on

The BioC-BioGRID corpus: full text articles annotated for curation of protein-protein and genetic interactions.

Science.gov (United States)

Islamaj Dogan, Rezarta; Kim, Sun; Chatr-Aryamontri, Andrew; Chang, Christie S; Oughtred, Rose; Rust, Jennifer; Wilbur, W John; Comeau, Donald C; Dolinski, Kara; Tyers, Mike

2017-01-01

A great deal of information on the molecular genetics and biochemistry of model organisms has been reported in the scientific literature. However, this data is typically described in free text form and is not readily amenable to computational analyses. To this end, the BioGRID database systematically curates the biomedical literature for genetic and protein interaction data. This data is provided in a standardized computationally tractable format and includes structured annotation of experimental evidence. BioGRID curation necessarily involves substantial human effort by expert curators who must read each publication to extract the relevant information. Computational text-mining methods offer the potential to augment and accelerate manual curation. To facilitate the development of practical text-mining strategies, a new challenge was organized in BioCreative V for the BioC task, the collaborative Biocurator Assistant Task. This was a non-competitive, cooperative task in which the participants worked together to build BioC-compatible modules into an integrated pipeline to assist BioGRID curators. As an integral part of this task, a test collection of full text articles was developed that contained both biological entity annotations (gene/protein and organism/species) and molecular interaction annotations (protein-protein and genetic interactions (PPIs and GIs)). This collection, which we call the BioC-BioGRID corpus, was annotated by four BioGRID curators over three rounds of annotation and contains 120 full text articles curated in a dataset representing two major model organisms, namely budding yeast and human. The BioC-BioGRID corpus contains annotations for 6409 mentions of genes and their Entrez Gene IDs, 186 mentions of organism names and their NCBI Taxonomy IDs, 1867 mentions of PPIs and 701 annotations of PPI experimental evidence statements, 856 mentions of GIs and 399 annotations of GI evidence statements. The purpose, characteristics and possible future

Reactome graph database: Efficient access to complex pathway data

Science.gov (United States)

Korninger, Florian; Viteri, Guilherme; Marin-Garcia, Pablo; Ping, Peipei; Wu, Guanming; Stein, Lincoln; D’Eustachio, Peter

2018-01-01

Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. One of its main priorities is to provide easy and efficient access to its high quality curated data. At present, biological pathway databases typically store their contents in relational databases. This limits access efficiency because there are performance issues associated with queries traversing highly interconnected data. The same data in a graph database can be queried more efficiently. Here we present the rationale behind the adoption of a graph database (Neo4j) as well as the new ContentService (REST API) that provides access to these data. The Neo4j graph database and its query language, Cypher, provide efficient access to the complex Reactome data model, facilitating easy traversal and knowledge discovery. The adoption of this technology greatly improved query efficiency, reducing the average query time by 93%. The web service built on top of the graph database provides programmatic access to Reactome data by object oriented queries, but also supports more complex queries that take advantage of the new underlying graph-based data storage. By adopting graph database technology we are providing a high performance pathway data resource to the community. The Reactome graph database use case shows the power of NoSQL database engines for complex biological data types. PMID:29377902

Reactome graph database: Efficient access to complex pathway data.

Directory of Open Access Journals (Sweden)

Antonio Fabregat

2018-01-01

Full Text Available Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. One of its main priorities is to provide easy and efficient access to its high quality curated data. At present, biological pathway databases typically store their contents in relational databases. This limits access efficiency because there are performance issues associated with queries traversing highly interconnected data. The same data in a graph database can be queried more efficiently. Here we present the rationale behind the adoption of a graph database (Neo4j as well as the new ContentService (REST API that provides access to these data. The Neo4j graph database and its query language, Cypher, provide efficient access to the complex Reactome data model, facilitating easy traversal and knowledge discovery. The adoption of this technology greatly improved query efficiency, reducing the average query time by 93%. The web service built on top of the graph database provides programmatic access to Reactome data by object oriented queries, but also supports more complex queries that take advantage of the new underlying graph-based data storage. By adopting graph database technology we are providing a high performance pathway data resource to the community. The Reactome graph database use case shows the power of NoSQL database engines for complex biological data types.

Reactome graph database: Efficient access to complex pathway data.

Science.gov (United States)

Fabregat, Antonio; Korninger, Florian; Viteri, Guilherme; Sidiropoulos, Konstantinos; Marin-Garcia, Pablo; Ping, Peipei; Wu, Guanming; Stein, Lincoln; D'Eustachio, Peter; Hermjakob, Henning

2018-01-01

Reactome is a free, open-source, open-data, curated and peer-reviewed knowledgebase of biomolecular pathways. One of its main priorities is to provide easy and efficient access to its high quality curated data. At present, biological pathway databases typically store their contents in relational databases. This limits access efficiency because there are performance issues associated with queries traversing highly interconnected data. The same data in a graph database can be queried more efficiently. Here we present the rationale behind the adoption of a graph database (Neo4j) as well as the new ContentService (REST API) that provides access to these data. The Neo4j graph database and its query language, Cypher, provide efficient access to the complex Reactome data model, facilitating easy traversal and knowledge discovery. The adoption of this technology greatly improved query efficiency, reducing the average query time by 93%. The web service built on top of the graph database provides programmatic access to Reactome data by object oriented queries, but also supports more complex queries that take advantage of the new underlying graph-based data storage. By adopting graph database technology we are providing a high performance pathway data resource to the community. The Reactome graph database use case shows the power of NoSQL database engines for complex biological data types.

Saccharomyces genome database informs human biology

OpenAIRE

Skrzypek, Marek S; Nash, Robert S; Wong, Edith D; MacPherson, Kevin A; Hellerstedt, Sage T; Engel, Stacia R; Karra, Kalpana; Weng, Shuai; Sheppard, Travis K; Binkley, Gail; Simison, Matt; Miyasato, Stuart R; Cherry, J Michael

2017-01-01

Abstract The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org) is an expertly curated database of literature-derived functional information for the model organism budding yeast, Saccharomyces cerevisiae. SGD constantly strives to synergize new types of experimental data and bioinformatics predictions with existing data, and to organize them into a comprehensive and up-to-date information resource. The primary mission of SGD is to facilitate research into the biology of yeast and...

Agile Data Curation Case Studies Leading to the Identification and Development of Data Curation Design Patterns

Science.gov (United States)

Benedict, K. K.; Lenhardt, W. C.; Young, J. W.; Gordon, L. C.; Hughes, S.; Santhana Vannan, S. K.

2017-12-01

The planning for and development of efficient workflows for the creation, reuse, sharing, documentation, publication and preservation of research data is a general challenge that research teams of all sizes face. In response to: requirements from funding agencies for full-lifecycle data management plans that will result in well documented, preserved, and shared research data products increasing requirements from publishers for shared data in conjunction with submitted papers interdisciplinary research team's needs for efficient data sharing within projects, and increasing reuse of research data for replication and new, unanticipated research, policy development, and public use alternative strategies to traditional data life cycle approaches must be developed and shared that enable research teams to meet these requirements while meeting the core science objectives of their projects within the available resources. In support of achieving these goals, the concept of Agile Data Curation has been developed in which there have been parallel activities in support of 1) identifying a set of shared values and principles that underlie the objectives of agile data curation, 2) soliciting case studies from the Earth science and other research communities that illustrate aspects of what the contributors consider agile data curation methods and practices, and 3) identifying or developing design patterns that are high-level abstractions from successful data curation practice that are related to common data curation problems for which common solution strategies may be employed. This paper provides a collection of case studies that have been contributed by the Earth science community, and an initial analysis of those case studies to map them to emerging shared data curation problems and their potential solutions. Following the initial analysis of these problems and potential solutions, existing design patterns from software engineering and related disciplines are identified as a

Somatic cancer variant curation and harmonization through consensus minimum variant level data

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Deborah I. Ritter

2016-11-01

Full Text Available Abstract Background To truly achieve personalized medicine in oncology, it is critical to catalog and curate cancer sequence variants for their clinical relevance. The Somatic Working Group (WG of the Clinical Genome Resource (ClinGen, in cooperation with ClinVar and multiple cancer variant curation stakeholders, has developed a consensus set of minimal variant level data (MVLD. MVLD is a framework of standardized data elements to curate cancer variants for clinical utility. With implementation of MVLD standards, and in a working partnership with ClinVar, we aim to streamline the somatic variant curation efforts in the community and reduce redundancy and time burden for the interpretation of cancer variants in clinical practice. Methods We developed MVLD through a consensus approach by i reviewing clinical actionability interpretations from institutions participating in the WG, ii conducting extensive literature search of clinical somatic interpretation schemas, and iii survey of cancer variant web portals. A forthcoming guideline on cancer variant interpretation, from the Association of Molecular Pathology (AMP, can be incorporated into MVLD. Results Along with harmonizing standardized terminology for allele interpretive and descriptive fields that are collected by many databases, the MVLD includes unique fields for cancer variants such as Biomarker Class, Therapeutic Context and Effect. In addition, MVLD includes recommendations for controlled semantics and ontologies. The Somatic WG is collaborating with ClinVar to evaluate MVLD use for somatic variant submissions. ClinVar is an open and centralized repository where sequencing laboratories can report summary-level variant data with clinical significance, and ClinVar accepts cancer variant data. Conclusions We expect the use of the MVLD to streamline clinical interpretation of cancer variants, enhance interoperability among multiple redundant curation efforts, and increase submission of

WikiPathways: a multifaceted pathway database bridging metabolomics to other omics research.

Science.gov (United States)

Slenter, Denise N; Kutmon, Martina; Hanspers, Kristina; Riutta, Anders; Windsor, Jacob; Nunes, Nuno; Mélius, Jonathan; Cirillo, Elisa; Coort, Susan L; Digles, Daniela; Ehrhart, Friederike; Giesbertz, Pieter; Kalafati, Marianthi; Martens, Marvin; Miller, Ryan; Nishida, Kozo; Rieswijk, Linda; Waagmeester, Andra; Eijssen, Lars M T; Evelo, Chris T; Pico, Alexander R; Willighagen, Egon L

2018-01-04

WikiPathways (wikipathways.org) captures the collective knowledge represented in biological pathways. By providing a database in a curated, machine readable way, omics data analysis and visualization is enabled. WikiPathways and other pathway databases are used to analyze experimental data by research groups in many fields. Due to the open and collaborative nature of the WikiPathways platform, our content keeps growing and is getting more accurate, making WikiPathways a reliable and rich pathway database. Previously, however, the focus was primarily on genes and proteins, leaving many metabolites with only limited annotation. Recent curation efforts focused on improving the annotation of metabolism and metabolic pathways by associating unmapped metabolites with database identifiers and providing more detailed interaction knowledge. Here, we report the outcomes of the continued growth and curation efforts, such as a doubling of the number of annotated metabolite nodes in WikiPathways. Furthermore, we introduce an OpenAPI documentation of our web services and the FAIR (Findable, Accessible, Interoperable and Reusable) annotation of resources to increase the interoperability of the knowledge encoded in these pathways and experimental omics data. New search options, monthly downloads, more links to metabolite databases, and new portals make pathway knowledge more effortlessly accessible to individual researchers and research communities. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Curating NASA's Past, Present, and Future Extraterrestrial Sample Collections

Science.gov (United States)

McCubbin, F. M.; Allton, J. H.; Evans, C. A.; Fries, M. D.; Nakamura-Messenger, K.; Righter, K.; Zeigler, R. A.; Zolensky, M.; Stansbery, E. K.

2016-01-01

The Astromaterials Acquisition and Curation Office (henceforth referred to herein as NASA Curation Office) at NASA Johnson Space Center (JSC) is responsible for curating all of NASA's extraterrestrial samples. Under the governing document, NASA Policy Directive (NPD) 7100.10E "Curation of Extraterrestrial Materials", JSC is charged with "...curation of all extra-terrestrial material under NASA control, including future NASA missions." The Directive goes on to define Curation as including "...documentation, preservation, preparation, and distribution of samples for research, education, and public outreach." Here we describe some of the past, present, and future activities of the NASA Curation Office.

The Danish Bladder Cancer Database

Directory of Open Access Journals (Sweden)

Hansen E

2016-10-01

Full Text Available Erik Hansen,1–3 Heidi Larsson,4 Mette Nørgaard,4 Peter Thind,3,5 Jørgen Bjerggaard Jensen1–3 1Department of Urology, Hospital of West Jutland-Holstebro, Holstebro, 2Department of Urology, Aarhus University Hospital, Aarhus, 3The Danish Bladder Cancer Database Group, 4Department of Clinical Epidemiology, Aarhus University Hospital, Aarhus, 5Department of Urology, Copenhagen University Hospital, Copenhagen, Denmark Aim of database: The aim of the Danish Bladder Cancer Database (DaBlaCa-data is to monitor the treatment of all patients diagnosed with invasive bladder cancer (BC in Denmark. Study population: All patients diagnosed with BC in Denmark from 2012 onward were included in the study. Results presented in this paper are predominantly from the 2013 population. Main variables: In 2013, 970 patients were diagnosed with BC in Denmark and were included in a preliminary report from the database. A total of 458 (47% patients were diagnosed with non-muscle-invasive BC (non-MIBC and 512 (53% were diagnosed with muscle-invasive BC (MIBC. A total of 300 (31% patients underwent cystectomy. Among the 135 patients diagnosed with MIBC, who were 75 years of age or younger, 67 (50% received neoadjuvent chemotherapy prior to cystectomy. In 2013, a total of 147 patients were treated with curative-intended radiation therapy. Descriptive data: One-year mortality was 28% (95% confidence interval [CI]: 15–21. One-year cancer-specific mortality was 25% (95% CI: 22–27%. One-year mortality after cystectomy was 14% (95% CI: 10–18. Ninety-day mortality after cystectomy was 3% (95% CI: 1–5 in 2013. One-year mortality following curative-intended radiation therapy was 32% (95% CI: 24–39 and 1-year cancer-specific mortality was 23% (95% CI: 16–31 in 2013. Conclusion: This preliminary DaBlaCa-data report showed that the treatment of MIBC in Denmark overall meet high international academic standards. The database is able to identify Danish BC patients and

Research Problems in Data Curation: Outcomes from the Data Curation Education in Research Centers Program

Science.gov (United States)

Palmer, C. L.; Mayernik, M. S.; Weber, N.; Baker, K. S.; Kelly, K.; Marlino, M. R.; Thompson, C. A.

2013-12-01

The need for data curation is being recognized in numerous institutional settings as national research funding agencies extend data archiving mandates to cover more types of research grants. Data curation, however, is not only a practical challenge. It presents many conceptual and theoretical challenges that must be investigated to design appropriate technical systems, social practices and institutions, policies, and services. This presentation reports on outcomes from an investigation of research problems in data curation conducted as part of the Data Curation Education in Research Centers (DCERC) program. DCERC is developing a new model for educating data professionals to contribute to scientific research. The program is organized around foundational courses and field experiences in research and data centers for both master's and doctoral students. The initiative is led by the Graduate School of Library and Information Science at the University of Illinois at Urbana-Champaign, in collaboration with the School of Information Sciences at the University of Tennessee, and library and data professionals at the National Center for Atmospheric Research (NCAR). At the doctoral level DCERC is educating future faculty and researchers in data curation and establishing a research agenda to advance the field. The doctoral seminar, Research Problems in Data Curation, was developed and taught in 2012 by the DCERC principal investigator and two doctoral fellows at the University of Illinois. It was designed to define the problem space of data curation, examine relevant concepts and theories related to both technical and social perspectives, and articulate research questions that are either unexplored or under theorized in the current literature. There was a particular emphasis on the Earth and environmental sciences, with guest speakers brought in from NCAR, National Snow and Ice Data Center (NSIDC), and Rensselaer Polytechnic Institute. Through the assignments, students

Curating research data a handbook of current practice

CERN Document Server

Johnston, Lisa R

2017-01-01

Curating Research Data, Volume Two: A Handbook of Current Practice guides you across the data lifecycle through the practical strategies and techniques for curating research data in a digital repository setting. The data curation steps for receiving, appraising, selecting, ingesting, transforming, describing, contextualizing, disseminating, and preserving digital research data are each explored, and then supplemented with detailed case studies written by more than forty international practitioners from national, disciplinary, and institutional data repositories. The steps in this volume detail the sequential actions that you might take to curate a data set from receiving the data (Step 1) to eventual reuse (Step 8). Data curators, archivists, research data management specialists, subject librarians, institutional repository managers, and digital library staff will benefit from these current and practical approaches to data curation.

Digital curation: a proposal of a semi-automatic digital object selection-based model for digital curation in Big Data environments

Directory of Open Access Journals (Sweden)

Moisés Lima Dutra

2016-08-01

Full Text Available Introduction: This work presents a new approach for Digital Curations from a Big Data perspective. Objective: The objective is to propose techniques to digital curations for selecting and evaluating digital objects that take into account volume, velocity, variety, reality, and the value of the data collected from multiple knowledge domains. Methodology: This is an exploratory research of applied nature, which addresses the research problem in a qualitative way. Heuristics allow this semi-automatic process to be done either by human curators or by software agents. Results: As a result, it was proposed a model for searching, processing, evaluating and selecting digital objects to be processed by digital curations. Conclusions: It is possible to use Big Data environments as a source of information resources for Digital Curation; besides, Big Data techniques and tools can support the search and selection process of information resources by Digital Curations.

Automatic vs. manual curation of a multi-source chemical dictionary: the impact on text mining

Science.gov (United States)

2010-01-01

Background Previously, we developed a combined dictionary dubbed Chemlist for the identification of small molecules and drugs in text based on a number of publicly available databases and tested it on an annotated corpus. To achieve an acceptable recall and precision we used a number of automatic and semi-automatic processing steps together with disambiguation rules. However, it remained to be investigated which impact an extensive manual curation of a multi-source chemical dictionary would have on chemical term identification in text. ChemSpider is a chemical database that has undergone extensive manual curation aimed at establishing valid chemical name-to-structure relationships. Results We acquired the component of ChemSpider containing only manually curated names and synonyms. Rule-based term filtering, semi-automatic manual curation, and disambiguation rules were applied. We tested the dictionary from ChemSpider on an annotated corpus and compared the results with those for the Chemlist dictionary. The ChemSpider dictionary of ca. 80 k names was only a 1/3 to a 1/4 the size of Chemlist at around 300 k. The ChemSpider dictionary had a precision of 0.43 and a recall of 0.19 before the application of filtering and disambiguation and a precision of 0.87 and a recall of 0.19 after filtering and disambiguation. The Chemlist dictionary had a precision of 0.20 and a recall of 0.47 before the application of filtering and disambiguation and a precision of 0.67 and a recall of 0.40 after filtering and disambiguation. Conclusions We conclude the following: (1) The ChemSpider dictionary achieved the best precision but the Chemlist dictionary had a higher recall and the best F-score; (2) Rule-based filtering and disambiguation is necessary to achieve a high precision for both the automatically generated and the manually curated dictionary. ChemSpider is available as a web service at http://www.chemspider.com/ and the Chemlist dictionary is freely available as an XML file in

Investigating Astromaterials Curation Applications for Dexterous Robotic Arms

Science.gov (United States)

Snead, C. J.; Jang, J. H.; Cowden, T. R.; McCubbin, F. M.

2018-01-01

The Astromaterials Acquisition and Curation office at NASA Johnson Space Center is currently investigating tools and methods that will enable the curation of future astromaterials collections. Size and temperature constraints for astromaterials to be collected by current and future proposed missions will require the development of new robotic sample and tool handling capabilities. NASA Curation has investigated the application of robot arms in the past, and robotic 3-axis micromanipulators are currently in use for small particle curation in the Stardust and Cosmic Dust laboratories. While 3-axis micromanipulators have been extremely successful for activities involving the transfer of isolated particles in the 5-20 micron range (e.g. from microscope slide to epoxy bullet tip, beryllium SEM disk), their limited ranges of motion and lack of yaw, pitch, and roll degrees of freedom restrict their utility in other applications. For instance, curators removing particles from cosmic dust collectors by hand often employ scooping and rotating motions to successfully free trapped particles from the silicone oil coatings. Similar scooping and rotating motions are also employed when isolating a specific particle of interest from an aliquot of crushed meteorite. While cosmic dust curators have been remarkably successful with these kinds of particle manipulations using handheld tools, operator fatigue limits the number of particles that can be removed during a given extraction session. The challenges for curation of small particles will be exacerbated by mission requirements that samples be processed in N2 sample cabinets (i.e. gloveboxes). We have been investigating the use of compact robot arms to facilitate sample handling within gloveboxes. Six-axis robot arms potentially have applications beyond small particle manipulation. For instance, future sample return missions may involve biologically sensitive astromaterials that can be easily compromised by physical interaction with

tRNA sequence data, annotation data and curation data - tRNADB-CE | LSDB Archive [Life Science Database Archive metadata

Lifescience Database Archive (English)

Full Text Available switchLanguage; BLAST Search Image Search Home About Archive Update History Data List Contact us tRNAD... tRNA sequence data, annotation data and curation data - tRNADB-CE | LSDB Archive ...

Self-Rerouting and Curative Interconnect Technology (SERCUIT)

Science.gov (United States)

2017-12-01

SPECIAL REPORT RDMR-CS-17-01 SELF-REROUTING AND CURATIVE INTERCONNECT TECHNOLOGY (SERCUIT) Shiv Joshi Concepts to Systems, Inc...Final 4. TITLE AND SUBTITLE Self-Rerouting and Curative Interconnect Technology (SERCUIT) 5. FUNDING NUMBERS 6. AUTHOR(S) Shiv Joshi...concepts2systems.com (p) 434-207-5189 x (f) Click to view full size Title Contract Number SELF-REROUTING AND CURATIVE INTERCONNECT TECHNOLOGY (SERCUIT) W911W6-17-C-0029

The plant phenological online database (PPODB): an online database for long-term phenological data

Science.gov (United States)

Dierenbach, Jonas; Badeck, Franz-W.; Schaber, Jörg

2013-09-01

We present an online database that provides unrestricted and free access to over 16 million plant phenological observations from over 8,000 stations in Central Europe between the years 1880 and 2009. Unique features are (1) a flexible and unrestricted access to a full-fledged database, allowing for a wide range of individual queries and data retrieval, (2) historical data for Germany before 1951 ranging back to 1880, and (3) more than 480 curated long-term time series covering more than 100 years for individual phenological phases and plants combined over Natural Regions in Germany. Time series for single stations or Natural Regions can be accessed through a user-friendly graphical geo-referenced interface. The joint databases made available with the plant phenological database PPODB render accessible an important data source for further analyses of long-term changes in phenology. The database can be accessed via www.ppodb.de .

NEMiD: a web-based curated microbial diversity database with geo-based plotting.

Science.gov (United States)

Bhattacharjee, Kaushik; Joshi, Santa Ram

2014-01-01

The majority of the Earth's microbes remain unknown, and that their potential utility cannot be exploited until they are discovered and characterized. They provide wide scope for the development of new strains as well as biotechnological uses. The documentation and bioprospection of microorganisms carry enormous significance considering their relevance to human welfare. This calls for an urgent need to develop a database with emphasis on the microbial diversity of the largest untapped reservoirs in the biosphere. The data annotated in the North-East India Microbial database (NEMiD) were obtained by the isolation and characterization of microbes from different parts of the Eastern Himalayan region. The database was constructed as a relational database management system (RDBMS) for data storage in MySQL in the back-end on a Linux server and implemented in an Apache/PHP environment. This database provides a base for understanding the soil microbial diversity pattern in this megabiodiversity hotspot and indicates the distribution patterns of various organisms along with identification. The NEMiD database is freely available at www.mblabnehu.info/nemid/.

NEMiD: A Web-Based Curated Microbial Diversity Database with Geo-Based Plotting

Science.gov (United States)

Bhattacharjee, Kaushik; Joshi, Santa Ram

2014-01-01

The majority of the Earth's microbes remain unknown, and that their potential utility cannot be exploited until they are discovered and characterized. They provide wide scope for the development of new strains as well as biotechnological uses. The documentation and bioprospection of microorganisms carry enormous significance considering their relevance to human welfare. This calls for an urgent need to develop a database with emphasis on the microbial diversity of the largest untapped reservoirs in the biosphere. The data annotated in the North-East India Microbial database (NEMiD) were obtained by the isolation and characterization of microbes from different parts of the Eastern Himalayan region. The database was constructed as a relational database management system (RDBMS) for data storage in MySQL in the back-end on a Linux server and implemented in an Apache/PHP environment. This database provides a base for understanding the soil microbial diversity pattern in this megabiodiversity hotspot and indicates the distribution patterns of various organisms along with identification. The NEMiD database is freely available at www.mblabnehu.info/nemid/. PMID:24714636

3DSwap: Curated knowledgebase of proteins involved in 3D domain swapping

KAUST Repository

Shameer, Khader

2011-09-29

Three-dimensional domain swapping is a unique protein structural phenomenon where two or more protein chains in a protein oligomer share a common structural segment between individual chains. This phenomenon is observed in an array of protein structures in oligomeric conformation. Protein structures in swapped conformations perform diverse functional roles and are also associated with deposition diseases in humans. We have performed in-depth literature curation and structural bioinformatics analyses to develop an integrated knowledgebase of proteins involved in 3D domain swapping. The hallmark of 3D domain swapping is the presence of distinct structural segments such as the hinge and swapped regions. We have curated the literature to delineate the boundaries of these regions. In addition, we have defined several new concepts like \\'secondary major interface\\' to represent the interface properties arising as a result of 3D domain swapping, and a new quantitative measure for the \\'extent of swapping\\' in structures. The catalog of proteins reported in 3DSwap knowledgebase has been generated using an integrated structural bioinformatics workflow of database searches, literature curation, by structure visualization and sequence-structure-function analyses. The current version of the 3DSwap knowledgebase reports 293 protein structures, the analysis of such a compendium of protein structures will further the understanding molecular factors driving 3D domain swapping. The Author(s) 2011.

AtomPy: an open atomic-data curation environment

Science.gov (United States)

Bautista, Manuel; Mendoza, Claudio; Boswell, Josiah S; Ajoku, Chukwuemeka

2014-06-01

We present a cloud-computing environment for atomic data curation, networking among atomic data providers and users, teaching-and-learning, and interfacing with spectral modeling software. The system is based on Google-Drive Sheets, Pandas (Python Data Analysis Library) DataFrames, and IPython Notebooks for open community-driven curation of atomic data for scientific and technological applications. The atomic model for each ionic species is contained in a multi-sheet Google-Drive workbook, where the atomic parameters from all known public sources are progressively stored. Metadata (provenance, community discussion, etc.) accompanying every entry in the database are stored through Notebooks. Education tools on the physics of atomic processes as well as their relevance to plasma and spectral modeling are based on IPython Notebooks that integrate written material, images, videos, and active computer-tool workflows. Data processing workflows and collaborative software developments are encouraged and managed through the GitHub social network. Relevant issues this platform intends to address are: (i) data quality by allowing open access to both data producers and users in order to attain completeness, accuracy, consistency, provenance and currentness; (ii) comparisons of different datasets to facilitate accuracy assessment; (iii) downloading to local data structures (i.e. Pandas DataFrames) for further manipulation and analysis by prospective users; and (iv) data preservation by avoiding the discard of outdated sets.

Alfred Drury: The Artist as Curator

Directory of Open Access Journals (Sweden)

Ben Thomas

2016-06-01

Full Text Available This article presents a series of reflections on the experience of curating the exhibition ‘Alfred Drury and the New Sculpture’ in 2013. In particular, it charts the evolution of the design of the exhibition, notably its central tableau based on a photograph of the sculptor Alfred Drury’s studio in 1900. This photograph records a display of Drury’s works for visiting Australian patrons, and could be said to record evidence of the artist curating his own work. The legitimacy of deriving a curatorial approach from this photographic evidence is discussed, along with the broader problem of ‘historicizing’ approaches to curating.

Advanced Curation Activities at NASA: Preparation for Upcoming Missions

Science.gov (United States)

Fries, M. D.; Evans, C. A.; McCubbin, F. M.; Harrington, A. D.; Regberg, A. B.; Snead, C. J.; Zeigler, R. A.

2017-07-01

NASA Curation cares for NASA's astromaterials and performs advanced curation so as to improve current practices and prepare for future collections. Cold curation, microbial monitoring, contamination control/knowledge and other aspects are reviewed.

DataShare: Empowering Researcher Data Curation

Directory of Open Access Journals (Sweden)

Stephen Abrams

2014-07-01

Full Text Available Researchers are increasingly being asked to ensure that all products of research activity – not just traditional publications – are preserved and made widely available for study and reuse as a precondition for publication or grant funding, or to conform to disciplinary best practices. In order to conform to these requirements, scholars need effective, easy-to-use tools and services for the long-term curation of their research data. The DataShare service, developed at the University of California, is being used by researchers to: (1 prepare for curation by reviewing best practice recommendations for the acquisition or creation of digital research data; (2 select datasets using intuitive file browsing and drag-and-drop interfaces; (3 describe their data for enhanced discoverability in terms of the DataCite metadata schema; (4 preserve their data by uploading to a public access collection in the UC3 Merritt curation repository; (5 cite their data in terms of persistent and globally-resolvable DOI identifiers; (6 expose their data through registration with well-known abstracting and indexing services and major internet search engines; (7 control the dissemination of their data through enforceable data use agreements; and (8 discover and retrieve datasets of interest through a faceted search and browse environment. Since the widespread adoption of effective data management practices is highly dependent on ease of use and integration into existing individual, institutional, and disciplinary workflows, the emphasis throughout the design and implementation of DataShare is to provide the highest level of curation service with the lowest possible technical barriers to entry by individual researchers. By enabling intuitive, self-service access to data curation functions, DataShare helps to contribute to more widespread adoption of good data curation practices that are critical to open scientific inquiry, discourse, and advancement.

Curating research data practical strategies for your digital repository

CERN Document Server

Johnston, Lisa R

2017-01-01

Volume One of Curating Research Data explores the variety of reasons, motivations, and drivers for why data curation services are needed in the context of academic and disciplinary data repository efforts. Twelve chapters, divided into three parts, take an in-depth look at the complex practice of data curation as it emerges around us. Part I sets the stage for data curation by describing current policies, data sharing cultures, and collaborative efforts currently underway that impact potential services. Part II brings several key issues, such as cost recovery and marketing strategy, into focus for practitioners when considering how to put data curation services in action. Finally, Part III describes the full lifecycle of data by examining the ethical and practical reuse issues that data curation practitioners must consider as we strive to prepare data for the future.

Comprehensive curation and analysis of global interaction networks in Saccharomyces cerevisiae

Science.gov (United States)

Reguly, Teresa; Breitkreutz, Ashton; Boucher, Lorrie; Breitkreutz, Bobby-Joe; Hon, Gary C; Myers, Chad L; Parsons, Ainslie; Friesen, Helena; Oughtred, Rose; Tong, Amy; Stark, Chris; Ho, Yuen; Botstein, David; Andrews, Brenda; Boone, Charles; Troyanskya, Olga G; Ideker, Trey; Dolinski, Kara; Batada, Nizar N; Tyers, Mike

2006-01-01

Background The study of complex biological networks and prediction of gene function has been enabled by high-throughput (HTP) methods for detection of genetic and protein interactions. Sparse coverage in HTP datasets may, however, distort network properties and confound predictions. Although a vast number of well substantiated interactions are recorded in the scientific literature, these data have not yet been distilled into networks that enable system-level inference. Results We describe here a comprehensive database of genetic and protein interactions, and associated experimental evidence, for the budding yeast Saccharomyces cerevisiae, as manually curated from over 31,793 abstracts and online publications. This literature-curated (LC) dataset contains 33,311 interactions, on the order of all extant HTP datasets combined. Surprisingly, HTP protein-interaction datasets currently achieve only around 14% coverage of the interactions in the literature. The LC network nevertheless shares attributes with HTP networks, including scale-free connectivity and correlations between interactions, abundance, localization, and expression. We find that essential genes or proteins are enriched for interactions with other essential genes or proteins, suggesting that the global network may be functionally unified. This interconnectivity is supported by a substantial overlap of protein and genetic interactions in the LC dataset. We show that the LC dataset considerably improves the predictive power of network-analysis approaches. The full LC dataset is available at the BioGRID () and SGD () databases. Conclusion Comprehensive datasets of biological interactions derived from the primary literature provide critical benchmarks for HTP methods, augment functional prediction, and reveal system-level attributes of biological networks. PMID:16762047

The Coral Trait Database, a curated database of trait information for coral species from the global oceans

Science.gov (United States)

Madin, Joshua S.; Anderson, Kristen D.; Andreasen, Magnus Heide; Bridge, Tom C. L.; Cairns, Stephen D.; Connolly, Sean R.; Darling, Emily S.; Diaz, Marcela; Falster, Daniel S.; Franklin, Erik C.; Gates, Ruth D.; Hoogenboom, Mia O.; Huang, Danwei; Keith, Sally A.; Kosnik, Matthew A.; Kuo, Chao-Yang; Lough, Janice M.; Lovelock, Catherine E.; Luiz, Osmar; Martinelli, Julieta; Mizerek, Toni; Pandolfi, John M.; Pochon, Xavier; Pratchett, Morgan S.; Putnam, Hollie M.; Roberts, T. Edward; Stat, Michael; Wallace, Carden C.; Widman, Elizabeth; Baird, Andrew H.

2016-03-01

Trait-based approaches advance ecological and evolutionary research because traits provide a strong link to an organism’s function and fitness. Trait-based research might lead to a deeper understanding of the functions of, and services provided by, ecosystems, thereby improving management, which is vital in the current era of rapid environmental change. Coral reef scientists have long collected trait data for corals; however, these are difficult to access and often under-utilized in addressing large-scale questions. We present the Coral Trait Database initiative that aims to bring together physiological, morphological, ecological, phylogenetic and biogeographic trait information into a single repository. The database houses species- and individual-level data from published field and experimental studies alongside contextual data that provide important framing for analyses. In this data descriptor, we release data for 56 traits for 1547 species, and present a collaborative platform on which other trait data are being actively federated. Our overall goal is for the Coral Trait Database to become an open-source, community-led data clearinghouse that accelerates coral reef research.

The Coral Trait Database, a curated database of trait information for coral species from the global oceans.

Science.gov (United States)

Madin, Joshua S; Anderson, Kristen D; Andreasen, Magnus Heide; Bridge, Tom C L; Cairns, Stephen D; Connolly, Sean R; Darling, Emily S; Diaz, Marcela; Falster, Daniel S; Franklin, Erik C; Gates, Ruth D; Harmer, Aaron; Hoogenboom, Mia O; Huang, Danwei; Keith, Sally A; Kosnik, Matthew A; Kuo, Chao-Yang; Lough, Janice M; Lovelock, Catherine E; Luiz, Osmar; Martinelli, Julieta; Mizerek, Toni; Pandolfi, John M; Pochon, Xavier; Pratchett, Morgan S; Putnam, Hollie M; Roberts, T Edward; Stat, Michael; Wallace, Carden C; Widman, Elizabeth; Baird, Andrew H

2016-03-29

Trait-based approaches advance ecological and evolutionary research because traits provide a strong link to an organism's function and fitness. Trait-based research might lead to a deeper understanding of the functions of, and services provided by, ecosystems, thereby improving management, which is vital in the current era of rapid environmental change. Coral reef scientists have long collected trait data for corals; however, these are difficult to access and often under-utilized in addressing large-scale questions. We present the Coral Trait Database initiative that aims to bring together physiological, morphological, ecological, phylogenetic and biogeographic trait information into a single repository. The database houses species- and individual-level data from published field and experimental studies alongside contextual data that provide important framing for analyses. In this data descriptor, we release data for 56 traits for 1547 species, and present a collaborative platform on which other trait data are being actively federated. Our overall goal is for the Coral Trait Database to become an open-source, community-led data clearinghouse that accelerates coral reef research.

Modern oncologic and operative outcomes for oesophageal cancer treated with curative intent.

LENUS (Irish Health Repository)

Reynolds, J V

2011-09-01

The curative approach to oesophageal cancer carries significant risks and a cure is achieved in approximately 20 per cent. There has been a recent trend internationally to observe improved operative and oncological outcomes. This report audits modern outcomes from a high volume centre with a prospective database for the period 2004-08. 603 patients were referred and 310 (52%) were treated with curative intent. Adenocarcinoma represented 68% of the cohort, squamous cell cancer 30%. Of the 310 cases, 227 (73%) underwent surgery, 105 (46%) underwent surgery alone, and 122 (54%) had chemotherapy or combination chemotherapy and radiation therapy. The postoperative mortality rate was 1.7%. The median and 5-year survival of the 310 patients based on intention to treat was 36 months and 36%, respectively, and of the 181 patients undergoing R0 resection, 52 months and 42%, respectively. An in-hospital postoperative mortality rate of less than 2 per cent, and 5-year survival of between 35 and 42% is consistent with benchmarks from international series.

The Princeton Protein Orthology Database (P-POD): a comparative genomics analysis tool for biologists.

OpenAIRE

Sven Heinicke; Michael S Livstone; Charles Lu; Rose Oughtred; Fan Kang; Samuel V Angiuoli; Owen White; David Botstein; Kara Dolinski

2007-01-01

Many biological databases that provide comparative genomics information and tools are now available on the internet. While certainly quite useful, to our knowledge none of the existing databases combine results from multiple comparative genomics methods with manually curated information from the literature. Here we describe the Princeton Protein Orthology Database (P-POD, http://ortholog.princeton.edu), a user-friendly database system that allows users to find and visualize the phylogenetic r...

Database Systems and Oracle: Experiences and Lessons Learned

Science.gov (United States)

Dunn, Deborah

2005-01-01

In a tight job market, IT professionals with database experience are likely to be in great demand. Companies need database personnel who can help improve access to and security of data. The events of September 11 have increased business' awareness of the need for database security, backup, and recovery procedures. It is our responsibility to…

ECOTOX Knowledgebase: New tools for data visualization and database interoperability (poster)

Science.gov (United States)

The ECOTOXicology knowledgebase (ECOTOX) is a comprehensive, curated database that summarizes toxicology data from single chemical exposure studies to terrestrial and aquatic organisms. The ECOTOX Knowledgebase provides risk assessors and researchers consistent information on tox...

Current Challenges in Development of a Database of Three-Dimensional Chemical Structures

Science.gov (United States)

Maeda, Miki H.

2015-01-01

We are developing a database named 3DMET, a three-dimensional structure database of natural metabolites. There are two major impediments to the creation of 3D chemical structures from a set of planar structure drawings: the limited accuracy of computer programs and insufficient human resources for manual curation. We have tested some 2D–3D converters to convert 2D structure files from external databases. These automatic conversion processes yielded an excessive number of improper conversions. To ascertain the quality of the conversions, we compared IUPAC Chemical Identifier and canonical SMILES notations before and after conversion. Structures whose notations correspond to each other were regarded as a correct conversion in our present work. We found that chiral inversion is the most serious factor during the improper conversion. In the current stage of our database construction, published books or articles have been resources for additions to our database. Chemicals are usually drawn as pictures on the paper. To save human resources, an optical structure reader was introduced. The program was quite useful but some particular errors were observed during our operation. We hope our trials for producing correct 3D structures will help other developers of chemical programs and curators of chemical databases. PMID:26075200

A comprehensive curated resource for follicle stimulating hormone signaling

Directory of Open Access Journals (Sweden)

Sharma Jyoti

2011-10-01

Full Text Available Abstract Background Follicle stimulating hormone (FSH is an important hormone responsible for growth, maturation and function of the human reproductive system. FSH regulates the synthesis of steroid hormones such as estrogen and progesterone, proliferation and maturation of follicles in the ovary and spermatogenesis in the testes. FSH is a glycoprotein heterodimer that binds and acts through the FSH receptor, a G-protein coupled receptor. Although online pathway repositories provide information about G-protein coupled receptor mediated signal transduction, the signaling events initiated specifically by FSH are not cataloged in any public database in a detailed fashion. Findings We performed comprehensive curation of the published literature to identify the components of FSH signaling pathway and the molecular interactions that occur upon FSH receptor activation. Our effort yielded 64 reactions comprising 35 enzyme-substrate reactions, 11 molecular association events, 11 activation events and 7 protein translocation events that occur in response to FSH receptor activation. We also cataloged 265 genes, which were differentially expressed upon FSH stimulation in normal human reproductive tissues. Conclusions We anticipate that the information provided in this resource will provide better insights into the physiological role of FSH in reproductive biology, its signaling mediators and aid in further research in this area. The curated FSH pathway data is freely available through NetPath (http://www.netpath.org, a pathway resource developed previously by our group.

Benchmarking of the 2010 BioCreative Challenge III text-mining competition by the BioGRID and MINT interaction databases

Directory of Open Access Journals (Sweden)

Cesareni Gianni

2011-10-01

Full Text Available Abstract Background The vast amount of data published in the primary biomedical literature represents a challenge for the automated extraction and codification of individual data elements. Biological databases that rely solely on manual extraction by expert curators are unable to comprehensively annotate the information dispersed across the entire biomedical literature. The development of efficient tools based on natural language processing (NLP systems is essential for the selection of relevant publications, identification of data attributes and partially automated annotation. One of the tasks of the Biocreative 2010 Challenge III was devoted to the evaluation of NLP systems developed to identify articles for curation and extraction of protein-protein interaction (PPI data. Results The Biocreative 2010 competition addressed three tasks: gene normalization, article classification and interaction method identification. The BioGRID and MINT protein interaction databases both participated in the generation of the test publication set for gene normalization, annotated the development and test sets for article classification, and curated the test set for interaction method classification. These test datasets served as a gold standard for the evaluation of data extraction algorithms. Conclusion The development of efficient tools for extraction of PPI data is a necessary step to achieve full curation of the biomedical literature. NLP systems can in the first instance facilitate expert curation by refining the list of candidate publications that contain PPI data; more ambitiously, NLP approaches may be able to directly extract relevant information from full-text articles for rapid inspection by expert curators. Close collaboration between biological databases and NLP systems developers will continue to facilitate the long-term objectives of both disciplines.

The MAR databases: development and implementation of databases specific for marine metagenomics.

Science.gov (United States)

Klemetsen, Terje; Raknes, Inge A; Fu, Juan; Agafonov, Alexander; Balasundaram, Sudhagar V; Tartari, Giacomo; Robertsen, Espen; Willassen, Nils P

2018-01-04

We introduce the marine databases; MarRef, MarDB and MarCat (https://mmp.sfb.uit.no/databases/), which are publicly available resources that promote marine research and innovation. These data resources, which have been implemented in the Marine Metagenomics Portal (MMP) (https://mmp.sfb.uit.no/), are collections of richly annotated and manually curated contextual (metadata) and sequence databases representing three tiers of accuracy. While MarRef is a database for completely sequenced marine prokaryotic genomes, which represent a marine prokaryote reference genome database, MarDB includes all incomplete sequenced prokaryotic genomes regardless level of completeness. The last database, MarCat, represents a gene (protein) catalog of uncultivable (and cultivable) marine genes and proteins derived from marine metagenomics samples. The first versions of MarRef and MarDB contain 612 and 3726 records, respectively. Each record is built up of 106 metadata fields including attributes for sampling, sequencing, assembly and annotation in addition to the organism and taxonomic information. Currently, MarCat contains 1227 records with 55 metadata fields. Ontologies and controlled vocabularies are used in the contextual databases to enhance consistency. The user-friendly web interface lets the visitors browse, filter and search in the contextual databases and perform BLAST searches against the corresponding sequence databases. All contextual and sequence databases are freely accessible and downloadable from https://s1.sfb.uit.no/public/mar/. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Curating Gothic Nightmares

Directory of Open Access Journals (Sweden)

Heather Tilley

2007-10-01

Full Text Available This review takes the occasion of a workshop given by Martin Myrone, curator of Gothic Nightmares: Fuseli, Blake, and the Romantic Imagination (Tate Britain, 2006 as a starting point to reflect on the practice of curating, and its relation to questions of the verbal and the visual in contemporary art historical practice. The exhibition prompted an engagement with questions of the genre of Gothic, through a dramatic display of the differences between ‘the Gothic' in literature and ‘the Gothic' in the visual arts within eighteenth- and early nineteenth-century culture. I also address the various ways in which 'the Gothic' was interpreted and reinscribed by visitors, especially those who dressed up for the exhibition. Finally, I consider some of the show's ‘marginalia' (specifically the catalogue, exploring the ways in which these extra events and texts shaped, and continue to shape, the cultural effect of the exhibition.

Data Curation in the World Data System: Proposed Framework

Directory of Open Access Journals (Sweden)

P Laughton

2013-09-01

Full Text Available The value of data in society is increasing rapidly. Organisations that work with data should have standard practices in place to ensure successful curation of data. The World Data System (WDS consists of a number of data centres responsible for curating research data sets for the scientific community. The WDS has no formal data curation framework or model in place to act as a guideline for member data centres. The objective of this research was to develop a framework for the curation of data in the WDS. A multiple-case case study was conducted. Interviews were used to gather qualitative data and analysis of the data, which led to the development of this framework. The proposed framework is largely based on the Open Archival Information System (OAIS functional model and caters for the curation of both analogue and digital data.

Gramene database: Navigating plant comparative genomics resources

Directory of Open Access Journals (Sweden)

Parul Gupta

2016-11-01

Full Text Available Gramene (http://www.gramene.org is an online, open source, curated resource for plant comparative genomics and pathway analysis designed to support researchers working in plant genomics, breeding, evolutionary biology, system biology, and metabolic engineering. It exploits phylogenetic relationships to enrich the annotation of genomic data and provides tools to perform powerful comparative analyses across a wide spectrum of plant species. It consists of an integrated portal for querying, visualizing and analyzing data for 44 plant reference genomes, genetic variation data sets for 12 species, expression data for 16 species, curated rice pathways and orthology-based pathway projections for 66 plant species including various crops. Here we briefly describe the functions and uses of the Gramene database.

Curating NASA's Future Extraterrestrial Sample Collections: How Do We Achieve Maximum Proficiency?

Science.gov (United States)

McCubbin, Francis; Evans, Cynthia; Zeigler, Ryan; Allton, Judith; Fries, Marc; Righter, Kevin; Zolensky, Michael

2016-01-01

The Astromaterials Acquisition and Curation Office (henceforth referred to herein as NASA Curation Office) at NASA Johnson Space Center (JSC) is responsible for curating all of NASA's extraterrestrial samples. Under the governing document, NASA Policy Directive (NPD) 7100.10E "Curation of Extraterrestrial Materials", JSC is charged with "The curation of all extraterrestrial material under NASA control, including future NASA missions." The Directive goes on to define Curation as including "... documentation, preservation, preparation, and distribution of samples for research, education, and public outreach." Here we describe some of the ongoing efforts to ensure that the future activities of the NASA Curation Office are working towards a state of maximum proficiency.

Opening Data in the Long Tail for Community Discovery, Curation and Action Using Active and Social Curation

Science.gov (United States)

Hedstrom, M. L.; Kumar, P.; Myers, J.; Plale, B. A.

2012-12-01

In data science, the most common sequence of steps for data curation are to 1) curate data, 2) enable data discovery, and 3) provide for data reuse. The Sustainable Environments - Actionable Data (SEAD) project, funded through NSF's DataNet program, is creating an environment for sustainability scientists to discover data first, reuse data next, and curate data though an on-going process that we call Active and Social Curation. For active curation we are developing tools and services that support data discovery, data management, and data enhancement for the community while the data is still being used actively for research. We are creating an Active Content Repository, using drop box, semantic web technologies, and a Flickr-like interface for researchers to "drop" data into a repository where it will be replicated and minimally discoverable. For social curation, we are deploying a social networking tool, VIVO, which will allow researchers to discover data-publications-people (e.g. expertise) through a route that can start at any of those entry points. The other dimension of social curation is developing mechanisms to open data for community input, for example, using ranking and commenting mechanisms for data sets and a community-sourcing capability to add tags, clean up and validate data sets. SEAD's strategies and services are aimed at the sustainability science community, which faces numerous challenges including discovery of useful data, cleaning noisy observational data, synthesizing data of different types, defining appropriate models, managing and preserving their research data, and conveying holistic results to colleagues, students, decision makers, and the public. Sustainability researchers make significant use of centrally managed data from satellites and national sensor networks, national scientific and statistical agencies, and data archives. At the same time, locally collected data and custom derived data products that combine observations and

Development of Database and Lecture Book for Nuclear Water Chemistry

International Nuclear Information System (INIS)

Maeng, Wan Young; Kim, U. C.; Na, J. W.; Choi, B. S.; Lee, E. H.; Kim, K. H.; Kim, K. M.; Kim, S. H.; Im, K. S.

2010-02-01

In order to establish a systematic and synthetic knowledge system of nuclear water chemistry, we held nuclear water chemistry experts group meetings. We discussed the way of buildup and propagation of nuclear water chemistry knowledge with domestic experts. We obtained a lot of various opinions that made the good use of this research project. The results will be applied to continuous buildup of domestic nuclear water chemistry knowledge database. Lessons in water chemistry of nuclear power plants (NPPs) have been opened in Nuclear Training and education Center, KAERI to educate the new generation who are working and will be working at the department of water chemistry of NPPs. The lessons were 17 and lesson period was from 12th May through 5th November. In order to progress the programs, many water chemistry experts were invited. They gave lectures to the younger generation once a week for 2 h about their experiences obtained during working on water chemistry of NPPs. The number of attendance was 290. The lessons were very effective and the lesson data will be used to make database for continuous use

An Emergent Micro-Services Approach to Digital Curation Infrastructure

OpenAIRE

Abrams, Stephen; Kunze, John; Loy, David

2010-01-01

In order better to meet the needs of its diverse University of California (UC) constituencies, the California Digital Library UC Curation Center is re-envisioning its approach to digital curation infrastructure by devolving function into a set of granular, independent, but interoperable micro-services. Since each of these services is small and self-contained, they are more easily developed, deployed, maintained, and enhanced; at the same time, complex curation function can emerge from the str...

Supervised Learning for Detection of Duplicates in Genomic Sequence Databases.

Directory of Open Access Journals (Sweden)

Qingyu Chen

Full Text Available First identified as an issue in 1996, duplication in biological databases introduces redundancy and even leads to inconsistency when contradictory information appears. The amount of data makes purely manual de-duplication impractical, and existing automatic systems cannot detect duplicates as precisely as can experts. Supervised learning has the potential to address such problems by building automatic systems that learn from expert curation to detect duplicates precisely and efficiently. While machine learning is a mature approach in other duplicate detection contexts, it has seen only preliminary application in genomic sequence databases.We developed and evaluated a supervised duplicate detection method based on an expert curated dataset of duplicates, containing over one million pairs across five organisms derived from genomic sequence databases. We selected 22 features to represent distinct attributes of the database records, and developed a binary model and a multi-class model. Both models achieve promising performance; under cross-validation, the binary model had over 90% accuracy in each of the five organisms, while the multi-class model maintains high accuracy and is more robust in generalisation. We performed an ablation study to quantify the impact of different sequence record features, finding that features derived from meta-data, sequence identity, and alignment quality impact performance most strongly. The study demonstrates machine learning can be an effective additional tool for de-duplication of genomic sequence databases. All Data are available as described in the supplementary material.

Supervised Learning for Detection of Duplicates in Genomic Sequence Databases.

Science.gov (United States)

Chen, Qingyu; Zobel, Justin; Zhang, Xiuzhen; Verspoor, Karin

2016-01-01

First identified as an issue in 1996, duplication in biological databases introduces redundancy and even leads to inconsistency when contradictory information appears. The amount of data makes purely manual de-duplication impractical, and existing automatic systems cannot detect duplicates as precisely as can experts. Supervised learning has the potential to address such problems by building automatic systems that learn from expert curation to detect duplicates precisely and efficiently. While machine learning is a mature approach in other duplicate detection contexts, it has seen only preliminary application in genomic sequence databases. We developed and evaluated a supervised duplicate detection method based on an expert curated dataset of duplicates, containing over one million pairs across five organisms derived from genomic sequence databases. We selected 22 features to represent distinct attributes of the database records, and developed a binary model and a multi-class model. Both models achieve promising performance; under cross-validation, the binary model had over 90% accuracy in each of the five organisms, while the multi-class model maintains high accuracy and is more robust in generalisation. We performed an ablation study to quantify the impact of different sequence record features, finding that features derived from meta-data, sequence identity, and alignment quality impact performance most strongly. The study demonstrates machine learning can be an effective additional tool for de-duplication of genomic sequence databases. All Data are available as described in the supplementary material.

SWEETLEAD: an in silico database of approved drugs, regulated chemicals, and herbal isolates for computer-aided drug discovery.

Directory of Open Access Journals (Sweden)

Paul A Novick

Full Text Available In the face of drastically rising drug discovery costs, strategies promising to reduce development timelines and expenditures are being pursued. Computer-aided virtual screening and repurposing approved drugs are two such strategies that have shown recent success. Herein, we report the creation of a highly-curated in silico database of chemical structures representing approved drugs, chemical isolates from traditional medicinal herbs, and regulated chemicals, termed the SWEETLEAD database. The motivation for SWEETLEAD stems from the observance of conflicting information in publicly available chemical databases and the lack of a highly curated database of chemical structures for the globally approved drugs. A consensus building scheme surveying information from several publicly accessible databases was employed to identify the correct structure for each chemical. Resulting structures are filtered for the active pharmaceutical ingredient, standardized, and differing formulations of the same drug were combined in the final database. The publically available release of SWEETLEAD (https://simtk.org/home/sweetlead provides an important tool to enable the successful completion of computer-aided repurposing and drug discovery campaigns.

dbEM: A database of epigenetic modifiers curated from cancerous and normal genomes

Science.gov (United States)

Singh Nanda, Jagpreet; Kumar, Rahul; Raghava, Gajendra P. S.

2016-01-01

We have developed a database called dbEM (database of Epigenetic Modifiers) to maintain the genomic information of about 167 epigenetic modifiers/proteins, which are considered as potential cancer targets. In dbEM, modifiers are classified on functional basis and comprise of 48 histone methyl transferases, 33 chromatin remodelers and 31 histone demethylases. dbEM maintains the genomic information like mutations, copy number variation and gene expression in thousands of tumor samples, cancer cell lines and healthy samples. This information is obtained from public resources viz. COSMIC, CCLE and 1000-genome project. Gene essentiality data retrieved from COLT database further highlights the importance of various epigenetic proteins for cancer survival. We have also reported the sequence profiles, tertiary structures and post-translational modifications of these epigenetic proteins in cancer. It also contains information of 54 drug molecules against different epigenetic proteins. A wide range of tools have been integrated in dbEM e.g. Search, BLAST, Alignment and Profile based prediction. In our analysis, we found that epigenetic proteins DNMT3A, HDAC2, KDM6A, and TET2 are highly mutated in variety of cancers. We are confident that dbEM will be very useful in cancer research particularly in the field of epigenetic proteins based cancer therapeutics. This database is available for public at URL: http://crdd.osdd.net/raghava/dbem.

JASPAR 2010: the greatly expanded open-access database of transcription factor binding profiles

Science.gov (United States)

Portales-Casamar, Elodie; Thongjuea, Supat; Kwon, Andrew T.; Arenillas, David; Zhao, Xiaobei; Valen, Eivind; Yusuf, Dimas; Lenhard, Boris; Wasserman, Wyeth W.; Sandelin, Albin

2010-01-01

JASPAR (http://jaspar.genereg.net) is the leading open-access database of matrix profiles describing the DNA-binding patterns of transcription factors (TFs) and other proteins interacting with DNA in a sequence-specific manner. Its fourth major release is the largest expansion of the core database to date: the database now holds 457 non-redundant, curated profiles. The new entries include the first batch of profiles derived from ChIP-seq and ChIP-chip whole-genome binding experiments, and 177 yeast TF binding profiles. The introduction of a yeast division brings the convenience of JASPAR to an active research community. As binding models are refined by newer data, the JASPAR database now uses versioning of matrices: in this release, 12% of the older models were updated to improved versions. Classification of TF families has been improved by adopting a new DNA-binding domain nomenclature. A curated catalog of mammalian TFs is provided, extending the use of the JASPAR profiles to additional TFs belonging to the same structural family. The changes in the database set the system ready for more rapid acquisition of new high-throughput data sources. Additionally, three new special collections provide matrix profile data produced by recent alternative high-throughput approaches. PMID:19906716

WeCurate: Designing for synchronised browsing and social negotiation

OpenAIRE

Hazelden, Katina; Yee-King, Matthew; d'Inverno, Mark; Confalonieri, Roberto; De Jonge, Dave; Amgoud, Leila; Osman, Nardine; Prade, Henri; Sierra, Carles

2012-01-01

WeCurate is a shared image browser for collaboratively curating a virtual exhibition from a cultural image archive. This paper is concerned with the evaluation and iteration of a prototype UI (User Interface) design to enable this community image browsing. In WeCurate, several remote users work together with autonomic agents to browse the archive and to select, through negotiation and voting, a set of images which are of the greatest interest to the group. The UI allows users to synchronize v...

MicroScope—an integrated microbial resource for the curation and comparative analysis of genomic and metabolic data

Science.gov (United States)

Vallenet, David; Belda, Eugeni; Calteau, Alexandra; Cruveiller, Stéphane; Engelen, Stefan; Lajus, Aurélie; Le Fèvre, François; Longin, Cyrille; Mornico, Damien; Roche, David; Rouy, Zoé; Salvignol, Gregory; Scarpelli, Claude; Thil Smith, Adam Alexander; Weiman, Marion; Médigue, Claudine

2013-01-01

MicroScope is an integrated platform dedicated to both the methodical updating of microbial genome annotation and to comparative analysis. The resource provides data from completed and ongoing genome projects (automatic and expert annotations), together with data sources from post-genomic experiments (i.e. transcriptomics, mutant collections) allowing users to perfect and improve the understanding of gene functions. MicroScope (http://www.genoscope.cns.fr/agc/microscope) combines tools and graphical interfaces to analyse genomes and to perform the manual curation of gene annotations in a comparative context. Since its first publication in January 2006, the system (previously named MaGe for Magnifying Genomes) has been continuously extended both in terms of data content and analysis tools. The last update of MicroScope was published in 2009 in the Database journal. Today, the resource contains data for >1600 microbial genomes, of which ∼300 are manually curated and maintained by biologists (1200 personal accounts today). Expert annotations are continuously gathered in the MicroScope database (∼50 000 a year), contributing to the improvement of the quality of microbial genomes annotations. Improved data browsing and searching tools have been added, original tools useful in the context of expert annotation have been developed and integrated and the website has been significantly redesigned to be more user-friendly. Furthermore, in the context of the European project Microme (Framework Program 7 Collaborative Project), MicroScope is becoming a resource providing for the curation and analysis of both genomic and metabolic data. An increasing number of projects are related to the study of environmental bacterial (meta)genomes that are able to metabolize a large variety of chemical compounds that may be of high industrial interest. PMID:23193269

Solving Guesstimation Problems Using the Semantic Web:Four Lessons from an Application

OpenAIRE

Bundy, Alan; Sasnauskas, Gintautas; Chan, Michael

2013-01-01

We draw on our experience of implementing a semi-automated guesstimation application of the Semantic Web, gort, to draw four lessons, which we claim are of general applicability. These are:1. Inference can unleash the Semantic Web: The full power of the web will only be realised when we can use it to infer new knowledge from old.2. The Semantic Web does not constrain the inference mechanisms: Since we must anyway curate the knowledge we extract from the web, we can take the opportunity to tra...

Screen Practice in Curating

DEFF Research Database (Denmark)

Toft, Tanya Søndergaard

2014-01-01

During the past one and a half decade, a curatorial orientation towards "screen practice" has expanded the moving image and digital art into the public domain, exploring alternative artistic uses of the screen. The emergence of urban LED screens in the late 1990s provided a new venue that allowed...... for digital art to expand into public space. It also offered a political point of departure, inviting for confrontation with the Spectacle and with the politics and ideology of the screen as a mass communication medium that instrumentalized spectator positions. In this article I propose that screen practice...... to the dispositif of screen practice in curating, resulting in a medium-based curatorial discourse. With reference to the nomadic exhibition project Nordic Outbreak that I co-curated with Nina Colosi in 2013 and 2014, I suggest that the topos of the defined visual display area, frequently still known as "the screen...

Toward an interactive article: integrating journals and biological databases

Directory of Open Access Journals (Sweden)

Marygold Steven J

2011-05-01

Full Text Available Abstract Background Journal articles and databases are two major modes of communication in the biological sciences, and thus integrating these critical resources is of urgent importance to increase the pace of discovery. Projects focused on bridging the gap between journals and databases have been on the rise over the last five years and have resulted in the development of automated tools that can recognize entities within a document and link those entities to a relevant database. Unfortunately, automated tools cannot resolve ambiguities that arise from one term being used to signify entities that are quite distinct from one another. Instead, resolving these ambiguities requires some manual oversight. Finding the right balance between the speed and portability of automation and the accuracy and flexibility of manual effort is a crucial goal to making text markup a successful venture. Results We have established a journal article mark-up pipeline that links GENETICS journal articles and the model organism database (MOD WormBase. This pipeline uses a lexicon built with entities from the database as a first step. The entity markup pipeline results in links from over nine classes of objects including genes, proteins, alleles, phenotypes and anatomical terms. New entities and ambiguities are discovered and resolved by a database curator through a manual quality control (QC step, along with help from authors via a web form that is provided to them by the journal. New entities discovered through this pipeline are immediately sent to an appropriate curator at the database. Ambiguous entities that do not automatically resolve to one link are resolved by hand ensuring an accurate link. This pipeline has been extended to other databases, namely Saccharomyces Genome Database (SGD and FlyBase, and has been implemented in marking up a paper with links to multiple databases. Conclusions Our semi-automated pipeline hyperlinks articles published in GENETICS to

XML: James Webb Space Telescope Database Issues, Lessons, and Status

Science.gov (United States)

Detter, Ryan; Mooney, Michael; Fatig, Curtis

2003-01-01

This paper will present the current concept using extensible Markup Language (XML) as the underlying structure for the James Webb Space Telescope (JWST) database. The purpose of using XML is to provide a JWST database, independent of any portion of the ground system, yet still compatible with the various systems using a variety of different structures. The testing of the JWST Flight Software (FSW) started in 2002, yet the launch is scheduled for 2011 with a planned 5-year mission and a 5-year follow on option. The initial database and ground system elements, including the commands, telemetry, and ground system tools will be used for 19 years, plus post mission activities. During the Integration and Test (I&T) phases of the JWST development, 24 distinct laboratories, each geographically dispersed, will have local database tools with an XML database. Each of these laboratories database tools will be used for the exporting and importing of data both locally and to a central database system, inputting data to the database certification process, and providing various reports. A centralized certified database repository will be maintained by the Space Telescope Science Institute (STScI), in Baltimore, Maryland, USA. One of the challenges for the database is to be flexible enough to allow for the upgrade, addition or changing of individual items without effecting the entire ground system. Also, using XML should allow for the altering of the import and export formats needed by the various elements, tracking the verification/validation of each database item, allow many organizations to provide database inputs, and the merging of the many existing database processes into one central database structure throughout the JWST program. Many National Aeronautics and Space Administration (NASA) projects have attempted to take advantage of open source and commercial technology. Often this causes a greater reliance on the use of Commercial-Off-The-Shelf (COTS), which is often limiting

Using the Pathogen-Host Interactions database (PHI-base to investigate plant pathogen genomes and genes implicated in virulence

Directory of Open Access Journals (Sweden)

Martin eUrban

2015-08-01

Full Text Available New pathogen-host interaction mechanisms can be revealed by integrating mutant phenotype data with genetic information. PHI-base is a multi-species manually curated database combining peer-reviewed published phenotype data from plant and animal pathogens and gene/protein information in a single database.

Data Curation Network: How Do We Compare? A Snapshot of Six Academic Library Institutions’ Data Repository and Curation Services

Directory of Open Access Journals (Sweden)

Lisa R. Johnston

2017-02-01

Full Text Available Objective: Many academic and research institutions are exploring opportunities to better support researchers in sharing their data. As partners in the Data Curation Network project, our six institutions developed a comparison of the current levels of support provided for researchers to meet their data sharing goals through library-based data repository and curation services. Methods: Each institutional lead provided a written summary of their services based on a previously developed structure, followed by group discussion and refinement of descriptions. Service areas assessed include the repository services for data, technologies used, policies, and staffing in place. Conclusions: Through this process we aim to better define the current levels of support offered by our institutions as a first step toward meeting our project's overarching goal to develop a shared staffing model for data curation across multiple institutions.

The Danish Bladder Cancer Database

DEFF Research Database (Denmark)

Hansen, Erik; Larsson, Heidi Jeanet; Nørgaard, Mette

2016-01-01

AIM OF DATABASE: The aim of the Danish Bladder Cancer Database (DaBlaCa-data) is to monitor the treatment of all patients diagnosed with invasive bladder cancer (BC) in Denmark. STUDY POPULATION: All patients diagnosed with BC in Denmark from 2012 onward were included in the study. Results......-intended radiation therapy. DESCRIPTIVE DATA: One-year mortality was 28% (95% confidence interval [CI]: 15-21). One-year cancer-specific mortality was 25% (95% CI: 22-27%). One-year mortality after cystectomy was 14% (95% CI: 10-18). Ninety-day mortality after cystectomy was 3% (95% CI: 1-5) in 2013. One......-year mortality following curative-intended radiation therapy was 32% (95% CI: 24-39) and 1-year cancer-specific mortality was 23% (95% CI: 16-31) in 2013. CONCLUSION: This preliminary DaBlaCa-data report showed that the treatment of MIBC in Denmark overall meet high international academic standards. The database...

The STRING database in 2017

DEFF Research Database (Denmark)

Szklarczyk, Damian; Morris, John H; Cook, Helen

2017-01-01

A system-wide understanding of cellular function requires knowledge of all functional interactions between the expressed proteins. The STRING database aims to collect and integrate this information, by consolidating known and predicted protein-protein association data for a large number of organi......A system-wide understanding of cellular function requires knowledge of all functional interactions between the expressed proteins. The STRING database aims to collect and integrate this information, by consolidating known and predicted protein-protein association data for a large number...... of organisms. The associations in STRING include direct (physical) interactions, as well as indirect (functional) interactions, as long as both are specific and biologically meaningful. Apart from collecting and reassessing available experimental data on protein-protein interactions, and importing known...... pathways and protein complexes from curated databases, interaction predictions are derived from the following sources: (i) systematic co-expression analysis, (ii) detection of shared selective signals across genomes, (iii) automated text-mining of the scientific literature and (iv) computational transfer...

Digital curation theory and practice

CERN Document Server

Hedges, Mark

2016-01-01

Digital curation is a multi-skilled profession with a key role to play not only in domains traditionally associated with the management of information, such as libraries and archives, but in a broad range of market sectors. Digital information is a defining feature of our age. As individuals we increasingly communicate and record our lives and memories in digital form, whether consciously or as a by-product of broader social, cultural and business activities. Throughout government and industry, there is a pressing need to manage complex information assets and to exploit their social, cultural and commercial value. This book addresses the key strategic, technical and practical issues around digital curation, curatorial practice, and locating the discussions within an appropriate theoretical context.

The Importance of Contamination Knowledge in Curation - Insights into Mars Sample Return

Science.gov (United States)

Harrington, A. D.; Calaway, M. J.; Regberg, A. B.; Mitchell, J. L.; Fries, M. D.; Zeigler, R. A.; McCubbin, F. M.

2018-01-01

The Astromaterials Acquisition and Curation Office at NASA Johnson Space Center (JSC), in Houston, TX (henceforth Curation Office) manages the curation of extraterrestrial samples returned by NASA missions and shared collections from international partners, preserving their integrity for future scientific study while providing the samples to the international community in a fair and unbiased way. The Curation Office also curates flight and non-flight reference materials and other materials from spacecraft assembly (e.g., lubricants, paints and gases) of sample return missions that would have the potential to cross-contaminate a present or future NASA astromaterials collection.

Curative radiotherapy of supraglottic cancer

International Nuclear Information System (INIS)

Kim, Yong Ho; Chai, Gyu Young

1998-01-01

The purpose of this study was to evaluate the efficacy of curative radiotherapy in the management of supraglottic cancer. Twenty-one patients with squamous cell carcinoma of the supraglottis were treated with radiotherapy at Gyeongsang National University Hospital between 1990 and 1994. Median follow-up period was 36 months and 95% were observed for at least 2 years. Actuarial survival rate at 5 years was 39.3% for 21 patients. The 5-year actuarial survival rate was 75.0% in Stage I, 42.9% in Stage II, 33.3% in Stage III, and 28.6% in Stage IV(p=0.54). The 5-year local control rate was 52.0% for 21 patients. The 5-year local control rate was 75.0% in Stage I, 57.1% in Stage II, 66.7% in Stage III, and 28.6% in Stage IV(p=0.33). Double primary cancer was developed in 3 patients and those were all esophageal cancers. In early stage(Stage I and II) supraglottic cancer, curative radiotherapy would be a treatment of choice and surgery would be better to be reserved for salvage of radiotherapy failure. In advanced stage(Stage III and IV), radiotherapy alone is inadequate for curative therapy and combination with surgery should be done in operable patients. This report emphasizes the importance of esophagoscopy and esophagogram at the follow-up of patients with supraglottic cancer

An Emergent Micro-Services Approach to Digital Curation Infrastructure

Directory of Open Access Journals (Sweden)

Stephen Abrams

2010-07-01

Full Text Available In order better to meet the needs of its diverse University of California (UC constituencies, the California Digital Library UC Curation Center is re-envisioning its approach to digital curation infrastructure by devolving function into a set of granular, independent, but interoperable micro-services. Since each of these services is small and self-contained, they are more easily developed, deployed, maintained, and enhanced; at the same time, complex curation function can emerge from the strategic combination of atomistic services. The emergent approach emphasizes the persistence of content rather than the systems in which that content is managemed, thus the paradigmatic archival culture is not unduly coupled to any particular technological context. This results in a curation environment that is comprehensive in scope, yet flexible with regard to local policies and practices and sustainable despite the inevitability of disruptive change in technology and user expectation.

The BDNYC database of low-mass stars, brown dwarfs, and planetary mass companions

Science.gov (United States)

Cruz, Kelle; Rodriguez, David; Filippazzo, Joseph; Gonzales, Eileen; Faherty, Jacqueline K.; Rice, Emily; BDNYC

2018-01-01

We present a web-interface to a database of low-mass stars, brown dwarfs, and planetary mass companions. Users can send SELECT SQL queries to the database, perform searches by coordinates or name, check the database inventory on specified objects, and even plot spectra interactively. The initial version of this database contains information for 198 objects and version 2 will contain over 1000 objects. The database currently includes photometric data from 2MASS, WISE, and Spitzer and version 2 will include a significant portion of the publicly available optical and NIR spectra for brown dwarfs. The database is maintained and curated by the BDNYC research group and we welcome contributions from other researchers via GitHub.

HSC-explorer: a curated database for hematopoietic stem cells.

Science.gov (United States)

Montrone, Corinna; Kokkaliaris, Konstantinos D; Loeffler, Dirk; Lechner, Martin; Kastenmüller, Gabi; Schroeder, Timm; Ruepp, Andreas

2013-01-01

HSC-Explorer (http://mips.helmholtz-muenchen.de/HSC/) is a publicly available, integrative database containing detailed information about the early steps of hematopoiesis. The resource aims at providing fast and easy access to relevant information, in particular to the complex network of interacting cell types and molecules, from the wealth of publications in the field through visualization interfaces. It provides structured information on more than 7000 experimentally validated interactions between molecules, bioprocesses and environmental factors. Information is manually derived by critical reading of the scientific literature from expert annotators. Hematopoiesis-relevant interactions are accompanied with context information such as model organisms and experimental methods for enabling assessment of reliability and relevance of experimental results. Usage of established vocabularies facilitates downstream bioinformatics applications and to convert the results into complex networks. Several predefined datasets (Selected topics) offer insights into stem cell behavior, the stem cell niche and signaling processes supporting hematopoietic stem cell maintenance. HSC-Explorer provides a versatile web-based resource for scientists entering the field of hematopoiesis enabling users to inspect the associated biological processes through interactive graphical presentation.

HSC-explorer: a curated database for hematopoietic stem cells.

Directory of Open Access Journals (Sweden)

Corinna Montrone

Full Text Available HSC-Explorer (http://mips.helmholtz-muenchen.de/HSC/ is a publicly available, integrative database containing detailed information about the early steps of hematopoiesis. The resource aims at providing fast and easy access to relevant information, in particular to the complex network of interacting cell types and molecules, from the wealth of publications in the field through visualization interfaces. It provides structured information on more than 7000 experimentally validated interactions between molecules, bioprocesses and environmental factors. Information is manually derived by critical reading of the scientific literature from expert annotators. Hematopoiesis-relevant interactions are accompanied with context information such as model organisms and experimental methods for enabling assessment of reliability and relevance of experimental results. Usage of established vocabularies facilitates downstream bioinformatics applications and to convert the results into complex networks. Several predefined datasets (Selected topics offer insights into stem cell behavior, the stem cell niche and signaling processes supporting hematopoietic stem cell maintenance. HSC-Explorer provides a versatile web-based resource for scientists entering the field of hematopoiesis enabling users to inspect the associated biological processes through interactive graphical presentation.

International survey of academic library data curation practices

CERN Document Server

2013-01-01

This survey looks closely at the data curation practices of a sample of research-oriented universities largely from the USA, the UK, Australia and Scandinavia but also including India, South Africa and other countries. The study looks at how major universities are assisting faculty in developing data curation and management plans for large scale data projects, largely in the sciences and social sciences, often as pre-conditions for major grants. The report looks at which departments of universities are shouldering the data curation burden, the personnel involved in the efforts, the costs involved, types of software used, difficulties in procuring scientific experiment logs and other hard to obtain information, types of training offered to faculty, and other issues in large scale data management.

Curating NASA's future extraterrestrial sample collections: How do we achieve maximum proficiency?

Science.gov (United States)

McCubbin, Francis; Evans, Cynthia; Allton, Judith; Fries, Marc; Righter, Kevin; Zolensky, Michael; Zeigler, Ryan

2016-07-01

Introduction: The Astromaterials Acquisition and Curation Office (henceforth referred to herein as NASA Curation Office) at NASA Johnson Space Center (JSC) is responsible for curating all of NASA's extraterrestrial samples. Under the governing document, NASA Policy Directive (NPD) 7100.10E "Curation of Extraterrestrial Materials", JSC is charged with "The curation of all extraterrestrial material under NASA control, including future NASA missions." The Directive goes on to define Curation as including "…documentation, preservation, preparation, and distribution of samples for research, education, and public outreach." Here we describe some of the ongoing efforts to ensure that the future activities of the NASA Curation Office are working to-wards a state of maximum proficiency. Founding Principle: Curatorial activities began at JSC (Manned Spacecraft Center before 1973) as soon as design and construction planning for the Lunar Receiving Laboratory (LRL) began in 1964 [1], not with the return of the Apollo samples in 1969, nor with the completion of the LRL in 1967. This practice has since proven that curation begins as soon as a sample return mission is conceived, and this founding principle continues to return dividends today [e.g., 2]. The Next Decade: Part of the curation process is planning for the future, and we refer to these planning efforts as "advanced curation" [3]. Advanced Curation is tasked with developing procedures, technology, and data sets necessary for curating new types of collections as envisioned by NASA exploration goals. We are (and have been) planning for future curation, including cold curation, extended curation of ices and volatiles, curation of samples with special chemical considerations such as perchlorate-rich samples, curation of organically- and biologically-sensitive samples, and the use of minimally invasive analytical techniques (e.g., micro-CT, [4]) to characterize samples. These efforts will be useful for Mars Sample Return

Content curation en periodismo (y en documentación periodística)

OpenAIRE

Guallar, Javier

2014-01-01

The last years we have seen the appearance of concepts such as content curation and content curator as, respectively, the activity or system and the professional or specialist. Although the term is originally linked to the world of marketing, -considering marketer's Rohit Bhargava 'Manifesto for the content curator' (2009) as its founding article-, and its features mostly identify with those of the Information Science professional, content curation goes beyond a specific discipline or profess...

[Curative effect of ozone hydrotherapy for pemphigus].

Science.gov (United States)

Jiang, Fuqiong; Deng, Danqi; Li, Xiaolan; Wang, Wenfang; Xie, Hong; Wu, Yongzhuo; Luan, Chunyan; Yang, Binbin

2018-02-28

To determine clinical curative effects of ozone therapy for pemphigus vulgaris.
 Methods: Ozone hydrotherapy was used as an aid treatment for 32 patients with pemphigus vulgaris. The hydropathic compression of potassium permanganate solution for 34 patients with pemphigus vulgaris served as a control. The main treatment for both groups were glucocorticoids and immune inhibitors. The lesions of patients, bacterial infection, usage of antibiotics, patient's satisfaction, and clinical curative effect were evaluated in the 2 groups.
 Results: There was no significant difference in the curative effect and the average length of staying at hospital between the 2 groups (P>0.05). But rate for the usage of antibiotics was significantly reduced in the group of ozone hydrotherapy (P=0.039). The patients were more satisfied in using ozone hydrotherapy than the potassium permanganate solution after 7-day therapy (P>0.05).
 Conclusion: Ozone hydrotherapy is a safe and effective aid method for pemphigus vulgaris. It can reduce the usage of antibiotics.

Consensus coding sequence (CCDS) database: a standardized set of human and mouse protein-coding regions supported by expert curation.

Science.gov (United States)

Pujar, Shashikant; O'Leary, Nuala A; Farrell, Catherine M; Loveland, Jane E; Mudge, Jonathan M; Wallin, Craig; Girón, Carlos G; Diekhans, Mark; Barnes, If; Bennett, Ruth; Berry, Andrew E; Cox, Eric; Davidson, Claire; Goldfarb, Tamara; Gonzalez, Jose M; Hunt, Toby; Jackson, John; Joardar, Vinita; Kay, Mike P; Kodali, Vamsi K; Martin, Fergal J; McAndrews, Monica; McGarvey, Kelly M; Murphy, Michael; Rajput, Bhanu; Rangwala, Sanjida H; Riddick, Lillian D; Seal, Ruth L; Suner, Marie-Marthe; Webb, David; Zhu, Sophia; Aken, Bronwen L; Bruford, Elspeth A; Bult, Carol J; Frankish, Adam; Murphy, Terence; Pruitt, Kim D

2018-01-04

The Consensus Coding Sequence (CCDS) project provides a dataset of protein-coding regions that are identically annotated on the human and mouse reference genome assembly in genome annotations produced independently by NCBI and the Ensembl group at EMBL-EBI. This dataset is the product of an international collaboration that includes NCBI, Ensembl, HUGO Gene Nomenclature Committee, Mouse Genome Informatics and University of California, Santa Cruz. Identically annotated coding regions, which are generated using an automated pipeline and pass multiple quality assurance checks, are assigned a stable and tracked identifier (CCDS ID). Additionally, coordinated manual review by expert curators from the CCDS collaboration helps in maintaining the integrity and high quality of the dataset. The CCDS data are available through an interactive web page (https://www.ncbi.nlm.nih.gov/CCDS/CcdsBrowse.cgi) and an FTP site (ftp://ftp.ncbi.nlm.nih.gov/pub/CCDS/). In this paper, we outline the ongoing work, growth and stability of the CCDS dataset and provide updates on new collaboration members and new features added to the CCDS user interface. We also present expert curation scenarios, with specific examples highlighting the importance of an accurate reference genome assembly and the crucial role played by input from the research community. Published by Oxford University Press on behalf of Nucleic Acids Research 2017.

NeuroRDF: semantic integration of highly curated data to prioritize biomarker candidates in Alzheimer's disease.

Science.gov (United States)

Iyappan, Anandhi; Kawalia, Shweta Bagewadi; Raschka, Tamara; Hofmann-Apitius, Martin; Senger, Philipp

2016-07-08

Neurodegenerative diseases are incurable and debilitating indications with huge social and economic impact, where much is still to be learnt about the underlying molecular events. Mechanistic disease models could offer a knowledge framework to help decipher the complex interactions that occur at molecular and cellular levels. This motivates the need for the development of an approach integrating highly curated and heterogeneous data into a disease model of different regulatory data layers. Although several disease models exist, they often do not consider the quality of underlying data. Moreover, even with the current advancements in semantic web technology, we still do not have cure for complex diseases like Alzheimer's disease. One of the key reasons accountable for this could be the increasing gap between generated data and the derived knowledge. In this paper, we describe an approach, called as NeuroRDF, to develop an integrative framework for modeling curated knowledge in the area of complex neurodegenerative diseases. The core of this strategy lies in the usage of well curated and context specific data for integration into one single semantic web-based framework, RDF. This increases the probability of the derived knowledge to be novel and reliable in a specific disease context. This infrastructure integrates highly curated data from databases (Bind, IntAct, etc.), literature (PubMed), and gene expression resources (such as GEO and ArrayExpress). We illustrate the effectiveness of our approach by asking real-world biomedical questions that link these resources to prioritize the plausible biomarker candidates. Among the 13 prioritized candidate genes, we identified MIF to be a potential emerging candidate due to its role as a pro-inflammatory cytokine. We additionally report on the effort and challenges faced during generation of such an indication-specific knowledge base comprising of curated and quality-controlled data. Although many alternative approaches

LeishCyc: a biochemical pathways database for Leishmania major

Directory of Open Access Journals (Sweden)

Doyle Maria A

2009-06-01

Full Text Available Abstract Background Leishmania spp. are sandfly transmitted protozoan parasites that cause a spectrum of diseases in more than 12 million people worldwide. Much research is now focusing on how these parasites adapt to the distinct nutrient environments they encounter in the digestive tract of the sandfly vector and the phagolysosome compartment of mammalian macrophages. While data mining and annotation of the genomes of three Leishmania species has provided an initial inventory of predicted metabolic components and associated pathways, resources for integrating this information into metabolic networks and incorporating data from transcript, protein, and metabolite profiling studies is currently lacking. The development of a reliable, expertly curated, and widely available model of Leishmania metabolic networks is required to facilitate systems analysis, as well as discovery and prioritization of new drug targets for this important human pathogen. Description The LeishCyc database was initially built from the genome sequence of Leishmania major (v5.2, based on the annotation published by the Wellcome Trust Sanger Institute. LeishCyc was manually curated to remove errors, correct automated predictions, and add information from the literature. The ongoing curation is based on public sources, literature searches, and our own experimental and bioinformatics studies. In a number of instances we have improved on the original genome annotation, and, in some ambiguous cases, collected relevant information from the literature in order to help clarify gene or protein annotation in the future. All genes in LeishCyc are linked to the corresponding entry in GeneDB (Wellcome Trust Sanger Institute. Conclusion The LeishCyc database describes Leishmania major genes, gene products, metabolites, their relationships and biochemical organization into metabolic pathways. LeishCyc provides a systematic approach to organizing the evolving information about Leishmania

Design database for quantitative trait loci (QTL) data warehouse, data mining, and meta-analysis.

Science.gov (United States)

Hu, Zhi-Liang; Reecy, James M; Wu, Xiao-Lin

2012-01-01

A database can be used to warehouse quantitative trait loci (QTL) data from multiple sources for comparison, genomic data mining, and meta-analysis. A robust database design involves sound data structure logistics, meaningful data transformations, normalization, and proper user interface designs. This chapter starts with a brief review of relational database basics and concentrates on issues associated with curation of QTL data into a relational database, with emphasis on the principles of data normalization and structure optimization. In addition, some simple examples of QTL data mining and meta-analysis are included. These examples are provided to help readers better understand the potential and importance of sound database design.

BGDB: a database of bivalent genes.

Science.gov (United States)

Li, Qingyan; Lian, Shuabin; Dai, Zhiming; Xiang, Qian; Dai, Xianhua

2013-01-01

Bivalent gene is a gene marked with both H3K4me3 and H3K27me3 epigenetic modification in the same area, and is proposed to play a pivotal role related to pluripotency in embryonic stem (ES) cells. Identification of these bivalent genes and understanding their functions are important for further research of lineage specification and embryo development. So far, lots of genome-wide histone modification data were generated in mouse and human ES cells. These valuable data make it possible to identify bivalent genes, but no comprehensive data repositories or analysis tools are available for bivalent genes currently. In this work, we develop BGDB, the database of bivalent genes. The database contains 6897 bivalent genes in human and mouse ES cells, which are manually collected from scientific literature. Each entry contains curated information, including genomic context, sequences, gene ontology and other relevant information. The web services of BGDB database were implemented with PHP + MySQL + JavaScript, and provide diverse query functions. Database URL: http://dailab.sysu.edu.cn/bgdb/

Lnc2Meth: a manually curated database of regulatory relationships between long non-coding RNAs and DNA methylation associated with human disease.

Science.gov (United States)

Zhi, Hui; Li, Xin; Wang, Peng; Gao, Yue; Gao, Baoqing; Zhou, Dianshuang; Zhang, Yan; Guo, Maoni; Yue, Ming; Shen, Weitao; Ning, Shangwei; Jin, Lianhong; Li, Xia

2018-01-04

Lnc2Meth (http://www.bio-bigdata.com/Lnc2Meth/), an interactive resource to identify regulatory relationships between human long non-coding RNAs (lncRNAs) and DNA methylation, is not only a manually curated collection and annotation of experimentally supported lncRNAs-DNA methylation associations but also a platform that effectively integrates tools for calculating and identifying the differentially methylated lncRNAs and protein-coding genes (PCGs) in diverse human diseases. The resource provides: (i) advanced search possibilities, e.g. retrieval of the database by searching the lncRNA symbol of interest, DNA methylation patterns, regulatory mechanisms and disease types; (ii) abundant computationally calculated DNA methylation array profiles for the lncRNAs and PCGs; (iii) the prognostic values for each hit transcript calculated from the patients clinical data; (iv) a genome browser to display the DNA methylation landscape of the lncRNA transcripts for a specific type of disease; (v) tools to re-annotate probes to lncRNA loci and identify the differential methylation patterns for lncRNAs and PCGs with user-supplied external datasets; (vi) an R package (LncDM) to complete the differentially methylated lncRNAs identification and visualization with local computers. Lnc2Meth provides a timely and valuable resource that can be applied to significantly expand our understanding of the regulatory relationships between lncRNAs and DNA methylation in various human diseases. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

Curated routes: the project of developing experiential tracks in sub-urban landscape

OpenAIRE

Papathanasiou, Maximi; Uyttenhove, Pieter

2015-01-01

The Curated Routes project reflects on the visiting routes’ ability to make apparent the internal characteristics of urban environments. The project’s name allude to the intellectual function of curation and the materiality of routes. Curate deals with the practice of arranging material –tangible or intangible- in a way that a new understanding of an area is revealed. The word routes refers to the linear associations that link places and guide movement. The Curated Routes aim to reinforce the...

Geocuration Lessons Learned from the Climate Data Initiative Project

Science.gov (United States)

Ramachandran, Rahul; Bugbee, Kaylin; Tilmes, Curt; Pinheiro Privette, Ana

2015-01-01

Curation is traditionally defined as the process of collecting and organizing information around a common subject matter or a topic of interest and typically occurs in museums, art galleries, and libraries. The task of organizing data around specific topics or themes is a vibrant and growing effort in the biological sciences but to date this effort has not been actively pursued in the Earth sciences. This presentation will introduce the concept of geocuration, which we define it as the act of searching, selecting, and synthesizing Earth science data/metadata and information from across disciplines and repositories into a single, cohesive, and useful compendium. We also present the Climate Data Initiative (CDI) project as an prototypical example. The CDI project is a systematic effort to manually curate and share openly available climate data from various federal agencies. CDI is a broad multi-agency effort of the U.S. government and seeks to leverage the extensive existing federal climate-relevant data to stimulate innovation and private-sector entrepreneurship to support national climate change preparedness. The geocuration process used in the CDI project, key lessons learned, and suggestions to improve similar geocuration efforts in the future will be part of this presentation.

Geocuration Lessons Learned from the Climate Data Initiative Project

Science.gov (United States)

Ramachandran, R.; Bugbee, K.; Tilmes, C.; Privette, A. P.

2015-12-01

Curation is traditionally defined as the process of collecting and organizing information around a common subject matter or a topic of interest and typically occurs in museums, art galleries, and libraries. The task of organizing data around specific topics or themes is a vibrant and growing effort in the biological sciences but to date this effort has not been actively pursued in the Earth sciences. This presentation will introduce the concept of geocuration, which we define it as the act of searching, selecting, and synthesizing Earth science data/metadata and information from across disciplines and repositories into a single, cohesive, and useful compendium.We also present the Climate Data Initiative (CDI) project as an exemplar example. The CDI project is a systematic effort to manually curate and share openly available climate data from various federal agencies. CDI is a broad multi-agency effort of the U.S. government and seeks to leverage the extensive existing federal climate-relevant data to stimulate innovation and private-sector entrepreneurship to support national climate-change preparedness. The geocuration process used in CDI project, key lessons learned, and suggestions to improve similar geocuration efforts in the future will be part of this presentation.

The immune epitope database: a historical retrospective of the first decade.

Science.gov (United States)

Salimi, Nima; Fleri, Ward; Peters, Bjoern; Sette, Alessandro

2012-10-01

As the amount of biomedical information available in the literature continues to increase, databases that aggregate this information continue to grow in importance and scope. The population of databases can occur either through fully automated text mining approaches or through manual curation by human subject experts. We here report our experiences in populating the National Institute of Allergy and Infectious Diseases sponsored Immune Epitope Database and Analysis Resource (IEDB, http://iedb.org), which was created in 2003, and as of 2012 captures the epitope information from approximately 99% of all papers published to date that describe immune epitopes (with the exception of cancer and HIV data). This was achieved using a hybrid model based on automated document categorization and extensive human expert involvement. This task required automated scanning of over 22 million PubMed abstracts followed by classification and curation of over 13 000 references, including over 7000 infectious disease-related manuscripts, over 1000 allergy-related manuscripts, roughly 4000 related to autoimmunity, and 1000 transplant/alloantigen-related manuscripts. The IEDB curation involves an unprecedented level of detail, capturing for each paper the actual experiments performed for each different epitope structure. Key to enabling this process was the extensive use of ontologies to ensure rigorous and consistent data representation as well as interoperability with other bioinformatics resources, including the Protein Data Bank, Chemical Entities of Biological Interest, and the NIAID Bioinformatics Resource Centers. A growing fraction of the IEDB data derives from direct submissions by research groups engaged in epitope discovery, and is being facilitated by the implementation of novel data submission tools. The present explosion of information contained in biological databases demands effective query and display capabilities to optimize the user experience. Accordingly, the

DREMECELS: A Curated Database for Base Excision and Mismatch Repair Mechanisms Associated Human Malignancies.

Directory of Open Access Journals (Sweden)

Ankita Shukla

Full Text Available DNA repair mechanisms act as a warrior combating various damaging processes that ensue critical malignancies. DREMECELS was designed considering the malignancies with frequent alterations in DNA repair pathways, that is, colorectal and endometrial cancers, associated with Lynch syndrome (also known as HNPCC. Since lynch syndrome carries high risk (~40-60% for both cancers, therefore we decided to cover all three diseases in this portal. Although a large population is presently affected by these malignancies, many resources are available for various cancer types but no database archives information on the genes specifically for only these cancers and disorders. The database contains 156 genes and two repair mechanisms, base excision repair (BER and mismatch repair (MMR. Other parameters include some of the regulatory processes that have roles in these disease progressions due to incompetent repair mechanisms, specifically BER and MMR. However, our unique database mainly provides qualitative and quantitative information on these cancer types along with methylation, drug sensitivity, miRNAs, copy number variation (CNV and somatic mutations data. This database would serve the scientific community by providing integrated information on these disease types, thus sustaining diagnostic and therapeutic processes. This repository would serve as an excellent accompaniment for researchers and biomedical professionals and facilitate in understanding such critical diseases. DREMECELS is publicly available at http://www.bioinfoindia.org/dremecels.

Advanced Curation Activities at NASA: Implications for Astrobiological Studies of Future Sample Collections

Science.gov (United States)

McCubbin, F. M.; Evans, C. A.; Fries, M. D.; Harrington, A. D.; Regberg, A. B.; Snead, C. J.; Zeigler, R. A.

2017-01-01

The Astromaterials Acquisition and Curation Office (henceforth referred to herein as NASA Curation Office) at NASA Johnson Space Center (JSC) is responsible for curating all of NASA's extraterrestrial samples. Under the governing document, NASA Policy Directive (NPD) 7100.10F JSC is charged with curation of all extraterrestrial material under NASA control, including future NASA missions. The Directive goes on to define Curation as including documentation, preservation, preparation, and distribution of samples for re-search, education, and public outreach. Here we briefly describe NASA's astromaterials collections and our ongoing efforts related to enhancing the utility of our current collections as well as our efforts to prepare for future sample return missions. We collectively refer to these efforts as advanced curation.

PathwayAccess: CellDesigner plugins for pathway databases.

Science.gov (United States)

Van Hemert, John L; Dickerson, Julie A

2010-09-15

CellDesigner provides a user-friendly interface for graphical biochemical pathway description. Many pathway databases are not directly exportable to CellDesigner models. PathwayAccess is an extensible suite of CellDesigner plugins, which connect CellDesigner directly to pathway databases using respective Java application programming interfaces. The process is streamlined for creating new PathwayAccess plugins for specific pathway databases. Three PathwayAccess plugins, MetNetAccess, BioCycAccess and ReactomeAccess, directly connect CellDesigner to the pathway databases MetNetDB, BioCyc and Reactome. PathwayAccess plugins enable CellDesigner users to expose pathway data to analytical CellDesigner functions, curate their pathway databases and visually integrate pathway data from different databases using standard Systems Biology Markup Language and Systems Biology Graphical Notation. Implemented in Java, PathwayAccess plugins run with CellDesigner version 4.0.1 and were tested on Ubuntu Linux, Windows XP and 7, and MacOSX. Source code, binaries, documentation and video walkthroughs are freely available at http://vrac.iastate.edu/~jlv.

The MetaCyc database of metabolic pathways and enzymes and the BioCyc collection of pathway/genome databases

Science.gov (United States)

Caspi, Ron; Altman, Tomer; Dale, Joseph M.; Dreher, Kate; Fulcher, Carol A.; Gilham, Fred; Kaipa, Pallavi; Karthikeyan, Athikkattuvalasu S.; Kothari, Anamika; Krummenacker, Markus; Latendresse, Mario; Mueller, Lukas A.; Paley, Suzanne; Popescu, Liviu; Pujar, Anuradha; Shearer, Alexander G.; Zhang, Peifen; Karp, Peter D.

2010-01-01

The MetaCyc database (MetaCyc.org) is a comprehensive and freely accessible resource for metabolic pathways and enzymes from all domains of life. The pathways in MetaCyc are experimentally determined, small-molecule metabolic pathways and are curated from the primary scientific literature. With more than 1400 pathways, MetaCyc is the largest collection of metabolic pathways currently available. Pathways reactions are linked to one or more well-characterized enzymes, and both pathways and enzymes are annotated with reviews, evidence codes, and literature citations. BioCyc (BioCyc.org) is a collection of more than 500 organism-specific Pathway/Genome Databases (PGDBs). Each BioCyc PGDB contains the full genome and predicted metabolic network of one organism. The network, which is predicted by the Pathway Tools software using MetaCyc as a reference, consists of metabolites, enzymes, reactions and metabolic pathways. BioCyc PGDBs also contain additional features, such as predicted operons, transport systems, and pathway hole-fillers. The BioCyc Web site offers several tools for the analysis of the PGDBs, including Omics Viewers that enable visualization of omics datasets on two different genome-scale diagrams and tools for comparative analysis. The BioCyc PGDBs generated by SRI are offered for adoption by any party interested in curation of metabolic, regulatory, and genome-related information about an organism. PMID:19850718

ExplorEnz: a MySQL database of the IUBMB enzyme nomenclature.

Science.gov (United States)

McDonald, Andrew G; Boyce, Sinéad; Moss, Gerard P; Dixon, Henry B F; Tipton, Keith F

2007-07-27

We describe the database ExplorEnz, which is the primary repository for EC numbers and enzyme data that are being curated on behalf of the IUBMB. The enzyme nomenclature is incorporated into many other resources, including the ExPASy-ENZYME, BRENDA and KEGG bioinformatics databases. The data, which are stored in a MySQL database, preserve the formatting of chemical and enzyme names. A simple, easy to use, web-based query interface is provided, along with an advanced search engine for more complex queries. The database is publicly available at http://www.enzyme-database.org. The data are available for download as SQL and XML files via FTP. ExplorEnz has powerful and flexible search capabilities and provides the scientific community with the most up-to-date version of the IUBMB Enzyme List.

DMPD: Infectious non-self recognition in invertebrates: lessons from Drosophila andother insect models. [Dynamic Macrophage Pathway CSML Database

Lifescience Database Archive (English)

Full Text Available 15476918 Infectious non-self recognition in invertebrates: lessons from Drosophila ...fectious non-self recognition in invertebrates: lessons from Drosophila andother insect models. PubmedID 154...76918 Title Infectious non-self recognition in invertebrates: lessons from Drosop

Bookshelf: a simple curation system for the storage of biomolecular simulation data.

Science.gov (United States)

Vohra, Shabana; Hall, Benjamin A; Holdbrook, Daniel A; Khalid, Syma; Biggin, Philip C

2010-01-01

Molecular dynamics simulations can now routinely generate data sets of several hundreds of gigabytes in size. The ability to generate this data has become easier over recent years and the rate of data production is likely to increase rapidly in the near future. One major problem associated with this vast amount of data is how to store it in a way that it can be easily retrieved at a later date. The obvious answer to this problem is a database. However, a key issue in the development and maintenance of such a database is its sustainability, which in turn depends on the ease of the deposition and retrieval process. Encouraging users to care about meta-data is difficult and thus the success of any storage system will ultimately depend on how well used by end-users the system is. In this respect we suggest that even a minimal amount of metadata if stored in a sensible fashion is useful, if only at the level of individual research groups. We discuss here, a simple database system which we call 'Bookshelf', that uses python in conjunction with a mysql database to provide an extremely simple system for curating and keeping track of molecular simulation data. It provides a user-friendly, scriptable solution to the common problem amongst biomolecular simulation laboratories; the storage, logging and subsequent retrieval of large numbers of simulations. Download URL: http://sbcb.bioch.ox.ac.uk/bookshelf/

Bisphosphonate adverse effects, lessons from large databases

DEFF Research Database (Denmark)

Abrahamsen, Bo

2010-01-01

To review the latest findings on bisphosphonate safety from health databases, in particular sources that can provide incidence rates for stress fractures, osteonecrosis of the jaw (ONJ), atrial fibrillation and gastrointestinal lesions including esophageal cancer. The main focus is on bisphosphon...

Human Ageing Genomic Resources: new and updated databases

Science.gov (United States)

Tacutu, Robi; Thornton, Daniel; Johnson, Emily; Budovsky, Arie; Barardo, Diogo; Craig, Thomas; Diana, Eugene; Lehmann, Gilad; Toren, Dmitri; Wang, Jingwei; Fraifeld, Vadim E

2018-01-01

Abstract In spite of a growing body of research and data, human ageing remains a poorly understood process. Over 10 years ago we developed the Human Ageing Genomic Resources (HAGR), a collection of databases and tools for studying the biology and genetics of ageing. Here, we present HAGR’s main functionalities, highlighting new additions and improvements. HAGR consists of six core databases: (i) the GenAge database of ageing-related genes, in turn composed of a dataset of >300 human ageing-related genes and a dataset with >2000 genes associated with ageing or longevity in model organisms; (ii) the AnAge database of animal ageing and longevity, featuring >4000 species; (iii) the GenDR database with >200 genes associated with the life-extending effects of dietary restriction; (iv) the LongevityMap database of human genetic association studies of longevity with >500 entries; (v) the DrugAge database with >400 ageing or longevity-associated drugs or compounds; (vi) the CellAge database with >200 genes associated with cell senescence. All our databases are manually curated by experts and regularly updated to ensure a high quality data. Cross-links across our databases and to external resources help researchers locate and integrate relevant information. HAGR is freely available online (http://genomics.senescence.info/). PMID:29121237

Pathbase: A new reference resource and database for laboratory mouse pathology

International Nuclear Information System (INIS)

Schofield, P. N.; Bard, J. B. L.; Boniver, J.; Covelli, V.; Delvenne, P.; Ellender, M.; Engstrom, W.; Goessner, W.; Gruenberger, M.; Hoefler, H.; Hopewell, J. W.; Mancuso, M.; Mothersill, C.; Quintanilla-Martinez, L.; Rozell, B.; Sariola, H.; Sundberg, J. P.; Ward, A.

2004-01-01

Pathbase (http:/www.pathbase.net) is a web accessible database of histopathological images of laboratory mice, developed as a resource for the coding and archiving of data derived from the analysis of mutant or genetically engineered mice and their background strains. The metadata for the images, which allows retrieval and inter-operability with other databases, is derived from a series of orthogonal ontologies, and controlled vocabularies. One of these controlled vocabularies, MPATH, was developed by the Pathbase Consortium as a formal description of the content of mouse histopathological images. The database currently has over 1000 images on-line with 2000 more under curation and presents a paradigm for the development of future databases dedicated to aspects of experimental biology. (authors)

The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

Science.gov (United States)

Reddy, T.B.K.; Thomas, Alex D.; Stamatis, Dimitri; Bertsch, Jon; Isbandi, Michelle; Jansson, Jakob; Mallajosyula, Jyothi; Pagani, Ioanna; Lobos, Elizabeth A.; Kyrpides, Nikos C.

2015-01-01

The Genomes OnLine Database (GOLD; http://www.genomesonline.org) is a comprehensive online resource to catalog and monitor genetic studies worldwide. GOLD provides up-to-date status on complete and ongoing sequencing projects along with a broad array of curated metadata. Here we report version 5 (v.5) of the database. The newly designed database schema and web user interface supports several new features including the implementation of a four level (meta)genome project classification system and a simplified intuitive web interface to access reports and launch search tools. The database currently hosts information for about 19 200 studies, 56 000 Biosamples, 56 000 sequencing projects and 39 400 analysis projects. More than just a catalog of worldwide genome projects, GOLD is a manually curated, quality-controlled metadata warehouse. The problems encountered in integrating disparate and varying quality data into GOLD are briefly highlighted. GOLD fully supports and follows the Genomic Standards Consortium (GSC) Minimum Information standards. PMID:25348402

The Genomes OnLine Database (GOLD) v.5: a metadata management system based on a four level (meta)genome project classification

Energy Technology Data Exchange (ETDEWEB)

Reddy, Tatiparthi B. K. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Thomas, Alex D. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Stamatis, Dimitri [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Bertsch, Jon [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Isbandi, Michelle [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Jansson, Jakob [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Mallajosyula, Jyothi [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Pagani, Ioanna [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Lobos, Elizabeth A. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); Kyrpides, Nikos C. [USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); King Abdulaziz Univ., Jeddah (Saudi Arabia)

2014-10-27

The Genomes OnLine Database (GOLD; http://www.genomesonline.org) is a comprehensive online resource to catalog and monitor genetic studies worldwide. GOLD provides up-to-date status on complete and ongoing sequencing projects along with a broad array of curated metadata. Within this paper, we report version 5 (v.5) of the database. The newly designed database schema and web user interface supports several new features including the implementation of a four level (meta)genome project classification system and a simplified intuitive web interface to access reports and launch search tools. The database currently hosts information for about 19 200 studies, 56 000 Biosamples, 56 000 sequencing projects and 39 400 analysis projects. More than just a catalog of worldwide genome projects, GOLD is a manually curated, quality-controlled metadata warehouse. The problems encountered in integrating disparate and varying quality data into GOLD are briefly highlighted. Lastly, GOLD fully supports and follows the Genomic Standards Consortium (GSC) Minimum Information standards.

The prognostic importance of jaundice in surgical resection with curative intent for gallbladder cancer.

Science.gov (United States)

Yang, Xin-wei; Yuan, Jian-mao; Chen, Jun-yi; Yang, Jue; Gao, Quan-gen; Yan, Xing-zhou; Zhang, Bao-hua; Feng, Shen; Wu, Meng-chao

2014-09-03

Preoperative jaundice is frequent in gallbladder cancer (GBC) and indicates advanced disease. Resection is rarely recommended to treat advanced GBC. An aggressive surgical approach for advanced GBC remains lacking because of the association of this disease with serious postoperative complications and poor prognosis. This study aims to re-assess the prognostic value of jaundice for the morbidity, mortality, and survival of GBC patients who underwent surgical resection with curative intent. GBC patients who underwent surgical resection with curative intent at a single institution between January 2003 and December 2012 were identified from a prospectively maintained database. A total of 192 patients underwent surgical resection with curative intent, of whom 47 had preoperative jaundice and 145 had none. Compared with the non-jaundiced patients, the jaundiced patients had significantly longer operative time (p jaundice was the only independent predictor of postoperative complications. The jaundiced patients had lower survival rates than the non-jaundiced patients (p jaundiced patients. The survival rates of the jaundiced patients with preoperative biliary drainage (PBD) were similar to those of the jaundiced patients without PBD (p = 0.968). No significant differences in the rate of postoperative intra-abdominal abscesses were found between the jaundiced patients with and without PBD (n = 4, 21.1% vs. n = 5, 17.9%, p = 0.787). Preoperative jaundice indicates poor prognosis and high postoperative morbidity but is not a surgical contraindication. Gallbladder neck tumors significantly increase the surgical difficulty and reduce the opportunities for radical resection. Gallbladder neck tumors can independently predict poor outcome. PBD correlates with neither a low rate of postoperative intra-abdominal abscesses nor a high survival rate.

Safety and Mission Assurance for In-House Design Lessons Learned from Ares I Upper Stage

Science.gov (United States)

Anderson, Joel M.

2011-01-01

This viewgraph presentation identifies lessons learned in the course of the Ares I Upper Stage design and in-house development effort. The contents include: 1) Constellation Organization; 2) Upper Stage Organization; 3) Presentation Structure; 4) Lesson-Importance of Systems Engineering/Integration; 5) Lesson-Importance of Early S&MA Involvement; 6) Lesson-Importance of Appropriate Staffing Levels; 7) Lesson-Importance S&MA Team Deployment; 8) Lesson-Understanding of S&MA In-Line Engineering versus Assurance; 9) Lesson-Importance of Close Coordination between Supportability and Reliability/Maintainability; 10) Lesson-Importance of Engineering Data Systems; 11) Lesson-Importance of Early Development of Supporting Databases; 12) Lesson-Importance of Coordination with Safety Assessment/Review Panels; 13) Lesson-Implementation of Software Reliability; 14) Lesson-Implementation of S&MA Technical Authority/Chief S&MA Officer; 15) Lesson-Importance of S&MA Evaluation of Project Risks; 16) Lesson-Implementation of Critical Items List and Government Mandatory Inspections; 17) Lesson-Implementation of Critical Items List Mandatory Inspections; 18) Lesson-Implementation of Test Article Safety Analysis; and 19) Lesson-Importance of Procurement Quality.

HEROD: a human ethnic and regional specific omics database.

Science.gov (United States)

Zeng, Xian; Tao, Lin; Zhang, Peng; Qin, Chu; Chen, Shangying; He, Weidong; Tan, Ying; Xia Liu, Hong; Yang, Sheng Yong; Chen, Zhe; Jiang, Yu Yang; Chen, Yu Zong

2017-10-15

Genetic and gene expression variations within and between populations and across geographical regions have substantial effects on the biological phenotypes, diseases, and therapeutic response. The development of precision medicines can be facilitated by the OMICS studies of the patients of specific ethnicity and geographic region. However, there is an inadequate facility for broadly and conveniently accessing the ethnic and regional specific OMICS data. Here, we introduced a new free database, HEROD, a human ethnic and regional specific OMICS database. Its first version contains the gene expression data of 53 070 patients of 169 diseases in seven ethnic populations from 193 cities/regions in 49 nations curated from the Gene Expression Omnibus (GEO), the ArrayExpress Archive of Functional Genomics Data (ArrayExpress), the Cancer Genome Atlas (TCGA) and the International Cancer Genome Consortium (ICGC). Geographic region information of curated patients was mainly manually extracted from referenced publications of each original study. These data can be accessed and downloaded via keyword search, World map search, and menu-bar search of disease name, the international classification of disease code, geographical region, location of sample collection, ethnic population, gender, age, sample source organ, patient type (patient or healthy), sample type (disease or normal tissue) and assay type on the web interface. The HEROD database is freely accessible at http://bidd2.nus.edu.sg/herod/index.php. The database and web interface are implemented in MySQL, PHP and HTML with all major browsers supported. phacyz@nus.edu.sg. © The Author (2017). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oup.com

DCC DIFFUSE Standards Frameworks: A Standards Path through the Curation Lifecycle

Directory of Open Access Journals (Sweden)

Sarah Higgins

2009-10-01

Full Text Available Normal 0 false false false MicrosoftInternetExplorer4 DCC DIFFUSE Standards Frameworks aims to offer domain specific advice on standards relevant to digital preservation and curation, to help curators identify which standards they should be using and where they can be appropriately implemented, to ensure authoritative digital material. The Project uses the DCC Curation Lifecycle Model and Web 2.0 technology, to visually present standards frameworks for a number of disciplines. The Digital Curation Centre (DCC is actively working with a different relevant organisations to present searchable frameworks of standards, for a number of domains. These include digital repositories, records management, the geo-information sector, archives and the museum sector. Other domains, such as e-science, will shortly be investigated.

Human Variome Project Quality Assessment Criteria for Variation Databases.

Science.gov (United States)

Vihinen, Mauno; Hancock, John M; Maglott, Donna R; Landrum, Melissa J; Schaafsma, Gerard C P; Taschner, Peter

2016-06-01

Numerous databases containing information about DNA, RNA, and protein variations are available. Gene-specific variant databases (locus-specific variation databases, LSDBs) are typically curated and maintained for single genes or groups of genes for a certain disease(s). These databases are widely considered as the most reliable information source for a particular gene/protein/disease, but it should also be made clear they may have widely varying contents, infrastructure, and quality. Quality is very important to evaluate because these databases may affect health decision-making, research, and clinical practice. The Human Variome Project (HVP) established a Working Group for Variant Database Quality Assessment. The basic principle was to develop a simple system that nevertheless provides a good overview of the quality of a database. The HVP quality evaluation criteria that resulted are divided into four main components: data quality, technical quality, accessibility, and timeliness. This report elaborates on the developed quality criteria and how implementation of the quality scheme can be achieved. Examples are provided for the current status of the quality items in two different databases, BTKbase, an LSDB, and ClinVar, a central archive of submissions about variants and their clinical significance. © 2016 WILEY PERIODICALS, INC.

The Annotometer; Encouraging uptake and use of freely available curation tools.

OpenAIRE

Zhe, Xiao Si; Edmunds, Scott; Li, Peter; Goodman, Laurie; Hunter, Christopher

2016-01-01

In recent years it has become clear that the amount of data being generated worldwide cannot be curated and annotated by any individual or small group. Currently, there is recognition that one of the best ways to provide ongoing curation is to employ the power of the community. To achieve this, the first hurdle to overcome was the development of user-friendly tools and apps that non-expert curators would be comfortable and capable of using. Such tools are now in place, inclu...

Teacher Training in Curative Education.

Science.gov (United States)

Juul, Kristen D.; Maier, Manfred

1992-01-01

This article considers the application of the philosophical and educational principles of Rudolf Steiner, called "anthroposophy," to the training of teachers and curative educators in the Waldorf schools. Special emphasis is on the Camphill movement which focuses on therapeutic schools and communities for children with special needs. (DB)

The Structure-Function Linkage Database.

Science.gov (United States)

Akiva, Eyal; Brown, Shoshana; Almonacid, Daniel E; Barber, Alan E; Custer, Ashley F; Hicks, Michael A; Huang, Conrad C; Lauck, Florian; Mashiyama, Susan T; Meng, Elaine C; Mischel, David; Morris, John H; Ojha, Sunil; Schnoes, Alexandra M; Stryke, Doug; Yunes, Jeffrey M; Ferrin, Thomas E; Holliday, Gemma L; Babbitt, Patricia C

2014-01-01

The Structure-Function Linkage Database (SFLD, http://sfld.rbvi.ucsf.edu/) is a manually curated classification resource describing structure-function relationships for functionally diverse enzyme superfamilies. Members of such superfamilies are diverse in their overall reactions yet share a common ancestor and some conserved active site features associated with conserved functional attributes such as a partial reaction. Thus, despite their different functions, members of these superfamilies 'look alike', making them easy to misannotate. To address this complexity and enable rational transfer of functional features to unknowns only for those members for which we have sufficient functional information, we subdivide superfamily members into subgroups using sequence information, and lastly into families, sets of enzymes known to catalyze the same reaction using the same mechanistic strategy. Browsing and searching options in the SFLD provide access to all of these levels. The SFLD offers manually curated as well as automatically classified superfamily sets, both accompanied by search and download options for all hierarchical levels. Additional information includes multiple sequence alignments, tab-separated files of functional and other attributes, and sequence similarity networks. The latter provide a new and intuitively powerful way to visualize functional trends mapped to the context of sequence similarity.

Managing expectations: assessment of chemistry databases generated by automated extraction of chemical structures from patents.

Science.gov (United States)

Senger, Stefan; Bartek, Luca; Papadatos, George; Gaulton, Anna

2015-12-01

First public disclosure of new chemical entities often takes place in patents, which makes them an important source of information. However, with an ever increasing number of patent applications, manual processing and curation on such a large scale becomes even more challenging. An alternative approach better suited for this large corpus of documents is the automated extraction of chemical structures. A number of patent chemistry databases generated by using the latter approach are now available but little is known that can help to manage expectations when using them. This study aims to address this by comparing two such freely available sources, SureChEMBL and IBM SIIP (IBM Strategic Intellectual Property Insight Platform), with manually curated commercial databases. When looking at the percentage of chemical structures successfully extracted from a set of patents, using SciFinder as our reference, 59 and 51 % were also found in our comparison in SureChEMBL and IBM SIIP, respectively. When performing this comparison with compounds as starting point, i.e. establishing if for a list of compounds the databases provide the links between chemical structures and patents they appear in, we obtained similar results. SureChEMBL and IBM SIIP found 62 and 59 %, respectively, of the compound-patent pairs obtained from Reaxys. In our comparison of automatically generated vs. manually curated patent chemistry databases, the former successfully provided approximately 60 % of links between chemical structure and patents. It needs to be stressed that only a very limited number of patents and compound-patent pairs were used for our comparison. Nevertheless, our results will hopefully help to manage expectations of users of patent chemistry databases of this type and provide a useful framework for more studies like ours as well as guide future developments of the workflows used for the automated extraction of chemical structures from patents. The challenges we have encountered

The Danish Microbiology Database (MiBa) 2010 to 2013.

Science.gov (United States)

Voldstedlund, M; Haarh, M; Mølbak, K

2014-01-09

The Danish Microbiology Database (MiBa) is a national database that receives copies of reports from all Danish departments of clinical microbiology. The database was launched in order to provide healthcare personnel with nationwide access to microbiology reports and to enable real-time surveillance of communicable diseases and microorganisms. The establishment and management of MiBa has been a collaborative process among stakeholders, and the present paper summarises lessons learned from this nationwide endeavour which may be relevant to similar projects in the rapidly changing landscape of health informatics.

Advanced Curation Protocols for Mars Returned Sample Handling

Science.gov (United States)

Bell, M.; Mickelson, E.; Lindstrom, D.; Allton, J.

Introduction: Johnson Space Center has over 30 years experience handling precious samples which include Lunar rocks and Antarctic meteorites. However, we recognize that future curation of samples from such missions as Genesis, Stardust, and Mars S mple Return, will require a high degree of biosafety combined witha extremely low levels of inorganic, organic, and biological contamination. To satisfy these requirements, research in the JSC Advanced Curation Lab is currently focused toward two major areas: preliminary examination techniques and cleaning and verification techniques . Preliminary Examination Techniques : In order to minimize the number of paths for contamination we are exploring the synergy between human &robotic sample handling in a controlled environment to help determine the limits of clean curation. Within the Advanced Curation Laboratory is a prototype, next-generation glovebox, which contains a robotic micromanipulator. The remotely operated manipulator has six degrees-of- freedom and can be programmed to perform repetitive sample handling tasks. Protocols are being tested and developed to perform curation tasks such as rock splitting, weighing, imaging, and storing. Techniques for sample transfer enabling more detailed remote examination without compromising the integrity of sample science are also being developed . The glovebox is equipped with a rapid transfer port through which samples can be passed without exposure. The transfer is accomplished by using a unique seal and engagement system which allows passage between containers while maintaining a first seal to the outside environment and a second seal to prevent the outside of the container cover and port door from becoming contaminated by the material being transferred. Cleaning and Verification Techniques: As part of the contamination control effort, innovative cleaning techniques are being identified and evaluated in conjunction with sensitive cleanliness verification methods. Towards this

TRENDS: The aeronautical post-test database management system

Science.gov (United States)

Bjorkman, W. S.; Bondi, M. J.

1990-01-01

TRENDS, an engineering-test database operating system developed by NASA to support rotorcraft flight tests, is described. Capabilities and characteristics of the system are presented, with examples of its use in recalling and analyzing rotorcraft flight-test data from a TRENDS database. The importance of system user-friendliness in gaining users' acceptance is stressed, as is the importance of integrating supporting narrative data with numerical data in engineering-test databases. Considerations relevant to the creation and maintenance of flight-test database are discussed and TRENDS' solutions to database management problems are described. Requirements, constraints, and other considerations which led to the system's configuration are discussed and some of the lessons learned during TRENDS' development are presented. Potential applications of TRENDS to a wide range of aeronautical and other engineering tests are identified.

Prioritizing PubMed articles for the Comparative Toxicogenomic Database utilizing semantic information.

Science.gov (United States)

Kim, Sun; Kim, Won; Wei, Chih-Hsuan; Lu, Zhiyong; Wilbur, W John

2012-01-01

The Comparative Toxicogenomics Database (CTD) contains manually curated literature that describes chemical-gene interactions, chemical-disease relationships and gene-disease relationships. Finding articles containing this information is the first and an important step to assist manual curation efficiency. However, the complex nature of named entities and their relationships make it challenging to choose relevant articles. In this article, we introduce a machine learning framework for prioritizing CTD-relevant articles based on our prior system for the protein-protein interaction article classification task in BioCreative III. To address new challenges in the CTD task, we explore a new entity identification method for genes, chemicals and diseases. In addition, latent topics are analyzed and used as a feature type to overcome the small size of the training set. Applied to the BioCreative 2012 Triage dataset, our method achieved 0.8030 mean average precision (MAP) in the official runs, resulting in the top MAP system among participants. Integrated with PubTator, a Web interface for annotating biomedical literature, the proposed system also received a positive review from the CTD curation team.

The Distinction Between Curative and Assistive Technology.

Science.gov (United States)

Stramondo, Joseph A

2018-05-01

Disability activists have sometimes claimed their disability has actually increased their well-being. Some even say they would reject a cure to keep these gains. Yet, these same activists often simultaneously propose improvements to the quality and accessibility of assistive technology. However, for any argument favoring assistive over curative technology (or vice versa) to work, there must be a coherent distinction between the two. This line is already vague and will become even less clear with the emergence of novel technologies. This paper asks and tries to answer the question: what is it about the paradigmatic examples of curative and assistive technologies that make them paradigmatic and how can these defining features help us clarify the hard cases? This analysis will begin with an argument that, while the common views of this distinction adequately explain the paradigmatic cases, they fail to accurately pick out the relevant features of those technologies that make them paradigmatic and to provide adequate guidance for parsing the hard cases. Instead, it will be claimed that these categories of curative or assistive technologies are defined by the role the technologies play in establishing a person's relational narrative identity as a member of one of two social groups: disabled people or non-disabled people.

REDfly: a Regulatory Element Database for Drosophila.

Science.gov (United States)

Gallo, Steven M; Li, Long; Hu, Zihua; Halfon, Marc S

2006-02-01

Bioinformatics studies of transcriptional regulation in the metazoa are significantly hindered by the absence of readily available data on large numbers of transcriptional cis-regulatory modules (CRMs). Even the richly annotated Drosophila melanogaster genome lacks extensive CRM information. We therefore present here a database of Drosophila CRMs curated from the literature complete with both DNA sequence and a searchable description of the gene expression pattern regulated by each CRM. This resource should greatly facilitate the development of computational approaches to CRM discovery as well as bioinformatics analyses of regulatory sequence properties and evolution.

Content curation en periodismo (y en documentación periodística

Directory of Open Access Journals (Sweden)

Javier Guallar

2014-05-01

Full Text Available Desde hace unos pocos años están con nosotros los conceptos de content curation y de content curator como actividad o sistema y como profesional o especialista, respectivamente. Aunque el origen del término se vincule al mundo del marketing –se considera como artículo fundacional “Manifesto for the content curator” del marketer Rohit Bhargava (2009-, y sus características se identifiquen en buena medida con las del profesional de la Información y la Documentación, la content curation va más allá de una disciplina concreta o de un rol profesional determinado. Ambos perfiles citados, marketers y bibliotecarios-documentalistas, pueden hacer content curation por supuesto, pero también otros, como educadores, por ejemplo. Y, como es el caso que tratamos aquí, periodistas (y documentalistas de prensa. Porque en estas breves líneas nos vamos a centrar en presentar el papel de la content curation en el ámbito del periodismo.

Advanced Curation: Solving Current and Future Sample Return Problems

Science.gov (United States)

Fries, M.; Calaway, M.; Evans, C.; McCubbin, F.

2015-01-01

Advanced Curation is a wide-ranging and comprehensive research and development effort at NASA Johnson Space Center that identifies and remediates sample related issues. For current collections, Advanced Curation investigates new cleaning, verification, and analytical techniques to assess their suitability for improving curation processes. Specific needs are also assessed for future sample return missions. For each need, a written plan is drawn up to achieve the requirement. The plan draws while upon current Curation practices, input from Curators, the analytical expertise of the Astromaterials Research and Exploration Science (ARES) team, and suitable standards maintained by ISO, IEST, NIST and other institutions. Additionally, new technologies are adopted on the bases of need and availability. Implementation plans are tested using customized trial programs with statistically robust courses of measurement, and are iterated if necessary until an implementable protocol is established. Upcoming and potential NASA missions such as OSIRIS-REx, the Asteroid Retrieval Mission (ARM), sample return missions in the New Frontiers program, and Mars sample return (MSR) all feature new difficulties and specialized sample handling requirements. The Mars 2020 mission in particular poses a suite of challenges since the mission will cache martian samples for possible return to Earth. In anticipation of future MSR, the following problems are among those under investigation: What is the most efficient means to achieve the less than 1.0 ng/sq cm total organic carbon (TOC) cleanliness required for all sample handling hardware? How do we maintain and verify cleanliness at this level? The Mars 2020 Organic Contamination Panel (OCP) predicts that organic carbon, if present, will be present at the "one to tens" of ppb level in martian near-surface samples. The same samples will likely contain wt% perchlorate salts, or approximately 1,000,000x as much perchlorate oxidizer as organic carbon

Protective, curative and eradicative activities of fungicides against grapevine rust

Directory of Open Access Journals (Sweden)

Francislene Angelotti

2014-01-01

Full Text Available The protective, eradicative and curative activities of the fungicides azoxystrobin, tebuconazole, pyraclostrobin+metiram, and ciproconazole against grapevine rust, were determined in greenhouse. To evaluate the protective activity, leaves of potted ´Niagara´ (Vitis labrusca vines were artificially inoculated with an urediniospore suspension of Phakopsora euvitis four, eight or forteen days after fungicidal spray; and to evaluate the curative and eradicative activities, leaves were sprayed with fungicides two, four or eight days after inoculation. Disease severity was assessed 14 days after each inoculation. All tested fungicides present excellent preventive activity against grapevine rust; however, tebuconazole and ciproconazole provide better curative activity than azoxystrobin and pyraclostrobin+metiram. It was observed also that all tested fungicides significantly reduced the germination of urediniospore produced on sprayed leaves.

A High School Student's Bill of Rights. Teaching Resources in the ERIC Database (TRIED) Series.

Science.gov (United States)

Gottlieb, Stephen S.

Designed to tap the rich collection of instructional techniques in the ERIC database, this compilation of lesson plans focuses on teaching high school students their Constitutional rights and responsibilities. The 40 lesson plans in the book cover the courts and basic rights, the rights of criminal suspects, the rights of minors and education law,…

Data Stewardship: Environmental Data Curation and a Web-of-Repositories

Directory of Open Access Journals (Sweden)

Karen S. Baker

2009-10-01

Full Text Available Scientific researchers today frequently package measurements and associated metadata as digital datasets in anticipation of storage in data repositories. Through the lens of environmental data stewardship, we consider the data repository as an organizational element central to data curation. One aspect of non-commercial repositories, their distance-from-origin of the data, is explored in terms of near and remote categories. Three idealized repository types are distinguished – local, center, and archive - paralleling research, resource, and reference collection categories respectively. Repository type characteristics such as scope, structure, and goals are discussed. Repository similarities in terms of roles, activities and responsibilities are also examined. Data stewardship is related to care of research data and responsible scientific communication supported by an infrastructure that coordinates curation activities; data curation is defined as a set of repeated and repeatable activities focusing on tending data and creating data products within a particular arena. The concept of “sphere-of-context” is introduced as an aid to distinguishing repository types. Conceptualizing a “web-of-repositories” accommodates a variety of repository types and represents an ecologically inclusive approach to data curation.

HIM-herbal ingredients in-vivo metabolism database.

Science.gov (United States)

Kang, Hong; Tang, Kailin; Liu, Qi; Sun, Yi; Huang, Qi; Zhu, Ruixin; Gao, Jun; Zhang, Duanfeng; Huang, Chenggang; Cao, Zhiwei

2013-05-31

Herbal medicine has long been viewed as a valuable asset for potential new drug discovery and herbal ingredients' metabolites, especially the in vivo metabolites were often found to gain better pharmacological, pharmacokinetic and even better safety profiles compared to their parent compounds. However, these herbal metabolite information is still scattered and waiting to be collected. HIM database manually collected so far the most comprehensive available in-vivo metabolism information for herbal active ingredients, as well as their corresponding bioactivity, organs and/or tissues distribution, toxicity, ADME and the clinical research profile. Currently HIM contains 361 ingredients and 1104 corresponding in-vivo metabolites from 673 reputable herbs. Tools of structural similarity, substructure search and Lipinski's Rule of Five are also provided. Various links were made to PubChem, PubMed, TCM-ID (Traditional Chinese Medicine Information database) and HIT (Herbal ingredients' targets databases). A curated database HIM is set up for the in vivo metabolites information of the active ingredients for Chinese herbs, together with their corresponding bioactivity, toxicity and ADME profile. HIM is freely accessible to academic researchers at http://www.bioinformatics.org.cn/.

Lessons Learned from Past and Ongoing Construction Projects

International Nuclear Information System (INIS)

Tabatabai, Omid

2011-01-01

Full text of publication follows: The nuclear industry in the U.S. faced many construction quality and design issues in the 1970's and 1980's. In 1984, the NRC issued NUREG-1055, 'Improving Quality and the Assurance of Quality in the Design and Construction of Nuclear Power Plants,' to document the lessons learned from nuclear power plant (NPP) construction in the U.S. In recent years, several countries have begun either planning for or actually constructing new NPPs. For instance, in the U.S., the nuclear industry has submitted several combined license and design certification applications to the NRC for licensing reviews and approval to build 30+ new NPP units. Latest construction experience from countries that are currently building new NPPs indicate that these countries are dealing with challenges that are similar to those issues that caused major quality assurance problems, delays, or even termination of several projects in U.S. in the 70's and 80's. The U.S. NRC is pro-actively taking measures to improve its regulatory programs as well as construction oversight activities before new NPPs construction begin in the U.S. In late 2007, the U.S. NRC's Office of New Reactors established a construction experience program (ConE) to obtain and evaluate construction and operating experience events and to identify the lessons learned from these events. In March 2009, the NRC published an Office Instruction to provide a process for incorporating the lessons learned and insights from the design, construction, and operation of the international and domestic NPPs into the licensing reviews, inspections, and construction of new reactors in the U.S. Additionally, the ConE program staff developed a Web-enabled database to store, manage, and make construction experience information available to all NRC technical reviewers as well as inspectors. Because this database contains information from other countries' regulators that are considered

Biocuration at the Saccharomyces genome database.

Science.gov (United States)

Skrzypek, Marek S; Nash, Robert S

2015-08-01

Saccharomyces Genome Database is an online resource dedicated to managing information about the biology and genetics of the model organism, yeast (Saccharomyces cerevisiae). This information is derived primarily from scientific publications through a process of human curation that involves manual extraction of data and their organization into a comprehensive system of knowledge. This system provides a foundation for further analysis of experimental data coming from research on yeast as well as other organisms. In this review we will demonstrate how biocuration and biocurators add a key component, the biological context, to our understanding of how genes, proteins, genomes and cells function and interact. We will explain the role biocurators play in sifting through the wealth of biological data to incorporate and connect key information. We will also discuss the many ways we assist researchers with their various research needs. We hope to convince the reader that manual curation is vital in converting the flood of data into organized and interconnected knowledge, and that biocurators play an essential role in the integration of scientific information into a coherent model of the cell. © 2015 Wiley Periodicals, Inc.

Data Curation Education Grounded in Earth Sciences and the Science of Data

Science.gov (United States)

Palmer, C. L.

2015-12-01

This presentation looks back over ten years of experience advancing data curation education at two Information Schools, highlighting the vital role of earth science case studies, expertise, and collaborations in development of curriculum and internships. We also consider current data curation practices and workforce demand in data centers in the geosciences, drawing on studies conducted in the Data Curation Education in Research Centers (DCERC) initiative and the Site-Based Data Curation project. Outcomes from this decade of data curation research and education has reinforced the importance of key areas of information science in preparing data professionals to respond to the needs of user communities, provide services across disciplines, invest in standards and interoperability, and promote open data practices. However, a serious void remains in principles to guide education and practice that are distinct to the development of data systems and services that meet both local and global aims. We identify principles emerging from recent empirical studies on the reuse value of data in the earth sciences and propose an approach for advancing data curation education that depends on systematic coordination with data intensive research and propagation of current best practices from data centers into curriculum. This collaborative model can increase both domain-based and cross-disciplinary expertise among data professionals, ultimately improving data systems and services in our universities and data centers while building the new base of knowledge needed for a foundational science of data.

The Structure–Function Linkage Database

Science.gov (United States)

Akiva, Eyal; Brown, Shoshana; Almonacid, Daniel E.; Barber, Alan E.; Custer, Ashley F.; Hicks, Michael A.; Huang, Conrad C.; Lauck, Florian; Mashiyama, Susan T.; Meng, Elaine C.; Mischel, David; Morris, John H.; Ojha, Sunil; Schnoes, Alexandra M.; Stryke, Doug; Yunes, Jeffrey M.; Ferrin, Thomas E.; Holliday, Gemma L.; Babbitt, Patricia C.

2014-01-01

The Structure–Function Linkage Database (SFLD, http://sfld.rbvi.ucsf.edu/) is a manually curated classification resource describing structure–function relationships for functionally diverse enzyme superfamilies. Members of such superfamilies are diverse in their overall reactions yet share a common ancestor and some conserved active site features associated with conserved functional attributes such as a partial reaction. Thus, despite their different functions, members of these superfamilies ‘look alike’, making them easy to misannotate. To address this complexity and enable rational transfer of functional features to unknowns only for those members for which we have sufficient functional information, we subdivide superfamily members into subgroups using sequence information, and lastly into families, sets of enzymes known to catalyze the same reaction using the same mechanistic strategy. Browsing and searching options in the SFLD provide access to all of these levels. The SFLD offers manually curated as well as automatically classified superfamily sets, both accompanied by search and download options for all hierarchical levels. Additional information includes multiple sequence alignments, tab-separated files of functional and other attributes, and sequence similarity networks. The latter provide a new and intuitively powerful way to visualize functional trends mapped to the context of sequence similarity. PMID:24271399

Lessons Learned from resolving massive IPS database change for SPADES+

International Nuclear Information System (INIS)

Kim, Jin-Soo

2016-01-01

Safety Parameter Display and Evaluation System+ (SPADES+) was implemented to meet the requirements for Safety Parameter Display System (SPDS) which are related to TMI Action Plan requirements. SPADES+ monitors continuously the critical safety function during normal, abnormal, and emergency operation mode and generates the alarm output to the alarm server when the tolerance related to safety functions are not satisfied. The alarm algorithm for critical safety function is performed in the NSSS Application Software (NAPS) server of the Information Process System (IPS) and the calculation result will be displayed on the flat panel display (FPD) of the IPS. SPADES+ provides the critical variable to the control room operators to aid them in rapidly and reliable determining the safety status of the plant. Many database point ID names (518 points) were changed. POINT_ID is used in the programming source code, the related documents such as SDS and SRS, and Graphic database. To reduce human errors, computer program and office program’s Macro are used. Though the automatic methods are used for changing POINT_IDs, it takes lots of time to resolve for editing the change list except for making computerized solutions. In IPS, there are many more programs than SPADES+ and over 30,000 POINT_IDs are in IPS database. Changing POINT_IDs could be a burden to software engineers. In case of Ovation system database, there is the Alias field to prevent this kind of problem. The Alias is a kind of secondary key in database

The Hayabusa Curation Facility at Johnson Space Center

Science.gov (United States)

Zolensky, M.; Bastien, R.; McCann, B.; Frank, D.; Gonzalez, C.; Rodriguez, M.

2013-01-01

The Japan Aerospace Exploration Agency (JAXA) Hayabusa spacecraft made contact with the asteroid 25143 Itokawa and collected regolith dust from Muses Sea region of smooth terrain [1]. The spacecraft returned to Earth with more than 10,000 grains ranging in size from just over 300 µm to less than 10 µm [2, 3]. These grains represent the only collection of material returned from an asteroid by a spacecraft. As part of the joint agreement between JAXA and NASA for the mission, 10% of the Hayabusa grains are being transferred to NASA for parallel curation and allocation. In order to properly receive process and curate these samples, a new curation facility was established at Johnson Space Center (JSC). Since the Hayabusa samples within the JAXA curation facility have been stored free from exposure to terrestrial atmosphere and contamination [4], one of the goals of the new NASA curation facility was to continue this treatment. An existing lab space at JSC was transformed into a 120 sq.ft. ISO class 4 (equivalent to the original class 10 standard) clean room. Hayabusa samples are stored, observed, processed, and packaged for allocation inside a stainless steel glove box under dry N2. Construction of the clean laboratory was completed in 2012. Currently, 25 Itokawa particles are lodged in NASA's Hayabusa Lab. Special care has been taken during lab construction to remove or contain materials that may contribute contaminant particles in the same size range as the Hayabusa grains. Several witness plates of various materials are installed around the clean lab and within the glove box to permit characterization of local contaminants at regular intervals by SEM and mass spectrometry, and particle counts of the lab environment are frequently acquired. Of particular interest is anodized aluminum, which contains copious sub-mm grains of a multitude of different materials embedded in its upper surface. Unfortunately the use of anodized aluminum was necessary in the construction

Building a genome database using an object-oriented approach.

Science.gov (United States)

Barbasiewicz, Anna; Liu, Lin; Lang, B Franz; Burger, Gertraud

2002-01-01

GOBASE is a relational database that integrates data associated with mitochondria and chloroplasts. The most important data in GOBASE, i. e., molecular sequences and taxonomic information, are obtained from the public sequence data repository at the National Center for Biotechnology Information (NCBI), and are validated by our experts. Maintaining a curated genomic database comes with a towering labor cost, due to the shear volume of available genomic sequences and the plethora of annotation errors and omissions in records retrieved from public repositories. Here we describe our approach to increase automation of the database population process, thereby reducing manual intervention. As a first step, we used Unified Modeling Language (UML) to construct a list of potential errors. Each case was evaluated independently, and an expert solution was devised, and represented as a diagram. Subsequently, the UML diagrams were used as templates for writing object-oriented automation programs in the Java programming language.

Organic Contamination Baseline Study: In NASA JSC Astromaterials Curation Laboratories. Summary Report

Science.gov (United States)

Calaway, Michael J.

2013-01-01

In preparation for OSIRIS-REx and other future sample return missions concerned with analyzing organics, we conducted an Organic Contamination Baseline Study for JSC Curation Labsoratories in FY12. For FY12 testing, organic baseline study focused only on molecular organic contamination in JSC curation gloveboxes: presumably future collections (i.e. Lunar, Mars, asteroid missions) would use isolation containment systems over only cleanrooms for primary sample storage. This decision was made due to limit historical data on curation gloveboxes, limited IR&D funds and Genesis routinely monitors organics in their ISO class 4 cleanrooms.

Refusal of curative radiation therapy and surgery among patients with cancer.

Science.gov (United States)

Aizer, Ayal A; Chen, Ming-Hui; Parekh, Arti; Choueiri, Toni K; Hoffman, Karen E; Kim, Simon P; Martin, Neil E; Hu, Jim C; Trinh, Quoc-Dien; Nguyen, Paul L

2014-07-15

Surgery and radiation therapy represent the only curative options for many patients with solid malignancies. However, despite the recommendations of their physicians, some patients refuse these therapies. This study characterized factors associated with refusal of surgical or radiation therapy as well as the impact of refusal of recommended therapy on patients with localized malignancies. We used the Surveillance, Epidemiology, and End Results program to identify a population-based sample of 925,127 patients who had diagnoses of 1 of 8 common malignancies for which surgery and/or radiation are believed to confer a survival benefit between 1995 and 2008. Refusal of oncologic therapy, as documented in the SEER database, was the primary outcome measure. Multivariable logistic regression was used to investigate factors associated with refusal. The impact of refusal of therapy on cancer-specific mortality was assessed with Fine and Gray's competing risks regression. In total, 2441 of 692,938 patients (0.4%) refused surgery, and 2113 of 232,189 patients (0.9%) refused radiation, despite the recommendations of their physicians. On multivariable analysis, advancing age, decreasing annual income, nonwhite race, and unmarried status were associated with refusal of surgery, whereas advancing age, decreasing annual income, Asian American race, and unmarried status were associated with refusal of radiation (PRefusal of surgery and radiation were associated with increased estimates of cancer-specific mortality for all malignancies evaluated (hazard ratio [HR], 2.80, 95% confidence interval [CI], 2.59-3.03; Prefuse curative surgical and/or radiation-based oncologic therapy, raising concern that socioeconomic factors may drive some patients to forego potentially life-saving care. Copyright © 2014 Elsevier Inc. All rights reserved.

Locus-Specific Databases and Recommendations to Strengthen Their Contribution to the Classification of Variants in Cancer Susceptibility Genes

NARCIS (Netherlands)

Greenblatt, Marc S.; Brody, Lawrence C.; Foulkes, William D.; Genuardi, Maurizio; Hofstra, Robert M. W.; Olivier, Magali; Plon, Sharon E.; Sijmons, Rolf H.; Sinilnikova, Olga; Spurdle, Amanda B.

2008-01-01

Locus-specific databases (LSDBs) are curated collections of sequence variants in genes associated with disease. LSDBs of cancer-related genes often serve as a critical resource to researchers, diagnostic laboratories, clinicians, and others in the cancer genetics community. LSDBs are poised to play

Kalium: a database of potassium channel toxins from scorpion venom.

Science.gov (United States)

Kuzmenkov, Alexey I; Krylov, Nikolay A; Chugunov, Anton O; Grishin, Eugene V; Vassilevski, Alexander A

2016-01-01

Kalium (http://kaliumdb.org/) is a manually curated database that accumulates data on potassium channel toxins purified from scorpion venom (KTx). This database is an open-access resource, and provides easy access to pages of other databases of interest, such as UniProt, PDB, NCBI Taxonomy Browser, and PubMed. General achievements of Kalium are a strict and easy regulation of KTx classification based on the unified nomenclature supported by researchers in the field, removal of peptides with partial sequence and entries supported by transcriptomic information only, classification of β-family toxins, and addition of a novel λ-family. Molecules presented in the database can be processed by the Clustal Omega server using a one-click option. Molecular masses of mature peptides are calculated and available activity data are compiled for all KTx. We believe that Kalium is not only of high interest to professional toxinologists, but also of general utility to the scientific community.Database URL:http://kaliumdb.org/. © The Author(s) 2016. Published by Oxford University Press.

Lessons Learned from resolving massive IPS database change for SPADES+

Energy Technology Data Exchange (ETDEWEB)

Kim, Jin-Soo [KEPCO Engineering and Construction Co., Deajeon (Korea, Republic of)

2016-10-15

Safety Parameter Display and Evaluation System+ (SPADES+) was implemented to meet the requirements for Safety Parameter Display System (SPDS) which are related to TMI Action Plan requirements. SPADES+ monitors continuously the critical safety function during normal, abnormal, and emergency operation mode and generates the alarm output to the alarm server when the tolerance related to safety functions are not satisfied. The alarm algorithm for critical safety function is performed in the NSSS Application Software (NAPS) server of the Information Process System (IPS) and the calculation result will be displayed on the flat panel display (FPD) of the IPS. SPADES+ provides the critical variable to the control room operators to aid them in rapidly and reliable determining the safety status of the plant. Many database point ID names (518 points) were changed. POINT{sub I}D is used in the programming source code, the related documents such as SDS and SRS, and Graphic database. To reduce human errors, computer program and office program’s Macro are used. Though the automatic methods are used for changing POINT{sub I}Ds, it takes lots of time to resolve for editing the change list except for making computerized solutions. In IPS, there are many more programs than SPADES+ and over 30,000 POINT{sub I}Ds are in IPS database. Changing POINT{sub I}Ds could be a burden to software engineers. In case of Ovation system database, there is the Alias field to prevent this kind of problem. The Alias is a kind of secondary key in database.

Data Curation Program Development in U.S. Universities: The Georgia Institute of Technology Example

Directory of Open Access Journals (Sweden)

Tyler O. Walters

2009-12-01

Full Text Available The curation of scientific research data at U.S. universities is a story of enterprising individuals and of incremental progress. A small number of libraries and data centers who see the possibilities of becoming “digital information management centers” are taking entrepreneurial steps to extend beyond their traditional information assets and include managing scientific and scholarly research data. The Georgia Institute of Technology (GT has had a similar development path toward a data curation program based in its library. This paper will articulate GT’s program development, which the author offers as an experience common in U.S. universities. The main characteristic is a program devoid of top-level mandates and incentives, but rich with independent, “bottom-up” action. The paper will address program antecedents and context, inter-institutional partnerships that advance the library’s curation program, library organizational developments, partnerships with campus research communities, and a proposed model for curation program development. It concludes that despite the clear need for data curation put forth by researchers such as the groups of neuroscientists and bioscientists referenced in this paper, the university experience examined suggests that gathering resources for developing data curation programs at the institutional level is proving to be a quite onerous. However, and in spite of the challenges, some U.S. research universities are beginning to establish perceptible data curation programs.

Curating Public Art 2.0: The case of Autopoiesis

DEFF Research Database (Denmark)

Ajana, Btihaj

2017-01-01

This article examines the intersections between public art, curation and Web 2.0 technology. Building on the case study of Autopoiesis, a digital art project focusing on the curation and online exhibition of artworks received from members of the public in the United Arab Emirates, the article...... to facilitate autonomous creative self-expressions and enable greater public participation in culture. By providing a critical reflection on the ‘material’ contexts of this digital project, the article also demonstrates the related tensions between the virtual and the physical, and the wider ‘local’ realities...

PHI-base: a new interface and further additions for the multi-species pathogen–host interactions database

Science.gov (United States)

Urban, Martin; Cuzick, Alayne; Rutherford, Kim; Irvine, Alistair; Pedro, Helder; Pant, Rashmi; Sadanadan, Vidyendra; Khamari, Lokanath; Billal, Santoshkumar; Mohanty, Sagar; Hammond-Kosack, Kim E.

2017-01-01

The pathogen–host interactions database (PHI-base) is available at www.phi-base.org. PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen–host interactions reported in peer reviewed research articles. In addition, literature that indicates specific gene alterations that did not affect the disease interaction phenotype are curated to provide complete datasets for comparative purposes. Viruses are not included. Here we describe a revised PHI-base Version 4 data platform with improved search, filtering and extended data display functions. A PHIB-BLAST search function is provided and a link to PHI-Canto, a tool for authors to directly curate their own published data into PHI-base. The new release of PHI-base Version 4.2 (October 2016) has an increased data content containing information from 2219 manually curated references. The data provide information on 4460 genes from 264 pathogens tested on 176 hosts in 8046 interactions. Prokaryotic and eukaryotic pathogens are represented in almost equal numbers. Host species belong ∼70% to plants and 30% to other species of medical and/or environmental importance. Additional data types included into PHI-base 4 are the direct targets of pathogen effector proteins in experimental and natural host organisms. The curation problems encountered and the future directions of the PHI-base project are briefly discussed. PMID:27915230

A framework for organizing cancer-related variations from existing databases, publications and NGS data using a High-performance Integrated Virtual Environment (HIVE).

Science.gov (United States)

Wu, Tsung-Jung; Shamsaddini, Amirhossein; Pan, Yang; Smith, Krista; Crichton, Daniel J; Simonyan, Vahan; Mazumder, Raja

2014-01-01

Years of sequence feature curation by UniProtKB/Swiss-Prot, PIR-PSD, NCBI-CDD, RefSeq and other database biocurators has led to a rich repository of information on functional sites of genes and proteins. This information along with variation-related annotation can be used to scan human short sequence reads from next-generation sequencing (NGS) pipelines for presence of non-synonymous single-nucleotide variations (nsSNVs) that affect functional sites. This and similar workflows are becoming more important because thousands of NGS data sets are being made available through projects such as The Cancer Genome Atlas (TCGA), and researchers want to evaluate their biomarkers in genomic data. BioMuta, an integrated sequence feature database, provides a framework for automated and manual curation and integration of cancer-related sequence features so that they can be used in NGS analysis pipelines. Sequence feature information in BioMuta is collected from the Catalogue of Somatic Mutations in Cancer (COSMIC), ClinVar, UniProtKB and through biocuration of information available from publications. Additionally, nsSNVs identified through automated analysis of NGS data from TCGA are also included in the database. Because of the petabytes of data and information present in NGS primary repositories, a platform HIVE (High-performance Integrated Virtual Environment) for storing, analyzing, computing and curating NGS data and associated metadata has been developed. Using HIVE, 31 979 nsSNVs were identified in TCGA-derived NGS data from breast cancer patients. All variations identified through this process are stored in a Curated Short Read archive, and the nsSNVs from the tumor samples are included in BioMuta. Currently, BioMuta has 26 cancer types with 13 896 small-scale and 308 986 large-scale study-derived variations. Integration of variation data allows identifications of novel or common nsSNVs that can be prioritized in validation studies. Database URL: BioMuta: http

Vaxjo: A Web-Based Vaccine Adjuvant Database and Its Application for Analysis of Vaccine Adjuvants and Their Uses in Vaccine Development

Directory of Open Access Journals (Sweden)

Samantha Sayers

2012-01-01

Full Text Available Vaccine adjuvants are compounds that enhance host immune responses to co-administered antigens in vaccines. Vaxjo is a web-based central database and analysis system that curates, stores, and analyzes vaccine adjuvants and their usages in vaccine development. Basic information of a vaccine adjuvant stored in Vaxjo includes adjuvant name, components, structure, appearance, storage, preparation, function, safety, and vaccines that use this adjuvant. Reliable references are curated and cited. Bioinformatics scripts are developed and used to link vaccine adjuvants to different adjuvanted vaccines stored in the general VIOLIN vaccine database. Presently, 103 vaccine adjuvants have been curated in Vaxjo. Among these adjuvants, 98 have been used in 384 vaccines stored in VIOLIN against over 81 pathogens, cancers, or allergies. All these vaccine adjuvants are categorized and analyzed based on adjuvant types, pathogens used, and vaccine types. As a use case study of vaccine adjuvants in infectious disease vaccines, the adjuvants used in Brucella vaccines are specifically analyzed. A user-friendly web query and visualization interface is developed for interactive vaccine adjuvant search. To support data exchange, the information of vaccine adjuvants is stored in the Vaccine Ontology (VO in the Web Ontology Language (OWL format.

Vaxjo: a web-based vaccine adjuvant database and its application for analysis of vaccine adjuvants and their uses in vaccine development.

Science.gov (United States)

Sayers, Samantha; Ulysse, Guerlain; Xiang, Zuoshuang; He, Yongqun

2012-01-01

Vaccine adjuvants are compounds that enhance host immune responses to co-administered antigens in vaccines. Vaxjo is a web-based central database and analysis system that curates, stores, and analyzes vaccine adjuvants and their usages in vaccine development. Basic information of a vaccine adjuvant stored in Vaxjo includes adjuvant name, components, structure, appearance, storage, preparation, function, safety, and vaccines that use this adjuvant. Reliable references are curated and cited. Bioinformatics scripts are developed and used to link vaccine adjuvants to different adjuvanted vaccines stored in the general VIOLIN vaccine database. Presently, 103 vaccine adjuvants have been curated in Vaxjo. Among these adjuvants, 98 have been used in 384 vaccines stored in VIOLIN against over 81 pathogens, cancers, or allergies. All these vaccine adjuvants are categorized and analyzed based on adjuvant types, pathogens used, and vaccine types. As a use case study of vaccine adjuvants in infectious disease vaccines, the adjuvants used in Brucella vaccines are specifically analyzed. A user-friendly web query and visualization interface is developed for interactive vaccine adjuvant search. To support data exchange, the information of vaccine adjuvants is stored in the Vaccine Ontology (VO) in the Web Ontology Language (OWL) format.

Fish Karyome version 2.1: a chromosome database of fishes and other aquatic organisms.

Science.gov (United States)

Nagpure, Naresh Sahebrao; Pathak, Ajey Kumar; Pati, Rameshwar; Rashid, Iliyas; Sharma, Jyoti; Singh, Shri Prakash; Singh, Mahender; Sarkar, Uttam Kumar; Kushwaha, Basdeo; Kumar, Ravindra; Murali, S

2016-01-01

A voluminous information is available on karyological studies of fishes; however, limited efforts were made for compilation and curation of the available karyological data in a digital form. 'Fish Karyome' database was the preliminary attempt to compile and digitize the available karyological information on finfishes belonging to the Indian subcontinent. But the database had limitations since it covered data only on Indian finfishes with limited search options. Perceiving the feedbacks from the users and its utility in fish cytogenetic studies, the Fish Karyome database was upgraded by applying Linux, Apache, MySQL and PHP (pre hypertext processor) (LAMP) technologies. In the present version, the scope of the system was increased by compiling and curating the available chromosomal information over the globe on fishes and other aquatic organisms, such as echinoderms, molluscs and arthropods, especially of aquaculture importance. Thus, Fish Karyome version 2.1 presently covers 866 chromosomal records for 726 species supported with 253 published articles and the information is being updated regularly. The database provides information on chromosome number and morphology, sex chromosomes, chromosome banding, molecular cytogenetic markers, etc. supported by fish and karyotype images through interactive tools. It also enables the users to browse and view chromosomal information based on habitat, family, conservation status and chromosome number. The system also displays chromosome number in model organisms, protocol for chromosome preparation and allied techniques and glossary of cytogenetic terms. A data submission facility has also been provided through data submission panel. The database can serve as a unique and useful resource for cytogenetic characterization, sex determination, chromosomal mapping, cytotaxonomy, karyo-evolution and systematics of fishes. Database URL: http://mail.nbfgr.res.in/Fish_Karyome. © The Author(s) 2016. Published by Oxford University Press.

Practices of research data curation in institutional repositories: A qualitative view from repository staff.

Science.gov (United States)

Lee, Dong Joon; Stvilia, Besiki

2017-01-01

The importance of managing research data has been emphasized by the government, funding agencies, and scholarly communities. Increased access to research data increases the impact and efficiency of scientific activities and funding. Thus, many research institutions have established or plan to establish research data curation services as part of their Institutional Repositories (IRs). However, in order to design effective research data curation services in IRs, and to build active research data providers and user communities around those IRs, it is essential to study current data curation practices and provide rich descriptions of the sociotechnical factors and relationships shaping those practices. Based on 13 interviews with 15 IR staff members from 13 large research universities in the United States, this paper provides a rich, qualitative description of research data curation and use practices in IRs. In particular, the paper identifies data curation and use activities in IRs, as well as their structures, roles played, skills needed, contradictions and problems present, solutions sought, and workarounds applied. The paper can inform the development of best practice guides, infrastructure and service templates, as well as education in research data curation in Library and Information Science (LIS) schools.

Crowdsourcing and curation: perspectives from biology and natural language processing.

Science.gov (United States)

Hirschman, Lynette; Fort, Karën; Boué, Stéphanie; Kyrpides, Nikos; Islamaj Doğan, Rezarta; Cohen, Kevin Bretonnel

2016-01-01

Crowdsourcing is increasingly utilized for performing tasks in both natural language processing and biocuration. Although there have been many applications of crowdsourcing in these fields, there have been fewer high-level discussions of the methodology and its applicability to biocuration. This paper explores crowdsourcing for biocuration through several case studies that highlight different ways of leveraging 'the crowd'; these raise issues about the kind(s) of expertise needed, the motivations of participants, and questions related to feasibility, cost and quality. The paper is an outgrowth of a panel session held at BioCreative V (Seville, September 9-11, 2015). The session consisted of four short talks, followed by a discussion. In their talks, the panelists explored the role of expertise and the potential to improve crowd performance by training; the challenge of decomposing tasks to make them amenable to crowdsourcing; and the capture of biological data and metadata through community editing.Database URL: http://www.mitre.org/publications/technical-papers/crowdsourcing-and-curation-perspectives. © The Author(s) 2016. Published by Oxford University Press.

Curation of US Martian Meteorites Collected in Antarctica

Science.gov (United States)

Lindstrom, M.; Satterwhite, C.; Allton, J.; Stansbury, E.

1998-01-01

To date the ANSMET field team has collected five martian meteorites (see below) in Antarctica and returned them for curation at the Johnson Space Center (JSC) Meteorite Processing Laboratory (MPL). ne meteorites were collected with the clean procedures used by ANSMET in collecting all meteorites: They were handled with JSC-cleaned tools, packaged in clean bags, and shipped frozen to JSC. The five martian meteorites vary significantly in size (12-7942 g) and rock type (basalts, lherzolites, and orthopyroxenite). Detailed descriptions are provided in the Mars Meteorite compendium, which describes classification, curation and research results. A table gives the names, classifications and original and curatorial masses of the martian meteorites. The MPL and measures for contamination control are described.

Curative and eradicant action of fungicides to control Phakopsora pachyrhizi in soybean plants

Directory of Open Access Journals (Sweden)

Erlei Melo Reis

Full Text Available ABSTRACT Experiments were carried out in a growth chamber and laboratory to quantify the curative and eradicant actions of fungicides in Asian soybean rust control. The experiments were conducted with the CD 214 RR cultivar, assessing the following fungicides, separately or in association, chlorothalonil, flutriafol, cyproconazole + trifloxystrobin, epoxiconazole + pyraclostrobin, cyproconazole + azoxystrobin, and cyproconazole + picoxystrobin. The fungicides were applied at four (curative and nine days after inoculation (eradicant treatment. Treatments were evaluated according to the density of lesions and uredia/cm2, and the eradicant treatment was assessed based on the necrosis of lesions/uredia and on uredospore viability. Except for the fungicide chlorothalonil, there was curative action of latent/virtual infections by the fungicides. Penetrant fungicides that are absorbed have curative and eradicant action to soybean rust.

An emerging role: the nurse content curator.

Science.gov (United States)

Brooks, Beth A

2015-01-01

A new phenomenon, the inverted or "flipped" classroom, assumes that students are no longer acquiring knowledge exclusively through textbooks or lectures. Instead, they are seeking out the vast amount of free information available to them online (the very essence of open source) to supplement learning gleaned in textbooks and lectures. With so much open-source content available to nursing faculty, it benefits the faculty to use readily available, technologically advanced content. The nurse content curator supports nursing faculty in its use of such content. Even more importantly, the highly paid, time-strapped faculty is not spending an inordinate amount of effort surfing for and evaluating content. The nurse content curator does that work, while the faculty uses its time more effectively to help students vet the truth, make meaning of the content, and learn to problem-solve. Brooks. © 2014 Wiley Periodicals, Inc.

CEBS: a comprehensive annotated database of toxicological data

Science.gov (United States)

Lea, Isabel A.; Gong, Hui; Paleja, Anand; Rashid, Asif; Fostel, Jennifer

2017-01-01

The Chemical Effects in Biological Systems database (CEBS) is a comprehensive and unique toxicology resource that compiles individual and summary animal data from the National Toxicology Program (NTP) testing program and other depositors into a single electronic repository. CEBS has undergone significant updates in recent years and currently contains over 11 000 test articles (exposure agents) and over 8000 studies including all available NTP carcinogenicity, short-term toxicity and genetic toxicity studies. Study data provided to CEBS are manually curated, accessioned and subject to quality assurance review prior to release to ensure high quality. The CEBS database has two main components: data collection and data delivery. To accommodate the breadth of data produced by NTP, the CEBS data collection component is an integrated relational design that allows the flexibility to capture any type of electronic data (to date). The data delivery component of the database comprises a series of dedicated user interface tables containing pre-processed data that support each component of the user interface. The user interface has been updated to include a series of nine Guided Search tools that allow access to NTP summary and conclusion data and larger non-NTP datasets. The CEBS database can be accessed online at http://www.niehs.nih.gov/research/resources/databases/cebs/. PMID:27899660

The DigCurV Curriculum Framework for Digital Curation in the Cultural Heritage Sector

Directory of Open Access Journals (Sweden)

Laura Molloy

2014-07-01

Full Text Available In 2013, the DigCurV collaborative network completed development of a Curriculum Framework for digital curation skills in the European cultural heritage sector. DigCurV synthesised a variety of established skills and competence models in the digital curation and LIS sectors with expertise from digital curation professionals, in order to develop a new Curriculum Framework. The resulting Framework provides a common language and helps define the skills, knowledge and abilities that are necessary for the development of digital curation training; for benchmarking existing programmes; and for promoting the continuing production, improvement and refinement of digital curation training programmes. This paper describes the salient points of this work, including how the project team conducted the research necessary to develop the Framework, the structure of the Framework, the processes used to validate the Framework, and three ‘lenses’ onto the Framework. The paper also provides suggestions as to how the Framework might be used, including a description of potential audiences and purposes.

AgdbNet – antigen sequence database software for bacterial typing

Directory of Open Access Journals (Sweden)

Maiden Martin CJ

2006-06-01

Full Text Available Abstract Background Bacterial typing schemes based on the sequences of genes encoding surface antigens require databases that provide a uniform, curated, and widely accepted nomenclature of the variants identified. Due to the differences in typing schemes, imposed by the diversity of genes targeted, creating these databases has typically required the writing of one-off code to link the database to a web interface. Here we describe agdbNet, widely applicable web database software that facilitates simultaneous BLAST querying of multiple loci using either nucleotide or peptide sequences. Results Databases are described by XML files that are parsed by a Perl CGI script. Each database can have any number of loci, which may be defined by nucleotide and/or peptide sequences. The software is currently in use on at least five public databases for the typing of Neisseria meningitidis, Campylobacter jejuni and Streptococcus equi and can be set up to query internal isolate tables or suitably-configured external isolate databases, such as those used for multilocus sequence typing. The style of the resulting website can be fully configured by modifying stylesheets and through the use of customised header and footer files that surround the output of the script. Conclusion The software provides a rapid means of setting up customised Internet antigen sequence databases. The flexible configuration options enable typing schemes with differing requirements to be accommodated.

Competencies for preservation and digital curation

Directory of Open Access Journals (Sweden)

Sonia Boeres

2016-09-01

Full Text Available Information Science, throughout its existence, has been a multi and interdisciplinary field, and has undergone constant change because of its object of study: information. Seen that this element is not static and is increasingly linked to information technology, we have witnessed a challenge arise: how to ensure the permanence of digital libraries? How to secure the terabytes generated with increasing speed, and in various formats, will be available and fully capable of use over time? This is a challenge that Information Science professionals are being challenged to solve in the process of so-called digital preservation and curation. Thus, this article aims to raise the skills that the information professional must have to carry out the process of preservation and digital curation. The article discusses the emergence of professions (from the perspective of Sociology, the need to work for the realization of the human being (Psychology and proficiencies of exercising the office of Information Science to ensure the preservation of digital information in information units.

Organic Contamination Baseline Study in NASA Johnson Space Center Astromaterials Curation Laboratories

Science.gov (United States)

Calaway, Michael J.; Allen, Carlton C.; Allton, Judith H.

2014-01-01

Future robotic and human spaceflight missions to the Moon, Mars, asteroids, and comets will require curating astromaterial samples with minimal inorganic and organic contamination to preserve the scientific integrity of each sample. 21st century sample return missions will focus on strict protocols for reducing organic contamination that have not been seen since the Apollo manned lunar landing program. To properly curate these materials, the Astromaterials Acquisition and Curation Office under the Astromaterial Research and Exploration Science Directorate at NASA Johnson Space Center houses and protects all extraterrestrial materials brought back to Earth that are controlled by the United States government. During fiscal year 2012, we conducted a year-long project to compile historical documentation and laboratory tests involving organic investigations at these facilities. In addition, we developed a plan to determine the current state of organic cleanliness in curation laboratories housing astromaterials. This was accomplished by focusing on current procedures and protocols for cleaning, sample handling, and storage. While the intention of this report is to give a comprehensive overview of the current state of organic cleanliness in JSC curation laboratories, it also provides a baseline for determining whether our cleaning procedures and sample handling protocols need to be adapted and/or augmented to meet the new requirements for future human spaceflight and robotic sample return missions.

Refusal of Curative Radiation Therapy and Surgery Among Patients With Cancer

International Nuclear Information System (INIS)

Aizer, Ayal A.; Chen, Ming-Hui; Parekh, Arti; Choueiri, Toni K.; Hoffman, Karen E.; Kim, Simon P.; Martin, Neil E.; Hu, Jim C.; Trinh, Quoc-Dien; Nguyen, Paul L.

2014-01-01

Purpose: Surgery and radiation therapy represent the only curative options for many patients with solid malignancies. However, despite the recommendations of their physicians, some patients refuse these therapies. This study characterized factors associated with refusal of surgical or radiation therapy as well as the impact of refusal of recommended therapy on patients with localized malignancies. Methods and Materials: We used the Surveillance, Epidemiology, and End Results program to identify a population-based sample of 925,127 patients who had diagnoses of 1 of 8 common malignancies for which surgery and/or radiation are believed to confer a survival benefit between 1995 and 2008. Refusal of oncologic therapy, as documented in the SEER database, was the primary outcome measure. Multivariable logistic regression was used to investigate factors associated with refusal. The impact of refusal of therapy on cancer-specific mortality was assessed with Fine and Gray's competing risks regression. Results: In total, 2441 of 692,938 patients (0.4%) refused surgery, and 2113 of 232,189 patients (0.9%) refused radiation, despite the recommendations of their physicians. On multivariable analysis, advancing age, decreasing annual income, nonwhite race, and unmarried status were associated with refusal of surgery, whereas advancing age, decreasing annual income, Asian American race, and unmarried status were associated with refusal of radiation (P<.001 in all cases). Refusal of surgery and radiation were associated with increased estimates of cancer-specific mortality for all malignancies evaluated (hazard ratio [HR], 2.80, 95% confidence interval [CI], 2.59-3.03; P<.001 and HR 1.97 [95% CI, 1.78-2.18]; P<.001, respectively). Conclusions: Nonwhite, less affluent, and unmarried patients are more likely to refuse curative surgical and/or radiation-based oncologic therapy, raising concern that socioeconomic factors may drive some patients to forego potentially life

Refusal of Curative Radiation Therapy and Surgery Among Patients With Cancer

Energy Technology Data Exchange (ETDEWEB)

Aizer, Ayal A., E-mail: aaaizer@partners.org [Harvard Radiation Oncology Program, Boston, Massachusetts (United States); Chen, Ming-Hui [Department of Statistics, University of Connecticut, Storrs, Connecticut (United States); Parekh, Arti [Boston University School of Medicine, Boston, Massachusetts (United States); Choueiri, Toni K. [Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute/Brigham and Women' s Hospital, Harvard Medical School, Boston, Massachusetts (United States); Hoffman, Karen E. [Department of Radiation Oncology, The University of Texas MD Anderson Cancer Center, Houston, Texas (United States); Kim, Simon P. [Department of Urology, Mayo Clinic, Rochester, Minnesota (United States); Martin, Neil E. [Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute/Brigham and Women' s Hospital, Harvard Medical School, Boston, Massachusetts (United States); Hu, Jim C. [Department of Urology, University of California, Los Angeles, California (United States); Trinh, Quoc-Dien [Cancer Prognostics and Health Outcomes Unit, University of Montreal Health Center, Montreal, Quebec (Canada); Nguyen, Paul L. [Lank Center for Genitourinary Oncology, Dana-Farber Cancer Institute/Brigham and Women' s Hospital, Harvard Medical School, Boston, Massachusetts (United States)

2014-07-15

Purpose: Surgery and radiation therapy represent the only curative options for many patients with solid malignancies. However, despite the recommendations of their physicians, some patients refuse these therapies. This study characterized factors associated with refusal of surgical or radiation therapy as well as the impact of refusal of recommended therapy on patients with localized malignancies. Methods and Materials: We used the Surveillance, Epidemiology, and End Results program to identify a population-based sample of 925,127 patients who had diagnoses of 1 of 8 common malignancies for which surgery and/or radiation are believed to confer a survival benefit between 1995 and 2008. Refusal of oncologic therapy, as documented in the SEER database, was the primary outcome measure. Multivariable logistic regression was used to investigate factors associated with refusal. The impact of refusal of therapy on cancer-specific mortality was assessed with Fine and Gray's competing risks regression. Results: In total, 2441 of 692,938 patients (0.4%) refused surgery, and 2113 of 232,189 patients (0.9%) refused radiation, despite the recommendations of their physicians. On multivariable analysis, advancing age, decreasing annual income, nonwhite race, and unmarried status were associated with refusal of surgery, whereas advancing age, decreasing annual income, Asian American race, and unmarried status were associated with refusal of radiation (P<.001 in all cases). Refusal of surgery and radiation were associated with increased estimates of cancer-specific mortality for all malignancies evaluated (hazard ratio [HR], 2.80, 95% confidence interval [CI], 2.59-3.03; P<.001 and HR 1.97 [95% CI, 1.78-2.18]; P<.001, respectively). Conclusions: Nonwhite, less affluent, and unmarried patients are more likely to refuse curative surgical and/or radiation-based oncologic therapy, raising concern that socioeconomic factors may drive some patients to forego potentially life

Creating Large Scale Database Servers

International Nuclear Information System (INIS)

Becla, Jacek

2001-01-01

The BaBar experiment at the Stanford Linear Accelerator Center (SLAC) is designed to perform a high precision investigation of the decays of the B-meson produced from electron-positron interactions. The experiment, started in May 1999, will generate approximately 300TB/year of data for 10 years. All of the data will reside in Objectivity databases accessible via the Advanced Multi-threaded Server (AMS). To date, over 70TB of data have been placed in Objectivity/DB, making it one of the largest databases in the world. Providing access to such a large quantity of data through a database server is a daunting task. A full-scale testbed environment had to be developed to tune various software parameters and a fundamental change had to occur in the AMS architecture to allow it to scale past several hundred terabytes of data. Additionally, several protocol extensions had to be implemented to provide practical access to large quantities of data. This paper will describe the design of the database and the changes that we needed to make in the AMS for scalability reasons and how the lessons we learned would be applicable to virtually any kind of database server seeking to operate in the Petabyte region

Creating Large Scale Database Servers

Energy Technology Data Exchange (ETDEWEB)

Becla, Jacek

2001-12-14

The BaBar experiment at the Stanford Linear Accelerator Center (SLAC) is designed to perform a high precision investigation of the decays of the B-meson produced from electron-positron interactions. The experiment, started in May 1999, will generate approximately 300TB/year of data for 10 years. All of the data will reside in Objectivity databases accessible via the Advanced Multi-threaded Server (AMS). To date, over 70TB of data have been placed in Objectivity/DB, making it one of the largest databases in the world. Providing access to such a large quantity of data through a database server is a daunting task. A full-scale testbed environment had to be developed to tune various software parameters and a fundamental change had to occur in the AMS architecture to allow it to scale past several hundred terabytes of data. Additionally, several protocol extensions had to be implemented to provide practical access to large quantities of data. This paper will describe the design of the database and the changes that we needed to make in the AMS for scalability reasons and how the lessons we learned would be applicable to virtually any kind of database server seeking to operate in the Petabyte region.

The baladi curative system of Cairo, Egypt.

Science.gov (United States)

Early, E A

1988-03-01

The article explores the symbolic structure of the baladi (traditional) cultural system as revealed in everyday narratives, with a focus on baladi curative action. The everyday illness narrative provides a cultural window to the principles of fluidity and restorative balance of baladi curative practices. The body is seen as a dynamic organism through which both foreign objects and physiological entities can move. The body should be in balance, as with any humorally-influenced system, and so baladi cures aim to restore normal balance and functioning of the body. The article examines in detail a narrative on treatment of a sick child, and another on treatment of fertility problems. It traces such cultural oppositions as insider: outsider; authentic:inauthentic; home remedy:cosmopolitan medicine. In the social as well as the medical arena these themes organize social/medical judgements about correct action and explanations of events.

Judson_Mansouri_Automated_Chemical_Curation_QSAREnvRes_Data

Data.gov (United States)

U.S. Environmental Protection Agency — Here we describe the development of an automated KNIME workflow to curate and correct errors in the structure and identity of chemicals using the publically...

Reducing Organic Contamination in NASA JSC Astromaterial Curation Facility

Science.gov (United States)

Calaway, M. J.; Allen, C. C.; Allton, J. H.

2013-01-01

Future robotic and human spaceflight missions to the Moon, Mars, asteroids and comets will require handling and storing astromaterial samples with minimal inorganic and organic contamination to preserve the scientific integrity of each sample. Much was learned from the rigorous attempts to minimize and monitor organic contamination during Apollo, but it was not adequate for current analytical requirements; thus [1]. OSIRIS-REx, Hayabusa-2, and future Mars sample return will require better protocols for reducing organic contamination. Future isolation con-tainment systems for astromaterials, possibly nitrogen enriched gloveboxes, must be able to reduce organic and inorganic cross-contamination. In 2012, a baseline study established the current state of organic cleanliness in gloveboxes used by NASA JSC astromaterials curation labs that could be used as a benchmark for future mission designs [2, 3]. After standard ultra-pure water (UPW) cleaning, the majority of organic contaminates found were hydrocarbons, plasticizers, silicones, and solvents. Hydro-carbons loads (> C7) ranged from 1.9 to 11.8 ng/cm2 for TD-GC-MS wafer exposure analyses and 5.0 to 19.5 ng/L for TD-GC-MS adsorbent tube exposure. Plasticizers included peracetic acid sterilization were used in the atmospheric de-contamination (R) cabinets. Later, Lunar curation gloveboxes were degreased with a pressurized Freon 113 wash. Today, UPW has replaced Freon as the standard cleaning procedure, but does not have the degreasing solvency power of Freon. Future Cleaning Studies: Cleaning experiments are cur-rently being orchestrated to study how to degrease and reduce organics in a JSC curation glovebox lower than the established baseline. Several new chemicals in the industry have replaced traditional degreasing solvents such as Freon and others that are now federally restricted. However, these new suites of chemicals remain untested for lowering organics in curation gloveboxes. 3M's HFE-7100DL and Du

PHI-base: a new interface and further additions for the multi-species pathogen-host interactions database.

Science.gov (United States)

Urban, Martin; Cuzick, Alayne; Rutherford, Kim; Irvine, Alistair; Pedro, Helder; Pant, Rashmi; Sadanadan, Vidyendra; Khamari, Lokanath; Billal, Santoshkumar; Mohanty, Sagar; Hammond-Kosack, Kim E

2017-01-04

The pathogen-host interactions database (PHI-base) is available at www.phi-base.org PHI-base contains expertly curated molecular and biological information on genes proven to affect the outcome of pathogen-host interactions reported in peer reviewed research articles. In addition, literature that indicates specific gene alterations that did not affect the disease interaction phenotype are curated to provide complete datasets for comparative purposes. Viruses are not included. Here we describe a revised PHI-base Version 4 data platform with improved search, filtering and extended data display functions. A PHIB-BLAST search function is provided and a link to PHI-Canto, a tool for authors to directly curate their own published data into PHI-base. The new release of PHI-base Version 4.2 (October 2016) has an increased data content containing information from 2219 manually curated references. The data provide information on 4460 genes from 264 pathogens tested on 176 hosts in 8046 interactions. Prokaryotic and eukaryotic pathogens are represented in almost equal numbers. Host species belong ∼70% to plants and 30% to other species of medical and/or environmental importance. Additional data types included into PHI-base 4 are the direct targets of pathogen effector proteins in experimental and natural host organisms. The curation problems encountered and the future directions of the PHI-base project are briefly discussed. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Sharing Responsibility for Data Stewardship Between Scientists and Curators

Science.gov (United States)

Hedstrom, M. L.

2012-12-01

Data stewardship is becoming increasingly important to support accurate conclusions from new forms of data, integration of and computation across heterogeneous data types, interactions between models and data, replication of results, data governance and long-term archiving. In addition to increasing recognition of the importance of data management, data science, and data curation by US and international scientific agencies, the National Academies of Science Board on Research Data and Information is sponsoring a study on Data Curation Education and Workforce Issues. Effective data stewardship requires a distributed effort among scientists who produce data, IT staff and/or vendors who provide data storage and computational facilities and services, and curators who enhance data quality, manage data governance, provide access to third parties, and assume responsibility for long-term archiving of data. The expertise necessary for scientific data management includes a mix of knowledge of the scientific domain; an understanding of domain data requirements, standards, ontologies and analytical methods; facility with leading edge information technology; and knowledge of data governance, standards, and best practices for long-term preservation and access that rarely are found in a single individual. Rather than developing data science and data curation as new and distinct occupations, this paper examines the set of tasks required for data stewardship. The paper proposes an alternative model that embeds data stewardship in scientific workflows and coordinates hand-offs between instruments, repositories, analytical processing, publishers, distributors, and archives. This model forms the basis for defining knowledge and skill requirements for specific actors in the processes required for data stewardship and the corresponding educational and training needs.

The PDS4 Information Model and its Role in Agile Science Data Curation

Science.gov (United States)

Hughes, J. S.; Crichton, D.

2017-12-01

PDS4 is an information model-driven service architecture supporting the capture, management, distribution and integration of massive planetary science data captured in distributed data archives world-wide. The PDS4 Information Model (IM), the core element of the architecture, was developed using lessons learned from 20 years of archiving Planetary Science Data and best practices for information model development. The foundational principles were adopted from the Open Archival Information System (OAIS) Reference Model (ISO 14721), the Metadata Registry Specification (ISO/IEC 11179), and W3C XML (Extensible Markup Language) specifications. These provided respectively an object oriented model for archive information systems, a comprehensive schema for data dictionaries and hierarchical governance, and rules for rules for encoding documents electronically. The PDS4 Information model is unique in that it drives the PDS4 infrastructure by providing the representation of concepts and their relationships, constraints, rules, and operations; a sharable, stable, and organized set of information requirements; and machine parsable definitions that are suitable for configuring and generating code. This presentation will provide an over of the PDS4 Information Model and how it is being leveraged to develop and evolve the PDS4 infrastructure and enable agile curation of over 30 years of science data collected by the international Planetary Science community.

Improving taxonomic accuracy for fungi in public sequence databases: applying ‘one name one species’ in well-defined genera with Trichoderma/Hypocrea as a test case

Science.gov (United States)

Strope, Pooja K; Chaverri, Priscila; Gazis, Romina; Ciufo, Stacy; Domrachev, Michael; Schoch, Conrad L

2017-01-01

Abstract The ITS (nuclear ribosomal internal transcribed spacer) RefSeq database at the National Center for Biotechnology Information (NCBI) is dedicated to the clear association between name, specimen and sequence data. This database is focused on sequences obtained from type material stored in public collections. While the initial ITS sequence curation effort together with numerous fungal taxonomy experts attempted to cover as many orders as possible, we extended our latest focus to the family and genus ranks. We focused on Trichoderma for several reasons, mainly because the asexual and sexual synonyms were well documented, and a list of proposed names and type material were recently proposed and published. In this case study the recent taxonomic information was applied to do a complete taxonomic audit for the genus Trichoderma in the NCBI Taxonomy database. A name status report is available here: https://www.ncbi.nlm.nih.gov/Taxonomy/TaxIdentifier/tax_identifier.cgi. As a result, the ITS RefSeq Targeted Loci database at NCBI has been augmented with more sequences from type and verified material from Trichoderma species. Additionally, to aid in the cross referencing of data from single loci and genomes we have collected a list of quality records of the RPB2 gene obtained from type material in GenBank that could help validate future submissions. During the process of curation misidentified genomes were discovered, and sequence records from type material were found hidden under previous classifications. Source metadata curation, although more cumbersome, proved to be useful as confirmation of the type material designation. Database URL: http://www.ncbi.nlm.nih.gov/bioproject/PRJNA177353 PMID:29220466

Enhanced annotations and features for comparing thousands of Pseudomonas genomes in the Pseudomonas genome database.

Science.gov (United States)

Winsor, Geoffrey L; Griffiths, Emma J; Lo, Raymond; Dhillon, Bhavjinder K; Shay, Julie A; Brinkman, Fiona S L

2016-01-04

The Pseudomonas Genome Database (http://www.pseudomonas.com) is well known for the application of community-based annotation approaches for producing a high-quality Pseudomonas aeruginosa PAO1 genome annotation, and facilitating whole-genome comparative analyses with other Pseudomonas strains. To aid analysis of potentially thousands of complete and draft genome assemblies, this database and analysis platform was upgraded to integrate curated genome annotations and isolate metadata with enhanced tools for larger scale comparative analysis and visualization. Manually curated gene annotations are supplemented with improved computational analyses that help identify putative drug targets and vaccine candidates or assist with evolutionary studies by identifying orthologs, pathogen-associated genes and genomic islands. The database schema has been updated to integrate isolate metadata that will facilitate more powerful analysis of genomes across datasets in the future. We continue to place an emphasis on providing high-quality updates to gene annotations through regular review of the scientific literature and using community-based approaches including a major new Pseudomonas community initiative for the assignment of high-quality gene ontology terms to genes. As we further expand from thousands of genomes, we plan to provide enhancements that will aid data visualization and analysis arising from whole-genome comparative studies including more pan-genome and population-based approaches. © The Author(s) 2015. Published by Oxford University Press on behalf of Nucleic Acids Research.

[Curative Effects of Hydroxyurea on the Patients with β-thalassaemia Intermadia].

Science.gov (United States)

Huang, Li; Yao, Hong-Xia

2016-06-01

To investigate the clinical features of β-thalassaemia intermediate (TI) patients and the curative effect and side reactions of hydroxyurea therapys. Twenty nine patients with TI were divided into hydroxyurea therapy group and no hydroxyurea therapy group; the curative effect and side reactions in 2 groups were compared; the situation of blood transfusion in the 2 groups was evaluated. In hydroxyurea therapy group, the hemoglobin level increased after treatment for 3 months; the reticulocyte percentage obviously decreased after treatment for 12 months; the serum ferritin had been maintained at a low level; while in no hydroxyurea therapy group, the levels of hemoglobin and reticulocytes were not significantly improved after treatment, the serum ferritin level gradually increased. In hydroxyurea therapy group, 12 cases were out of blood transfusion after treatment for 12 months, effective rate of treatment was 85.71%; while in no hydroxyurea therapy group, the blood transfusion dependency was not improved after treatment. No serious side reactions were found in all the hydroxyurea treated patients. The hydroxyurea shows a better curative effect on TI patients, no serious side reactions occur in all the patients treated with hydroxyurea, but the long-term curative effect and side reactions should be observed continuously.

CAZymes Analysis Toolkit (CAT): web service for searching and analyzing carbohydrate-active enzymes in a newly sequenced organism using CAZy database.

Science.gov (United States)

Park, Byung H; Karpinets, Tatiana V; Syed, Mustafa H; Leuze, Michael R; Uberbacher, Edward C

2010-12-01

The Carbohydrate-Active Enzyme (CAZy) database provides a rich set of manually annotated enzymes that degrade, modify, or create glycosidic bonds. Despite rich and invaluable information stored in the database, software tools utilizing this information for annotation of newly sequenced genomes by CAZy families are limited. We have employed two annotation approaches to fill the gap between manually curated high-quality protein sequences collected in the CAZy database and the growing number of other protein sequences produced by genome or metagenome sequencing projects. The first approach is based on a similarity search against the entire nonredundant sequences of the CAZy database. The second approach performs annotation using links or correspondences between the CAZy families and protein family domains. The links were discovered using the association rule learning algorithm applied to sequences from the CAZy database. The approaches complement each other and in combination achieved high specificity and sensitivity when cross-evaluated with the manually curated genomes of Clostridium thermocellum ATCC 27405 and Saccharophagus degradans 2-40. The capability of the proposed framework to predict the function of unknown protein domains and of hypothetical proteins in the genome of Neurospora crassa is demonstrated. The framework is implemented as a Web service, the CAZymes Analysis Toolkit, and is available at http://cricket.ornl.gov/cgi-bin/cat.cgi.

TIPdb-3D: the three-dimensional structure database of phytochemicals from Taiwan indigenous plants.

Science.gov (United States)

Tung, Chun-Wei; Lin, Ying-Chi; Chang, Hsun-Shuo; Wang, Chia-Chi; Chen, Ih-Sheng; Jheng, Jhao-Liang; Li, Jih-Heng

2014-01-01

The rich indigenous and endemic plants in Taiwan serve as a resourceful bank for biologically active phytochemicals. Based on our TIPdb database curating bioactive phytochemicals from Taiwan indigenous plants, this study presents a three-dimensional (3D) chemical structure database named TIPdb-3D to support the discovery of novel pharmacologically active compounds. The Merck Molecular Force Field (MMFF94) was used to generate 3D structures of phytochemicals in TIPdb. The 3D structures could facilitate the analysis of 3D quantitative structure-activity relationship, the exploration of chemical space and the identification of potential pharmacologically active compounds using protein-ligand docking. Database URL: http://cwtung.kmu.edu.tw/tipdb. © The Author(s) 2014. Published by Oxford University Press.

Non-animal methods to predict skin sensitization (I): the Cosmetics Europe database.

Science.gov (United States)

Hoffmann, Sebastian; Kleinstreuer, Nicole; Alépée, Nathalie; Allen, David; Api, Anne Marie; Ashikaga, Takao; Clouet, Elodie; Cluzel, Magalie; Desprez, Bertrand; Gellatly, Nichola; Goebel, Carsten; Kern, Petra S; Klaric, Martina; Kühnl, Jochen; Lalko, Jon F; Martinozzi-Teissier, Silvia; Mewes, Karsten; Miyazawa, Masaaki; Parakhia, Rahul; van Vliet, Erwin; Zang, Qingda; Petersohn, Dirk

2018-05-01

Cosmetics Europe, the European Trade Association for the cosmetics and personal care industry, is conducting a multi-phase program to develop regulatory accepted, animal-free testing strategies enabling the cosmetics industry to conduct safety assessments. Based on a systematic evaluation of test methods for skin sensitization, five non-animal test methods (DPRA (Direct Peptide Reactivity Assay), KeratinoSens TM , h-CLAT (human cell line activation test), U-SENS TM , SENS-IS) were selected for inclusion in a comprehensive database of 128 substances. Existing data were compiled and completed with newly generated data, the latter amounting to one-third of all data. The database was complemented with human and local lymph node assay (LLNA) reference data, physicochemical properties and use categories, and thoroughly curated. Focused on the availability of human data, the substance selection resulted nevertheless resulted in a high diversity of chemistries in terms of physico-chemical property ranges and use categories. Predictivities of skin sensitization potential and potency, where applicable, were calculated for the LLNA as compared to human data and for the individual test methods compared to both human and LLNA reference data. In addition, various aspects of applicability of the test methods were analyzed. Due to its high level of curation, comprehensiveness, and completeness, we propose our database as a point of reference for the evaluation and development of testing strategies, as done for example in the associated work of Kleinstreuer et al. We encourage the community to use it to meet the challenge of conducting skin sensitization safety assessment without generating new animal data.

Observations on the Curative Effect of Acupuncture on Depressive Neurosis

Institute of Scientific and Technical Information of China (English)

FU Wen-bin; WANG Si-you

2003-01-01

Purpose To evaluate the curative effect of acupuncture on depressive neurosis. Method Sixty-two patients were randomly divided into a treatment group of 32 cases and a control group of 30 cases. The treatment group and the control group were treated with acupuncture and Fluoxetine, respectively. The curative effects were evaluated by HAMD. Results There was a significant difference between pretreatment and posttreatmentin each group ( P 0.05). But acupuncture had no side effects and was good in compliance. Conclusion Acupuncture is an effective method for treating depressive neurosis.

Jean-Paul Martinon, ed. - The Curatorial: A Philosophy of Curating

Directory of Open Access Journals (Sweden)

Sofia Romualdo

2015-12-01

Full Text Available In the words of Jean-Paul Martinon, this book’s editor, The Curatorial: A Philosophy of Curating originated from a “wish to talk about curating”, the same wish that led to the creation, in 2006, of a practice-led PhD programme at Goldsmiths College, called Curatorial/Knowledge. The anthology features contributions from tutors, guest speakers and students, all of whom delve into what “the curatorial” is and what it might mean in the future. Curating, or the act of organizing exhibitions, paral...

Solubility Study of Curatives in Various Rubbers

NARCIS (Netherlands)

Guo, R.; Talma, Auke; Datta, Rabin; Dierkes, Wilma K.; Noordermeer, Jacobus W.M.

2008-01-01

The previous works on solubility of curatives in rubbers were mainly carried out in natural rubber. Not too much information available on dissimilar rubbers and this is important because most of the compounds today are blends of dissimilar rubbers. Although solubility can be expected to certain

The Molecular Signatures Database (MSigDB) hallmark gene set collection.

Science.gov (United States)

Liberzon, Arthur; Birger, Chet; Thorvaldsdóttir, Helga; Ghandi, Mahmoud; Mesirov, Jill P; Tamayo, Pablo

2015-12-23

The Molecular Signatures Database (MSigDB) is one of the most widely used and comprehensive databases of gene sets for performing gene set enrichment analysis. Since its creation, MSigDB has grown beyond its roots in metabolic disease and cancer to include >10,000 gene sets. These better represent a wider range of biological processes and diseases, but the utility of the database is reduced by increased redundancy across, and heterogeneity within, gene sets. To address this challenge, here we use a combination of automated approaches and expert curation to develop a collection of "hallmark" gene sets as part of MSigDB. Each hallmark in this collection consists of a "refined" gene set, derived from multiple "founder" sets, that conveys a specific biological state or process and displays coherent expression. The hallmarks effectively summarize most of the relevant information of the original founder sets and, by reducing both variation and redundancy, provide more refined and concise inputs for gene set enrichment analysis.

Hayabusa Asteroidal Sample Preliminary Examination Team (HASPET) and the Astromaterial Curation Facility at JAXA/ISAS

Science.gov (United States)

Yano, H.; Fujiwara, A.

After the successful launch in May 2003, the Hayabusa (MUSES-C) mission of JAXA/ISAS will collect surface materials (e.g., regolith) of several hundred mg to several g in total from the S-type near Earth asteroid (25143) Itokawa in late 2005 and bring them back to ground laboratories in the summer of 2007. The retrieved samples will be given initial analysis at the JAXA/ISAS astromaterial curation facility, which is currently in the preparation for its construction, by the Hayabusa Asteroidal Sample Preliminary Examination Team (HASPET). HASPET is consisted of the ISAS Hayabusa team, the international partners from NASA and Australia and all-Japan meteoritic scientists to be selected as outsourcing parts of the initial analyses. The initial analysis to characterize general aspects of returned samples can consume only 15 % of its total mass and must complete the whole analyses including the database building before international AO for detailed analyses within the maximum of 1 year. Confident exercise of non-destructive, micro-analyses whenever possible are thus vital for the HASPET analysis. In the purpose to survey what kinds and levels of micro-analysis techniques in respective fields, from major elements and mineralogy to trace and isotopic elements and organics, are available in Japan at present, ISAS has conducted the HASPET open competitions in 2000-01 and 2004. The initial evaluation was made by multiple domestic peer reviews. Applicants were then provided two kinds of unknown asteroid sample analogs in order to conduct proposed analysis with self-claimed amount of samples in self-claimed duration. After the completion of multiple, international peer reviews, the Selection Committee compiled evaluations and recommended the finalists of each round. The final members of the HASPET will be appointed about 2 years prior to the Earth return. Then they will conduct a test-run of the whole initial analysis procedures at the ISAS astromaterial curation facility and

HIPdb: a database of experimentally validated HIV inhibiting peptides.

Science.gov (United States)

Qureshi, Abid; Thakur, Nishant; Kumar, Manoj

2013-01-01

Besides antiretroviral drugs, peptides have also demonstrated potential to inhibit the Human immunodeficiency virus (HIV). For example, T20 has been discovered to effectively block the HIV entry and was approved by the FDA as a novel anti-HIV peptide (AHP). We have collated all experimental information on AHPs at a single platform. HIPdb is a manually curated database of experimentally verified HIV inhibiting peptides targeting various steps or proteins involved in the life cycle of HIV e.g. fusion, integration, reverse transcription etc. This database provides experimental information of 981 peptides. These are of varying length obtained from natural as well as synthetic sources and tested on different cell lines. Important fields included are peptide sequence, length, source, target, cell line, inhibition/IC(50), assay and reference. The database provides user friendly browse, search, sort and filter options. It also contains useful services like BLAST and 'Map' for alignment with user provided sequences. In addition, predicted structure and physicochemical properties of the peptides are also included. HIPdb database is freely available at http://crdd.osdd.net/servers/hipdb. Comprehensive information of this database will be helpful in selecting/designing effective anti-HIV peptides. Thus it may prove a useful resource to researchers for peptide based therapeutics development.

IRID: specifications for the Ionising Radiations Incident Database

International Nuclear Information System (INIS)

Thomas, G.O.; Croft, J.R.; Williams, M.K.; McHugh, J.O.

1996-01-01

Technologies that make use of ionising radiations are widespread. They provide many benefits but, as with other technologies, the use of ionising radiations carries with it the potential for incidents and accidents. Their severity can vary from the trivial to the fatal and may involve substantial economic penalties. In order to minimise the number of incidents and their consequences it is important that there is a mechanism to learn the lessons from those that do occur. To help pursue this objective the National Radiological Protection Board, the Health and Safety Executive and the Environment Agency have established a national Ionising Radiations Incident Database (IRID) to cover radiation incidents in industry, medicine, research and teaching. This publication details the specifications for IRID and its methods of operation. All information in the database will be unattributable and names of persons or organisations will not be included. It is a personal computer based system with 24 fields to categorise an incident, including a text field that will provide a description of the incident giving the causes, consequences, follow-up actions and lessons to be learned. These descriptions will be used in subsequent publications to provide feedback to the users. (UK)

Thirty years after Alma-Ata: a systematic review of the impact of community health workers delivering curative interventions against malaria, pneumonia and diarrhoea on child mortality and morbidity in sub-Saharan Africa

Directory of Open Access Journals (Sweden)

Lewin Simon

2011-10-01

Full Text Available Abstract Background Over thirty years have passed since the Alma-Ata Declaration on primary health care in 1978. Many governments in the first decade following the declaration responded by developing national programmes of community health workers (CHWs, but evaluations of these often demonstrated poor outcomes. As many CHW programmes have responded to the HIV/AIDS pandemic, international interest in them has returned and their role in the response to other diseases should be examined carefully so that lessons can be applied to their new roles. Over half of the deaths in African children under five years of age are due to malaria, diarrhoea and pneumonia - a situation which could be addressed through the use of cheap and effective interventions delivered by CHWs. However, to date there is very little evidence from randomised controlled trials of the impacts of CHW programmes on child mortality in Africa. Evidence from non-randomised controlled studies has not previously been reviewed systematically. Methods We searched databases of published and unpublished studies for RCTs and non-randomised studies evaluating CHW programmes delivering curative treatments, with or without preventive components, for malaria, diarrhoea or pneumonia, in children in sub-Saharan Africa from 1987 to 2007. The impact of these programmes on morbidity or mortality in children under six years of age was reviewed. A descriptive analysis of interventional and contextual factors associated with these impacts was attempted. Results The review identified seven studies evaluating CHWs, delivering a range of interventions. Limited descriptive data on programmes, contexts or process outcomes for these CHW programmes were available. CHWs in national programmes achieved large mortality reductions of 63% and 36% respectively, when insecticide-treated nets and anti-malarial chemoprophylaxis were delivered, in addition to curative interventions. Conclusions CHW programmes could

State of the Art of Cost and Benefit Models for Digital Curation

DEFF Research Database (Denmark)

Kejser, Ulla Bøgvad; Davidson, Joy; Wang, David

2014-01-01

, to support decision-making and for selecting the most efficient processes – all of which are critical for ensuring sustainability of digital curation investment. The evaluation revealed that the most prominent challenges are associated with the models’ usability, their inability to model quality and benefits......This paper presents the results of an evaluation carried out by the EU 4C project to assess how well current digital curation cost and benefit models meet a range of stakeholders’ needs. This work aims to elicit a means of modelling that enables comparing financial information across organisations...... of curation, and the lack of a clear terminology and conceptual description of costs and benefits. The paper provides recommendations on how these gaps in cost and benefit modelling can be bridged....

HCVpro: Hepatitis C virus protein interaction database

KAUST Repository

Kwofie, Samuel K.

2011-12-01

It is essential to catalog characterized hepatitis C virus (HCV) protein-protein interaction (PPI) data and the associated plethora of vital functional information to augment the search for therapies, vaccines and diagnostic biomarkers. In furtherance of these goals, we have developed the hepatitis C virus protein interaction database (HCVpro) by integrating manually verified hepatitis C virus-virus and virus-human protein interactions curated from literature and databases. HCVpro is a comprehensive and integrated HCV-specific knowledgebase housing consolidated information on PPIs, functional genomics and molecular data obtained from a variety of virus databases (VirHostNet, VirusMint, HCVdb and euHCVdb), and from BIND and other relevant biology repositories. HCVpro is further populated with information on hepatocellular carcinoma (HCC) related genes that are mapped onto their encoded cellular proteins. Incorporated proteins have been mapped onto Gene Ontologies, canonical pathways, Online Mendelian Inheritance in Man (OMIM) and extensively cross-referenced to other essential annotations. The database is enriched with exhaustive reviews on structure and functions of HCV proteins, current state of drug and vaccine development and links to recommended journal articles. Users can query the database using specific protein identifiers (IDs), chromosomal locations of a gene, interaction detection methods, indexed PubMed sources as well as HCVpro, BIND and VirusMint IDs. The use of HCVpro is free and the resource can be accessed via http://apps.sanbi.ac.za/hcvpro/ or http://cbrc.kaust.edu.sa/hcvpro/. © 2011 Elsevier B.V.

A scalable machine-learning approach to recognize chemical names within large text databases

Directory of Open Access Journals (Sweden)

Wren Jonathan D

2006-09-01

Full Text Available Abstract Motivation The use or study of chemical compounds permeates almost every scientific field and in each of them, the amount of textual information is growing rapidly. There is a need to accurately identify chemical names within text for a number of informatics efforts such as database curation, report summarization, tagging of named entities and keywords, or the development/curation of reference databases. Results A first-order Markov Model (MM was evaluated for its ability to distinguish chemical names from words, yielding ~93% recall in recognizing chemical terms and ~99% precision in rejecting non-chemical terms on smaller test sets. However, because total false-positive events increase with the number of words analyzed, the scalability of name recognition was measured by processing 13.1 million MEDLINE records. The method yielded precision ranges from 54.7% to 100%, depending upon the cutoff score used, averaging 82.7% for approximately 1.05 million putative chemical terms extracted. Extracted chemical terms were analyzed to estimate the number of spelling variants per term, which correlated with the total number of times the chemical name appeared in MEDLINE. This variability in term construction was found to affect both information retrieval and term mapping when using PubMed and Ovid.

JSC Advanced Curation: Research and Development for Current Collections and Future Sample Return Mission Demands

Science.gov (United States)

Fries, M. D.; Allen, C. C.; Calaway, M. J.; Evans, C. A.; Stansbery, E. K.

2015-01-01

Curation of NASA's astromaterials sample collections is a demanding and evolving activity that supports valuable science from NASA missions for generations, long after the samples are returned to Earth. For example, NASA continues to loan hundreds of Apollo program samples to investigators every year and those samples are often analyzed using instruments that did not exist at the time of the Apollo missions themselves. The samples are curated in a manner that minimizes overall contamination, enabling clean, new high-sensitivity measurements and new science results over 40 years after their return to Earth. As our exploration of the Solar System progresses, upcoming and future NASA sample return missions will return new samples with stringent contamination control, sample environmental control, and Planetary Protection requirements. Therefore, an essential element of a healthy astromaterials curation program is a research and development (R&D) effort that characterizes and employs new technologies to maintain current collections and enable new missions - an Advanced Curation effort. JSC's Astromaterials Acquisition & Curation Office is continually performing Advanced Curation research, identifying and defining knowledge gaps about research, development, and validation/verification topics that are critical to support current and future NASA astromaterials sample collections. The following are highlighted knowledge gaps and research opportunities.

Updates to the Cool Season Food Legume Genome Database: Resources for pea, lentil, faba bean and chickpea genetics, genomics and breeding

Science.gov (United States)

The Cool Season Food Legume Genome database (CSFL, www.coolseasonfoodlegume.org) is an online resource for genomics, genetics, and breeding research for chickpea, lentil,pea, and faba bean. The user-friendly and curated website allows for all publicly available map,marker,trait, gene,transcript, ger...

Sample Transport for a European Sample Curation Facility

Science.gov (United States)

Berthoud, L.; Vrublevskis, J. B.; Bennett, A.; Pottage, T.; Bridges, J. C.; Holt, J. M. C.; Dirri, F.; Longobardo, A.; Palomba, E.; Russell, S.; Smith, C.

2018-04-01

This work has looked at the recovery of Mars Sample Return capsule once it arrives on Earth. It covers possible landing sites, planetary protection requirements, and transportation from the landing site to a European Sample Curation Facility.

Curative efficacy and safety of traditional Chinese medicine xuebijing injections combined with ulinastatin for treating sepsis in the Chinese population: A meta-analysis.

Science.gov (United States)

Xiao, Shi-Hui; Luo, Liang; Liu, Xiang-Hong; Zhou, Yu-Ming; Liu, Hong-Ming; Huang, Zhen-Fei

2018-06-01

Sepsis is a clinically critical disease. However, it is still controversial whether the combined use of traditional Chinese medicine Xuebijing injections (XBJI) and western medicine can enhance curative efficacy and ensure safety compared with western medicine alone. Thus, this research consisted of a systematic review of the curative efficacy and safety of traditional Chinese medicine XBJI combined with ulinastatin for treating sepsis in the Chinese population. A total of 8 databases were retrieved: 4 foreign databases, namely, PubMed, The Cochrane Library, Embase, and Web of Science; and 4 Chinese databases, namely, Sino Med, China National Knowledge Infrastructure (CNKI), VIP, and Wangfang Data. The time span of retrieval began from the establishment of each database and ended on August 1, 2017. Published randomized controlled trials about the combined use of traditional Chinese medicine XBJI and western medicine were included, regardless of language. Stata12.0 software was used for statistical analysis. Finally, 16 papers involving 1335 cases were included. The result of meta-analysis showed that compared with the single use of ulinastatin, traditional Chinese medicine XBJI combined with ulinastatin could reduce the time of mechanical ventilation, shorten the length of intensive care unit (ICU) stay, improve the 28-day survival rate, and decrease the occurrence rate of multiple organ dysfunction syndrome, case fatality rate, procalcitonin (PCT) content, APACKEII score, tumor necrosis factor (TNF)-α level, and interleukin (IL)-6 level. On the basis of the common basic therapeutic regimen, the combined use of traditional Chinese medicine XBJI and ulinastatin was compared with the use of ulinastatin alone for treating sepsis in the Chinese population. It was found that the number of adverse events of combination therapy is not significantly increased, and its clinical safety is well within the permitted range. However, considering the limitations of this

Curating and Nudging in Virtual CLIL Environments

Science.gov (United States)

Nielsen, Helle Lykke

2014-01-01

Foreign language teachers can benefit substantially from the notions of curation and nudging when scaffolding CLIL activities on the internet. This article shows how these principles can be integrated into CLILstore, a free multimedia-rich learning tool with seamless access to online dictionaries, and presents feedback from first and second year…

Outcomes of the 'Data Curation for Geobiology at Yellowstone National Park' Workshop

Science.gov (United States)

Thomer, A.; Palmer, C. L.; Fouke, B. W.; Rodman, A.; Choudhury, G. S.; Baker, K. S.; Asangba, A. E.; Wickett, K.; DiLauro, T.; Varvel, V.

2013-12-01

The continuing proliferation of geological and biological data generated at scientifically significant sites (such as hot springs, coral reefs, volcanic fields and other unique, data-rich locales) has created a clear need for the curation and active management of these data. However, there has been little exploration of what these curation processes and policies would entail. To that end, the Site-Based Data Curation (SBDC) project is developing a framework of guidelines and processes for the curation of research data generated at scientifically significant sites. A workshop was held in April 2013 at Yellowstone National Park (YNP) to gather input from scientists and stakeholders. Workshop participants included nine researchers actively conducting geobiology research at YNP, and seven YNP representatives, including permitting staff and information professionals from the YNP research library and archive. Researchers came from a range of research areas -- geology, molecular and microbial biology, ecology, environmental engineering, and science education. Through group discussions, breakout sessions and hands-on activities, we sought to generate policy recommendations and curation guidelines for the collection, representation, sharing and quality control of geobiological datasets. We report on key themes that emerged from workshop discussions, including: - participants' broad conceptions of the long-term usefulness, reusability and value of data. - the benefits of aggregating site-specific data in general, and geobiological data in particular. - the importance of capturing a dataset's originating context, and the potential usefulness of photographs as a reliable and easy way of documenting context. - researchers' and resource managers' overlapping priorities with regards to 'big picture' data collection and management in the long-term. Overall, we found that workshop participants were enthusiastic and optimistic about future collaboration and development of community

Greengenes: Chimera-checked 16S rRNA gene database and workbenchcompatible in ARB

Energy Technology Data Exchange (ETDEWEB)

DeSantis, T.Z.; Hugenholtz, P.; Larsen, N.; Rojas, M.; Brodie,E.L; Keller, K.; Huber, T.; Dalevi, D.; Hu, P.; Andersen, G.L.

2006-02-01

A 16S rRNA gene database (http://greengenes.lbl.gov) addresses limitations of public repositories by providing chimera-screening, standard alignments and taxonomic classification using multiple published taxonomies. It was revealed that incongruent taxonomic nomenclature exists among curators even at the phylum-level. Putative chimeras were identified in 3% of environmental sequences and 0.2% of records derived from isolates. Environmental sequences were classified into 100 phylum-level lineages within the Archaea and Bacteria.

Organic Contamination Baseline Study on NASA JSC Astromaterial Curation Gloveboxes

Science.gov (United States)

Calaway, Michael J.; Allton, J. H.; Allen, C. C.; Burkett, P. J.

2013-01-01

Future planned sample return missions to carbon-rich asteroids and Mars in the next two decades will require strict handling and curation protocols as well as new procedures for reducing organic contamination. After the Apollo program, astromaterial collections have mainly been concerned with inorganic contamination [1-4]. However, future isolation containment systems for astromaterials, possibly nitrogen enriched gloveboxes, must be able to reduce organic and inorganic cross-contamination. In 2012, a baseline study was orchestrated to establish the current state of organic cleanliness in gloveboxes used by NASA JSC astromaterials curation labs that could be used as a benchmark for future mission designs.

Xylella fastidiosa comparative genomic database is an information resource to explore the annotation, genomic features, and biology of different strains

Directory of Open Access Journals (Sweden)

Alessandro M. Varani

2012-01-01

Full Text Available The Xylella fastidiosa comparative genomic database is a scientific resource with the aim to provide a user-friendly interface for accessing high-quality manually curated genomic annotation and comparative sequence analysis, as well as for identifying and mapping prophage-like elements, a marked feature of Xylella genomes. Here we describe a database and tools for exploring the biology of this important plant pathogen. The hallmarks of this database are the high quality genomic annotation, the functional and comparative genomic analysis and the identification and mapping of prophage-like elements. It is available from web site http://www.xylella.lncc.br.

Curating Media Learning: Towards a Porous Expertise

Science.gov (United States)

McDougall, Julian; Potter, John

2015-01-01

This article combines research results from a range of projects with two consistent themes. Firstly, we explore the potential for curation to offer a productive metaphor for the convergence of digital media learning across and between home/lifeworld and formal educational/system-world spaces--or between the public and private spheres. Secondly, we…

Hospital of Diagnosis Influences the Probability of Receiving Curative Treatment for Esophageal Cancer.

Science.gov (United States)

van Putten, Margreet; Koëter, Marijn; van Laarhoven, Hanneke W M; Lemmens, Valery E P P; Siersema, Peter D; Hulshof, Maarten C C M; Verhoeven, Rob H A; Nieuwenhuijzen, Grard A P

2018-02-01

The aim of this article was to study the influence of hospital of diagnosis on the probability of receiving curative treatment and its impact on survival among patients with esophageal cancer (EC). Although EC surgery is centralized in the Netherlands, the disease is often diagnosed in hospitals that do not perform this procedure. Patients with potentially curable esophageal or gastroesophageal junction tumors diagnosed between 2005 and 2013 who were potentially curable (cT1-3,X, any N, M0,X) were selected from the Netherlands Cancer Registry. Multilevel logistic regression was performed to examine the probability to undergo curative treatment (resection with or without neoadjuvant treatment, definitive chemoradiotherapy, or local tumor excision) according to hospital of diagnosis. Effects of variation in probability of undergoing curative treatment among these hospitals on survival were investigated by Cox regression. All 13,017 patients with potentially curable EC, diagnosed in 91 hospitals, were included. The proportion of patients receiving curative treatment ranged from 37% to 83% and from 45% to 86% in the periods 2005-2009 and 2010-2013, respectively, depending on hospital of diagnosis. After adjustment for patient- and hospital-related characteristics these proportions ranged from 41% to 77% and from 50% to 82%, respectively (both P < 0.001). Multivariable survival analyses showed that patients diagnosed in hospitals with a low probability of undergoing curative treatment had a worse overall survival (hazard ratio = 1.13, 95% confidence interval 1.06-1.20; hazard ratio = 1.15, 95% confidence interval 1.07-1.24). The variation in probability of undergoing potentially curative treatment for EC between hospitals of diagnosis and its impact on survival indicates that treatment decision making in EC may be improved.

Curator's process of meaning-making in National museums

DEFF Research Database (Denmark)

Cole, Anne Jodon

2014-01-01

The paper aims to understand the meaning-making process curators engage in designing/developing exhibitions of the nations indigenous peoples. How indigenous people are represented can with perpetuate stereotypes or mediate change while strengthening their personal and group identity. Analysis...

Curation and Computational Design of Bioenergy-Related Metabolic Pathways

Energy Technology Data Exchange (ETDEWEB)

Karp, Peter D. [SRI International, Menlo Park, CA (United States)

2014-09-12

Pathway Tools is a systems-biology software package written by SRI International (SRI) that produces Pathway/Genome Databases (PGDBs) for organisms with a sequenced genome. Pathway Tools also provides a wide range of capabilities for analyzing predicted metabolic networks and user-generated omics data. More than 5,000 academic, industrial, and government groups have licensed Pathway Tools. This user community includes researchers at all three DOE bioenergy centers, as well as academic and industrial metabolic engineering (ME) groups. An integral part of the Pathway Tools software is MetaCyc, a large, multiorganism database of metabolic pathways and enzymes that SRI and its academic collaborators manually curate. This project included two main goals: I. Enhance the MetaCyc content of bioenergy-related enzymes and pathways. II. Develop computational tools for engineering metabolic pathways that satisfy specified design goals, in particular for bioenergy-related pathways. In part I, SRI proposed to significantly expand the coverage of bioenergy-related metabolic information in MetaCyc, followed by the generation of organism-specific PGDBs for all energy-relevant organisms sequenced at the DOE Joint Genome Institute (JGI). Part I objectives included: 1: Expand the content of MetaCyc to include bioenergy-related enzymes and pathways. 2: Enhance the Pathway Tools software to enable display of complex polymer degradation processes. 3: Create new PGDBs for the energy-related organisms sequenced by JGI, update existing PGDBs with new MetaCyc content, and make these data available to JBEI via the BioCyc website. In part II, SRI proposed to develop an efficient computational tool for the engineering of metabolic pathways. Part II objectives included: 4: Develop computational tools for generating metabolic pathways that satisfy specified design goals, enabling users to specify parameters such as starting and ending compounds, and preferred or disallowed intermediate compounds

Observation of curative effect of 131I in treatment of hyperthyroidism

International Nuclear Information System (INIS)

Huang Kebin; Xu Fan; Zhang Yaping; Wang Jingchang; Zhao Mingli; Ye Ming

2012-01-01

Objective: To explore the curative effect of 131 I in the treatment of hyperthyroidism. Method: 126 patients with hyperthyroidism were treated with 131 I and the curative effect was analyzed. Result: The results showed that among 126 cases of hyperthyroidism treated with 131 I, 117 cases had recovered and the cure rate was 92.9%. 9 cases were found hypothyroidism in one-year follow-up and the occurrence rate was 7.1%. Conclusion: The treatment of hyperthyroidism with 131 I is safe and effective method. (authors)

Planform: an application and database of graph-encoded planarian regenerative experiments.

Science.gov (United States)

Lobo, Daniel; Malone, Taylor J; Levin, Michael

2013-04-15

Understanding the mechanisms governing the regeneration capabilities of many organisms is a fundamental interest in biology and medicine. An ever-increasing number of manipulation and molecular experiments are attempting to discover a comprehensive model for regeneration, with the planarian flatworm being one of the most important model species. Despite much effort, no comprehensive, constructive, mechanistic models exist yet, and it is now clear that computational tools are needed to mine this huge dataset. However, until now, there is no database of regenerative experiments, and the current genotype-phenotype ontologies and databases are based on textual descriptions, which are not understandable by computers. To overcome these difficulties, we present here Planform (Planarian formalization), a manually curated database and software tool for planarian regenerative experiments, based on a mathematical graph formalism. The database contains more than a thousand experiments from the main publications in the planarian literature. The software tool provides the user with a graphical interface to easily interact with and mine the database. The presented system is a valuable resource for the regeneration community and, more importantly, will pave the way for the application of novel artificial intelligence tools to extract knowledge from this dataset. The database and software tool are freely available at http://planform.daniel-lobo.com.

AT_CHLORO, a comprehensive chloroplast proteome database with subplastidial localization and curated information on envelope proteins.

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Ferro, Myriam; Brugière, Sabine; Salvi, Daniel; Seigneurin-Berny, Daphné; Court, Magali; Moyet, Lucas; Ramus, Claire; Miras, Stéphane; Mellal, Mourad; Le Gall, Sophie; Kieffer-Jaquinod, Sylvie; Bruley, Christophe; Garin, Jérôme; Joyard, Jacques; Masselon, Christophe; Rolland, Norbert

2010-06-01

Recent advances in the proteomics field have allowed a series of high throughput experiments to be conducted on chloroplast samples, and the data are available in several public databases. However, the accurate localization of many chloroplast proteins often remains hypothetical. This is especially true for envelope proteins. We went a step further into the knowledge of the chloroplast proteome by focusing, in the same set of experiments, on the localization of proteins in the stroma, the thylakoids, and envelope membranes. LC-MS/MS-based analyses first allowed building the AT_CHLORO database (http://www.grenoble.prabi.fr/protehome/grenoble-plant-proteomics/), a comprehensive repertoire of the 1323 proteins, identified by 10,654 unique peptide sequences, present in highly purified chloroplasts and their subfractions prepared from Arabidopsis thaliana leaves. This database also provides extensive proteomics information (peptide sequences and molecular weight, chromatographic retention times, MS/MS spectra, and spectral count) for a unique chloroplast protein accurate mass and time tag database gathering identified peptides with their respective and precise analytical coordinates, molecular weight, and retention time. We assessed the partitioning of each protein in the three chloroplast compartments by using a semiquantitative proteomics approach (spectral count). These data together with an in-depth investigation of the literature were compiled to provide accurate subplastidial localization of previously known and newly identified proteins. A unique knowledge base containing extensive information on the proteins identified in envelope fractions was thus obtained, allowing new insights into this membrane system to be revealed. Altogether, the data we obtained provide unexpected information about plastidial or subplastidial localization of some proteins that were not suspected to be associated to this membrane system. The spectral counting-based strategy was further

Neural systems language: a formal modeling language for the systematic description, unambiguous communication, and automated digital curation of neural connectivity.

Science.gov (United States)

Brown, Ramsay A; Swanson, Larry W

2013-09-01

Systematic description and the unambiguous communication of findings and models remain among the unresolved fundamental challenges in systems neuroscience. No common descriptive frameworks exist to describe systematically the connective architecture of the nervous system, even at the grossest level of observation. Furthermore, the accelerating volume of novel data generated on neural connectivity outpaces the rate at which this data is curated into neuroinformatics databases to synthesize digitally systems-level insights from disjointed reports and observations. To help address these challenges, we propose the Neural Systems Language (NSyL). NSyL is a modeling language to be used by investigators to encode and communicate systematically reports of neural connectivity from neuroanatomy and brain imaging. NSyL engenders systematic description and communication of connectivity irrespective of the animal taxon described, experimental or observational technique implemented, or nomenclature referenced. As a language, NSyL is internally consistent, concise, and comprehensible to both humans and computers. NSyL is a promising development for systematizing the representation of neural architecture, effectively managing the increasing volume of data on neural connectivity and streamlining systems neuroscience research. Here we present similar precedent systems, how NSyL extends existing frameworks, and the reasoning behind NSyL's development. We explore NSyL's potential for balancing robustness and consistency in representation by encoding previously reported assertions of connectivity from the literature as examples. Finally, we propose and discuss the implications of a framework for how NSyL will be digitally implemented in the future to streamline curation of experimental results and bridge the gaps among anatomists, imagers, and neuroinformatics databases. Copyright © 2013 Wiley Periodicals, Inc.

Curating NASA's Astromaterials Collections: Past, Present, and Future

Science.gov (United States)

Zeigler, Ryan

2015-01-01

Planning for the curation of samples from future sample return missions must begin during the initial planning stages of a mission. Waiting until the samples have been returned to Earth, or even when you begin to physically build the spacecraft is too late. A lack of proper planning could lead to irreversible contamination of the samples, which in turn would compromise the scientific integrity of the mission. For example, even though the Apollo missions first returned samples in 1969, planning for the curation facility began in the early 1960s, and construction of the Lunar Receiving Laboratory was completed in 1967. In addition to designing the receiving facility and laboratory that the samples will be characterized and stored in, there are many aspects of contamination that must be addressed during the planning and building of the spacecraft: planetary protection (both outbound and inbound); cataloging, documenting, and preserving the materials used to build spacecraft (also known as coupons); near real-time monitoring of the environment in which the spacecraft is being built using witness plates for critical aspects of contamination (known as contamination control); and long term monitoring and preservation of the environment in which the spacecraft is being built for most aspects of potential contamination through the use of witness plates (known as contamination knowledge). The OSIRIS REx asteroid sample return mission, currently being built, is dealing with all of these aspects of contamination in order to ensure they return the best preserved sample possible. Coupons and witness plates from OSIRIS REx are currently being studied and stored (for future studies) at the Johnson Space Center. Similarly, planning for the clean room facility at Johnson Space Center to house the OSIRIS-REx samples is well advanced, and construction of the facility should begin in early 2017 (despite a nominal 2023 return date for OSIRIS-REx samples). Similar development is being

H2DB: a heritability database across multiple species by annotating trait-associated genomic loci.

Science.gov (United States)

Kaminuma, Eli; Fujisawa, Takatomo; Tanizawa, Yasuhiro; Sakamoto, Naoko; Kurata, Nori; Shimizu, Tokurou; Nakamura, Yasukazu

2013-01-01

H2DB (http://tga.nig.ac.jp/h2db/), an annotation database of genetic heritability estimates for humans and other species, has been developed as a knowledge database to connect trait-associated genomic loci. Heritability estimates have been investigated for individual species, particularly in human twin studies and plant/animal breeding studies. However, there appears to be no comprehensive heritability database for both humans and other species. Here, we introduce an annotation database for genetic heritabilities of various species that was annotated by manually curating online public resources in PUBMED abstracts and journal contents. The proposed heritability database contains attribute information for trait descriptions, experimental conditions, trait-associated genomic loci and broad- and narrow-sense heritability specifications. Annotated trait-associated genomic loci, for which most are single-nucleotide polymorphisms derived from genome-wide association studies, may be valuable resources for experimental scientists. In addition, we assigned phenotype ontologies to the annotated traits for the purposes of discussing heritability distributions based on phenotypic classifications.

A justification for semantic training in data curation frameworks development

Science.gov (United States)

Ma, X.; Branch, B. D.; Wegner, K.

2013-12-01

In the complex data curation activities involving proper data access, data use optimization and data rescue, opportunities exist where underlying skills in semantics may play a crucial role in data curation professionals ranging from data scientists, to informaticists, to librarians. Here, We provide a conceptualization of semantics use in the education data curation framework (EDCF) [1] under development by Purdue University and endorsed by the GLOBE program [2] for further development and application. Our work shows that a comprehensive data science training includes both spatial and non-spatial data, where both categories are promoted by standard efforts of organizations such as the Open Geospatial Consortium (OGC) and the World Wide Web Consortium (W3C), as well as organizations such as the Federation of Earth Science Information Partners (ESIP) that share knowledge and propagate best practices in applications. Outside the context of EDCF, semantics training may be same critical to such data scientists, informaticists or librarians in other types of data curation activity. Past works by the authors have suggested that such data science should augment an ontological literacy where data science may become sustainable as a discipline. As more datasets are being published as open data [3] and made linked to each other, i.e., in the Resource Description Framework (RDF) format, or at least their metadata are being published in such a way, vocabularies and ontologies of various domains are being created and used in the data management, such as the AGROVOC [4] for agriculture and the GCMD keywords [5] and CLEAN vocabulary [6] for climate sciences. The new generation of data scientist should be aware of those technologies and receive training where appropriate to incorporate those technologies into their reforming daily works. References [1] Branch, B.D., Fosmire, M., 2012. The role of interdisciplinary GIS and data curation librarians in enhancing authentic scientific

Collecting, curating, and researching writers' libraries a handbook

CERN Document Server

Oram, Richard W

2014-01-01

Collecting, Curating, and Researching Writers' Libraries: A Handbook is the first book to examine the history, acquisition, cataloging, and scholarly use of writers' personal libraries. This book also includes interviews with several well-known writers, who discuss their relationship with their books.

A relevancy algorithm for curating earth science data around phenomenon

Science.gov (United States)

Maskey, Manil; Ramachandran, Rahul; Li, Xiang; Weigel, Amanda; Bugbee, Kaylin; Gatlin, Patrick; Miller, J. J.

2017-09-01

Earth science data are being collected for various science needs and applications, processed using different algorithms at multiple resolutions and coverages, and then archived at different archiving centers for distribution and stewardship causing difficulty in data discovery. Curation, which typically occurs in museums, art galleries, and libraries, is traditionally defined as the process of collecting and organizing information around a common subject matter or a topic of interest. Curating data sets around topics or areas of interest addresses some of the data discovery needs in the field of Earth science, especially for unanticipated users of data. This paper describes a methodology to automate search and selection of data around specific phenomena. Different components of the methodology including the assumptions, the process, and the relevancy ranking algorithm are described. The paper makes two unique contributions to improving data search and discovery capabilities. First, the paper describes a novel methodology developed for automatically curating data around a topic using Earth science metadata records. Second, the methodology has been implemented as a stand-alone web service that is utilized to augment search and usability of data in a variety of tools.

Reservation Application System Of Private Lesson At Easyspeak Denpasar Based On Web And Android

Directory of Open Access Journals (Sweden)

Ferry yudhitama putra

2016-06-01

Full Text Available Abstract— English Private lessons institutes are now widely facilitates a person to develop English skills in speaking and writing. Currently the service users private lessons English book private lessons manually, that is by coming directly to the place as well as through the telephone service, but with the operator even then still have difficulties in user validation that requires a long time. To facilitate the user in terms of the reservation, then the system will be built based on web and Android. Development of private lessons reservation application built with PHP and Java programming language using CodeIgniter framework on the web side , while on the Android using Eclipse tools , and MySQL as database storage media . Applications reservation private lessons has several functions to make a reservation time and tutor can be done by the student of Easyspeak and on the side of the tutor application can provide information about the student will be taught , as well as on the side of the operator to provide ease in setting booking private lessons because it computerized not manually as before. Applications reservation private lessons are also equipped with a reminder or reminders are made on the side of Android apps , using alarmmanager system.

Learning relationships: Church of England curates and training ...

African Journals Online (AJOL)

2017-06-20

Jun 20, 2017 ... exploring how this affects the dynamic of the relationship with their curates. Scripture is also ... factors, as employed in the models of personality advanced by Costa and .... psychological type preferences of their training incumbents. The data ..... to conceptualising and implementing Christian vocation.

GarlicESTdb: an online database and mining tool for garlic EST sequences

Directory of Open Access Journals (Sweden)

Choi Sang-Haeng

2009-05-01

Full Text Available Abstract Background Allium sativum., commonly known as garlic, is a species in the onion genus (Allium, which is a large and diverse one containing over 1,250 species. Its close relatives include chives, onion, leek and shallot. Garlic has been used throughout recorded history for culinary, medicinal use and health benefits. Currently, the interest in garlic is highly increasing due to nutritional and pharmaceutical value including high blood pressure and cholesterol, atherosclerosis and cancer. For all that, there are no comprehensive databases available for Expressed Sequence Tags(EST of garlic for gene discovery and future efforts of genome annotation. That is why we developed a new garlic database and applications to enable comprehensive analysis of garlic gene expression. Description GarlicESTdb is an integrated database and mining tool for large-scale garlic (Allium sativum EST sequencing. A total of 21,595 ESTs collected from an in-house cDNA library were used to construct the database. The analysis pipeline is an automated system written in JAVA and consists of the following components: automatic preprocessing of EST reads, assembly of raw sequences, annotation of the assembled sequences, storage of the analyzed information into MySQL databases, and graphic display of all processed data. A web application was implemented with the latest J2EE (Java 2 Platform Enterprise Edition software technology (JSP/EJB/JavaServlet for browsing and querying the database, for creation of dynamic web pages on the client side, and for mapping annotated enzymes to KEGG pathways, the AJAX framework was also used partially. The online resources, such as putative annotation, single nucleotide polymorphisms (SNP and tandem repeat data sets, can be searched by text, explored on the website, searched using BLAST, and downloaded. To archive more significant BLAST results, a curation system was introduced with which biologists can easily edit best-hit annotation

GarlicESTdb: an online database and mining tool for garlic EST sequences.

Science.gov (United States)

Kim, Dae-Won; Jung, Tae-Sung; Nam, Seong-Hyeuk; Kwon, Hyuk-Ryul; Kim, Aeri; Chae, Sung-Hwa; Choi, Sang-Haeng; Kim, Dong-Wook; Kim, Ryong Nam; Park, Hong-Seog

2009-05-18

Allium sativum., commonly known as garlic, is a species in the onion genus (Allium), which is a large and diverse one containing over 1,250 species. Its close relatives include chives, onion, leek and shallot. Garlic has been used throughout recorded history for culinary, medicinal use and health benefits. Currently, the interest in garlic is highly increasing due to nutritional and pharmaceutical value including high blood pressure and cholesterol, atherosclerosis and cancer. For all that, there are no comprehensive databases available for Expressed Sequence Tags(EST) of garlic for gene discovery and future efforts of genome annotation. That is why we developed a new garlic database and applications to enable comprehensive analysis of garlic gene expression. GarlicESTdb is an integrated database and mining tool for large-scale garlic (Allium sativum) EST sequencing. A total of 21,595 ESTs collected from an in-house cDNA library were used to construct the database. The analysis pipeline is an automated system written in JAVA and consists of the following components: automatic preprocessing of EST reads, assembly of raw sequences, annotation of the assembled sequences, storage of the analyzed information into MySQL databases, and graphic display of all processed data. A web application was implemented with the latest J2EE (Java 2 Platform Enterprise Edition) software technology (JSP/EJB/JavaServlet) for browsing and querying the database, for creation of dynamic web pages on the client side, and for mapping annotated enzymes to KEGG pathways, the AJAX framework was also used partially. The online resources, such as putative annotation, single nucleotide polymorphisms (SNP) and tandem repeat data sets, can be searched by text, explored on the website, searched using BLAST, and downloaded. To archive more significant BLAST results, a curation system was introduced with which biologists can easily edit best-hit annotation information for others to view. The Garlic

ProCarDB: a database of bacterial carotenoids.

Science.gov (United States)

Nupur, L N U; Vats, Asheema; Dhanda, Sandeep Kumar; Raghava, Gajendra P S; Pinnaka, Anil Kumar; Kumar, Ashwani

2016-05-26

Carotenoids have important functions in bacteria, ranging from harvesting light energy to neutralizing oxidants and acting as virulence factors. However, information pertaining to the carotenoids is scattered throughout the literature. Furthermore, information about the genes/proteins involved in the biosynthesis of carotenoids has tremendously increased in the post-genomic era. A web server providing the information about microbial carotenoids in a structured manner is required and will be a valuable resource for the scientific community working with microbial carotenoids. Here, we have created a manually curated, open access, comprehensive compilation of bacterial carotenoids named as ProCarDB- Prokaryotic Carotenoid Database. ProCarDB includes 304 unique carotenoids arising from 50 biosynthetic pathways distributed among 611 prokaryotes. ProCarDB provides important information on carotenoids, such as 2D and 3D structures, molecular weight, molecular formula, SMILES, InChI, InChIKey, IUPAC name, KEGG Id, PubChem Id, and ChEBI Id. The database also provides NMR data, UV-vis absorption data, IR data, MS data and HPLC data that play key roles in the identification of carotenoids. An important feature of this database is the extension of biosynthetic pathways from the literature and through the presence of the genes/enzymes in different organisms. The information contained in the database was mined from published literature and databases such as KEGG, PubChem, ChEBI, LipidBank, LPSN, and Uniprot. The database integrates user-friendly browsing and searching with carotenoid analysis tools to help the user. We believe that this database will serve as a major information centre for researchers working on bacterial carotenoids.

GDR (Genome Database for Rosaceae): integrated web-database for Rosaceae genomics and genetics data.

Science.gov (United States)

Jung, Sook; Staton, Margaret; Lee, Taein; Blenda, Anna; Svancara, Randall; Abbott, Albert; Main, Dorrie

2008-01-01

The Genome Database for Rosaceae (GDR) is a central repository of curated and integrated genetics and genomics data of Rosaceae, an economically important family which includes apple, cherry, peach, pear, raspberry, rose and strawberry. GDR contains annotated databases of all publicly available Rosaceae ESTs, the genetically anchored peach physical map, Rosaceae genetic maps and comprehensively annotated markers and traits. The ESTs are assembled to produce unigene sets of each genus and the entire Rosaceae. Other annotations include putative function, microsatellites, open reading frames, single nucleotide polymorphisms, gene ontology terms and anchored map position where applicable. Most of the published Rosaceae genetic maps can be viewed and compared through CMap, the comparative map viewer. The peach physical map can be viewed using WebFPC/WebChrom, and also through our integrated GDR map viewer, which serves as a portal to the combined genetic, transcriptome and physical mapping information. ESTs, BACs, markers and traits can be queried by various categories and the search result sites are linked to the mapping visualization tools. GDR also provides online analysis tools such as a batch BLAST/FASTA server for the GDR datasets, a sequence assembly server and microsatellite and primer detection tools. GDR is available at http://www.rosaceae.org.

The Candidate Cancer Gene Database: a database of cancer driver genes from forward genetic screens in mice.

Science.gov (United States)

Abbott, Kenneth L; Nyre, Erik T; Abrahante, Juan; Ho, Yen-Yi; Isaksson Vogel, Rachel; Starr, Timothy K

2015-01-01

Identification of cancer driver gene mutations is crucial for advancing cancer therapeutics. Due to the overwhelming number of passenger mutations in the human tumor genome, it is difficult to pinpoint causative driver genes. Using transposon mutagenesis in mice many laboratories have conducted forward genetic screens and identified thousands of candidate driver genes that are highly relevant to human cancer. Unfortunately, this information is difficult to access and utilize because it is scattered across multiple publications using different mouse genome builds and strength metrics. To improve access to these findings and facilitate meta-analyses, we developed the Candidate Cancer Gene Database (CCGD, http://ccgd-starrlab.oit.umn.edu/). The CCGD is a manually curated database containing a unified description of all identified candidate driver genes and the genomic location of transposon common insertion sites (CISs) from all currently published transposon-based screens. To demonstrate relevance to human cancer, we performed a modified gene set enrichment analysis using KEGG pathways and show that human cancer pathways are highly enriched in the database. We also used hierarchical clustering to identify pathways enriched in blood cancers compared to solid cancers. The CCGD is a novel resource available to scientists interested in the identification of genetic drivers of cancer. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

A tuberculosis biomarker database: the key to novel TB diagnostics

Directory of Open Access Journals (Sweden)

Seda Yerlikaya

2017-03-01

Full Text Available New diagnostic innovations for tuberculosis (TB, including point-of-care solutions, are critical to reach the goals of the End TB Strategy. However, despite decades of research, numerous reports on new biomarker candidates, and significant investment, no well-performing, simple and rapid TB diagnostic test is yet available on the market, and the search for accurate, non-DNA biomarkers remains a priority. To help overcome this ‘biomarker pipeline problem’, FIND and partners are working on the development of a well-curated and user-friendly TB biomarker database. The web-based database will enable the dynamic tracking of evidence surrounding biomarker candidates in relation to target product profiles (TPPs for needed TB diagnostics. It will be able to accommodate raw datasets and facilitate the verification of promising biomarker candidates and the identification of novel biomarker combinations. As such, the database will simplify data and knowledge sharing, empower collaboration, help in the coordination of efforts and allocation of resources, streamline the verification and validation of biomarker candidates, and ultimately lead to an accelerated translation into clinically useful tools.

Use of Ontologies for Data Integration and Curation

Directory of Open Access Journals (Sweden)

Judith Gelernter

2011-03-01

Full Text Available Data curation includes the goal of facilitating the re-use and combination of datasets, which is often impeded by incompatible data schema. Can we use ontologies to help with data integration? We suggest a semi-automatic process that involves the use of automatic text searching to help identify overlaps in metadata that accompany data schemas, plus human validation of suggested data matches.Problems include different text used to describe the same concept, different forms of data recording and different organizations of data. Ontologies can help by focussing attention on important words, providing synonyms to assist matching, and indicating in what context words are used. Beyond ontologies, data on the statistical behavior of data can be used to decide which data elements appear to be compatible with which other data elements. When curating data which may have hundreds or even thousands of data labels, semi-automatic assistance with data fusion should be of great help.

Curating the Poster

DEFF Research Database (Denmark)

Christensen, Line Hjorth

2017-01-01

Parallel to the primary functions performed by posters in the urban environment, we find a range of curatorial practices that tie the poster, a mass-produced graphic design media, to the museum institution. Yet little research has attempted to uncover the diverse subject of curatorial work...... and the process where posters created to live in a real-world environment are relocated in a museum. According to Peter Bil’ak (2006), it creates a situation where ”the entire raison d’être of the work is lost as a side effect of losing the context of the work”. The article investigates how environmental...... structures can work as guidelines for curating posters and graphic design in a museum context. By applying an ecological view to design, specifically the semiotic notion “counter-ability”, it stresses the reciprocal relationship of humans and their built and product-designed environments. It further suggests...

A Phase Blending Study on Rubber Blends Based on the Solubility Preference of Curatives

NARCIS (Netherlands)

Guo, R.; Talma, Auke; Datta, Rabin; Dierkes, Wilma K.; Noordermeer, Jacobus W.M.

2009-01-01

Using previously obtained data on the solubilities of curatives in SBR, EPDM and in NBR, different mixing procedures were performed on 50/50 SBR/EPDM and NBR/EPDM blends. In contrast to a previous phase-mixing study, the curatives were added to separate phases before final blending, in an attempt to

DB-PABP: a database of polyanion-binding proteins.

Science.gov (United States)

Fang, Jianwen; Dong, Yinghua; Salamat-Miller, Nazila; Middaugh, C Russell

2008-01-01

The interactions between polyanions (PAs) and polyanion-binding proteins (PABPs) have been found to play significant roles in many essential biological processes including intracellular organization, transport and protein folding. Furthermore, many neurodegenerative disease-related proteins are PABPs. Thus, a better understanding of PA/PABP interactions may not only enhance our understandings of biological systems but also provide new clues to these deadly diseases. The literature in this field is widely scattered, suggesting the need for a comprehensive and searchable database of PABPs. The DB-PABP is a comprehensive, manually curated and searchable database of experimentally characterized PABPs. It is freely available and can be accessed online at http://pabp.bcf.ku.edu/DB_PABP/. The DB-PABP was implemented as a MySQL relational database. An interactive web interface was created using Java Server Pages (JSP). The search page of the database is organized into a main search form and a section for utilities. The main search form enables custom searches via four menus: protein names, polyanion names, the source species of the proteins and the methods used to discover the interactions. Available utilities include a commonality matrix, a function of listing PABPs by the number of interacting polyanions and a string search for author surnames. The DB-PABP is maintained at the University of Kansas. We encourage users to provide feedback and submit new data and references.

Smart Mobility Stakeholders - Curating Urban Data & Models

Energy Technology Data Exchange (ETDEWEB)

Sperling, Joshua [National Renewable Energy Laboratory (NREL), Golden, CO (United States)

2017-09-01

This presentation provides an overview of the curation of urban data and models through engaging SMART mobility stakeholders. SMART Mobility Urban Science Efforts are helping to expose key data sets, models, and roles for the U.S. Department of Energy in engaging across stakeholders to ensure useful insights. This will help to support other Urban Science and broader SMART initiatives.

HemaExplorer: a database of mRNA expression profiles in normal and malignant haematopoiesis

DEFF Research Database (Denmark)

Bagger, Frederik Otzen; Rapin, Nicolas; Theilgaard-Mönch, Kim

2013-01-01

lead to full integrity of the data in the database. The HemaExplorer has comprehensive visualization interface that can make it useful as a daily tool for biologists and cancer researchers to assess the expression patterns of genes encountered in research or literature. HemaExplorer is relevant for all......The HemaExplorer (http://servers.binf.ku.dk/hemaexplorer) is a curated database of processed mRNA Gene expression profiles (GEPs) that provides an easy display of gene expression in haematopoietic cells. HemaExplorer contains GEPs derived from mouse/human haematopoietic stem and progenitor cells...... as well as from more differentiated cell types. Moreover, data from distinct subtypes of human acute myeloid leukemia is included in the database allowing researchers to directly compare gene expression of leukemic cells with those of their closest normal counterpart. Normalization and batch correction...

AtomPy: An Open Atomic Data Curation Environment for Astrophysical Applications

Directory of Open Access Journals (Sweden)

Claudio Mendoza

2014-05-01

Full Text Available We present a cloud-computing environment, referred to as AtomPy, based on Google-Drive Sheets and Pandas (Python Data Analysis Library DataFrames to promote community-driven curation of atomic data for astrophysical applications, a stage beyond database development. The atomic model for each ionic species is contained in a multi-sheet workbook, tabulating representative sets of energy levels, A-values and electron impact effective collision strengths from different sources. The relevant issues that AtomPy intends to address are: (i data quality by allowing open access to both data producers and users; (ii comparisons of different datasets to facilitate accuracy assessments; (iii downloading to local data structures (i.e., Pandas DataFrames for further manipulation and analysis by prospective users; and (iv data preservation by avoiding the discard of outdated sets. Data processing workflows are implemented by means of IPython Notebooks, and collaborative software developments are encouraged and managed within the GitHub social network. The facilities of AtomPy are illustrated with the critical assessment of the transition probabilities for ions in the hydrogen and helium isoelectronic sequences with atomic number Z ≤ 10.

HIVsirDB: a database of HIV inhibiting siRNAs.

Directory of Open Access Journals (Sweden)

Atul Tyagi

Full Text Available Human immunodeficiency virus (HIV is responsible for millions of deaths every year. The current treatment involves the use of multiple antiretroviral agents that may harm patients due to their toxic nature. RNA interference (RNAi is a potent candidate for the future treatment of HIV, uses short interfering RNA (siRNA/shRNA for silencing HIV genes. In this study, attempts have been made to create a database HIVsirDB of siRNAs responsible for silencing HIV genes.HIVsirDB is a manually curated database of HIV inhibiting siRNAs that provides comprehensive information about each siRNA or shRNA. Information was collected and compiled from literature and public resources. This database contains around 750 siRNAs that includes 75 partially complementary siRNAs differing by one or more bases with the target sites and over 100 escape mutant sequences. HIVsirDB structure contains sixteen fields including siRNA sequence, HIV strain, targeted genome region, efficacy and conservation of target sequences. In order to facilitate user, many tools have been integrated in this database that includes; i siRNAmap for mapping siRNAs on target sequence, ii HIVsirblast for BLAST search against database, iii siRNAalign for aligning siRNAs.HIVsirDB is a freely accessible database of siRNAs which can silence or degrade HIV genes. It covers 26 types of HIV strains and 28 cell types. This database will be very useful for developing models for predicting efficacy of HIV inhibiting siRNAs. In summary this is a useful resource for researchers working in the field of siRNA based HIV therapy. HIVsirDB database is accessible at http://crdd.osdd.net/raghava/hivsir/.

A site-specific curated database for the microorganisms of activated sludge and anaerobic digesters

DEFF Research Database (Denmark)

McIlroy, Simon Jon; Kirkegaard, Rasmus Hansen; McIlroy, Bianca

RNA gene amplicon sequencing (V1-3 region), including full-scale AS (20 plants, 8 years) and AD systems (36 reactors, 18 plants, 4 years). Surveys also include the Archaea (V3-5 region). The MiDAS field guide is intended as a collaborative platform for researchers and wastewater treatment practitioners...... taxonomy, proposes putative names for each genus-level-taxon that can be used as a common vocabulary for all researchers in the field. The online database covers >250 genera found to be abundant and/or important in biological nutrient removal treatment plants, based on extensive in-house surveys with 16S r...

Recovery, Transportation and Acceptance to the Curation Facility of the Hayabusa Re-Entry Capsule

Science.gov (United States)

Abe, M.; Fujimura, A.; Yano, H.; Okamoto, C.; Okada, T.; Yada, T.; Ishibashi, Y.; Shirai, K.; Nakamura, T.; Noguchi, T.;

Discovering New Global Climate Patterns: Curating a 21-Year High Temporal (Hourly) and Spatial (40km) Resolution Reanalysis Dataset

Science.gov (United States)

Hou, C. Y.; Dattore, R.; Peng, G. S.

2014-12-01

The National Center for Atmospheric Research's Global Climate Four-Dimensional Data Assimilation (CFDDA) Hourly 40km Reanalysis dataset is a dynamically downscaled dataset with high temporal and spatial resolution. The dataset contains three-dimensional hourly analyses in netCDF format for the global atmospheric state from 1985 to 2005 on a 40km horizontal grid (0.4°grid increment) with 28 vertical levels, providing good representation of local forcing and diurnal variation of processes in the planetary boundary layer. This project aimed to make the dataset publicly available, accessible, and usable in order to provide a unique resource to allow and promote studies of new climate characteristics. When the curation project started, it had been five years since the data files were generated. Also, although the Principal Investigator (PI) had generated a user document at the end of the project in 2009, the document had not been maintained. Furthermore, the PI had moved to a new institution, and the remaining team members were reassigned to other projects. These factors made data curation in the areas of verifying data quality, harvest metadata descriptions, documenting provenance information especially challenging. As a result, the project's curation process found that: Data curator's skill and knowledge helped make decisions, such as file format and structure and workflow documentation, that had significant, positive impact on the ease of the dataset's management and long term preservation. Use of data curation tools, such as the Data Curation Profiles Toolkit's guidelines, revealed important information for promoting the data's usability and enhancing preservation planning. Involving data curators during each stage of the data curation life cycle instead of at the end could improve the curation process' efficiency. Overall, the project showed that proper resources invested in the curation process would give datasets the best chance to fulfill their potential to

AllergenOnline: A peer-reviewed, curated allergen database to assess novel food proteins for potential cross-reactivity.

Science.gov (United States)

Goodman, Richard E; Ebisawa, Motohiro; Ferreira, Fatima; Sampson, Hugh A; van Ree, Ronald; Vieths, Stefan; Baumert, Joseph L; Bohle, Barbara; Lalithambika, Sreedevi; Wise, John; Taylor, Steve L

2016-05-01

Increasingly regulators are demanding evaluation of potential allergenicity of foods prior to marketing. Primary risks are the transfer of allergens or potentially cross-reactive proteins into new foods. AllergenOnline was developed in 2005 as a peer-reviewed bioinformatics platform to evaluate risks of new dietary proteins in genetically modified organisms (GMO) and novel foods. The process used to identify suspected allergens and evaluate the evidence of allergenicity was refined between 2010 and 2015. Candidate proteins are identified from the NCBI database using keyword searches, the WHO/IUIS nomenclature database and peer reviewed publications. Criteria to classify proteins as allergens are described. Characteristics of the protein, the source and human subjects, test methods and results are evaluated by our expert panel and archived. Food, inhalant, salivary, venom, and contact allergens are included. Users access allergen sequences through links to the NCBI database and relevant references are listed online. Version 16 includes 1956 sequences from 778 taxonomic-protein groups that are accepted with evidence of allergic serum IgE-binding and/or biological activity. AllergenOnline provides a useful peer-reviewed tool for identifying the primary potential risks of allergy for GMOs and novel foods based on criteria described by the Codex Alimentarius Commission (2003). © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

BioModels Database: a repository of mathematical models of biological processes.

Science.gov (United States)

Chelliah, Vijayalakshmi; Laibe, Camille; Le Novère, Nicolas

2013-01-01

BioModels Database is a public online resource that allows storing and sharing of published, peer-reviewed quantitative, dynamic models of biological processes. The model components and behaviour are thoroughly checked to correspond the original publication and manually curated to ensure reliability. Furthermore, the model elements are annotated with terms from controlled vocabularies as well as linked to relevant external data resources. This greatly helps in model interpretation and reuse. Models are stored in SBML format, accepted in SBML and CellML formats, and are available for download in various other common formats such as BioPAX, Octave, SciLab, VCML, XPP and PDF, in addition to SBML. The reaction network diagram of the models is also available in several formats. BioModels Database features a search engine, which provides simple and more advanced searches. Features such as online simulation and creation of smaller models (submodels) from the selected model elements of a larger one are provided. BioModels Database can be accessed both via a web interface and programmatically via web services. New models are available in BioModels Database at regular releases, about every 4 months.

NPACT: Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database.

Science.gov (United States)

Mangal, Manu; Sagar, Parul; Singh, Harinder; Raghava, Gajendra P S; Agarwal, Subhash M

2013-01-01

Plant-derived molecules have been highly valued by biomedical researchers and pharmaceutical companies for developing drugs, as they are thought to be optimized during evolution. Therefore, we have collected and compiled a central resource Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database (NPACT, http://crdd.osdd.net/raghava/npact/) that gathers the information related to experimentally validated plant-derived natural compounds exhibiting anti-cancerous activity (in vitro and in vivo), to complement the other databases. It currently contains 1574 compound entries, and each record provides information on their structure, manually curated published data on in vitro and in vivo experiments along with reference for users referral, inhibitory values (IC(50)/ED(50)/EC(50)/GI(50)), properties (physical, elemental and topological), cancer types, cell lines, protein targets, commercial suppliers and drug likeness of compounds. NPACT can easily be browsed or queried using various options, and an online similarity tool has also been made available. Further, to facilitate retrieval of existing data, each record is hyperlinked to similar databases like SuperNatural, Herbal Ingredients' Targets, Comparative Toxicogenomics Database, PubChem and NCI-60 GI(50) data.

NPACT: Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database

Science.gov (United States)

Mangal, Manu; Sagar, Parul; Singh, Harinder; Raghava, Gajendra P. S.; Agarwal, Subhash M.

2013-01-01

Plant-derived molecules have been highly valued by biomedical researchers and pharmaceutical companies for developing drugs, as they are thought to be optimized during evolution. Therefore, we have collected and compiled a central resource Naturally Occurring Plant-based Anti-cancer Compound-Activity-Target database (NPACT, http://crdd.osdd.net/raghava/npact/) that gathers the information related to experimentally validated plant-derived natural compounds exhibiting anti-cancerous activity (in vitro and in vivo), to complement the other databases. It currently contains 1574 compound entries, and each record provides information on their structure, manually curated published data on in vitro and in vivo experiments along with reference for users referral, inhibitory values (IC50/ED50/EC50/GI50), properties (physical, elemental and topological), cancer types, cell lines, protein targets, commercial suppliers and drug likeness of compounds. NPACT can easily be browsed or queried using various options, and an online similarity tool has also been made available. Further, to facilitate retrieval of existing data, each record is hyperlinked to similar databases like SuperNatural, Herbal Ingredients’ Targets, Comparative Toxicogenomics Database, PubChem and NCI-60 GI50 data. PMID:23203877

Preventive but Not Curative Efficacy of Celecoxib on Bladder Carcinogenesis in a Rat Model

Directory of Open Access Journals (Sweden)

José Sereno

2010-01-01

Full Text Available To evaluate the effect of a cyclooxygenase 2 inhibitor, celecoxib (CEL, on bladder cancer inhibition in a rat model, when used as preventive versus as curative treatment. The study comprised 52 male Wistar rats, divided in 5 groups, during a 20-week protocol: control: vehicle, carcinogen: 0.05% of N-butyl-N-(4-hydroxybutyl nitrosamine (BBN, CEL: 10 mg/kg/day of the selective COX-2 inhibitor Celebrex, preventive CEL (CEL+BBN-P, and curative CEL (BBN+CEL-C groups. Although tumor growth was markedly inhibited by the preventive application of CEL, it was even aggravated by the curative treatment. The incidence of gross bladder carcinoma was: control 0/8(0%, BBN 13/20(65%, CEL 0/8(0%, CEL+BBN-P 1/8(12.5%, and BBN+CEL-C 6/8(75%. The number and volume of carcinomas were significantly lower in the CEL+BBN-P versus BBN, accompanied by an ample reduction in hyperplasia, dysplasia, and papillary tumors as well as COX-2 immunostaining. In spite of the reduction of tumor volumes in the curative BBN+CEL-C group, tumor malignancy was augmented. An anti-inflammatory and antioxidant profile was encountered only in the group under preventive treatment. In conclusion, preventive, but not curative, celecoxib treatment promoted a striking inhibitory effect on bladder cancer development, reinforcing the potential role of chemopreventive strategies based on cyclooxygenase 2 inhibition.

Case Study III: The Construction of a Nanotoxicity Database - The MOD-ENP-TOX Experience.

Science.gov (United States)

Vriens, Hanne; Mertens, Dominik; Regret, Renaud; Lin, Pinpin; Locquet, Jean-Pierre; Hoet, Peter

2017-01-01

The amount of experimental studies on the toxicity of nanomaterials is growing fast. Interpretation and comparison of these studies is a complex issue due to the high amount of variables possibly determining the toxicity of nanomaterials.Qualitative databases providing a structured combination, integration and quality evaluation of the existing data could reveal insights that cannot be seen from different studies alone. A few database initiatives are under development but in practice very little data is publicly available and collaboration between physicists, toxicologists, computer scientists and modellers is needed to further develop databases, standards and analysis tools.In this case study the process of building a database on the in vitro toxicity of amorphous silica nanoparticles (NPs) is described in detail. Experimental data were systematically collected from peer reviewed papers, manually curated and stored in a standardised format. The result is a database in ISA-Tab-Nano including 68 peer reviewed papers on the toxicity of 148 amorphous silica NPs. Both the physicochemical characterization of the particles and their biological effect (described in 230 in vitro assays) were stored in the database. A scoring system was elaborated in order to evaluate the reliability of the stored data.

Surveillance Patterns After Curative-Intent Colorectal Cancer Surgery in Ontario

Directory of Open Access Journals (Sweden)

Jensen Tan

2014-01-01

Full Text Available BACKGROUND: Postoperative surveillance following curative-intent resection of colorectal cancer (CRC is variably performed due to existing guideline differences and to the limited data supporting different strategies.

A Practice and Value Proposal for Doctoral Dissertation Data Curation

Directory of Open Access Journals (Sweden)

W. Aaron Collie

2011-10-01

Full Text Available The preparation and publication of dissertations can be viewed as a subsystem of scholarly communication, and the treatment of data that support doctoral research can be mapped in a very controlled manner to the data curation lifecycle. Dissertation datasets represent “low-hanging fruit” for universities who are developing institutional data collections. The current workflow for processing electronic theses and dissertations (ETD at a typical American university is presented, and a new practice is proposed that includes datasets in the process of formulating, awarding, and disseminating dissertations in a way that enables them to be linked and curated together. The value proposition and new roles for the university and its student-authors, faculty, graduate programs and librarians are explored.

Hmrbase: a database of hormones and their receptors

Science.gov (United States)

Rashid, Mamoon; Singla, Deepak; Sharma, Arun; Kumar, Manish; Raghava, Gajendra PS

2009-01-01

Background Hormones are signaling molecules that play vital roles in various life processes, like growth and differentiation, physiology, and reproduction. These molecules are mostly secreted by endocrine glands, and transported to target organs through the bloodstream. Deficient, or excessive, levels of hormones are associated with several diseases such as cancer, osteoporosis, diabetes etc. Thus, it is important to collect and compile information about hormones and their receptors. Description This manuscript describes a database called Hmrbase which has been developed for managing information about hormones and their receptors. It is a highly curated database for which information has been collected from the literature and the public databases. The current version of Hmrbase contains comprehensive information about ~2000 hormones, e.g., about their function, source organism, receptors, mature sequences, structures etc. Hmrbase also contains information about ~3000 hormone receptors, in terms of amino acid sequences, subcellular localizations, ligands, and post-translational modifications etc. One of the major features of this database is that it provides data about ~4100 hormone-receptor pairs. A number of online tools have been integrated into the database, to provide the facilities like keyword search, structure-based search, mapping of a given peptide(s) on the hormone/receptor sequence, sequence similarity search. This database also provides a number of external links to other resources/databases in order to help in the retrieving of further related information. Conclusion Owing to the high impact of endocrine research in the biomedical sciences, the Hmrbase could become a leading data portal for researchers. The salient features of Hmrbase are hormone-receptor pair-related information, mapping of peptide stretches on the protein sequences of hormones and receptors, Pfam domain annotations, categorical browsing options, online data submission, Drug

Distribution and utilization of curative primary healthcare services in Lahej, Yemen.

Science.gov (United States)

Bawazir, A A; Bin Hawail, T S; Al-Sakkaf, K A Z; Basaleem, H O; Muhraz, A F; Al-Shehri, A M

2013-09-01

No evidence-based data exist on the availability, accessibility and utilization of healthcare services in Lahej Governorate, Yemen. The aim of this study was to assess the distribution and utilization of curative services in primary healthcare units and centres in Lahej. Cross-sectional study (clustering sample). This study was conducted in three of the 15 districts in Lahej between December 2009 and August 2010. Household members were interviewed using a questionnaire to determine sociodemographic characteristics and types of healthcare services available in the area. The distribution of health centres, health units and hospitals did not match the size of the populations or areas of the districts included in this study. Geographical accessibility was the main obstacle to utilization. Factors associated with the utilization of curative services were significantly related to the time required to reach the nearest facility, seeking curative services during illness and awareness of the availability of health facilities (P < 0.01). There is an urgent need to look critically and scientifically at the distribution of healthcare services in the region in order to ensure accessibility and quality of services. Copyright © 2013 The Royal Society for Public Health. Published by Elsevier Ltd. All rights reserved.

Kin-Driver: a database of driver mutations in protein kinases.

Science.gov (United States)

Simonetti, Franco L; Tornador, Cristian; Nabau-Moretó, Nuria; Molina-Vila, Miguel A; Marino-Buslje, Cristina

2014-01-01

Somatic mutations in protein kinases (PKs) are frequent driver events in many human tumors, while germ-line mutations are associated with hereditary diseases. Here we present Kin-driver, the first database that compiles driver mutations in PKs with experimental evidence demonstrating their functional role. Kin-driver is a manual expert-curated database that pays special attention to activating mutations (AMs) and can serve as a validation set to develop new generation tools focused on the prediction of gain-of-function driver mutations. It also offers an easy and intuitive environment to facilitate the visualization and analysis of mutations in PKs. Because all mutations are mapped onto a multiple sequence alignment, analogue positions between kinases can be identified and tentative new mutations can be proposed for studying by transferring annotation. Finally, our database can also be of use to clinical and translational laboratories, helping them to identify uncommon AMs that can correlate with response to new antitumor drugs. The website was developed using PHP and JavaScript, which are supported by all major browsers; the database was built using MySQL server. Kin-driver is available at: http://kin-driver.leloir.org.ar/ © The Author(s) 2014. Published by Oxford University Press.

Digital Curation as a Core Competency in Current Learning and Literacy: A Higher Education Perspective

Science.gov (United States)

Ungerer, Leona M.

2016-01-01

Digital curation may be regarded as a core competency in higher education since it contributes to establishing a sense of metaliteracy (an essential requirement for optimally functioning in a modern media environment) among students. Digital curation is gradually finding its way into higher education curricula aimed at fostering social media…

The latest evidence for possible HIV-1 curative strategies.

Science.gov (United States)

Pham, Hanh Thi; Mesplède, Thibault

2018-01-01

Human immunodeficiency virus type 1 (HIV-1) infection remains a major health issue worldwide. In developed countries, antiretroviral therapy has extended its reach from treatment of people living with HIV-1 to post-exposure prophylaxis, treatment as prevention, and, more recently, pre-exposure prophylaxis. These healthcare strategies offer the epidemiological tools to curve the epidemic in rich settings and will be concomitantly implemented in developing countries. One of the remaining challenges is to identify an efficacious curative strategy. This review manuscript will focus on some of the current curative strategies aiming at providing a sterilizing or functional cure to HIV-1-positive individuals. These include the following: early treatment initiation in post-treatment controllers as a long-term HIV-1 remission strategy, latency reversal, gene editing with or without stem cell transplantation, and antibodies against either the viral envelope protein or the host integrin α4β7.

Data Preservation and Curation for the Planetary Science Community

Science.gov (United States)

Hughes, J. S.; Crichton, D. J.; Joyner, R.; Hardman, S.; Rye, E.

2013-12-01

The Planetary Data System (PDS) has just released PDS4 Version 1.0, its next generation data standards for the planetary science archive. These data standards are the result of a multi-year effort to develop an information model based on accepted standards for data preservation, data curation, metadata management, and model development. The resulting information model is subsequently used to drive information system development from the generation of data standards documentation to the configuration of federated registries and search engines. This paper will provide an overview of the development of the PDS4 Information Model and focus on the application of the Open Archive Information System (OAIS) Reference Model - ISO 14721:2003, the Metadata Registry (MDR) Standard - ISO/IEC 11179, and the E-Business XML Standard to help ensure the long-term preservation and curation of planetary science data. Copyright 2013 California Institute of Technology Government sponsorship acknowledged

Virtual Collections: An Earth Science Data Curation Service

Science.gov (United States)

Bugbee, Kaylin; Ramachandran, Rahul; Maskey, Manil; Gatlin, Patrick

2016-01-01

The role of Earth science data centers has traditionally been to maintain central archives that serve openly available Earth observation data. However, in order to ensure data are as useful as possible to a diverse user community, Earth science data centers must move beyond simply serving as an archive to offering innovative data services to user communities. A virtual collection, the end product of a curation activity that searches, selects, and synthesizes diffuse data and information resources around a specific topic or event, is a data curation service that improves the discoverability, accessibility, and usability of Earth science data and also supports the needs of unanticipated users. Virtual collections minimize the amount of the time and effort needed to begin research by maximizing certainty of reward and by providing a trustworthy source of data for unanticipated users. This presentation will define a virtual collection in the context of an Earth science data center and will highlight a virtual collection case study created at the Global Hydrology Resource Center data center.

Virtual Collections: An Earth Science Data Curation Service

Science.gov (United States)

Bugbee, K.; Ramachandran, R.; Maskey, M.; Gatlin, P. N.

2016-12-01

The role of Earth science data centers has traditionally been to maintain central archives that serve openly available Earth observation data. However, in order to ensure data are as useful as possible to a diverse user community, Earth science data centers must move beyond simply serving as an archive to offering innovative data services to user communities. A virtual collection, the end product of a curation activity that searches, selects, and synthesizes diffuse data and information resources around a specific topic or event, is a data curation service that improves the discoverability, accessibility and usability of Earth science data and also supports the needs of unanticipated users. Virtual collections minimize the amount of time and effort needed to begin research by maximizing certainty of reward and by providing a trustworthy source of data for unanticipated users. This presentation will define a virtual collection in the context of an Earth science data center and will highlight a virtual collection case study created at the Global Hydrology Resource Center data center.

Ambiguity of non-systematic chemical identifiers within and between small-molecule databases.

Science.gov (United States)

Akhondi, Saber A; Muresan, Sorel; Williams, Antony J; Kors, Jan A

2015-01-01

A wide range of chemical compound databases are currently available for pharmaceutical research. To retrieve compound information, including structures, researchers can query these chemical databases using non-systematic identifiers. These are source-dependent identifiers (e.g., brand names, generic names), which are usually assigned to the compound at the point of registration. The correctness of non-systematic identifiers (i.e., whether an identifier matches the associated structure) can only be assessed manually, which is cumbersome, but it is possible to automatically check their ambiguity (i.e., whether an identifier matches more than one structure). In this study we have quantified the ambiguity of non-systematic identifiers within and between eight widely used chemical databases. We also studied the effect of chemical structure standardization on reducing the ambiguity of non-systematic identifiers. The ambiguity of non-systematic identifiers within databases varied from 0.1 to 15.2 % (median 2.5 %). Standardization reduced the ambiguity only to a small extent for most databases. A wide range of ambiguity existed for non-systematic identifiers that are shared between databases (17.7-60.2 %, median of 40.3 %). Removing stereochemistry information provided the largest reduction in ambiguity across databases (median reduction 13.7 percentage points). Ambiguity of non-systematic identifiers within chemical databases is generally low, but ambiguity of non-systematic identifiers that are shared between databases, is high. Chemical structure standardization reduces the ambiguity to a limited extent. Our findings can help to improve database integration, curation, and maintenance.

RNA STRAND: The RNA Secondary Structure and Statistical Analysis Database

Directory of Open Access Journals (Sweden)

Andronescu Mirela

2008-08-01

Full Text Available Abstract Background The ability to access, search and analyse secondary structures of a large set of known RNA molecules is very important for deriving improved RNA energy models, for evaluating computational predictions of RNA secondary structures and for a better understanding of RNA folding. Currently there is no database that can easily provide these capabilities for almost all RNA molecules with known secondary structures. Results In this paper we describe RNA STRAND – the RNA secondary STRucture and statistical ANalysis Database, a curated database containing known secondary structures of any type and organism. Our new database provides a wide collection of known RNA secondary structures drawn from public databases, searchable and downloadable in a common format. Comprehensive statistical information on the secondary structures in our database is provided using the RNA Secondary Structure Analyser, a new tool we have developed to analyse RNA secondary structures. The information thus obtained is valuable for understanding to which extent and with which probability certain structural motifs can appear. We outline several ways in which the data provided in RNA STRAND can facilitate research on RNA structure, including the improvement of RNA energy models and evaluation of secondary structure prediction programs. In order to keep up-to-date with new RNA secondary structure experiments, we offer the necessary tools to add solved RNA secondary structures to our database and invite researchers to contribute to RNA STRAND. Conclusion RNA STRAND is a carefully assembled database of trusted RNA secondary structures, with easy on-line tools for searching, analyzing and downloading user selected entries, and is publicly available at http://www.rnasoft.ca/strand.

Missing "Links" in Bioinformatics Education: Expanding Students' Conceptions of Bioinformatics Using a Biodiversity Database of Living and Fossil Reef Corals

Science.gov (United States)

Nehm, Ross H.; Budd, Ann F.

2006-01-01

NMITA is a reef coral biodiversity database that we use to introduce students to the expansive realm of bioinformatics beyond genetics. We introduce a series of lessons that have students use this database, thereby accessing real data that can be used to test hypotheses about biodiversity and evolution while targeting the "National Science …

Antarctic Meteorite Classification and Petrographic Database

Science.gov (United States)

Todd, Nancy S.; Satterwhite, C. E.; Righter, Kevin

2011-01-01

The Antarctic Meteorite collection, which is comprised of over 18,700 meteorites, is one of the largest collections of meteorites in the world. These meteorites have been collected since the late 1970's as part of a three-agency agreement between NASA, the National Science Foundation, and the Smithsonian Institution [1]. Samples collected each season are analyzed at NASA s Meteorite Lab and the Smithsonian Institution and results are published twice a year in the Antarctic Meteorite Newsletter, which has been in publication since 1978. Each newsletter lists the samples collected and processed and provides more in-depth details on selected samples of importance to the scientific community. Data about these meteorites is also published on the NASA Curation website [2] and made available through the Meteorite Classification Database allowing scientists to search by a variety of parameters

Determination of protective properties of Bardejovske Kuple spa curative waters by rotational viscometry and ABTS assay

Directory of Open Access Journals (Sweden)

TOPOLSKA Dominika

2014-02-01

Full Text Available Mineral waters from Bardejovske Kupele spa are natural, strongly mineralized, with healing effects. They are classified as hydrocarbonic - containing chloride and sodium - carbonic, cold, hypotonic, with a relatively high boric acid content. Potential anti-oxidative effects of curative waters from Bardejovske Kupele were investigated against the hyaluronan (HA degradation. High-molar-mass HA was exposed to the action of ascorbate and cupric ions, which initiate free-radical chain degradation. Time-dependent changes of dynamic viscosity (h of the HA solutions were monitored by rotational viscometry. The radical scavenging capacity of curative waters was determined by the ABTS assay. Despite a significantly high content of transition metal ions, especially iron, remarkable protective effects of the two curative spa waters were found, namely Alzbeta and Klara. Even though “Alzbeta´s“ iron content was 3.5-fold higher than “Klara´s“, “Alzbeta“ was shown to have better protective properties against the HA degradation compared to “Klara“. Bolus addition of ferric ions to the reaction system instead of the natural iron-containing curative water caused a significant HA degradation. The ABTS decolorization assay revealed that the curative spa waters were proven as poorly effective scavengers of the ABTS·+ cation radical.

Irinotecan and Oxaliplatin Might Provide Equal Benefit as Adjuvant Chemotherapy for Patients with Resectable Synchronous Colon Cancer and Liver-confined Metastases: A Nationwide Database Study.

Science.gov (United States)

Liang, Yi-Hsin; Shao, Yu-Yun; Chen, Ho-Min; Cheng, Ann-Lii; Lai, Mei-Shu; Yeh, Kun-Huei

2017-12-01

Although irinotecan and oxaliplatin are both standard treatments for advanced colon cancer, it remains unknown whether either is effective for patients with resectable synchronous colon cancer and liver-confined metastasis (SCCLM) after curative surgery. A population-based cohort of patients diagnosed with de novo SCCLM between 2004 and 2009 was established by searching the database of the Taiwan Cancer Registry and the National Health Insurance Research Database of Taiwan. Patients who underwent curative surgery as their first therapy followed by chemotherapy doublets were classified into the irinotecan group or oxaliplatin group accordingly. Patients who received radiotherapy or did not receive chemotherapy doublets were excluded. We included 6,533 patients with de novo stage IV colon cancer. Three hundred and nine of them received chemotherapy doublets after surgery; 77 patients received irinotecan and 232 patients received oxaliplatin as adjuvant chemotherapy. The patients in both groups exhibited similar overall survival (median: not reached vs. 40.8 months, p=0.151) and time to the next line of treatment (median: 16.5 vs. 14.3 months, p=0.349) in both univariate and multivariate analyses. Additionally, patients with resectable SCCLM had significantly shorter median overall survival than patients with stage III colon cancer who underwent curative surgery and subsequent adjuvant chemotherapy, but longer median overall survival than patients with de novo stage IV colon cancer who underwent surgery only at the primary site followed by standard systemic chemotherapy (p<0.001). Irinotecan and oxaliplatin exhibited similar efficacy in patients who underwent curative surgery for resectable SCCLM. Copyright© 2017, International Institute of Anticancer Research (Dr. George J. Delinasios), All rights reserved.

The curative effect analysis of 131I-therapy on patients with Graves' disease

International Nuclear Information System (INIS)

Cui Qin; Lu Shujun; Lu Tianhe

2002-01-01

To investigate the curative effect of 131 I-therapy on Graves' disease, the authors analyse conditions of patients who have received 131 I-therapy (n -674). These results showed that the incidence of fully recover, improve, Graves' disease and invalid is 80.11%, 7.28%, 11.87% and 0.74% respectively. Therefore, 131 I-therapy on Graves' disease is convenient. It has little side effect, low cost and better curative effect, it is one of the best therapeutic methods to treat hyperthyroidism

EURO-CARES as Roadmap for a European Sample Curation Facility

Science.gov (United States)

Brucato, J. R.; Russell, S.; Smith, C.; Hutzler, A.; Meneghin, A.; Aléon, J.; Bennett, A.; Berthoud, L.; Bridges, J.; Debaille, V.; Ferrière, L.; Folco, L.; Foucher, F.; Franchi, I.; Gounelle, M.; Grady, M.; Leuko, S.; Longobardo, A.; Palomba, E.; Pottage, T.; Rettberg, P.; Vrublevskis, J.; Westall, F.; Zipfel, J.; Euro-Cares Team

2018-04-01

EURO-CARES is a three-year multinational project funded under the European Commission Horizon2020 research program to develop a roadmap for a European Extraterrestrial Sample Curation Facility for samples returned from solar system missions.

Perioperative and long-term outcome of intrahepatic cholangiocarcinoma involving the hepatic hilus after curative-intent resection: comparison with peripheral intrahepatic cholangiocarcinoma and hilar cholangiocarcinoma.

Science.gov (United States)

Zhang, Xu-Feng; Bagante, Fabio; Chen, Qinyu; Beal, Eliza W; Lv, Yi; Weiss, Matthew; Popescu, Irinel; Marques, Hugo P; Aldrighetti, Luca; Maithel, Shishir K; Pulitano, Carlo; Bauer, Todd W; Shen, Feng; Poultsides, George A; Soubrane, Olivier; Martel, Guillaume; Koerkamp, B Groot; Guglielmi, Alfredo; Itaru, Endo; Pawlik, Timothy M

2018-05-01

Intrahepatic cholangiocarcinoma with hepatic hilus involvement has been either classified as intrahepatic cholangiocarcinoma or hilar cholangiocarcinoma. The present study aimed to investigate the clinicopathologic characteristics and short- and long-term outcomes after curative resection for hilar type intrahepatic cholangiocarcinoma in comparison with peripheral intrahepatic cholangiocarcinoma and hilar cholangiocarcinoma. A total of 912 patients with mass-forming peripheral intrahepatic cholangiocarcinoma, 101 patients with hilar type intrahepatic cholangiocarcinoma, and 159 patients with hilar cholangiocarcinoma undergoing curative resection from 2000 to 2015 were included from two multi-institutional databases. Clinicopathologic characteristics and short- and long-term outcomes were compared among the 3 groups. Patients with hilar type intrahepatic cholangiocarcinoma had more aggressive tumor characteristics (eg, higher frequency of vascular invasion and lymph nodes metastasis) and experienced more extensive resections in comparison with either peripheral intrahepatic cholangiocarcinoma or hilar cholangiocarcinoma patients. The odds of lymphadenectomy and R0 resection rate among patients with hilar type intrahepatic cholangiocarcinoma were comparable with hilar cholangiocarcinoma patients, but higher than peripheral intrahepatic cholangiocarcinoma patients (lymphadenectomy incidence, 85.1% vs 42.5%, P hilar type intrahepatic cholangiocarcinoma experienced a higher rate of technical-related complications compared with peripheral intrahepatic cholangiocarcinoma patients. Of note, hilar type intrahepatic cholangiocarcinoma was associated with worse disease-specific survival and recurrence-free survival after curative resection versus peripheral intrahepatic cholangiocarcinoma (median disease-specific survival, 26.0 vs 54.0 months, P hilar cholangiocarcinoma (median disease-specific survival, 26.0 vs 49.0 months, P = .003; median recurrence-free survival

Curative care through administration of plant-derived medicines in ...

African Journals Online (AJOL)

Curative care through administration of plant-derived medicines in Sekhukhune district municipality of Limpopo province, South Africa. ... Sources of medicine were mostly herbs followed by shrubs, trees, creepers and aloe collected from the communal land. The leaves, bark, roots and bulbs were prepared into decoctions ...

An Integrated Database of Unit Training Performance: Description an Lessons Learned

National Research Council Canada - National Science Library

Leibrecht, Bruce

1997-01-01

The Army Research Institute (ARI) has developed a prototype relational database for processing and archiving unit performance data from home station, training area, simulation based, and Combat Training Center training exercises...

GEAR: A database of Genomic Elements Associated with drug Resistance

Science.gov (United States)

Wang, Yin-Ying; Chen, Wei-Hua; Xiao, Pei-Pei; Xie, Wen-Bin; Luo, Qibin; Bork, Peer; Zhao, Xing-Ming

2017-01-01

Drug resistance is becoming a serious problem that leads to the failure of standard treatments, which is generally developed because of genetic mutations of certain molecules. Here, we present GEAR (A database of Genomic Elements Associated with drug Resistance) that aims to provide comprehensive information about genomic elements (including genes, single-nucleotide polymorphisms and microRNAs) that are responsible for drug resistance. Right now, GEAR contains 1631 associations between 201 human drugs and 758 genes, 106 associations between 29 human drugs and 66 miRNAs, and 44 associations between 17 human drugs and 22 SNPs. These relationships are firstly extracted from primary literature with text mining and then manually curated. The drug resistome deposited in GEAR provides insights into the genetic factors underlying drug resistance. In addition, new indications and potential drug combinations can be identified based on the resistome. The GEAR database can be freely accessed through http://gear.comp-sysbio.org. PMID:28294141

ChimerDB 3.0: an enhanced database for fusion genes from cancer transcriptome and literature data mining.

Science.gov (United States)

Lee, Myunggyo; Lee, Kyubum; Yu, Namhee; Jang, Insu; Choi, Ikjung; Kim, Pora; Jang, Ye Eun; Kim, Byounggun; Kim, Sunkyu; Lee, Byungwook; Kang, Jaewoo; Lee, Sanghyuk

2017-01-04

Fusion gene is an important class of therapeutic targets and prognostic markers in cancer. ChimerDB is a comprehensive database of fusion genes encompassing analysis of deep sequencing data and manual curations. In this update, the database coverage was enhanced considerably by adding two new modules of The Cancer Genome Atlas (TCGA) RNA-Seq analysis and PubMed abstract mining. ChimerDB 3.0 is composed of three modules of ChimerKB, ChimerPub and ChimerSeq. ChimerKB represents a knowledgebase including 1066 fusion genes with manual curation that were compiled from public resources of fusion genes with experimental evidences. ChimerPub includes 2767 fusion genes obtained from text mining of PubMed abstracts. ChimerSeq module is designed to archive the fusion candidates from deep sequencing data. Importantly, we have analyzed RNA-Seq data of the TCGA project covering 4569 patients in 23 cancer types using two reliable programs of FusionScan and TopHat-Fusion. The new user interface supports diverse search options and graphic representation of fusion gene structure. ChimerDB 3.0 is available at http://ercsb.ewha.ac.kr/fusiongene/. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

Biocuration workflows and text mining: overview of the BioCreative 2012 Workshop Track II.

Science.gov (United States)

Lu, Zhiyong; Hirschman, Lynette

2012-01-01

Manual curation of data from the biomedical literature is a rate-limiting factor for many expert curated databases. Despite the continuing advances in biomedical text mining and the pressing needs of biocurators for better tools, few existing text-mining tools have been successfully integrated into production literature curation systems such as those used by the expert curated databases. To close this gap and better understand all aspects of literature curation, we invited submissions of written descriptions of curation workflows from expert curated databases for the BioCreative 2012 Workshop Track II. We received seven qualified contributions, primarily from model organism databases. Based on these descriptions, we identified commonalities and differences across the workflows, the common ontologies and controlled vocabularies used and the current and desired uses of text mining for biocuration. Compared to a survey done in 2009, our 2012 results show that many more databases are now using text mining in parts of their curation workflows. In addition, the workshop participants identified text-mining aids for finding gene names and symbols (gene indexing), prioritization of documents for curation (document triage) and ontology concept assignment as those most desired by the biocurators. DATABASE URL: http://www.biocreative.org/tasks/bc-workshop-2012/workflow/.

Climate Signals: An On-Line Digital Platform for Mapping Climate Change Impacts in Real Time

Science.gov (United States)

Cutting, H.

2016-12-01

Climate Signals is an on-line digital platform for cataloging and mapping the impacts of climate change. The CS platform specifies and details the chains of connections between greenhouse gas emissions and individual climate events. Currently in open-beta release, the platform is designed to to engage and serve the general public, news media, and policy-makers, particularly in real-time during extreme climate events. Climate Signals consists of a curated relational database of events and their links to climate change, a mapping engine, and a gallery of climate change monitors offering real-time data. For each event in the database, an infographic engine provides a custom attribution "tree" that illustrates the connections to climate change. In addition, links to key contextual resources are aggregated and curated for each event. All event records are fully annotated with detailed source citations and corresponding hyper links. The system of attribution used to link events to climate change in real-time is detailed here. This open-beta release is offered for public user testing and engagement. Launched in May 2016, the operation of this platform offers lessons for public engagement in climate change impacts.

JASPAR 2014: an extensively expanded and updated open-access database of transcription factor binding profiles.

Science.gov (United States)

Mathelier, Anthony; Zhao, Xiaobei; Zhang, Allen W; Parcy, François; Worsley-Hunt, Rebecca; Arenillas, David J; Buchman, Sorana; Chen, Chih-yu; Chou, Alice; Ienasescu, Hans; Lim, Jonathan; Shyr, Casper; Tan, Ge; Zhou, Michelle; Lenhard, Boris; Sandelin, Albin; Wasserman, Wyeth W

2014-01-01

JASPAR (http://jaspar.genereg.net) is the largest open-access database of matrix-based nucleotide profiles describing the binding preference of transcription factors from multiple species. The fifth major release greatly expands the heart of JASPAR-the JASPAR CORE subcollection, which contains curated, non-redundant profiles-with 135 new curated profiles (74 in vertebrates, 8 in Drosophila melanogaster, 10 in Caenorhabditis elegans and 43 in Arabidopsis thaliana; a 30% increase in total) and 43 older updated profiles (36 in vertebrates, 3 in D. melanogaster and 4 in A. thaliana; a 9% update in total). The new and updated profiles are mainly derived from published chromatin immunoprecipitation-seq experimental datasets. In addition, the web interface has been enhanced with advanced capabilities in browsing, searching and subsetting. Finally, the new JASPAR release is accompanied by a new BioPython package, a new R tool package and a new R/Bioconductor data package to facilitate access for both manual and automated methods.

The reactive metabolite target protein database (TPDB)--a web-accessible resource.

Science.gov (United States)

Hanzlik, Robert P; Koen, Yakov M; Theertham, Bhargav; Dong, Yinghua; Fang, Jianwen

2007-03-16

The toxic effects of many simple organic compounds stem from their biotransformation to chemically reactive metabolites which bind covalently to cellular proteins. To understand the mechanisms of cytotoxic responses it may be important to know which proteins become adducted and whether some may be common targets of multiple toxins. The literature of this field is widely scattered but expanding rapidly, suggesting the need for a comprehensive, searchable database of reactive metabolite target proteins. The Reactive Metabolite Target Protein Database (TPDB) is a comprehensive, curated, searchable, documented compilation of publicly available information on the protein targets of reactive metabolites of 18 well-studied chemicals and drugs of known toxicity. TPDB software enables i) string searches for author names and proteins names/synonyms, ii) more complex searches by selecting chemical compound, animal species, target tissue and protein names/synonyms from pull-down menus, and iii) commonality searches over multiple chemicals. Tabulated search results provide information, references and links to other databases. The TPDB is a unique on-line compilation of information on the covalent modification of cellular proteins by reactive metabolites of chemicals and drugs. Its comprehensiveness and searchability should facilitate the elucidation of mechanisms of reactive metabolite toxicity. The database is freely available at http://tpdb.medchem.ku.edu/tpdb.html.

TIPdb: A Database of Anticancer, Antiplatelet, and Antituberculosis Phytochemicals from Indigenous Plants in Taiwan

Directory of Open Access Journals (Sweden)

Ying-Chi Lin

2013-01-01

Full Text Available The unique geographic features of Taiwan are attributed to the rich indigenous and endemic plant species in Taiwan. These plants serve as resourceful bank for biologically active phytochemicals. Given that these plant-derived chemicals are prototypes of potential drugs for diseases, databases connecting the chemical structures and pharmacological activities may facilitate drug development. To enhance the utility of the data, it is desirable to develop a database of chemical compounds and corresponding activities from indigenous plants in Taiwan. A database of anticancer, antiplatelet, and antituberculosis phytochemicals from indigenous plants in Taiwan was constructed. The database, TIPdb, is composed of a standardized format of published anticancer, antiplatelet, and antituberculosis phytochemicals from indigenous plants in Taiwan. A browse function was implemented for users to browse the database in a taxonomy-based manner. Search functions can be utilized to filter records of interest by botanical name, part, chemical class, or compound name. The structured and searchable database TIPdb was constructed to serve as a comprehensive and standardized resource for anticancer, antiplatelet, and antituberculosis compounds search. The manually curated chemical structures and activities provide a great opportunity to develop quantitative structure-activity relationship models for the high-throughput screening of potential anticancer, antiplatelet, and antituberculosis drugs.

TIPdb: a database of anticancer, antiplatelet, and antituberculosis phytochemicals from indigenous plants in Taiwan.

Science.gov (United States)

Lin, Ying-Chi; Wang, Chia-Chi; Chen, Ih-Sheng; Jheng, Jhao-Liang; Li, Jih-Heng; Tung, Chun-Wei

2013-01-01

The unique geographic features of Taiwan are attributed to the rich indigenous and endemic plant species in Taiwan. These plants serve as resourceful bank for biologically active phytochemicals. Given that these plant-derived chemicals are prototypes of potential drugs for diseases, databases connecting the chemical structures and pharmacological activities may facilitate drug development. To enhance the utility of the data, it is desirable to develop a database of chemical compounds and corresponding activities from indigenous plants in Taiwan. A database of anticancer, antiplatelet, and antituberculosis phytochemicals from indigenous plants in Taiwan was constructed. The database, TIPdb, is composed of a standardized format of published anticancer, antiplatelet, and antituberculosis phytochemicals from indigenous plants in Taiwan. A browse function was implemented for users to browse the database in a taxonomy-based manner. Search functions can be utilized to filter records of interest by botanical name, part, chemical class, or compound name. The structured and searchable database TIPdb was constructed to serve as a comprehensive and standardized resource for anticancer, antiplatelet, and antituberculosis compounds search. The manually curated chemical structures and activities provide a great opportunity to develop quantitative structure-activity relationship models for the high-throughput screening of potential anticancer, antiplatelet, and antituberculosis drugs.

Curating for engagement: Identifying the nature and impact of organizational marketing strategies on Pinterest

OpenAIRE

Saxton, Gregory D.; Ghosh, Amanda

2016-01-01

In an increasingly overloaded information environment sparked by the explosion of digital media, the ability to curate content has taken on greater importance. This study begins with the supposition that businesses that are able to adopt a content curation role and help consumers sort through the daily influx of information may be more successful in attracting, engaging, and retaining customers while fostering brand awareness and word of mouth. Accordingly, this study investigates organizatio...

The value of imaging examinations in diagnosis and curative effect evaluation of breast cancer

International Nuclear Information System (INIS)

Xia Xiaotian; Zhang Yongxue

2010-01-01

Breast cancer is a serious impact on women's physical and mental health and a life-threatening common disease. Imaging examinations have great significances in diagnosing and evaluating curative effect on breast cancer. This article aims to introduce and comprehensive the value of diagnosis and curative effect evaluation of breast cancer in the context of imaging examinations (ultrasonography, mammography, breast CT, breast MRI, breast 99 Tc m -MIBI imaging, PET, PET-CT, etc). (authors)

Visualizing information across multidimensional post-genomic structured and textual databases.

Science.gov (United States)

Tao, Ying; Friedman, Carol; Lussier, Yves A

2005-04-15

Visualizing relationships among biological information to facilitate understanding is crucial to biological research during the post-genomic era. Although different systems have been developed to view gene-phenotype relationships for specific databases, very few have been designed specifically as a general flexible tool for visualizing multidimensional genotypic and phenotypic information together. Our goal is to develop a method for visualizing multidimensional genotypic and phenotypic information and a model that unifies different biological databases in order to present the integrated knowledge using a uniform interface. We developed a novel, flexible and generalizable visualization tool, called PhenoGenesviewer (PGviewer), which in this paper was used to display gene-phenotype relationships from a human-curated database (OMIM) and from an automatic method using a Natural Language Processing tool called BioMedLEE. Data obtained from multiple databases were first integrated into a uniform structure and then organized by PGviewer. PGviewer provides a flexible query interface that allows dynamic selection and ordering of any desired dimension in the databases. Based on users' queries, results can be visualized using hierarchical expandable trees that present views specified by users according to their research interests. We believe that this method, which allows users to dynamically organize and visualize multiple dimensions, is a potentially powerful and promising tool that should substantially facilitate biological research. PhenogenesViewer as well as its support and tutorial are available at http://www.dbmi.columbia.edu/pgviewer/ Lussier@dbmi.columbia.edu.

Curating and nudging in virtual CLIL environments

Directory of Open Access Journals (Sweden)

Helle Lykke Nielsen

2014-03-01

Full Text Available Foreign language teachers can benefit substantially from the notions of curation and nudging when scaffolding CLIL activities on the internet. This article shows how these principles can be integrated into CLILstore, a free multimedia-rich learning tool with seamless access to online dictionaries, and presents feedback from first and second year university students of Arabic as a second language to inform foreign language teachers about students’ needs and preferences in virtual learning environments.

Supporting ontology-based keyword search over medical databases.

Science.gov (United States)

Kementsietsidis, Anastasios; Lim, Lipyeow; Wang, Min

2008-11-06

The proliferation of medical terms poses a number of challenges in the sharing of medical information among different stakeholders. Ontologies are commonly used to establish relationships between different terms, yet their role in querying has not been investigated in detail. In this paper, we study the problem of supporting ontology-based keyword search queries on a database of electronic medical records. We present several approaches to support this type of queries, study the advantages and limitations of each approach, and summarize the lessons learned as best practices.

A new version of the RDP (Ribosomal Database Project)

Science.gov (United States)

Maidak, B. L.; Cole, J. R.; Parker, C. T. Jr; Garrity, G. M.; Larsen, N.; Li, B.; Lilburn, T. G.; McCaughey, M. J.; Olsen, G. J.; Overbeek, R.;

Technology Development and Advanced Planning for Curation of Returned Mars Samples

Science.gov (United States)

Lindstrom, David J.; Allen, Carlton C.

2002-01-01

NASA Johnson Space Center (JSC) curates extraterrestrial samples, providing the international science community with lunar rock and soil returned by the Apollo astronauts, meteorites collected in Antarctica, cosmic dust collected in the stratosphere, and hardware exposed to the space environment. Curation comprises initial characterization of new samples, preparation and allocation of samples for research, and clean, secure long-term storage. The foundations of this effort are the specialized cleanrooms (class 10 to 10,000) for each of the four types of materials, the supporting facilities, and the people, many of whom have been doing detailed work in clean environments for decades. JSC is also preparing to curate the next generation of extraterrestrial samples. These include samples collected from the solar wind, a comet, and an asteroid. Early planning and R\\&D are underway to support post-mission sample handling and curation of samples returned from Mars. One of the strong scientific reasons for returning samples from Mars is to search for evidence of current or past life in the samples. Because of the remote possibility that the samples may contain life forms that are hazardous to the terrestrial biosphere, the National Research Council has recommended that all samples returned from Mars be kept under strict biological containment until tests show that they can safely be released to other laboratories. It is possible that Mars samples may contain only scarce or subtle traces of life or prebiotic chemistry that could readily be overwhelmed by terrestrial contamination . Thus, the facilities used to contain, process, and analyze samples from Mars must have a combination of high-level biocontainment and organic / inorganic chemical cleanliness that is unprecedented. JSC has been conducting feasibility studies and developing designs for a sample receiving facility that would offer biocontainment at least the equivalent of current maximum containment BSL-4 (Bio

IAEA Radiation Events Database (RADEV)

International Nuclear Information System (INIS)

Wheatley, J.; Ortiz-Lopez, P.

2001-01-01

Whilst the use of ionizing radiation continues to bring benefits to many people throughout the world there is increasing concern at the number of reported accidents involving radiation. Such accidents have had an impact on the lives of patients, workers and members of the public, the consequences of which have ranged from trivial health effects to fatalities. In order to reduce the number of accidents and to mitigate their consequences it is, therefore, necessary to raise awareness of the causes of accidents and to note the lessons that can be learned. The IAEA's database on unusual radiation events (RADEV) is intended to provide a world-wide focal point for such information. (author)

Annotation error in public databases: misannotation of molecular function in enzyme superfamilies.

Directory of Open Access Journals (Sweden)

Alexandra M Schnoes

2009-12-01

Full Text Available Due to the rapid release of new data from genome sequencing projects, the majority of protein sequences in public databases have not been experimentally characterized; rather, sequences are annotated using computational analysis. The level of misannotation and the types of misannotation in large public databases are currently unknown and have not been analyzed in depth. We have investigated the misannotation levels for molecular function in four public protein sequence databases (UniProtKB/Swiss-Prot, GenBank NR, UniProtKB/TrEMBL, and KEGG for a model set of 37 enzyme families for which extensive experimental information is available. The manually curated database Swiss-Prot shows the lowest annotation error levels (close to 0% for most families; the two other protein sequence databases (GenBank NR and TrEMBL and the protein sequences in the KEGG pathways database exhibit similar and surprisingly high levels of misannotation that average 5%-63% across the six superfamilies studied. For 10 of the 37 families examined, the level of misannotation in one or more of these databases is >80%. Examination of the NR database over time shows that misannotation has increased from 1993 to 2005. The types of misannotation that were found fall into several categories, most associated with "overprediction" of molecular function. These results suggest that misannotation in enzyme superfamilies containing multiple families that catalyze different reactions is a larger problem than has been recognized. Strategies are suggested for addressing some of the systematic problems contributing to these high levels of misannotation.

Annotation error in public databases: misannotation of molecular function in enzyme superfamilies.

Science.gov (United States)

Schnoes, Alexandra M; Brown, Shoshana D; Dodevski, Igor; Babbitt, Patricia C

2009-12-01

Due to the rapid release of new data from genome sequencing projects, the majority of protein sequences in public databases have not been experimentally characterized; rather, sequences are annotated using computational analysis. The level of misannotation and the types of misannotation in large public databases are currently unknown and have not been analyzed in depth. We have investigated the misannotation levels for molecular function in four public protein sequence databases (UniProtKB/Swiss-Prot, GenBank NR, UniProtKB/TrEMBL, and KEGG) for a model set of 37 enzyme families for which extensive experimental information is available. The manually curated database Swiss-Prot shows the lowest annotation error levels (close to 0% for most families); the two other protein sequence databases (GenBank NR and TrEMBL) and the protein sequences in the KEGG pathways database exhibit similar and surprisingly high levels of misannotation that average 5%-63% across the six superfamilies studied. For 10 of the 37 families examined, the level of misannotation in one or more of these databases is >80%. Examination of the NR database over time shows that misannotation has increased from 1993 to 2005. The types of misannotation that were found fall into several categories, most associated with "overprediction" of molecular function. These results suggest that misannotation in enzyme superfamilies containing multiple families that catalyze different reactions is a larger problem than has been recognized. Strategies are suggested for addressing some of the systematic problems contributing to these high levels of misannotation.

ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii.

Science.gov (United States)

May, Patrick; Christian, Jan-Ole; Kempa, Stefan; Walther, Dirk

2009-05-04

The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic model organism for the study of photosynthesis and plant growth. In the era of modern high-throughput technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using computational methods and database resources to provide comprehensive information about the molecular and cellular organization of a single organism. In the framework of the German Systems Biology initiative GoFORSYS, a pathway database and web-portal for Chlamydomonas (ChlamyCyc) was established, which currently features about 250 metabolic pathways with associated genes, enzymes, and compound information. ChlamyCyc was assembled using an integrative approach combining the recently published genome sequence, bioinformatics methods, and experimental data from metabolomics and proteomics experiments. We analyzed and integrated a combination of primary and secondary database resources, such as existing genome annotations from JGI, EST collections, orthology information, and MapMan classification. ChlamyCyc provides a curated and integrated systems biology repository that will enable and assist in systematic studies of fundamental cellular processes in Chlamydomonas. The ChlamyCyc database and web-portal is freely available under http://chlamycyc.mpimp-golm.mpg.de.

Analysis of a radiological incident and lessons to be learned: a case of industrial radiographic incident in great Britain

International Nuclear Information System (INIS)

Croft, J.; Lefaure, Ch.

2000-01-01

This note describes a case study to provide feedback analysis and lessons to be learned from a radiological incident. This one occurred in the UK. It has been published in the European ALARA Newsletter no. 2 (January 1997) and has been selected from the IRID database (Ionising Radiation Incident Database) managed by the Health and Safety Executive, National Radiological Protection Board and Environmental Agency. (authors)

QA lessons learned for parameter control from the WIPP Project

International Nuclear Information System (INIS)

Richards, R.R.

1998-01-01

This paper provides a summary of lessons learned from experiences on the Waste Isolation Pilot Plant (WJPP) Project in implementation of quality assurance controls surrounding inputs for performance assessment analysis. Since the performance assessment (PA) process is inherent in compliance determination for any waste repository, these lessons-learned are intended to be useful to investigators, analysts, and Quality Assurance (QA) practitioners working on high level waste disposal projects. On the WIPP Project, PA analyses for regulatory-compliance determination utilized several inter-related computer programs (codes) that mathematically modeled phenomena such as radionuclide release, retardation, and transport. The input information for those codes are the parameters that are the subject of this paper. Parameters were maintained in a computer database, which was then queried electronically by the PA codes whenever input was needed as the analyses were run

Breathing Life into Engineering: A Lesson Study Life Science Lesson

Science.gov (United States)

Lawrence, Maria; Yang, Li-Ling; Briggs, May; Hession, Alicia; Koussa, Anita; Wagoner, Lisa

2016-01-01

A fifth grade life science lesson was implemented through a lesson study approach in two fifth grade classrooms. The research lesson was designed by a team of four elementary school teachers with the goal of emphasizing engineering practices consistent with the "Next Generation Science Standards" (NGSS) (Achieve Inc. 2013). The fifth…

Patient-reported symptoms during radiotherapy : Clinically relevant symptom burden in patients treated with palliative and curative intent.

Science.gov (United States)

Körner, Philipp; Ehrmann, Katja; Hartmannsgruber, Johann; Metz, Michaela; Steigerwald, Sabrina; Flentje, Michael; van Oorschot, Birgitt

2017-07-01

The benefits of patient-reported symptom assessment combined with integrated palliative care are well documented. This study assessed the symptom burden of palliative and curative-intent radiation oncology patients. Prior to first consultation and at the end of RT, all adult cancer patients planned to receive fractionated percutaneous radiotherapy (RT) were asked to answer the Edmonton Symptom Assessment Scale (ESAS; nine symptoms from 0 = no symptoms to 10 = worst possible symptoms). Mean values were used for curative vs. palliative and pre-post comparisons, and the clinical relevance was evaluated (symptom values ≥ 4). Of 163 participating patients, 151 patients (90.9%) completed both surveys (116 curative and 35 palliative patients). Before beginning RT, 88.6% of palliative and 72.3% of curative patients showed at least one clinically relevant symptom. Curative patients most frequently named decreased general wellbeing (38.6%), followed by tiredness (35.0%), anxiety (32.4%), depression (30.0%), pain (26.3%), lack of appetite (23.5%), dyspnea (17.8%), drowsiness (8.0%) and nausea (6.1%). Palliative patients most frequently named decreased general wellbeing (62.8%), followed by pain (62.8%), tiredness (60.0%), lack of appetite (40.0%), anxiety (38.0%), depression (33.3%), dyspnea (28.5%), drowsiness (25.7%) and nausea (14.2%). At the end of RT, the proportion of curative and palliative patients with a clinically relevant symptom had increased significantly to 79.8 and 91.4%, respectively; whereas the proportion of patients reporting clinically relevant pain had decreased significantly (42.8 vs. 62.8%, respectively). Palliative patients had significantly increased tiredness. Curative patients reported significant increases in pain, tiredness, nausea, drowsiness, lack of appetite and restrictions in general wellbeing. Assessment of patient-reported symptoms was successfully realized in radiation oncology routine. Overall, both groups showed a high symptom

Patient-reported symptoms during radiotherapy. Clinically relevant symptom burden in patients treated with palliative and curative intent

International Nuclear Information System (INIS)

Koerner, Philipp; Ehrmann, Katja; Hartmannsgruber, Johann; Metz, Michaela; Steigerwald, Sabrina; Flentje, Michael; Oorschot, Birgitt van

2017-01-01

The benefits of patient-reported symptom assessment combined with integrated palliative care are well documented. This study assessed the symptom burden of palliative and curative-intent radiation oncology patients. Prior to first consultation and at the end of RT, all adult cancer patients planned to receive fractionated percutaneous radiotherapy (RT) were asked to answer the Edmonton Symptom Assessment Scale (ESAS; nine symptoms from 0 = no symptoms to 10 = worst possible symptoms). Mean values were used for curative vs. palliative and pre-post comparisons, and the clinical relevance was evaluated (symptom values ≥ 4). Of 163 participating patients, 151 patients (90.9%) completed both surveys (116 curative and 35 palliative patients). Before beginning RT, 88.6% of palliative and 72.3% of curative patients showed at least one clinically relevant symptom. Curative patients most frequently named decreased general wellbeing (38.6%), followed by tiredness (35.0%), anxiety (32.4%), depression (30.0%), pain (26.3%), lack of appetite (23.5%), dyspnea (17.8%), drowsiness (8.0%) and nausea (6.1%). Palliative patients most frequently named decreased general wellbeing (62.8%), followed by pain (62.8%), tiredness (60.0%), lack of appetite (40.0%), anxiety (38.0%), depression (33.3%), dyspnea (28.5%), drowsiness (25.7%) and nausea (14.2%). At the end of RT, the proportion of curative and palliative patients with a clinically relevant symptom had increased significantly to 79.8 and 91.4%, respectively; whereas the proportion of patients reporting clinically relevant pain had decreased significantly (42.8 vs. 62.8%, respectively). Palliative patients had significantly increased tiredness. Curative patients reported significant increases in pain, tiredness, nausea, drowsiness, lack of appetite and restrictions in general wellbeing. Assessment of patient-reported symptoms was successfully realized in radiation oncology routine. Overall, both groups showed a high symptom burden

Curative resection of transverse colon cancer via minilaparotomy.

Science.gov (United States)

Ishida, Hideyuki; Ishiguro, Tohru; Ishibashi, Keiichiro; Ohsawa, Tomonori; Okada, Norimichi; Kumamoto, Kensuke; Haga, Norihiro

2011-01-01

Minilaparotomy has been reported to be a minimally invasive alternative to laparoscopically assisted surgery. We retrospectively evaluated the usefulness of minilaparotomy for the resection of transverse colon cancer, which has generally been considered difficult to resect laparoscopically. Patients for whom curative resection was attempted for transverse colon cancer (n = 21) or sigmoid colon cancer (n = 81) via minilaparotomy (skin incision, transverse colon cancer as well as those with sigmoid colon cancer.

Advancing Site-Based Data Curation for Geobiology: The Yellowstone Exemplar (Invited)

Science.gov (United States)

Palmer, C. L.; Fouke, B. W.; Rodman, A.; Choudhury, G. S.

2013-12-01

While advances in the management and archiving of scientific digital data are proceeding apace, there is an urgent need for data curation services to collect and provide access to high-value data fit for reuse. The Site-Based Data Curation (SBDC) project is establishing a framework of guidelines and processes for the curation of research data generated at scientifically significant sites. The project is a collaboration among information scientists, geobiologists, data archiving experts, and resource managers at Yellowstone National Park (YNP). Based on our previous work with the Data Conservancy on indicators of value for research data, several factors made YNP an optimal site for developing the SBDC framework, including unique environmental conditions, a permitting process for data collection, and opportunities for geo-located longitudinal data and multiple data sources for triangulation and context. Stakeholder analysis is informing the SBDC requirements, through engagement with geologists, geochemists, and microbiologists conducting research at YNP and personnel from the Yellowstone Center for Resources and other YNP units. To date, results include data value indicators specific to site-based research, minimum and optimal parameters for data description and metadata, and a strategy for organizing data around sampling events. New value indicators identified by the scientists include ease of access to park locations for verification and correction of data, and stable environmental conditions important for controlling variables. Researchers see high potential for data aggregated from the many individual investigators conducting permitted research at YNP, however reuse is clearly contingent on detailed and consistent sampling records. Major applications of SBDC include identifying connections in dynamic systems, spatial temporal synthesis, analyzing variability within and across geological features, tracking site evolution, assessing anomalies, and greater awareness

dbPAF: an integrative database of protein phosphorylation in animals and fungi.

Science.gov (United States)

Ullah, Shahid; Lin, Shaofeng; Xu, Yang; Deng, Wankun; Ma, Lili; Zhang, Ying; Liu, Zexian; Xue, Yu

2016-03-24

Protein phosphorylation is one of the most important post-translational modifications (PTMs) and regulates a broad spectrum of biological processes. Recent progresses in phosphoproteomic identifications have generated a flood of phosphorylation sites, while the integration of these sites is an urgent need. In this work, we developed a curated database of dbPAF, containing known phosphorylation sites in H. sapiens, M. musculus, R. norvegicus, D. melanogaster, C. elegans, S. pombe and S. cerevisiae. From the scientific literature and public databases, we totally collected and integrated 54,148 phosphoproteins with 483,001 phosphorylation sites. Multiple options were provided for accessing the data, while original references and other annotations were also present for each phosphoprotein. Based on the new data set, we computationally detected significantly over-represented sequence motifs around phosphorylation sites, predicted potential kinases that are responsible for the modification of collected phospho-sites, and evolutionarily analyzed phosphorylation conservation states across different species. Besides to be largely consistent with previous reports, our results also proposed new features of phospho-regulation. Taken together, our database can be useful for further analyses of protein phosphorylation in human and other model organisms. The dbPAF database was implemented in PHP + MySQL and freely available at http://dbpaf.biocuckoo.org.

The Knitting Lesson.

Science.gov (United States)

Smith, Pamela

1987-01-01

Based on Jean-Francois Millet's 1869 painting, "The Knitting Lesson," this lesson's goal is to introduce students in grades seven through nine to genre (everyday life) painting the nineteenth century. The lesson is also designed to show that some aspects of genre may be timeless. (BSR)

Follicle Online: an integrated database of follicle assembly, development and ovulation.

Science.gov (United States)

Hua, Juan; Xu, Bo; Yang, Yifan; Ban, Rongjun; Iqbal, Furhan; Cooke, Howard J; Zhang, Yuanwei; Shi, Qinghua

2015-01-01

Folliculogenesis is an important part of ovarian function as it provides the oocytes for female reproductive life. Characterizing genes/proteins involved in folliculogenesis is fundamental for understanding the mechanisms associated with this biological function and to cure the diseases associated with folliculogenesis. A large number of genes/proteins associated with folliculogenesis have been identified from different species. However, no dedicated public resource is currently available for folliculogenesis-related genes/proteins that are validated by experiments. Here, we are reporting a database 'Follicle Online' that provides the experimentally validated gene/protein map of the folliculogenesis in a number of species. Follicle Online is a web-based database system for storing and retrieving folliculogenesis-related experimental data. It provides detailed information for 580 genes/proteins (from 23 model organisms, including Homo sapiens, Mus musculus, Rattus norvegicus, Mesocricetus auratus, Bos Taurus, Drosophila and Xenopus laevis) that have been reported to be involved in folliculogenesis, POF (premature ovarian failure) and PCOS (polycystic ovary syndrome). The literature was manually curated from more than 43,000 published articles (till 1 March 2014). The Follicle Online database is implemented in PHP + MySQL + JavaScript and this user-friendly web application provides access to the stored data. In summary, we have developed a centralized database that provides users with comprehensive information about genes/proteins involved in folliculogenesis. This database can be accessed freely and all the stored data can be viewed without any registration. Database URL: http://mcg.ustc.edu.cn/sdap1/follicle/index.php © The Author(s) 2015. Published by Oxford University Press.

Controlling Nutritional Status (CONUT) score is a prognostic marker for gastric cancer patients after curative resection.

Science.gov (United States)

Kuroda, Daisuke; Sawayama, Hiroshi; Kurashige, Junji; Iwatsuki, Masaaki; Eto, Tsugio; Tokunaga, Ryuma; Kitano, Yuki; Yamamura, Kensuke; Ouchi, Mayuko; Nakamura, Kenichi; Baba, Yoshifumi; Sakamoto, Yasuo; Yamashita, Yoichi; Yoshida, Naoya; Chikamoto, Akira; Baba, Hideo

2018-03-01

Controlling Nutritional Status (CONUT), as calculated from serum albumin, total cholesterol concentration, and total lymphocyte count, was previously shown to be useful for nutritional assessment. The current study investigated the potential use of CONUT as a prognostic marker in gastric cancer patients after curative resection. Preoperative CONUT was retrospectively calculated in 416 gastric cancer patients who underwent curative resection at Kumamoto University Hospital from 2005 to 2014. The patients were divided into two groups: CONUT-high (≥4) and CONUT-low (≤3), according to time-dependent receiver operating characteristic (ROC) analysis. The associations of CONUT with clinicopathological factors and survival were evaluated. CONUT-high patients were significantly older (p nutritional status but also for predicting long-term OS in gastric cancer patients after curative resection.

Strategies for the Curation of CAD Engineering Models

Directory of Open Access Journals (Sweden)

Manjula Patel

2009-06-01

Full Text Available Normal 0 Product Lifecycle Management (PLM has become increasingly important in the engineering community over the last decade or so, due to the globalisation of markets and the rising popularity of products provided as services. It demands the efficient capture, representation, organisation, retrieval and reuse of product data over its entire life. Simultaneously, there is now a much greater reliance on CAD models for communicating designs to manufacturers, builders, maintenance crews and regulators, and for definitively expressing designs. Creating the engineering record digitally, however, presents problems not only for its long-term maintenance and accessibility - due in part to the rapid obsolescence of the hardware, software and file formats involved - but also for recording the evolution of designs, artefacts and products. We examine the curation and preservation requirements in PLM and suggest ways of alleviating the problems of sustaining CAD engineering models through the use of lightweight formats, layered annotation and the collection of Representation Information as defined in the Open Archival Information System (OAIS Reference Model.  We describe two tools which have been specifically developed to aid in the curation of CAD engineering models in the context of PLM: Lightweight Models with Multilayered Annotation (LiMMA and a Registry/Repository of Representation Information for Engineering (RRoRIfE.

Local high voltage radiotherapy with curative intent for prostatic carcinoma

International Nuclear Information System (INIS)

Jacobi, G.H.; Kurth, K.H.; Hohenfellner, R.

1979-01-01

In a 10-year interval 179 patients with prostatic carcinoma were treated by cobalt-60 teletherapy (7600 R). A selected group of 47 patients with localized disease and irradiated with curative intent had serial prostatic biopsies and were analized after a minimum follow-up of 1 year. Biopsies of half of the patients rendered definitively negative, on an average 14 months after radiotherapy. 8 patients with initial negative biopsy changed to positive secondarily. In one third of the patients histological conversion was missed, considered as radiation persister. Persistent carcinoma were of predominant low grade. 5 patients developed distant metastases 30 months after irradiation on an average. These patients had persistent positive tissue studies. Over all cumulative 5-years survival was 89%. In patients with prostatic carcinoma and local high voltage radiotherapy with curative intent (stage A through C) serial prostatic biopsies to document therapy effect seen mandatory. (orig.) 891 AJ/orig. 892 BRE [de

InverPep: A database of invertebrate antimicrobial peptides.

Science.gov (United States)

Gómez, Esteban A; Giraldo, Paula; Orduz, Sergio

2017-03-01

The aim of this work was to construct InverPep, a database specialised in experimentally validated antimicrobial peptides (AMPs) from invertebrates. AMP data contained in InverPep were manually curated from other databases and the scientific literature. MySQL was integrated with the development platform Laravel; this framework allows to integrate programming in PHP with HTML and was used to design the InverPep web page's interface. InverPep contains 18 separated fields, including InverPep code, phylum and species source, peptide name, sequence, peptide length, secondary structure, molar mass, charge, isoelectric point, hydrophobicity, Boman index, aliphatic index and percentage of hydrophobic amino acids. CALCAMPI, an algorithm to calculate the physicochemical properties of multiple peptides simultaneously, was programmed in PERL language. To date, InverPep contains 702 experimentally validated AMPs from invertebrate species. All of the peptides contain information associated with their source, physicochemical properties, secondary structure, biological activity and links to external literature. Most AMPs in InverPep have a length between 10 and 50 amino acids, a positive charge, a Boman index between 0 and 2 kcal/mol, and 30-50% hydrophobic amino acids. InverPep includes 33 AMPs not reported in other databases. Besides, CALCAMPI and statistical analysis of InverPep data is presented. The InverPep database is available in English and Spanish. InverPep is a useful database to study invertebrate AMPs and its information could be used for the design of new peptides. The user-friendly interface of InverPep and its information can be freely accessed via a web-based browser at http://ciencias.medellin.unal.edu.co/gruposdeinvestigacion/prospeccionydisenobiomoleculas/InverPep/public/home_en. Copyright © 2016 International Society for Chemotherapy of Infection and Cancer. Published by Elsevier Ltd. All rights reserved.

The history of a lesson

DEFF Research Database (Denmark)

Rasmussen, Mikkel Vedby

2003-01-01

and emphasises the need to study the history of lessons rather than the lessons of history. This approach shows that Munich is the end point of a constitutive history that begins in the failure of the Versailles treaty to create a durable European order following the First World War. The Munich lesson is thus......The article investigates the concept of lessons in IR. By means of a constructivist critique of the 'lessons literature', the article analyses one of the most important of IR lessons: that of Munich. Examining how the Munich lesson came about, the article shows the praxeological nature of lessons...... one element of the lesson of Versailles, which is a praxeology that defines how the West is to make peace, and against whom peace must be defended. The lesson of Versailles has been, at least in part, constitutive of the outbreak of the Cold War, and it continues to define the Western conception...

Planning Related to the Curation and Processing of Returned Martian Samples

Science.gov (United States)

McCubbin, F. M.; Harrington, A. D.

2018-04-01

Many of the planning activities in the NASA Astromaterials Acquisition and Curation Office at JSC are centered around Mars Sample Return. The importance of contamination knowledge and the benefits of a mobile/modular receiving facility are discussed.

A systematic review of randomized controlled trials on curative and health enhancement effects of forest therapy

Directory of Open Access Journals (Sweden)

Kamioka H

2012-07-01

Full Text Available Hiroharu Kamioka,1 Kiichiro Tsutani,2 Yoshiteru Mutoh,3 Takuya Honda,4 Nobuyoshi Shiozawa,5 Shinpei Okada,6 Sang-Jun Park,6 Jun Kitayuguchi,7 Masamitsu Kamada,8 Hiroyasu Okuizumi,9 Shuichi Handa91Faculty of Regional Environment Science, Tokyo University of Agriculture, Tokyo, 2Department of Drug Policy and Management, Graduate School of Pharmaceutical Sciences, The University of Tokyo, Tokyo, 3Todai Policy Alternatives Research Institute, The University of Tokyo, Tokyo, 4Japanese Society for the Promotion of Science, Tokyo, 5Food Labeling Division, Consumer Affairs Agency, Cabinet Office, Government of Japan, Tokyo, 6Physical Education and Medicine Research Foundation, Nagano, 7Physical Education and Medicine Research Center Unnan, Shimane, 8Department of Environmental and Preventive Medicine, Shimane University School of Medicine, Shimane, 9Mimaki Onsen (Spa Clinic, Tomi City, Nagano, JapanObjective: To summarize the evidence for curative and health enhancement effects through forest therapy and to assess the quality of studies based on a review of randomized controlled trials (RCTs.Study design: A systematic review based on RCTs.Methods: Studies were eligible if they were RCTs. Studies included one treatment group in which forest therapy was applied. The following databases – from 1990 to November 9, 2010 – were searched: MEDLINE via PubMed, CINAHL, Web of Science, and Ichushi-Web. All Cochrane databases and Campbell Systematic Reviews were also searched up to November 9, 2010.Results: Two trials met all inclusion criteria. No specific diseases were evaluated, and both studies reported significant effectiveness in one or more outcomes for health enhancement. However, the results of evaluations with the CONSORT (Consolidated Standards of Reporting Trials 2010 and CLEAR NPT (A Checklist to Evaluate a Report of a Nonpharmacological Trial checklists generally showed a remarkable lack of description in the studies. Furthermore, there was a

Active and Social Data Curation: Reinventing the Business of Community-scale Lifecycle Data Management

Science.gov (United States)

McDonald, R. H.; Kumar, P.; Plale, B. A.; Myers, J.; Hedstrom, M. L.

2012-12-01

Effective long-term curation and preservation of data for community use has historically been limited to high-value and homogeneous collections produced by mission-oriented organizations. The technologies and practices that have been applied in these cases, e.g. relational data bases, development of comprehensive standardized vocabularies, and centralized support for reference data collections, are arguably applicable to the much broader range of data generated by the long tail of investigator-led research, with the logical conclusion of such an argument leading to the call for training, evangelism, and vastly increased funding as the best means of broadening community-scale data management. In this paper, we question this reasoning and explore how alternative approaches focused on the overall data lifecycle and the sociological and business realities of distributed multi-disciplinary research communities might dramatically lower costs, increase value, and consequently drive dramatic advances in our ability to use and re-use data, and ultimately enable more rapid scientific advance. Specifically, we introduce the concepts of active and social curation as a means to decrease coordination costs, align costs and values for individual data producers and data consumers, and improve the immediacy of returns for data curation investments. Further, we describe the specific architecture and services for active and social curation that are being prototyped within the Sustainable Environment - Actionable Data (SEAD) project within NSF's DataNet network and discuss how they are motivated by the long-tail dynamics in the cross-disciplinary sustainability research community.

Quality controls in integrative approaches to detect errors and inconsistencies in biological databases

Directory of Open Access Journals (Sweden)

Ghisalberti Giorgio

2010-12-01

Full Text Available Numerous biomolecular data are available, but they are scattered in many databases and only some of them are curated by experts. Most available data are computationally derived and include errors and inconsistencies. Effective use of available data in order to derive new knowledge hence requires data integration and quality improvement. Many approaches for data integration have been proposed. Data warehousing seams to be the most adequate when comprehensive analysis of integrated data is required. This makes it the most suitable also to implement comprehensive quality controls on integrated data. We previously developed GFINDer (http://www.bioinformatics.polimi.it/GFINDer/, a web system that supports scientists in effectively using available information. It allows comprehensive statistical analysis and mining of functional and phenotypic annotations of gene lists, such as those identified by high-throughput biomolecular experiments. GFINDer backend is composed of a multi-organism genomic and proteomic data warehouse (GPDW. Within the GPDW, several controlled terminologies and ontologies, which describe gene and gene product related biomolecular processes, functions and phenotypes, are imported and integrated, together with their associations with genes and proteins of several organisms. In order to ease maintaining updated the GPDW and to ensure the best possible quality of data integrated in subsequent updating of the data warehouse, we developed several automatic procedures. Within them, we implemented numerous data quality control techniques to test the integrated data for a variety of possible errors and inconsistencies. Among other features, the implemented controls check data structure and completeness, ontological data consistency, ID format and evolution, unexpected data quantification values, and consistency of data from single and multiple sources. We use the implemented controls to analyze the quality of data available from several

The curative effects of radiotherapy-based therapies for human epidermal growth factor receptor 2-positive breast cancer: A meta-analysis.

Science.gov (United States)

Shao, Minghai; Zhang, Chi; Qin, Qin; Zhang, Zhaoyue; Zhu, Hongcheng; Di, Xiaoke; Sun, Xinchen

2017-09-01

This meta-analysis was designed to fully assess the curative effects of radiotherapy-based therapies for human epidermal growth factor receptor 2-positive (HER2+) breast cancer (BC). English articles were retrieved through searching Cochrane library, PubMed, and Embase databases updated to February 2017. Studies were selected based on the inclusion and exclusion criteria. The curative effects of radiotherapy-based therapies forHER2+ BC patients were assessed using hazard rates (HRs) or odds ratios (ORs), as well as their 95% confidence intervals (CIs). In addition, Egger test was used to assess publication bias, followed by sensitivity analysis. All statistic methods were conducted using R 3.12 software. A total of 9 eligible studies were included into this meta-analysis, which involved 2236 HER2+ BC patients. Egger test showed that the eligible studies had no publication bias (t = 2.198, P = .05918). Sensitivity analysis demonstrated that the results were stable. HER2+ BC patients in radiotherapy group had lower locoregional recurrences than those in other groups. Moreover, meta-analysis showed that no significant difference was found between HER2+ BC patients in radiotherapy group and other groups on the 1-year overall survival (P = 0.5263, I = 65.4%), 3-year overall survival (P = 0.4591, I = 0), and 5-year overall survival (P = 0.06277, I = 0). Radiotherapy-based therapies might have certain advantages in treating HER2+ BC patients.

Lesson Learning at JPL

Science.gov (United States)

Oberhettinger, David

2011-01-01

A lessons learned system is a hallmark of a mature engineering organization A formal lessons learned process can help assure that valuable lessons get written and published, that they are well-written, and that the essential information is "infused" into institutional practice. Requires high-level institutional commitment, and everyone's participation in gathering, disseminating, and using the lessons

MetaboLights: An Open-Access Database Repository for Metabolomics Data.

Science.gov (United States)

Kale, Namrata S; Haug, Kenneth; Conesa, Pablo; Jayseelan, Kalaivani; Moreno, Pablo; Rocca-Serra, Philippe; Nainala, Venkata Chandrasekhar; Spicer, Rachel A; Williams, Mark; Li, Xuefei; Salek, Reza M; Griffin, Julian L; Steinbeck, Christoph

2016-03-24

MetaboLights is the first general purpose, open-access database repository for cross-platform and cross-species metabolomics research at the European Bioinformatics Institute (EMBL-EBI). Based upon the open-source ISA framework, MetaboLights provides Metabolomics Standard Initiative (MSI) compliant metadata and raw experimental data associated with metabolomics experiments. Users can upload their study datasets into the MetaboLights Repository. These studies are then automatically assigned a stable and unique identifier (e.g., MTBLS1) that can be used for publication reference. The MetaboLights Reference Layer associates metabolites with metabolomics studies in the archive and is extensively annotated with data fields such as structural and chemical information, NMR and MS spectra, target species, metabolic pathways, and reactions. The database is manually curated with no specific release schedules. MetaboLights is also recommended by journals for metabolomics data deposition. This unit provides a guide to using MetaboLights, downloading experimental data, and depositing metabolomics datasets using user-friendly submission tools. Copyright © 2016 John Wiley & Sons, Inc.

Interview with Smithsonian NASM Spacesuit Curator Dr. Cathleen Lewis

Science.gov (United States)

Lewis, Cathleen; Wright, Rebecca

2012-01-01

Dr. Cathleen Lewis was interviewed by Rebecca Wright during the presentation of an "Interview with Smithsonian NASM Spacesuit Curator Dr. Cathleen Lewis" on May 14, 2012. Topics included the care, size, and history of the spacesuit collection at the Smithsonian and the recent move to the state-of-the-art permanent storage facility at the Udvar-Hazy facility in Virginia.

The role of non-governmental organizations in providing curative health services in North Darfur State, Sudan.

Science.gov (United States)

Yagub, Abdallah I A; Mtshali, Khondlo

2015-09-01

Conflict in North Darfur state, Western Sudan started in 2003, and the delivering of curative health services was becoming a greater challenge for the country's limited resources. NGOs have played an important role in providing curative health services. To examine the role that Non-Governmental Organizations (NGOs) have played in providing curative health services, as well as to identify the difficulties and challenges that affect NGOs in delivering curative health services. Secondary data was collected from different sources, including government offices and medical organizations in Sudan and in North Darfur state. Primary data was obtained through interviews with government and NGOs representatives. The interviews were conducted with (1) expatriates working for international NGOs (N=15) (2) health professionals and administrators working in health sector (N= 45) in the period from November 2010 to January 2011. The government in North Darfur state spent 70% of its financial budget on security, while it spent it less than 1% on providing health services. The international NGOs have been providing 70% of curative health services to the State's population by contributing 52.9% of the health budget and 1 390 health personnel. Since 2003 NGOs have provided technical assistance to the health staff. As a result, more than fifty nurses have been trained to provide care and treatment, more than twenty-three doctors have been trained in laboratory equipment operation, and approximately six senior doctors and hospital directors have received management training. NGOs have been managing and supporting 89 public health facilities, and established 24 health centres in IDP camps, and 20 health centres across all the districts in North Darfur state. The NGOs have played an important role in providing curative health services and in establishing good health facilities, but a future problem is how the government will run these health facilities after a peaceful settlement has been

Data Albums: An Event Driven Search, Aggregation and Curation Tool for Earth Science

Science.gov (United States)

Ramachandran, Rahul; Kulkarni, Ajinkya; Maskey, Manil; Bakare, Rohan; Basyal, Sabin; Li, Xiang; Flynn, Shannon

2014-01-01

Approaches used in Earth science research such as case study analysis and climatology studies involve discovering and gathering diverse data sets and information to support the research goals. To gather relevant data and information for case studies and climatology analysis is both tedious and time consuming. Current Earth science data systems are designed with the assumption that researchers access data primarily by instrument or geophysical parameter. In cases where researchers are interested in studying a significant event, they have to manually assemble a variety of datasets relevant to it by searching the different distributed data systems. This paper presents a specialized search, aggregation and curation tool for Earth science to address these challenges. The search rool automatically creates curated 'Data Albums', aggregated collections of information related to a specific event, containing links to relevant data files [granules] from different instruments, tools and services for visualization and analysis, and information about the event contained in news reports, images or videos to supplement research analysis. Curation in the tool is driven via an ontology based relevancy ranking algorithm to filter out non relevant information and data.

[Two Cases of Curative Resection of Locally Advanced Rectal Cancer after Preoperative Chemotherapy].

Science.gov (United States)

Mitsuhashi, Noboru; Shimizu, Yoshiaki; Kuboki, Satoshi; Yoshitomi, Hideyuki; Kato, Atsushi; Ohtsuka, Masayuki; Shimizu, Hiroaki; Miyazaki, Masaru

2015-11-01

Reports of conversion in cases of locally advanced colorectal cancer have been increasing. Here, we present 2 cases in which curative resection of locally advanced rectal cancer accompanied by intestinal obstruction was achieved after establishing a stoma and administering chemotherapy. The first case was of a 46-year-old male patient diagnosed with upper rectal cancer and intestinal obstruction. Because of a high level of retroperitoneal invasion, after establishing a sigmoid colostomy, 13 courses of mFOLFOX6 plus Pmab were administered. Around 6 months after the initial surgery, low anterior resection for rectal cancer and surgery to close the stoma were performed. Fourteen days after curative resection, the patient was discharged from the hospital. The second case was of a 66-year-old male patient with a circumferential tumor extending from Rs to R, accompanied by right ureter infiltration and sub-intestinal obstruction. After establishing a sigmoid colostomy, 11 courses of mFOLFOX6 plus Pmab were administered. Five months after the initial surgery, anterior resection of the rectum and surgery to close the stoma were performed. Twenty days after curative resection, the patient was released from the hospital. No recurrences have been detected in either case.

The EcoCyc database: reflecting new knowledge about Escherichia coli K-12.

Science.gov (United States)

Keseler, Ingrid M; Mackie, Amanda; Santos-Zavaleta, Alberto; Billington, Richard; Bonavides-Martínez, César; Caspi, Ron; Fulcher, Carol; Gama-Castro, Socorro; Kothari, Anamika; Krummenacker, Markus; Latendresse, Mario; Muñiz-Rascado, Luis; Ong, Quang; Paley, Suzanne; Peralta-Gil, Martin; Subhraveti, Pallavi; Velázquez-Ramírez, David A; Weaver, Daniel; Collado-Vides, Julio; Paulsen, Ian; Karp, Peter D

2017-01-04

EcoCyc (EcoCyc.org) is a freely accessible, comprehensive database that collects and summarizes experimental data for Escherichia coli K-12, the best-studied bacterial model organism. New experimental discoveries about gene products, their function and regulation, new metabolic pathways, enzymes and cofactors are regularly added to EcoCyc. New SmartTable tools allow users to browse collections of related EcoCyc content. SmartTables can also serve as repositories for user- or curator-generated lists. EcoCyc now supports running and modifying E. coli metabolic models directly on the EcoCyc website. © The Author(s) 2016. Published by Oxford University Press on behalf of Nucleic Acids Research.

BioData: a national aquatic bioassessment database

Science.gov (United States)

MacCoy, Dorene

2011-01-01

BioData is a U.S. Geological Survey (USGS) web-enabled database that for the first time provides for the capture, curation, integration, and delivery of bioassessment data collected by local, regional, and national USGS projects. BioData offers field biologists advanced capabilities for entering, editing, and reviewing the macroinvertebrate, algae, fish, and supporting habitat data from rivers and streams. It offers data archival and curation capabilities that protect and maintain data for the long term. BioData provides the Federal, State, and local governments, as well as the scientific community, resource managers, the private sector, and the public with easy access to tens of thousands of samples collected nationwide from thousands of stream and river sites. BioData also provides the USGS with centralized data storage for delivering data to other systems and applications through automated web services. BioData allows users to combine data sets of known quality from different projects in various locations over time. It provides a nationally aggregated database for users to leverage data from many independent projects that, until now, was not feasible at this scale. For example, from 1991 to 2011, the USGS Idaho Water Science Center collected more than 816 bioassessment samples from 63 sites for the National Water Quality Assessment (NAWQA) Program and more than 477 samples from 39 sites for a cooperative USGS and State of Idaho Statewide Water Quality Network (fig. 1). Using BioData, 20 years of samples collected for both of these projects can be combined for analysis. BioData delivers all of the data using current taxonomic nomenclature, thus relieving users of the difficult and time-consuming task of harmonizing taxonomy among samples collected during different time periods. Fish data are reported using the Integrated Taxonomic Information Service (ITIS) Taxonomic Serial Numbers (TSN's). A simple web-data input interface and self-guided, public data

YPED: an integrated bioinformatics suite and database for mass spectrometry-based proteomics research.

Science.gov (United States)

Colangelo, Christopher M; Shifman, Mark; Cheung, Kei-Hoi; Stone, Kathryn L; Carriero, Nicholas J; Gulcicek, Erol E; Lam, TuKiet T; Wu, Terence; Bjornson, Robert D; Bruce, Can; Nairn, Angus C; Rinehart, Jesse; Miller, Perry L; Williams, Kenneth R

2015-02-01

We report a significantly-enhanced bioinformatics suite and database for proteomics research called Yale Protein Expression Database (YPED) that is used by investigators at more than 300 institutions worldwide. YPED meets the data management, archival, and analysis needs of a high-throughput mass spectrometry-based proteomics research ranging from a single laboratory, group of laboratories within and beyond an institution, to the entire proteomics community. The current version is a significant improvement over the first version in that it contains new modules for liquid chromatography-tandem mass spectrometry (LC-MS/MS) database search results, label and label-free quantitative proteomic analysis, and several scoring outputs for phosphopeptide site localization. In addition, we have added both peptide and protein comparative analysis tools to enable pairwise analysis of distinct peptides/proteins in each sample and of overlapping peptides/proteins between all samples in multiple datasets. We have also implemented a targeted proteomics module for automated multiple reaction monitoring (MRM)/selective reaction monitoring (SRM) assay development. We have linked YPED's database search results and both label-based and label-free fold-change analysis to the Skyline Panorama repository for online spectra visualization. In addition, we have built enhanced functionality to curate peptide identifications into an MS/MS peptide spectral library for all of our protein database search identification results. Copyright © 2015 The Authors. Production and hosting by Elsevier Ltd.. All rights reserved.

The phytophthora genome initiative database: informatics and analysis for distributed pathogenomic research.

Science.gov (United States)

Waugh, M; Hraber, P; Weller, J; Wu, Y; Chen, G; Inman, J; Kiphart, D; Sobral, B

2000-01-01

The Phytophthora Genome Initiative (PGI) is a distributed collaboration to study the genome and evolution of a particularly destructive group of plant pathogenic oomycete, with the goal of understanding the mechanisms of infection and resistance. NCGR provides informatics support for the collaboration as well as a centralized data repository. In the pilot phase of the project, several investigators prepared Phytophthora infestans and Phytophthora sojae EST and Phytophthora sojae BAC libraries and sent them to another laboratory for sequencing. Data from sequencing reactions were transferred to NCGR for analysis and curation. An analysis pipeline transforms raw data by performing simple analyses (i.e., vector removal and similarity searching) that are stored and can be retrieved by investigators using a web browser. Here we describe the database and access tools, provide an overview of the data therein and outline future plans. This resource has provided a unique opportunity for the distributed, collaborative study of a genus from which relatively little sequence data are available. Results may lead to insight into how better to control these pathogens. The homepage of PGI can be accessed at http:www.ncgr.org/pgi, with database access through the database access hyperlink.

Palliative or curative treatment intent affects communication in radiation therapy consultations.

NARCIS (Netherlands)

Timmermans, L.; Maazen, R.W.M. van der; Leer, J.W.H.; Kraaimaat, F.W.

2006-01-01

OBJECTIVE: To assess whether communication in radiotherapy consultations is affected by palliative or curative treatment intent. SUBJECTS AND METHODS: The study involved 160 patients and 8 radiation oncologists. Eighty patients visited the radiation oncologist (RO) for palliative treatment and 80

Lessons learned while building the Deepwater Horizon Database: Toward improved data sharing in coastal science

Science.gov (United States)

Thessen, Anne E.; McGinnis, Sean; North, Elizabeth W.

2016-02-01

Process studies and coupled-model validation efforts in geosciences often require integration of multiple data types across time and space. For example, improved prediction of hydrocarbon fate and transport is an important societal need which fundamentally relies upon synthesis of oceanography and hydrocarbon chemistry. Yet, there are no publically accessible databases which integrate these diverse data types in a georeferenced format, nor are there guidelines for developing such a database. The objective of this research was to analyze the process of building one such database to provide baseline information on data sources and data sharing and to document the challenges and solutions that arose during this major undertaking. The resulting Deepwater Horizon Database was approximately 2.4 GB in size and contained over 8 million georeferenced data points collected from industry, government databases, volunteer networks, and individual researchers. The major technical challenges that were overcome were reconciliation of terms, units, and quality flags which were necessary to effectively integrate the disparate data sets. Assembling this database required the development of relationships with individual researchers and data managers which often involved extensive e-mail contacts. The average number of emails exchanged per data set was 7.8. Of the 95 relevant data sets that were discovered, 38 (40%) were obtained, either in whole or in part. Over one third (36%) of the requests for data went unanswered. The majority of responses were received after the first request (64%) and within the first week of the first request (67%). Although fewer than half of the potentially relevant datasets were incorporated into the database, the level of sharing (40%) was high compared to some other disciplines where sharing can be as low as 10%. Our suggestions for building integrated databases include budgeting significant time for e-mail exchanges, being cognizant of the cost versus

ChlamyCyc: an integrative systems biology database and web-portal for Chlamydomonas reinhardtii

Directory of Open Access Journals (Sweden)

Kempa Stefan

2009-05-01

Full Text Available Abstract Background The unicellular green alga Chlamydomonas reinhardtii is an important eukaryotic model organism for the study of photosynthesis and plant growth. In the era of modern high-throughput technologies there is an imperative need to integrate large-scale data sets from high-throughput experimental techniques using computational methods and database resources to provide comprehensive information about the molecular and cellular organization of a single organism. Results In the framework of the German Systems Biology initiative GoFORSYS, a pathway database and web-portal for Chlamydomonas (ChlamyCyc was established, which currently features about 250 metabolic pathways with associated genes, enzymes, and compound information. ChlamyCyc was assembled using an integrative approach combining the recently published genome sequence, bioinformatics methods, and experimental data from metabolomics and proteomics experiments. We analyzed and integrated a combination of primary and secondary database resources, such as existing genome annotations from JGI, EST collections, orthology information, and MapMan classification. Conclusion ChlamyCyc provides a curated and integrated systems biology repository that will enable and assist in systematic studies of fundamental cellular processes in Chlamydomonas. The ChlamyCyc database and web-portal is freely available under http://chlamycyc.mpimp-golm.mpg.de.

3DSwap: Curated knowledgebase of proteins involved in 3D domain swapping

KAUST Repository

Shameer, Khader; Shingate, Prashant N.; Manjunath, S. C. P.; Karthika, M.; Pugalenthi, Ganesan; Sowdhamini, Ramanathan

2011-01-01

structures in oligomeric conformation. Protein structures in swapped conformations perform diverse functional roles and are also associated with deposition diseases in humans. We have performed in-depth literature curation and structural bioinformatics

Sample Curation at a Lunar Outpost

Science.gov (United States)

Allen, Carlton C.; Lofgren, Gary E.; Treiman, A. H.; Lindstrom, Marilyn L.

2007-01-01

The six Apollo surface missions returned 2,196 individual rock and soil samples, with a total mass of 381.6 kg. Samples were collected based on visual examination by the astronauts and consultation with geologists in the science back room in Houston. The samples were photographed during collection, packaged in uniquely-identified containers, and transported to the Lunar Module. All samples collected on the Moon were returned to Earth. NASA's upcoming return to the Moon will be different. Astronauts will have extended stays at an out-post and will collect more samples than they will return. They will need curation and analysis facilities on the Moon in order to carefully select samples for return to Earth.

Ginseng Genome Database: an open-access platform for genomics of Panax ginseng.

Science.gov (United States)

Jayakodi, Murukarthick; Choi, Beom-Soon; Lee, Sang-Choon; Kim, Nam-Hoon; Park, Jee Young; Jang, Woojong; Lakshmanan, Meiyappan; Mohan, Shobhana V G; Lee, Dong-Yup; Yang, Tae-Jin

2018-04-12

The ginseng (Panax ginseng C.A. Meyer) is a perennial herbaceous plant that has been used in traditional oriental medicine for thousands of years. Ginsenosides, which have significant pharmacological effects on human health, are the foremost bioactive constituents in this plant. Having realized the importance of this plant to humans, an integrated omics resource becomes indispensable to facilitate genomic research, molecular breeding and pharmacological study of this herb. The first draft genome sequences of P. ginseng cultivar "Chunpoong" were reported recently. Here, using the draft genome, transcriptome, and functional annotation datasets of P. ginseng, we have constructed the Ginseng Genome Database http://ginsengdb.snu.ac.kr /, the first open-access platform to provide comprehensive genomic resources of P. ginseng. The current version of this database provides the most up-to-date draft genome sequence (of approximately 3000 Mbp of scaffold sequences) along with the structural and functional annotations for 59,352 genes and digital expression of genes based on transcriptome data from different tissues, growth stages and treatments. In addition, tools for visualization and the genomic data from various analyses are provided. All data in the database were manually curated and integrated within a user-friendly query page. This database provides valuable resources for a range of research fields related to P. ginseng and other species belonging to the Apiales order as well as for plant research communities in general. Ginseng genome database can be accessed at http://ginsengdb.snu.ac.kr /.

Immunisation in a curative setting

DEFF Research Database (Denmark)

Kofoed, Poul-Erik; Nielsen, B; Rahman, A K

1990-01-01

OBJECTIVE: To study the uptake of vaccination offered to women and children attending a curative health facility. DESIGN: Prospective survey over eight months of the uptake of vaccination offered to unimmunised women and children attending a diarrhoeal treatment centre as patients or attendants....... SETTING: The International Centre for Diarrhoeal Disease Research, Dhaka, Bangladesh. SUBJECTS: An estimated 19,349 unimmunised women aged 15 to 45 and 17,372 children attending the centre for treatment or accompanying patients between 1 January and 31 August 1989. MAIN OUTCOME MEASURES: The number...... of women and children who were unimmunised or incompletely immunised was calculated and the percentage of this target population accepting vaccination was recorded. RESULTS: 7530 (84.2%) Of 8944 eligible children and 7730 (40.4%) of 19,138 eligible women were vaccinated. Of the children, 63.8% were boys...

Semi-automated curation of metabolic models via flux balance analysis: a case study with Mycoplasma gallisepticum.

Directory of Open Access Journals (Sweden)

Eddy J Bautista

Full Text Available Primarily used for metabolic engineering and synthetic biology, genome-scale metabolic modeling shows tremendous potential as a tool for fundamental research and curation of metabolism. Through a novel integration of flux balance analysis and genetic algorithms, a strategy to curate metabolic networks and facilitate identification of metabolic pathways that may not be directly inferable solely from genome annotation was developed. Specifically, metabolites involved in unknown reactions can be determined, and potentially erroneous pathways can be identified. The procedure developed allows for new fundamental insight into metabolism, as well as acting as a semi-automated curation methodology for genome-scale metabolic modeling. To validate the methodology, a genome-scale metabolic model for the bacterium Mycoplasma gallisepticum was created. Several reactions not predicted by the genome annotation were postulated and validated via the literature. The model predicted an average growth rate of 0.358±0.12[Formula: see text], closely matching the experimentally determined growth rate of M. gallisepticum of 0.244±0.03[Formula: see text]. This work presents a powerful algorithm for facilitating the identification and curation of previously known and new metabolic pathways, as well as presenting the first genome-scale reconstruction of M. gallisepticum.

Database citation in supplementary data linked to Europe PubMed Central full text biomedical articles.

Science.gov (United States)

Kafkas, Şenay; Kim, Jee-Hyub; Pi, Xingjun; McEntyre, Johanna R

2015-01-01

In this study, we present an analysis of data citation practices in full text research articles and their corresponding supplementary data files, made available in the Open Access set of articles from Europe PubMed Central. Our aim is to investigate whether supplementary data files should be considered as a source of information for integrating the literature with biomolecular databases. Using text-mining methods to identify and extract a variety of core biological database accession numbers, we found that the supplemental data files contain many more database citations than the body of the article, and that those citations often take the form of a relatively small number of articles citing large collections of accession numbers in text-based files. Moreover, citation of value-added databases derived from submission databases (such as Pfam, UniProt or Ensembl) is common, demonstrating the reuse of these resources as datasets in themselves. All the database accession numbers extracted from the supplementary data are publicly accessible from http://dx.doi.org/10.5281/zenodo.11771. Our study suggests that supplementary data should be considered when linking articles with data, in curation pipelines, and in information retrieval tasks in order to make full use of the entire research article. These observations highlight the need to improve the management of supplemental data in general, in order to make this information more discoverable and useful.

Predicting prognosis in hepatocellular carcinoma after curative surgery with common clinicopathologic parameters

International Nuclear Information System (INIS)

Hao, Ke; Sham, Pak C; Poon, Ronnie TP; Luk, John M; Lee, Nikki PY; Mao, Mao; Zhang, Chunsheng; Ferguson, Mark D; Lamb, John; Dai, Hongyue; Ng, Irene O

2009-01-01

Surgical resection is one important curative treatment for hepatocellular carcinoma (HCC), but the prognosis following surgery differs substantially and such large variation is mainly unexplained. A review of the literature yields a number of clinicopathologic parameters associated with HCC prognosis. However, the results are not consistent due to lack of systemic approach to establish a prediction model incorporating all these parameters. We conducted a retrospective analysis on the common clinicopathologic parameters from a cohort of 572 ethnic Chinese HCC patients who received curative surgery. The cases were randomly divided into training (n = 272) and validation (n = 300) sets. Each parameter was individually tested and the significant parameters were entered into a linear classifier for model building, and the prediction accuracy was assessed in the validation set Our findings based on the training set data reveal 6 common clinicopathologic parameters (tumor size, number of tumor nodules, tumor stage, venous infiltration status, and serum α-fetoprotein and total albumin levels) that were significantly associated with the overall HCC survival and disease-free survival (time to recurrence). We next built a linear classifier model by multivariate Cox regression to predict prognostic outcomes of HCC patients after curative surgery This analysis detected a considerable fraction of variance in HCC prognosis and the area under the ROC curve was about 70%. We further evaluated the model using two other protocols; leave-one-out procedure (n = 264) and independent validation (n = 300). Both were found to have excellent prediction power. The predicted score could separate patients into distinct groups with respect to survival (p-value = 1.8e-12) and disease free survival (p-value = 3.2e-7). This described model will provide valuable guidance on prognosis after curative surgery for HCC in clinical practice. The adaptive nature allows easy accommodation for future new

A qualitative content analysis of global health engagements in Peacekeeping and Stability Operations Institute's stability operations lessons learned and information management system.

Science.gov (United States)

Nang, Roberto N; Monahan, Felicia; Diehl, Glendon B; French, Daniel

2015-04-01

Many institutions collect reports in databases to make important lessons-learned available to their members. The Uniformed Services University of the Health Sciences collaborated with the Peacekeeping and Stability Operations Institute to conduct a descriptive and qualitative analysis of global health engagements (GHEs) contained in the Stability Operations Lessons Learned and Information Management System (SOLLIMS). This study used a summative qualitative content analysis approach involving six steps: (1) a comprehensive search; (2) two-stage reading and screening process to identify first-hand, health-related records; (3) qualitative and quantitative data analysis using MAXQDA, a software program; (4) a word cloud to illustrate word frequencies and interrelationships; (5) coding of individual themes and validation of the coding scheme; and (6) identification of relationships in the data and overarching lessons-learned. The individual codes with the most number of text segments coded included: planning, personnel, interorganizational coordination, communication/information sharing, and resources/supplies. When compared to the Department of Defense's (DoD's) evolving GHE principles and capabilities, the SOLLIMS coding scheme appeared to align well with the list of GHE capabilities developed by the Department of Defense Global Health Working Group. The results of this study will inform practitioners of global health and encourage additional qualitative analysis of other lessons-learned databases. Reprint & Copyright © 2015 Association of Military Surgeons of the U.S.

WEB-BASED DATABASE ON RENEWAL TECHNOLOGIES ...

Science.gov (United States)

As U.S. utilities continue to shore up their aging infrastructure, renewal needs now represent over 43% of annual expenditures compared to new construction for drinking water distribution and wastewater collection systems (Underground Construction [UC], 2016). An increased understanding of renewal options will ultimately assist drinking water utilities in reducing water loss and help wastewater utilities to address infiltration and inflow issues in a cost-effective manner. It will also help to extend the service lives of both drinking water and wastewater mains. This research effort involved collecting case studies on the use of various trenchless pipeline renewal methods and providing the information in an online searchable database. The overall objective was to further support technology transfer and information sharing regarding emerging and innovative renewal technologies for water and wastewater mains. The result of this research is a Web-based, searchable database that utility personnel can use to obtain technology performance and cost data, as well as case study references. The renewal case studies include: technologies used; the conditions under which the technology was implemented; costs; lessons learned; and utility contact information. The online database also features a data mining tool for automated review of the technologies selected and cost data. Based on a review of the case study results and industry data, several findings are presented on tren

Sharing and community curation of mass spectrometry data with Global Natural Products Social Molecular Networking

DEFF Research Database (Denmark)

Wang, Mingxun; Carver, Jeremy J.; Pevzner, Pavel

2016-01-01

are well-suited to high-throughput characterization of NP, there is a pressing need for an infrastructure to enable sharing and curation of data. We present Global Natural Products Social Molecular Networking (GNPS; http://gnps.ucsd.edu), an open-access knowledge base for community-wide organization...... and sharing of raw, processed or identified tandem mass (MS/MS) spectrometry data. In GNPS, crowdsourced curation of freely available community-wide reference MS libraries will underpin improved annotations. Data-driven social-networking should facilitate identification of spectra and foster collaborations...

The reactive metabolite target protein database (TPDB – a web-accessible resource

Directory of Open Access Journals (Sweden)

Dong Yinghua

2007-03-01

Full Text Available Abstract Background The toxic effects of many simple organic compounds stem from their biotransformation to chemically reactive metabolites which bind covalently to cellular proteins. To understand the mechanisms of cytotoxic responses it may be important to know which proteins become adducted and whether some may be common targets of multiple toxins. The literature of this field is widely scattered but expanding rapidly, suggesting the need for a comprehensive, searchable database of reactive metabolite target proteins. Description The Reactive Metabolite Target Protein Database (TPDB is a comprehensive, curated, searchable, documented compilation of publicly available information on the protein targets of reactive metabolites of 18 well-studied chemicals and drugs of known toxicity. TPDB software enables i string searches for author names and proteins names/synonyms, ii more complex searches by selecting chemical compound, animal species, target tissue and protein names/synonyms from pull-down menus, and iii commonality searches over multiple chemicals. Tabulated search results provide information, references and links to other databases. Conclusion The TPDB is a unique on-line compilation of information on the covalent modification of cellular proteins by reactive metabolites of chemicals and drugs. Its comprehensiveness and searchability should facilitate the elucidation of mechanisms of reactive metabolite toxicity. The database is freely available at http://tpdb.medchem.ku.edu/tpdb.html

DDEC: Dragon database of genes implicated in esophageal cancer

International Nuclear Information System (INIS)

Essack, Magbubah; Radovanovic, Aleksandar; Schaefer, Ulf; Schmeier, Sebastian; Seshadri, Sundararajan V; Christoffels, Alan; Kaur, Mandeep; Bajic, Vladimir B

2009-01-01

Esophageal cancer ranks eighth in order of cancer occurrence. Its lethality primarily stems from inability to detect the disease during the early organ-confined stage and the lack of effective therapies for advanced-stage disease. Moreover, the understanding of molecular processes involved in esophageal cancer is not complete, hampering the development of efficient diagnostics and therapy. Efforts made by the scientific community to improve the survival rate of esophageal cancer have resulted in a wealth of scattered information that is difficult to find and not easily amendable to data-mining. To reduce this gap and to complement available cancer related bioinformatic resources, we have developed a comprehensive database (Dragon Database of Genes Implicated in Esophageal Cancer) with esophageal cancer related information, as an integrated knowledge database aimed at representing a gateway to esophageal cancer related data. Manually curated 529 genes differentially expressed in EC are contained in the database. We extracted and analyzed the promoter regions of these genes and complemented gene-related information with transcription factors that potentially control them. We further, precompiled text-mined and data-mined reports about each of these genes to allow for easy exploration of information about associations of EC-implicated genes with other human genes and proteins, metabolites and enzymes, toxins, chemicals with pharmacological effects, disease concepts and human anatomy. The resulting database, DDEC, has a useful feature to display potential associations that are rarely reported and thus difficult to identify. Moreover, DDEC enables inspection of potentially new 'association hypotheses' generated based on the precompiled reports. We hope that this resource will serve as a useful complement to the existing public resources and as a good starting point for researchers and physicians interested in EC genetics. DDEC is freely accessible to academic

Ebola Preparedness in the Netherlands: The Need for Coordination Between the Public Health and the Curative Sector.

Science.gov (United States)

Swaan, Corien M; Öry, Alexander V; Schol, Lianne G C; Jacobi, André; Richardus, Jan Hendrik; Timen, Aura

During the Ebola outbreak in West Africa in 2014-2015, close cooperation between the curative sector and the public health sector in the Netherlands was necessary for timely identification, referral, and investigation of patients with suspected Ebola virus disease (EVD). In this study, we evaluated experiences in preparedness among stakeholders of both curative and public health sectors to formulate recommendations for optimizing preparedness protocols. Timeliness of referred patients with suspected EVD was used as indicator for preparedness. In focus group sessions and semistructured interviews, experiences of curative and public health stakeholders about the regional and national process of preparedness and response were listed. Timeliness recordings of all referred patients with suspected EVD (13) were collected from first date of illness until arrival in the referral academic hospital. Ebola preparedness was considered extensive compared with the risk of an actual patient, however necessary. Regional coordination varied between regions. More standardization of regional preparation and operational guidelines was requested, as well as nationally standardized contingency criteria, and the National Centre for Infectious Disease Control was expected to coordinate the development of these guidelines. For the timeliness of referred patients with suspected EVD, the median delay between first date of illness until triage was 2.0 days (range: 0-10 days), and between triage and arrival in the referral hospital, it was 5.0 hours (range: 2-7.5 hours). In none of these patients Ebola infection was confirmed. Coordination between the public health sector and the curative sector needs improvement to reduce delay in patient management in emerging infectious diseases. Standardization of preparedness and response practices, through guidelines for institutional preparedness and blueprints for regional and national coordination, is necessary, as preparedness for emerging infectious

FmMDb: a versatile database of foxtail millet markers for millets and bioenergy grasses research.

Directory of Open Access Journals (Sweden)

Venkata Suresh B

Full Text Available The prominent attributes of foxtail millet (Setaria italica L. including its small genome size, short life cycle, inbreeding nature, and phylogenetic proximity to various biofuel crops have made this crop an excellent model system to investigate various aspects of architectural, evolutionary and physiological significances in Panicoid bioenergy grasses. After release of its whole genome sequence, large-scale genomic resources in terms of molecular markers were generated for the improvement of both foxtail millet and its related species. Hence it is now essential to congregate, curate and make available these genomic resources for the benefit of researchers and breeders working towards crop improvement. In view of this, we have constructed the Foxtail millet Marker Database (FmMDb; http://www.nipgr.res.in/foxtail.html, a comprehensive online database for information retrieval, visualization and management of large-scale marker datasets with unrestricted public access. FmMDb is the first database which provides complete marker information to the plant science community attempting to produce elite cultivars of millet and bioenergy grass species, thus addressing global food insecurity.

A theoretical and experimental study on solubility of curatives in rubbers

NARCIS (Netherlands)

Guo, R.; Talma, Auke; Datta, Rabin; Dierkes, Wilma K.; Noordermeer, Jacobus W.M.

2009-01-01

The current study provides indications for improving the properties of dissimilar rubber blends. As solubility is a key factor for the distribution and a driving force for the migration of curatives in dissimilar rubber blends, it is of importance to have precise data of their solubilities. The

A predictive model for swallowing dysfunction after curative radiotherapy in head and neck cancer

International Nuclear Information System (INIS)

Langendijk, Johannes A.; Doornaert, Patricia; Rietveld, Derek H.F.; Verdonck-de Leeuw, Irma M.; Rene Leemans, C.; Slotman, Ben J.

2009-01-01

Introduction: Recently, we found that swallowing dysfunction after curative (chemo) radiation (CH) RT has a strong negative impact on health-related quality of life (HRQoL), even more than xerostomia. The purpose of this study was to design a predictive model for swallowing dysfunction after curative radiotherapy or chemoradiation. Materials and methods: A prospective study was performed including 529 patients with head and neck squamous cell carcinoma (HNSCC) treated with curative (CH) RT. In all patients, acute and late radiation-induced morbidity (RTOG Acute and Late Morbidity Scoring System) was scored prospectively. To design the model univariate and multivariate logistic regression analyses were carried out with grade 2 or higher RTOG swallowing dysfunction at 6 months as the primary (SWALL 6months ) endpoint. The model was validated by comparing the predicted and observed complication rates and by testing if the model also predicted acute dysphagia and late dysphagia at later time points (12, 18 and 24 months). Results: After univariate and multivariate logistic regression analyses, the following factors turned out to be independent prognostic factors for SWALL 6months : T3-T4, bilateral neck irradiation, weight loss prior to radiation, oropharyngeal and nasopharyngeal tumours, accelerated radiotherapy and concomitant chemoradiation. By summation of the regression coefficients derived from the multivariate model, the Total Dysphagia Risk Score (TDRS) could be calculated. In the logistic regression model, the TDRS was significantly associated with SWALL 6months ((p 6months was 5%, 24% and 46% in case of low-, intermediate- and high-risk patients, respectively. These observed percentages were within the 95% confidence intervals of the predicted values. The TDRS risk group classification was also significantly associated with acute dysphagia (P < 0.001 at all time points) and with late swallowing dysfunction at 12, 18 and 24 months (p < 0.001 at all time points

The importance of community building for establishing data management and curation practices for physical samples

Science.gov (United States)

Ramdeen, S.; Hangsterfer, A.; Stanley, V. L.

2017-12-01

There is growing enthusiasm for curation of physical samples in the Earth Science community (see sessions at AGU, GSA, ESIP). Multiple federally funded efforts aim to develop best practices for curation of physical samples; however, these efforts have not yet been consolidated. Harmonizing these concurrent efforts would enable the community as a whole to build the necessary tools and community standards to move forward together. Preliminary research indicate the various groups focused on this topic are working in isolation, and the development of standards needs to come from the broadest view of `community'. We will investigate the gaps between communities by collecting information about preservation policies and practices from curators, who can provide a diverse cross-section of the grand challenges to the overall community. We will look at existing reports and study results to identify example cases, then develop a survey to gather large scale data to reinforce or clarify the example cases. We will be targeting the various community groups which are working on similar issues, and use the survey to improve the visibility of developed best practices. Given that preservation and digital collection management for physical samples are both important and difficult at present (GMRWG, 2015; NRC, 2002), barriers to both need to be addressed in order to achieve open science goals for the entire community. To address these challenges, EarthCube's iSamples, a research coordination network established to advance discoverability, access, and curation of physical samples using cyberinfrastructure, has formed a working group to collect use cases to examine the breadth of earth scientists' work with physical samples. This research team includes curators of state survey and oceanographic geological collections, and a researcher from information science. In our presentation, we will share our research and the design of the proposed survey. Our goal is to engage the audience in a

Searching Harvard Business Review Online. . . Lessons in Searching a Full Text Database.

Science.gov (United States)

Tenopir, Carol

1985-01-01

This article examines the Harvard Business Review Online (HBRO) database (bibliographic description fields, abstracts, extracted information, full text, subject descriptors) and reports on 31 sample HBRO searches conducted in Bibliographic Retrieval Services to test differences between searching full text and searching bibliographic record. Sample…

The immune epitope database (IEDB) 3.0

Science.gov (United States)

Vita, Randi; Overton, James A.; Greenbaum, Jason A.; Ponomarenko, Julia; Clark, Jason D.; Cantrell, Jason R.; Wheeler, Daniel K.; Gabbard, Joseph L.; Hix, Deborah; Sette, Alessandro; Peters, Bjoern

2015-01-01

The IEDB, www.iedb.org, contains information on immune epitopes—the molecular targets of adaptive immune responses—curated from the published literature and submitted by National Institutes of Health funded epitope discovery efforts. From 2004 to 2012 the IEDB curation of journal articles published since 1960 has caught up to the present day, with >95% of relevant published literature manually curated amounting to more than 15 000 journal articles and more than 704 000 experiments to date. The revised curation target since 2012 has been to make recent research findings quickly available in the IEDB and thereby ensure that it continues to be an up-to-date resource. Having gathered a comprehensive dataset in the IEDB, a complete redesign of the query and reporting interface has been performed in the IEDB 3.0 release to improve how end users can access this information in an intuitive and biologically accurate manner. We here present this most recent release of the IEDB and describe the user testing procedures as well as the use of external ontologies that have enabled it. PMID:25300482

Curation Pedagogy for Media Studies: (Further Towards the Inexpert

Directory of Open Access Journals (Sweden)

Ben Andrews

2012-12-01

Full Text Available An educational ‘model’ for participatory learning and media literacy in the contemporary context of digitally mediated lifeworlds is emerging (Jenkins, 2010; Gauntlett, 2011; Fraser and Wardle, 2011. The critical problem, we argue, for its ‘adequacy’ is the privilege granted to curriculum content and skills over pedagogy. Elsewhere, we offered a ‘pedagogy of the inexpert’ as such a model for textconscious disciplines such as, but not restricted to, Media Studies. This strategy removes ‘the media’ from our gaze and looks awry to develop new ways of working with students – to ‘show and tell’ textual agency and more reflexive deconstruction of what it is to read and make media, and to ‘be’ in mediation. In this article, we develop this approach further towards a model of ‘curation’. Understood in this way, students ‘show’ media literacy in new spaces – not by recourse to skills, competences or analytical unmasking of the properties of a (contained text, but by exhibiting, by curating a moment in time of textual meaningmaking and meaning-taking, but with a mindfulness – a critical acceptance of such an attempt to hold and curate the flow of meaning as an artifice.

Curating Research: e-Merging New Roles and Responsibilities in the European Landscape (Conference Report

Directory of Open Access Journals (Sweden)

Inge Angevaare

2009-11-01

Full Text Available On 17 April 2009 LIBER, the Koninklijke Bibliotheek (KB and the Netherlands Coalition for Digital Preservation (NCDD co-organised LIBER’s first workshop on digital curation/preservation, providing an introduction to the theme of digital curation and different perspectives on the roles research libraries can and/or must play in keeping the digital records of science safe for future generations. Speakers included Eileen Fenton (Portico, Dale Peters (DRIVER, Maria Heijne (TU Delft Library, Jeffrey van der Hoeven (KB, PARSE.insight and ninety workshop attendees. The paper includes the conference report and some results of the PARSE.insight online survey into digital preservation practices of LIBER libraries.

Strict follow-up programme including CT and (18) F-FDG-PET after curative surgery for colorectal cancer

DEFF Research Database (Denmark)

Sørensen, N F; Jensen, A B; Wille-Jørgensen, P

2010-01-01

Aim The risk of local recurrence following curative surgery for colorectal cancer (CRC) is up to 50%. A rigorous follow-up program may increase survival. Guidelines on suitable methods for scheduled follow up examinations are needed. This study evaluates a strict follow-up program including...... supported a strict follow-up program following curative surgery for colorectal cancer. FDG-PET combined with CT should be included in control programs....

ExtraTrain: a database of Extragenic regions and Transcriptional information in prokaryotic organisms

Science.gov (United States)

Pareja, Eduardo; Pareja-Tobes, Pablo; Manrique, Marina; Pareja-Tobes, Eduardo; Bonal, Javier; Tobes, Raquel

2006-01-01

Background Transcriptional regulation processes are the principal mechanisms of adaptation in prokaryotes. In these processes, the regulatory proteins and the regulatory DNA signals located in extragenic regions are the key elements involved. As all extragenic spaces are putative regulatory regions, ExtraTrain covers all extragenic regions of available genomes and regulatory proteins from bacteria and archaea included in the UniProt database. Description ExtraTrain provides integrated and easily manageable information for 679816 extragenic regions and for the genes delimiting each of them. In addition ExtraTrain supplies a tool to explore extragenic regions, named Palinsight, oriented to detect and search palindromic patterns. This interactive visual tool is totally integrated in the database, allowing the search for regulatory signals in user defined sets of extragenic regions. The 26046 regulatory proteins included in ExtraTrain belong to the families AraC/XylS, ArsR, AsnC, Cold shock domain, CRP-FNR, DeoR, GntR, IclR, LacI, LuxR, LysR, MarR, MerR, NtrC/Fis, OmpR and TetR. The database follows the InterPro criteria to define these families. The information about regulators includes manually curated sets of references specifically associated to regulator entries. In order to achieve a sustainable and maintainable knowledge database ExtraTrain is a platform open to the contribution of knowledge by the scientific community providing a system for the incorporation of textual knowledge. Conclusion ExtraTrain is a new database for exploring Extragenic regions and Transcriptional information in bacteria and archaea. ExtraTrain database is available at . PMID:16539733

FJET Database Project: Extract, Transform, and Load

Science.gov (United States)

Samms, Kevin O.

2015-01-01

The Data Mining & Knowledge Management team at Kennedy Space Center is providing data management services to the Frangible Joint Empirical Test (FJET) project at Langley Research Center (LARC). FJET is a project under the NASA Engineering and Safety Center (NESC). The purpose of FJET is to conduct an assessment of mild detonating fuse (MDF) frangible joints (FJs) for human spacecraft separation tasks in support of the NASA Commercial Crew Program. The Data Mining & Knowledge Management team has been tasked with creating and managing a database for the efficient storage and retrieval of FJET test data. This paper details the Extract, Transform, and Load (ETL) process as it is related to gathering FJET test data into a Microsoft SQL relational database, and making that data available to the data users. Lessons learned, procedures implemented, and programming code samples are discussed to help detail the learning experienced as the Data Mining & Knowledge Management team adapted to changing requirements and new technology while maintaining flexibility of design in various aspects of the data management project.

Improving Access to NASA Earth Science Data through Collaborative Metadata Curation

Science.gov (United States)

Sisco, A. W.; Bugbee, K.; Shum, D.; Baynes, K.; Dixon, V.; Ramachandran, R.

2017-12-01

The NASA-developed Common Metadata Repository (CMR) is a high-performance metadata system that currently catalogs over 375 million Earth science metadata records. It serves as the authoritative metadata management system of NASA's Earth Observing System Data and Information System (EOSDIS), enabling NASA Earth science data to be discovered and accessed by a worldwide user community. The size of the EOSDIS data archive is steadily increasing, and the ability to manage and query this archive depends on the input of high quality metadata to the CMR. Metadata that does not provide adequate descriptive information diminishes the CMR's ability to effectively find and serve data to users. To address this issue, an innovative and collaborative review process is underway to systematically improve the completeness, consistency, and accuracy of metadata for approximately 7,000 data sets archived by NASA's twelve EOSDIS data centers, or Distributed Active Archive Centers (DAACs). The process involves automated and manual metadata assessment of both collection and granule records by a team of Earth science data specialists at NASA Marshall Space Flight Center. The team communicates results to DAAC personnel, who then make revisions and reingest improved metadata into the CMR. Implementation of this process relies on a network of interdisciplinary collaborators leveraging a variety of communication platforms and long-range planning strategies. Curating metadata at this scale and resolving metadata issues through community consensus improves the CMR's ability to serve current and future users and also introduces best practices for stewarding the next generation of Earth Observing System data. This presentation will detail the metadata curation process, its outcomes thus far, and also share the status of ongoing curation activities.

Improved Functionality and Curation Support in the ADS

Science.gov (United States)

Accomazzi, Alberto; Kurtz, Michael J.; Henneken, Edwin A.; Grant, Carolyn S.; Thompson, Donna; Chyla, Roman; Holachek, Alexandra; Sudilovsky, Vladimir; Murray, Stephen S.

2015-01-01

In this poster we describe the developments of the new ADS platform over the past year, focusing on the functionality which improves its discovery and curation capabilities.The ADS Application Programming Interface (API) is being updated to support authenticated access to the entire suite of ADS services, in addition to the search functionality itself. This allows programmatic access to resources which are specific to a user or class of users.A new interface, built directly on top of the API, now provides a more intuitive search experience and takes into account the best practices in web usability and responsive design. The interface now incorporates in-line views of graphics from the AAS Astroexplorer and the ADS All-Sky Survey image collections.The ADS Private Libraries, first introduced over 10 years ago, are now being enhanced to allow the bookmarking, tagging and annotation of records of interest. In addition, libraries can be shared with one or more ADS users, providing an easy way to collaborate in the curation of lists of papers. A library can also be explicitly made public and shared at large via the publishing of its URL.In collaboration with the AAS, the ADS plans to support the adoption of ORCID identifiers by implementing a plugin which will simplify the import of papers in ORCID via a query to the ADS API. Deeper integration between the two systems will depend on available resources and feedback from the community.

The Pathogen-Host Interactions database (PHI-base): additions and future developments.

Science.gov (United States)

Urban, Martin; Pant, Rashmi; Raghunath, Arathi; Irvine, Alistair G; Pedro, Helder; Hammond-Kosack, Kim E

2015-01-01

Rapidly evolving pathogens cause a diverse array of diseases and epidemics that threaten crop yield, food security as well as human, animal and ecosystem health. To combat infection greater comparative knowledge is required on the pathogenic process in multiple species. The Pathogen-Host Interactions database (PHI-base) catalogues experimentally verified pathogenicity, virulence and effector genes from bacterial, fungal and protist pathogens. Mutant phenotypes are associated with gene information. The included pathogens infect a wide range of hosts including humans, animals, plants, insects, fish and other fungi. The current version, PHI-base 3.6, available at http://www.phi-base.org, stores information on 2875 genes, 4102 interactions, 110 host species, 160 pathogenic species (103 plant, 3 fungal and 54 animal infecting species) and 181 diseases drawn from 1243 references. Phenotypic and gene function information has been obtained by manual curation of the peer-reviewed literature. A controlled vocabulary consisting of nine high-level phenotype terms permits comparisons and data analysis across the taxonomic space. PHI-base phenotypes were mapped via their associated gene information to reference genomes available in Ensembl Genomes. Virulence genes and hotspots can be visualized directly in genome browsers. Future plans for PHI-base include development of tools facilitating community-led curation and inclusion of the corresponding host target(s). © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

The observation of curative effects by therapy with low-dose 131I in younger with Graves' disease

International Nuclear Information System (INIS)

Cui Liqun; Li Lingling; Zhang Chenggang

2007-01-01

Objective: To observe the the curative effects in younger with Graves disease therapied by 131 I. Methods: The dose of 131 I is administrated with 1480-2220kBq/g of thyroid tissue which was decided by many factors that include the paticnt's Age, volume of thyroid, course and if antihyroid drug is administrated. The curative effects was classfide into four groups: complete remission, excellence, parts of remission, no effect. Results: 47 were complete remission, 34 were excellence, 10 were the parts of remission and 0 was no effects. The total effective power was 100%. Conclusions: Therapy with low-dose of mi for younger with Graves' disease is an effect, simple and safe method. Repeating treatment with 131 I will improve the curative rate of Graves' disease in younger, and the incidence of hypothyroidism cannot be increased. (authors)

Intelligent databases assist transparent and sound economic valuation of ecosystem services.

Science.gov (United States)

Villa, Ferdinando; Ceroni, Marta; Krivov, Sergey

2007-06-01

Assessment and economic valuation of services provided by ecosystems to humans has become a crucial phase in environmental management and policy-making. As primary valuation studies are out of the reach of many institutions, secondary valuation or benefit transfer, where the results of previous studies are transferred to the geographical, environmental, social, and economic context of interest, is becoming increasingly common. This has brought to light the importance of environmental valuation databases, which provide reliable valuation data to inform secondary valuation with enough detail to enable the transfer of values across contexts. This paper describes the role of next-generation, intelligent databases (IDBs) in assisting the activity of valuation. Such databases employ artificial intelligence to inform the transfer of values across contexts, enforcing comparability of values and allowing users to generate custom valuation portfolios that synthesize previous studies and provide aggregated value estimates to use as a base for secondary valuation. After a general introduction, we introduce the Ecosystem Services Database, the first IDB for environmental valuation to be made available to the public, describe its functionalities and the lessons learned from its usage, and outline the remaining needs and expected future developments in the field.

Harmonizing Access to Federal Data - Lessons Learned Through the Climate Data Initiative

Science.gov (United States)

Bugbee, K.; Pinheiro Privette, A. C.; Meyer, D. J.; Ramachandran, R.

2016-12-01

The Climate Data Initiative (CDI), launched by the Obama Administration in March of 2014, is an effort to leverage the extensive open Federal data to spur innovation and private-sector entrepreneurship in order to advance awareness of and preparedness for the impacts of climate change (see the White House fact sheet). The project includes an online catalog of climate-related datasets and data products in key areas of climate change risk and vulnerability from across the U.S. federal government through http://Climate.Data.gov. NASA was tasked with the implementation and management of the project and has been working closely with Subject Matter Experts (SMEs) and Data Curators (DCs) from across the Federal Government to identify and catalog federal datasets relevant for assessing climate risks and impacts. These datasets are organized around key themes and are framed by key climate questions. The current themes within CDI include: Arctic, Coastal Flooding, Ecosystem Vulnerability, Energy Infrastructure, Food Resilience, Human Health, Transportation, Tribal Nations and Water. This paper summarizes the main lessons learned from the last 2.5 years of CDI implementation.

Experience and Lessons learnt from running High Availability Databases on Network Attached Storage

CERN Document Server

Guijarro, Manuel

2008-01-01

The Database and Engineering Services Group of CERN's Information Technology Department supplies the Oracle Central Database services used in many activities at CERN. In order to provide High Availability and ease management for those services, a NAS (Network Attached Storage) based infrastructure has been setup. It runs several instances of the Oracle RAC (Real Application Cluster) using NFS (Network File System) as shared disk space for RAC purposes and Data hosting. It is composed of two private LANs (Local Area Network), one to provide access to the NAS filers and a second to implement the Oracle RAC private interconnect, both using Network Bonding. NAS filers are configured in partnership to prevent having single points of failure and to provide automatic NAS filer fail-over.

Experience and lessons learnt from running high availability databases on network attached storage

International Nuclear Information System (INIS)

Guijarro, M; Gaspar, R

2008-01-01

The Database and Engineering Services Group of CERN's Information Technology Department supplies the Oracle Central Database services used in many activities at CERN. In order to provide High Availability and ease management for those services, a NAS (Network Attached Storage) based infrastructure has been setup. It runs several instances of the Oracle RAC (Real Application Cluster) using NFS (Network File System) as shared disk space for RAC purposes and Data hosting. It is composed of two private LANs (Local Area Network), one to provide access to the NAS filers and a second to implement the Oracle RAC private interconnect, both using Network Bonding. NAS filers are configured in partnership to prevent having single points of failure and to provide automatic NAS filer fail-over

Locally Advanced Rectal Carcinoma: Curative Surgery Alone vs. postoperative Radiotherapy and Chemotherapy

International Nuclear Information System (INIS)

Ahn, Seung Do; Choi, Eun Kyung; Kim, Jin Cheon; Kim, Sang Hee

1995-01-01

Purpose : To evaluate the effects of postoperative radiotherapy and chemotherapy on the pattern of failure and survival for locally advanced rectal carcinoma, we analyzed the two groups of patients who received curative resection only and who received postoperative radiochemotherapy retrospectively. Materials and Methods : From June 1989 to December 1992, ninety nine patients with rectal cancer were treated by curative resection and staged as B2-3 or C. Group I(25) patients received curative resection only and group II(74) patients postoperative adjuvant therapy. Postoperative adjuvant group received radiation therapy (4500 cGy/ 25fx to whole pelvis)with 5-FU (500 mg/m 2 , day 1-3 IV infusion) as radiosensitizer and maintenance chemotherapy with 5-FU(400mg/m 2 for 5 days) and leucovorin (20mg/m 2 for 5 days) for 6 cycles. Results : The patients in group I and group II were comparable in terms of age, sex, performance status, but in group II 74% of patients showed stage C compared with 56% of group I. All patients were flowed from 6 to 60 months with a median follow up of 29 months. Three year overall survival rates and disease free survival rates were 68%, 64% respectively in group I and 64%, 61%, respectively in group II. There was no statistical difference between the two treatment groups in overall survival rate and disease free survival rate. Local recurrences occurred in 28% of group I, 21% of group II (p>.05) and distant metastases occurred in 20% of group I, 27% of group II(p>.05). The prognostic value of several variables other that treatment modality was assessed. In multivariate analysis for prognostic factors stage and histologic grade showed statistically significant effect on local recurrences, and lymphatic or vessel invasion on distant metastasis. Conclusion : This retrospective study showed no statistical difference between two groups on the pattern of failure and survival. But considering that group II had more advanced stage and poor prognostic

Human transporter database: comprehensive knowledge and discovery tools in the human transporter genes.

Directory of Open Access Journals (Sweden)

Adam Y Ye

Full Text Available Transporters are essential in homeostatic exchange of endogenous and exogenous substances at the systematic, organic, cellular, and subcellular levels. Gene mutations of transporters are often related to pharmacogenetics traits. Recent developments in high throughput technologies on genomics, transcriptomics and proteomics allow in depth studies of transporter genes in normal cellular processes and diverse disease conditions. The flood of high throughput data have resulted in urgent need for an updated knowledgebase with curated, organized, and annotated human transporters in an easily accessible way. Using a pipeline with the combination of automated keywords query, sequence similarity search and manual curation on transporters, we collected 1,555 human non-redundant transporter genes to develop the Human Transporter Database (HTD (http://htd.cbi.pku.edu.cn. Based on the extensive annotations, global properties of the transporter genes were illustrated, such as expression patterns and polymorphisms in relationships with their ligands. We noted that the human transporters were enriched in many fundamental biological processes such as oxidative phosphorylation and cardiac muscle contraction, and significantly associated with Mendelian and complex diseases such as epilepsy and sudden infant death syndrome. Overall, HTD provides a well-organized interface to facilitate research communities to search detailed molecular and genetic information of transporters for development of personalized medicine.

Uptake of [3H]PAH and [14C]urate into isolated proximal tubular segments of the pig kidney

International Nuclear Information System (INIS)

Schali, C.; Roch-Ramel, F.

1981-01-01

Segments of proximal convoluted (PCT) and proximal straight (PST) tubules of minipigs and normal-sized pigs were microdissected (without collagenase treatment) and incubated (30 min, 37 0 C, pH 7.4) in Ringer solution (under O 2 ) containing [ 3 H]PAH (3.10 -5 M) or [ 14 C]urate (9.10 -5 M) and, in inhibitor studies, probenecid, pyrazinoic acid (PZA), urate, or PAH, all at 1 mM. In both strains the uptake of [ 3 H]PAH expressed as mean T/M ratio (cpm per ml tissue water/cpm per ml incubation medium) was significantly higher (P 14 C]urate. In eight minipigs the T/M was 4.9 +/- 0.5 in 24 PCT and 2 +/- 0.2 in 25 PST. In normal-sized pigs the T/M was 3.8 +/- 0.3 in 35 PCT (five pigs) and 1.9 +/- 0.4 in eight PST (two pigs). In inhibitor studies urate significantly depressed the uptake of [ 3 H]PAH, and unlabeled PAH depressed the uptake of [ 14 C]urate. PZA significantly inhibited the uptake of [ 14 C]urate but not that of [ 3 H]PAH, whereas probenecid had a strong inhibitory efect on the uptake of both compounds. These results suggest that [ 14 C]urate and [ 3 H]PAH are transported by a transport system located mainly in the proximal convoluted tubule. These findings are in contrast in the findings are in contrast to the findings obtained in rabbits in which the transport system of PAH and urate is mainly located in the proximal part of the pars recta

Angiosarcoma of the scalp treated with curative radiotherapy plus recombinant interleukin-2 immunotherapy

International Nuclear Information System (INIS)

Ohguri, Takayuki; Imada, Hajime; Nomoto, Satoshi; Yahara, Katsuya; Hisaoka, Masanori; Hashimoto, Hiroshi; Tokura, Yoshiki; Nakamura, Katsumasa; Shioyama, Yoshiyuki; Honda, Hiroshi; Terashima, Hiromi; Moroi, Yoiichi; Furue, Masutaka; Korogi, Yukunori

2005-01-01

Purpose: To evaluate the effectiveness of curative radiotherapy (RT) plus recombinant interleukin-2 (rIL-2) immunotherapy regarding the treatment results for angiosarcoma of the scalp. Curative resection of angiosarcoma of the scalp is usually difficult because of the diffuse, clinically undetectable local spread. RT is a rational therapeutic approach, because a wide region of the dermis can be treated, while sparing the underlying normal tissues. Recently, the effectiveness of immunotherapy with rIL-2 has also been reported in the treatment of angiosarcoma of the scalp. Methods and Materials: The data of 20 patients with angiosarcoma of the scalp treated with curative RT plus rIL-2 immunotherapy between January 1988 and June 2002 were retrospectively analyzed. The total radiation dose was 70.3 ± 6.9 Gy. The fractions were 2-3 Gy daily, given 5 d/wk. rIL-2 immunotherapy was performed by transcatheter arterial administration in 10 patients, systemic administration in 11 during the course of RT, and intratumoral injection in 10 during and/or after RT; 12 patients received a combination of two. Five patients underwent limited surgery, and concomitant pacilitaxel chemotherapy was also used in 2 patients. Results: The median survival time for overall, local recurrence-free, and distant metastasis-free survival was 36.2, 11.1, and 17.8 months, respectively. Local recurrence developed in 7 patients (35%), 4 of whom also had evidence of distant metastases. An additional 7 patients (35%) developed distant metastases alone. Recurrence within the radiation field was recognized in 2 patients with systemic rIL-2 administration alone (p < 0.05). Arterial or intratumoral administration combined with systemic administration of rIL-2 resulted in better distant metaststasis-free survival rates (p < 0.05). Conclusion: Curative RT plus rIL-2 immunotherapy provided an efficient, effective means of treating angiosarcoma of the scalp. Arterial or intratumoral administration combined

When a Patient Declines Curative Care: Management of a Ruptured Aortic Aneurysm

Directory of Open Access Journals (Sweden)

Sangeeta Lamba

2013-09-01

Full Text Available The management of major vascular emergencies in the emergency department (ED involves rapid, aggressive resuscitation followed by emergent definitive surgery. However, for some patients this traditional approach may not be consistent with their goals and values. We explore the appropriate way to determine best treatment practices when patients elect to forego curative care in the ED, while reviewing such a case. We present the case of a 72-year-old patient who presented to the ED with a ruptured abdominal aortic aneurysm, but refused surgery. We discuss the transition of the patient from a curative to a comfort care approach with appropriate direct referral to hospice from the ED. Using principles of autonomy, decision-making capacity, informed consent, prognostication, and goals-of-care, ED clinicians are best able to align their approach with patients’ goals and values. [West J Emerg Med. 2013;14(5:555–558.

User-generated content curation with deep convolutional neural networks

OpenAIRE

Tous Liesa, Rubén; Wust, Otto; Gómez, Mauro; Poveda, Jonatan; Elena, Marc; Torres Viñals, Jordi; Makni, Mouna; Ayguadé Parra, Eduard

2016-01-01

In this paper, we report a work consisting in using deep convolutional neural networks (CNNs) for curating and filtering photos posted by social media users (Instagram and Twitter). The final goal is to facilitate searching and discovering user-generated content (UGC) with potential value for digital marketing tasks. The images are captured in real time and automatically annotated with multiple CNNs. Some of the CNNs perform generic object recognition tasks while others perform what we call v...

Interacting with the National Database for Autism Research (NDAR) via the LONI Pipeline workflow environment.

Science.gov (United States)

Torgerson, Carinna M; Quinn, Catherine; Dinov, Ivo; Liu, Zhizhong; Petrosyan, Petros; Pelphrey, Kevin; Haselgrove, Christian; Kennedy, David N; Toga, Arthur W; Van Horn, John Darrell

2015-03-01

Under the umbrella of the National Database for Clinical Trials (NDCT) related to mental illnesses, the National Database for Autism Research (NDAR) seeks to gather, curate, and make openly available neuroimaging data from NIH-funded studies of autism spectrum disorder (ASD). NDAR has recently made its database accessible through the LONI Pipeline workflow design and execution environment to enable large-scale analyses of cortical architecture and function via local, cluster, or "cloud"-based computing resources. This presents a unique opportunity to overcome many of the customary limitations to fostering biomedical neuroimaging as a science of discovery. Providing open access to primary neuroimaging data, workflow methods, and high-performance computing will increase uniformity in data collection protocols, encourage greater reliability of published data, results replication, and broaden the range of researchers now able to perform larger studies than ever before. To illustrate the use of NDAR and LONI Pipeline for performing several commonly performed neuroimaging processing steps and analyses, this paper presents example workflows useful for ASD neuroimaging researchers seeking to begin using this valuable combination of online data and computational resources. We discuss the utility of such database and workflow processing interactivity as a motivation for the sharing of additional primary data in ASD research and elsewhere.

Human Ageing Genomic Resources: Integrated databases and tools for the biology and genetics of ageing

Science.gov (United States)

Tacutu, Robi; Craig, Thomas; Budovsky, Arie; Wuttke, Daniel; Lehmann, Gilad; Taranukha, Dmitri; Costa, Joana; Fraifeld, Vadim E.; de Magalhães, João Pedro

2013-01-01

The Human Ageing Genomic Resources (HAGR, http://genomics.senescence.info) is a freely available online collection of research databases and tools for the biology and genetics of ageing. HAGR features now several databases with high-quality manually curated data: (i) GenAge, a database of genes associated with ageing in humans and model organisms; (ii) AnAge, an extensive collection of longevity records and complementary traits for >4000 vertebrate species; and (iii) GenDR, a newly incorporated database, containing both gene mutations that interfere with dietary restriction-mediated lifespan extension and consistent gene expression changes induced by dietary restriction. Since its creation about 10 years ago, major efforts have been undertaken to maintain the quality of data in HAGR, while further continuing to develop, improve and extend it. This article briefly describes the content of HAGR and details the major updates since its previous publications, in terms of both structure and content. The completely redesigned interface, more intuitive and more integrative of HAGR resources, is also presented. Altogether, we hope that through its improvements, the current version of HAGR will continue to provide users with the most comprehensive and accessible resources available today in the field of biogerontology. PMID:23193293

mirPub: a database for searching microRNA publications.

Science.gov (United States)

Vergoulis, Thanasis; Kanellos, Ilias; Kostoulas, Nikos; Georgakilas, Georgios; Sellis, Timos; Hatzigeorgiou, Artemis; Dalamagas, Theodore

2015-05-01

Identifying, amongst millions of publications available in MEDLINE, those that are relevant to specific microRNAs (miRNAs) of interest based on keyword search faces major obstacles. References to miRNA names in the literature often deviate from standard nomenclature for various reasons, since even the official nomenclature evolves. For instance, a single miRNA name may identify two completely different molecules or two different names may refer to the same molecule. mirPub is a database with a powerful and intuitive interface, which facilitates searching for miRNA literature, addressing the aforementioned issues. To provide effective search services, mirPub applies text mining techniques on MEDLINE, integrates data from several curated databases and exploits data from its user community following a crowdsourcing approach. Other key features include an interactive visualization service that illustrates intuitively the evolution of miRNA data, tag clouds summarizing the relevance of publications to particular diseases, cell types or tissues and access to TarBase 6.0 data to oversee genes related to miRNA publications. mirPub is freely available at http://www.microrna.gr/mirpub/. vergoulis@imis.athena-innovation.gr or dalamag@imis.athena-innovation.gr Supplementary data are available at Bioinformatics online. © The Author 2014. Published by Oxford University Press.

Long Duration Exposure Facility (LDEF) optical systems SIG summary and database

Science.gov (United States)

Bohnhoff-Hlavacek, Gail

1992-01-01

The main objectives of the Long Duration Exposure Facility (LDEF) Optical Systems Special Investigative Group (SIG) Discipline are to develop a database of experimental findings on LDEF optical systems and elements hardware, and provide an optical system overview. Unlike the electrical and mechanical disciplines, the optics effort relies primarily on the testing of hardware at the various principal investigator's laboratories, since minimal testing of optical hardware was done at Boeing. This is because all space-exposed optics hardware are part of other individual experiments. At this time, all optical systems and elements testing by experiment investigator teams is not complete, and in some cases has hardly begun. Most experiment results to date, document observations and measurements that 'show what happened'. Still to come from many principal investigators is a critical analysis to explain 'why it happened' and future design implications. The original optical system related concerns and the lessons learned at a preliminary stage in the Optical Systems Investigations are summarized. The design of the Optical Experiments Database and how to acquire and use the database to review the LDEF results are described.

Long Duration Exposure Facility (LDEF) optical systems SIG summary and database

Science.gov (United States)

Bohnhoff-Hlavacek, Gail

1992-09-01

The main objectives of the Long Duration Exposure Facility (LDEF) Optical Systems Special Investigative Group (SIG) Discipline are to develop a database of experimental findings on LDEF optical systems and elements hardware, and provide an optical system overview. Unlike the electrical and mechanical disciplines, the optics effort relies primarily on the testing of hardware at the various principal investigator's laboratories, since minimal testing of optical hardware was done at Boeing. This is because all space-exposed optics hardware are part of other individual experiments. At this time, all optical systems and elements testing by experiment investigator teams is not complete, and in some cases has hardly begun. Most experiment results to date, document observations and measurements that 'show what happened'. Still to come from many principal investigators is a critical analysis to explain 'why it happened' and future design implications. The original optical system related concerns and the lessons learned at a preliminary stage in the Optical Systems Investigations are summarized. The design of the Optical Experiments Database and how to acquire and use the database to review the LDEF results are described.

Comprehensive analysis of the N-glycan biosynthetic pathway using bioinformatics to generate UniCorn: A theoretical N-glycan structure database.

Science.gov (United States)

Akune, Yukie; Lin, Chi-Hung; Abrahams, Jodie L; Zhang, Jingyu; Packer, Nicolle H; Aoki-Kinoshita, Kiyoko F; Campbell, Matthew P

2016-08-05

Glycan structures attached to proteins are comprised of diverse monosaccharide sequences and linkages that are produced from precursor nucleotide-sugars by a series of glycosyltransferases. Databases of these structures are an essential resource for the interpretation of analytical data and the development of bioinformatics tools. However, with no template to predict what structures are possible the human glycan structure databases are incomplete and rely heavily on the curation of published, experimentally determined, glycan structure data. In this work, a library of 45 human glycosyltransferases was used to generate a theoretical database of N-glycan structures comprised of 15 or less monosaccharide residues. Enzyme specificities were sourced from major online databases including Kyoto Encyclopedia of Genes and Genomes (KEGG) Glycan, Consortium for Functional Glycomics (CFG), Carbohydrate-Active enZymes (CAZy), GlycoGene DataBase (GGDB) and BRENDA. Based on the known activities, more than 1.1 million theoretical structures and 4.7 million synthetic reactions were generated and stored in our database called UniCorn. Furthermore, we analyzed the differences between the predicted glycan structures in UniCorn and those contained in UniCarbKB (www.unicarbkb.org), a database which stores experimentally described glycan structures reported in the literature, and demonstrate that UniCorn can be used to aid in the assignment of ambiguous structures whilst also serving as a discovery database. Copyright © 2016 Elsevier Ltd. All rights reserved.

A Lesson about the Circular Flow. Active Learning Lessons. Economics International.

Science.gov (United States)

Landfried, Janet

This lesson plan was developed through "Economics International," an international program to help build economic education infrastructures in the emerging market economies. It provides a lesson description; appropriate grade level; economic concepts; content standards and benchmarks; related subjects; instructional objectives; time…

An Intelligent Web Digital Image Metadata Service Platform for Social Curation Commerce Environment

Directory of Open Access Journals (Sweden)

Seong-Yong Hong

2015-01-01

Full Text Available Information management includes multimedia data management, knowledge management, collaboration, and agents, all of which are supporting technologies for XML. XML technologies have an impact on multimedia databases as well as collaborative technologies and knowledge management. That is, e-commerce documents are encoded in XML and are gaining much popularity for business-to-business or business-to-consumer transactions. Recently, the internet sites, such as e-commerce sites and shopping mall sites, deal with a lot of image and multimedia information. This paper proposes an intelligent web digital image information retrieval platform, which adopts XML technology for social curation commerce environment. To support object-based content retrieval on product catalog images containing multiple objects, we describe multilevel metadata structures representing the local features, global features, and semantics of image data. To enable semantic-based and content-based retrieval on such image data, we design an XML-Schema for the proposed metadata. We also describe how to automatically transform the retrieval results into the forms suitable for the various user environments, such as web browser or mobile device, using XSLT. The proposed scheme can be utilized to enable efficient e-catalog metadata sharing between systems, and it will contribute to the improvement of the retrieval correctness and the user’s satisfaction on semantic-based web digital image information retrieval.

Tools and Databases of the KOMICS Web Portal for Preprocessing, Mining, and Dissemination of Metabolomics Data

Directory of Open Access Journals (Sweden)

Nozomu Sakurai

2014-01-01

Full Text Available A metabolome—the collection of comprehensive quantitative data on metabolites in an organism—has been increasingly utilized for applications such as data-intensive systems biology, disease diagnostics, biomarker discovery, and assessment of food quality. A considerable number of tools and databases have been developed to date for the analysis of data generated by various combinations of chromatography and mass spectrometry. We report here a web portal named KOMICS (The Kazusa Metabolomics Portal, where the tools and databases that we developed are available for free to academic users. KOMICS includes the tools and databases for preprocessing, mining, visualization, and publication of metabolomics data. Improvements in the annotation of unknown metabolites and dissemination of comprehensive metabolomic data are the primary aims behind the development of this portal. For this purpose, PowerGet and FragmentAlign include a manual curation function for the results of metabolite feature alignments. A metadata-specific wiki-based database, Metabolonote, functions as a hub of web resources related to the submitters' work. This feature is expected to increase citation of the submitters' work, thereby promoting data publication. As an example of the practical use of KOMICS, a workflow for a study on Jatropha curcas is presented. The tools and databases available at KOMICS should contribute to enhanced production, interpretation, and utilization of metabolomic Big Data.

Tools and databases of the KOMICS web portal for preprocessing, mining, and dissemination of metabolomics data.

Science.gov (United States)

Sakurai, Nozomu; Ara, Takeshi; Enomoto, Mitsuo; Motegi, Takeshi; Morishita, Yoshihiko; Kurabayashi, Atsushi; Iijima, Yoko; Ogata, Yoshiyuki; Nakajima, Daisuke; Suzuki, Hideyuki; Shibata, Daisuke

2014-01-01

A metabolome--the collection of comprehensive quantitative data on metabolites in an organism--has been increasingly utilized for applications such as data-intensive systems biology, disease diagnostics, biomarker discovery, and assessment of food quality. A considerable number of tools and databases have been developed to date for the analysis of data generated by various combinations of chromatography and mass spectrometry. We report here a web portal named KOMICS (The Kazusa Metabolomics Portal), where the tools and databases that we developed are available for free to academic users. KOMICS includes the tools and databases for preprocessing, mining, visualization, and publication of metabolomics data. Improvements in the annotation of unknown metabolites and dissemination of comprehensive metabolomic data are the primary aims behind the development of this portal. For this purpose, PowerGet and FragmentAlign include a manual curation function for the results of metabolite feature alignments. A metadata-specific wiki-based database, Metabolonote, functions as a hub of web resources related to the submitters' work. This feature is expected to increase citation of the submitters' work, thereby promoting data publication. As an example of the practical use of KOMICS, a workflow for a study on Jatropha curcas is presented. The tools and databases available at KOMICS should contribute to enhanced production, interpretation, and utilization of metabolomic Big Data.

Experience of introducing a new database for an approved coordination and record keeping service

International Nuclear Information System (INIS)

Garratt, N. J.

2011-01-01

The Health Protection Agency (and its predecessors) has many years experience of running Approved Dosimetry Services, including coordination and record keeping. This paper describes the experiences gained whilst introducing a new web-based system for coordination and record keeping to replace the ageing mainframe database. This includes the planning of the project, the migration of the data between the two systems, parallel running of all the operational tasks and lessons learned during the process. (authors)

Long-term results of curative intraluminal high dose rate brachytherapy for endobronchial carcinoma

Directory of Open Access Journals (Sweden)

Kawamura Hidemasa

2012-07-01

Full Text Available Abstract Background The treatment strategy of central lung tumors is not established. Intraluminal brachytherapy (ILBT is widely used for palliative treatment of endobronchial tumors, however, it is also a promising option for curative treatment with limited data. This study evaluates the results after ILBT for endobronchial carcinoma. Method Sixteen-endobronchial carcinoma of 13 patients treated with ILBT in curative intent for 2000 to 2008 were retrospectively reviewed. ILBT using high dose rate 192 iridium thin wire system was performed with 5 Gy/fraction at mucosal surface. The patient age ranged from 57 to 82 years old with median 75 years old. The 16 lesions consisted of 13 central endobronchial cancers including 7 roentgenographically occult lung cancers and 3 of tracheal cancers. Of them, 10 lesions were treated with ILBT of median 20 Gy combined with external beam radiation therapy of median 45 Gy and 6 lesions were treated with ILBT alone of median 25 Gy. Results Median follow-up time was 32.5 months. Two-year survival rate and local control rate were 92.3% and 86.2%, respectively. Local recurrences were observed in 2 lesions. Three patients died due to lung cancer (1 patient and intercurrent disease (2 patients. Complications greater than grade 2 were not observed except for one grade 3 dyspnea. Conclusions ILBT combined with or without EBRT might be a curative treatment option in inoperable endobronchial carcinoma patients with tolerable complication.

Classroom Management and Lesson Planning(4)

Institute of Scientific and Technical Information of China (English)

2006-01-01

Lesson PlanningTask 1As teachers,we all need to plan our lessons before we teach.Make a list of things that you think need tobe included in a lesson plan.Then compare and discuss your list with another teacher.Also think about reasonswhy we need to plan our lessons.

Data management and database framework for the MICE experiment

Science.gov (United States)

Martyniak, J.; Nebrensky, J. J.; Rajaram, D.; MICE Collaboration

2017-10-01

The international Muon Ionization Cooling Experiment (MICE) currently operating at the Rutherford Appleton Laboratory in the UK, is designed to demonstrate the principle of muon ionization cooling for application to a future Neutrino Factory or Muon Collider. We present the status of the framework for the movement and curation of both raw and reconstructed data. A raw data-mover has been designed to safely upload data files onto permanent tape storage as soon as they have been written out. The process has been automated, and checks have been built in to ensure the integrity of data at every stage of the transfer. The data processing framework has been recently redesigned in order to provide fast turnaround of reconstructed data for analysis. The automated reconstruction is performed on a dedicated machine in the MICE control room and any reprocessing is done at Tier-2 Grid sites. In conjunction with this redesign, a new reconstructed-data-mover has been designed and implemented. We also review the implementation of a robust database system that has been designed for MICE. The processing of data, whether raw or Monte Carlo, requires accurate knowledge of the experimental conditions. MICE has several complex elements ranging from beamline magnets to particle identification detectors to superconducting magnets. A Configuration Database, which contains information about the experimental conditions (magnet currents, absorber material, detector calibrations, etc.) at any given time has been developed to ensure accurate and reproducible simulation and reconstruction. A fully replicated, hot-standby database system has been implemented with a firewall-protected read-write master running in the control room, and a read-only slave running at a different location. The actual database is hidden from end users by a Web Service layer, which provides platform and programming language-independent access to the data.

Constellation Program Lessons Learned. Volume 2; Detailed Lessons Learned

Science.gov (United States)

Rhatigan, Jennifer; Neubek, Deborah J.; Thomas, L. Dale

2011-01-01

These lessons learned are part of a suite of hardware, software, test results, designs, knowledge base, and documentation that comprises the legacy of the Constellation Program. The context, summary information, and lessons learned are presented in a factual format, as known and described at the time. While our opinions might be discernable in the context, we have avoided all but factually sustainable statements. Statements should not be viewed as being either positive or negative; their value lies in what we did and what we learned that is worthy of passing on. The lessons include both "dos" and "don ts." In many cases, one person s "do" can be viewed as another person s "don t"; therefore, we have attempted to capture both perspectives when applicable and useful. While Volume I summarizes the views of those who managed the program, this Volume II encompasses the views at the working level, describing how the program challenges manifested in day-to-day activities. Here we see themes that were perhaps hinted at, but not completely addressed, in Volume I: unintended consequences of policies that worked well at higher levels but lacked proper implementation at the working level; long-term effects of the "generation gap" in human space flight development, the need to demonstrate early successes at the expense of thorough planning, and the consequences of problems and challenges not yet addressed because other problems and challenges were more immediate or manifest. Not all lessons learned have the benefit of being operationally vetted, since the program was cancelled shortly after Preliminary Design Review. We avoid making statements about operational consequences (with the exception of testing and test flights that did occur), but we do attempt to provide insight into how operational thinking influenced design and testing. The lessons have been formatted with a description, along with supporting information, a succinct statement of the lesson learned, and

Classroom Management and Lesson Planning(4)

Institute of Scientific and Technical Information of China (English)

2006-01-01

@@ Lesson Planning Task 1 As teachers,we all need to plan our lessons before we teach.Make a list of things that you think need to be included in a lesson plan.Then compare and discuss your list with another teacher.Also think about reasons why we need to plan our lessons.

THPdb: Database of FDA-approved peptide and protein therapeutics.

Directory of Open Access Journals (Sweden)

Salman Sadullah Usmani

Full Text Available THPdb (http://crdd.osdd.net/raghava/thpdb/ is a manually curated repository of Food and Drug Administration (FDA approved therapeutic peptides and proteins. The information in THPdb has been compiled from 985 research publications, 70 patents and other resources like DrugBank. The current version of the database holds a total of 852 entries, providing comprehensive information on 239 US-FDA approved therapeutic peptides and proteins and their 380 drug variants. The information on each peptide and protein includes their sequences, chemical properties, composition, disease area, mode of activity, physical appearance, category or pharmacological class, pharmacodynamics, route of administration, toxicity, target of activity, etc. In addition, we have annotated the structure of most of the protein and peptides. A number of user-friendly tools have been integrated to facilitate easy browsing and data analysis. To assist scientific community, a web interface and mobile App have also been developed.

Experiences and lessons learned from creating a generalized workflow for data publication of field campaign datasets

Science.gov (United States)

Santhana Vannan, S. K.; Ramachandran, R.; Deb, D.; Beaty, T.; Wright, D.

2017-12-01

This paper summarizes the workflow challenges of curating and publishing data produced from disparate data sources and provides a generalized workflow solution to efficiently archive data generated by researchers. The Oak Ridge National Laboratory Distributed Active Archive Center (ORNL DAAC) for biogeochemical dynamics and the Global Hydrology Resource Center (GHRC) DAAC have been collaborating on the development of a generalized workflow solution to efficiently manage the data publication process. The generalized workflow presented here are built on lessons learned from implementations of the workflow system. Data publication consists of the following steps: Accepting the data package from the data providers, ensuring the full integrity of the data files. Identifying and addressing data quality issues Assembling standardized, detailed metadata and documentation, including file level details, processing methodology, and characteristics of data files Setting up data access mechanisms Setup of the data in data tools and services for improved data dissemination and user experience Registering the dataset in online search and discovery catalogues Preserving the data location through Digital Object Identifiers (DOI) We will describe the steps taken to automate, and realize efficiencies to the above process. The goals of the workflow system are to reduce the time taken to publish a dataset, to increase the quality of documentation and metadata, and to track individual datasets through the data curation process. Utilities developed to achieve these goal will be described. We will also share metrics driven value of the workflow system and discuss the future steps towards creation of a common software framework.

Comparative analysis of four active compounds of Baikal skullcap and its classical TCM prescriptions according to different clinical curative effects

Directory of Open Access Journals (Sweden)

Guang-Wei Zhu

2017-05-01

Full Text Available Objective: A sensitive HPLC-DAD detection method was established for the comparative analysis of the four active compounds (including baicalin, baicalein, wogonoside and wogonin of Baikal Skullcap and its classical TCM prescriptions according to different clinical curative effects. And analyze the relationship between compatibility of medicines, content and clinical curative effect.

Lessons learned from external hazards

Energy Technology Data Exchange (ETDEWEB)

Peinador, Miguel; Zerger, Benoit [European Commisison Joint Research Centre, Petten (Netherlands). Inst. for Energy and Transport; Ramos, Manuel Martin [European Commission Joint Research Centre, Brussels (Belgium). Nuclear Safety and Security Coordination; Wattrelos, Didier [Institut de Radioprotection et de Surete Nucleaire (IRSN), Fontenay-aux-Roses (France); Maqua, Michael [Gesellschaft fuer Anlagen- und Reaktorsicherheit (GRS) mbH, Koeln (Germany)

2014-01-15

This paper presents a study performed by the European Clearinghouse of the Joint Research Centre on Operational Experience for nuclear power plants in cooperation with IRSN and GRS covering events reported by nuclear power plants in relation to external hazards. It summarizes the review of 235 event reports from 3 different databases. The events were grouped in 9 categories according to the nature of the external hazard involved, and the specific lessons learned and recommendations that can be derived from each of these categories are presented. Additional 'cross-cutting' recommendations covering several or all the external hazards considered are also discussed. These recommendations can be useful in preventing this type of events from happening again or in limiting their consequences. The study was launched in 2010 and therefore it does not cover the Fukushima event. This paper presents the main findings and recommendations raised by this study. (orig.)

Lesson Planning the Kodaly Way.

Science.gov (United States)

Boshkoff, Ruth

1991-01-01

Discusses the contribution of Zoltan Kodaly to music lesson planning. Emphasizes preparation, presentation, and practice as the three important strategies in teaching concepts and skills to be included in a lesson plan. Includes a sample lesson plan covering a semester and advice on choosing song material. (DK)

Database Resources of the BIG Data Center in 2018.

Science.gov (United States)

2018-01-04

The BIG Data Center at Beijing Institute of Genomics (BIG) of the Chinese Academy of Sciences provides freely open access to a suite of database resources in support of worldwide research activities in both academia and industry. With the vast amounts of omics data generated at ever-greater scales and rates, the BIG Data Center is continually expanding, updating and enriching its core database resources through big-data integration and value-added curation, including BioCode (a repository archiving bioinformatics tool codes), BioProject (a biological project library), BioSample (a biological sample library), Genome Sequence Archive (GSA, a data repository for archiving raw sequence reads), Genome Warehouse (GWH, a centralized resource housing genome-scale data), Genome Variation Map (GVM, a public repository of genome variations), Gene Expression Nebulas (GEN, a database of gene expression profiles based on RNA-Seq data), Methylation Bank (MethBank, an integrated databank of DNA methylomes), and Science Wikis (a series of biological knowledge wikis for community annotations). In addition, three featured web services are provided, viz., BIG Search (search as a service; a scalable inter-domain text search engine), BIG SSO (single sign-on as a service; a user access control system to gain access to multiple independent systems with a single ID and password) and Gsub (submission as a service; a unified submission service for all relevant resources). All of these resources are publicly accessible through the home page of the BIG Data Center at http://bigd.big.ac.cn. © The Author(s) 2017. Published by Oxford University Press on behalf of Nucleic Acids Research.

On Curating Multimodal Sensory Data for Health and Wellness Platforms

Directory of Open Access Journals (Sweden)

Muhammad Bilal Amin

2016-06-01

Full Text Available In recent years, the focus of healthcare and wellness technologies has shown a significant shift towards personal vital signs devices. The technology has evolved from smartphone-based wellness applications to fitness bands and smartwatches. The novelty of these devices is the accumulation of activity data as their users go about their daily life routine. However, these implementations are device specific and lack the ability to incorporate multimodal data sources. Data accumulated in their usage does not offer rich contextual information that is adequate for providing a holistic view of a user’s lifelog. As a result, making decisions and generating recommendations based on this data are single dimensional. In this paper, we present our Data Curation Framework (DCF which is device independent and accumulates a user’s sensory data from multimodal data sources in real time. DCF curates the context of this accumulated data over the user’s lifelog. DCF provides rule-based anomaly detection over this context-rich lifelog in real time. To provide computation and persistence over the large volume of sensory data, DCF utilizes the distributed and ubiquitous environment of the cloud platform. DCF has been evaluated for its performance, correctness, ability to detect complex anomalies, and management support for a large volume of sensory data.

On Curating Multimodal Sensory Data for Health and Wellness Platforms

Science.gov (United States)

Amin, Muhammad Bilal; Banos, Oresti; Khan, Wajahat Ali; Muhammad Bilal, Hafiz Syed; Gong, Jinhyuk; Bui, Dinh-Mao; Cho, Soung Ho; Hussain, Shujaat; Ali, Taqdir; Akhtar, Usman; Chung, Tae Choong; Lee, Sungyoung

2016-01-01

In recent years, the focus of healthcare and wellness technologies has shown a significant shift towards personal vital signs devices. The technology has evolved from smartphone-based wellness applications to fitness bands and smartwatches. The novelty of these devices is the accumulation of activity data as their users go about their daily life routine. However, these implementations are device specific and lack the ability to incorporate multimodal data sources. Data accumulated in their usage does not offer rich contextual information that is adequate for providing a holistic view of a user’s lifelog. As a result, making decisions and generating recommendations based on this data are single dimensional. In this paper, we present our Data Curation Framework (DCF) which is device independent and accumulates a user’s sensory data from multimodal data sources in real time. DCF curates the context of this accumulated data over the user’s lifelog. DCF provides rule-based anomaly detection over this context-rich lifelog in real time. To provide computation and persistence over the large volume of sensory data, DCF utilizes the distributed and ubiquitous environment of the cloud platform. DCF has been evaluated for its performance, correctness, ability to detect complex anomalies, and management support for a large volume of sensory data. PMID:27355955

New perspectives in toxicological information management, and the role of ISSTOX databases in assessing chemical mutagenicity and carcinogenicity.

Science.gov (United States)

Benigni, Romualdo; Battistelli, Chiara Laura; Bossa, Cecilia; Tcheremenskaia, Olga; Crettaz, Pierre

2013-07-01

Currently, the public has access to a variety of databases containing mutagenicity and carcinogenicity data. These resources are crucial for the toxicologists and regulators involved in the risk assessment of chemicals, which necessitates access to all the relevant literature, and the capability to search across toxicity databases using both biological and chemical criteria. Towards the larger goal of screening chemicals for a wide range of toxicity end points of potential interest, publicly available resources across a large spectrum of biological and chemical data space must be effectively harnessed with current and evolving information technologies (i.e. systematised, integrated and mined), if long-term screening and prediction objectives are to be achieved. A key to rapid progress in the field of chemical toxicity databases is that of combining information technology with the chemical structure as identifier of the molecules. This permits an enormous range of operations (e.g. retrieving chemicals or chemical classes, describing the content of databases, finding similar chemicals, crossing biological and chemical interrogations, etc.) that other more classical databases cannot allow. This article describes the progress in the technology of toxicity databases, including the concepts of Chemical Relational Database and Toxicological Standardized Controlled Vocabularies (Ontology). Then it describes the ISSTOX cluster of toxicological databases at the Istituto Superiore di Sanitá. It consists of freely available databases characterised by the use of modern information technologies and by curation of the quality of the biological data. Finally, this article provides examples of analyses and results made possible by ISSTOX.

DDEC: Dragon database of genes implicated in esophageal cancer

KAUST Repository

Essack, Magbubah

2009-07-06

Background: Esophageal cancer ranks eighth in order of cancer occurrence. Its lethality primarily stems from inability to detect the disease during the early organ-confined stage and the lack of effective therapies for advanced-stage disease. Moreover, the understanding of molecular processes involved in esophageal cancer is not complete, hampering the development of efficient diagnostics and therapy. Efforts made by the scientific community to improve the survival rate of esophageal cancer have resulted in a wealth of scattered information that is difficult to find and not easily amendable to data-mining. To reduce this gap and to complement available cancer related bioinformatic resources, we have developed a comprehensive database (Dragon Database of Genes Implicated in Esophageal Cancer) with esophageal cancer related information, as an integrated knowledge database aimed at representing a gateway to esophageal cancer related data. Description: Manually curated 529 genes differentially expressed in EC are contained in the database. We extracted and analyzed the promoter regions of these genes and complemented gene-related information with transcription factors that potentially control them. We further, precompiled text-mined and data-mined reports about each of these genes to allow for easy exploration of information about associations of EC-implicated genes with other human genes and proteins, metabolites and enzymes, toxins, chemicals with pharmacological effects, disease concepts and human anatomy. The resulting database, DDEC, has a useful feature to display potential associations that are rarely reported and thus difficult to identify. Moreover, DDEC enables inspection of potentially new \\'association hypotheses\\' generated based on the precompiled reports. Conclusion: We hope that this resource will serve as a useful complement to the existing public resources and as a good starting point for researchers and physicians interested in EC genetics. DDEC is

Analysing the integration of engineering in science lessons with the Engineering-Infused Lesson Rubric

Science.gov (United States)

Peterman, Karen; Daugherty, Jenny L.; Custer, Rodney L.; Ross, Julia M.

2017-09-01

Science teachers are being called on to incorporate engineering practices into their classrooms. This study explores whether the Engineering-Infused Lesson Rubric, a new rubric designed to target best practices in engineering education, could be used to evaluate the extent to which engineering is infused into online science lessons. Eighty lessons were selected at random from three online repositories, and coded with the rubric. Overall results documented the strengths of existing lessons, as well as many components that teachers might strengthen. In addition, a subset of characteristics was found to distinguish lessons with the highest level of engineering infusion. Findings are discussed in relation to the potential of the rubric to help teachers use research evidence-informed practice generally, and in relation to the new content demands of the U.S. Next Generation Science Standards, in particular.

libChEBI: an API for accessing the ChEBI database.

Science.gov (United States)

Swainston, Neil; Hastings, Janna; Dekker, Adriano; Muthukrishnan, Venkatesh; May, John; Steinbeck, Christoph; Mendes, Pedro

2016-01-01

ChEBI is a database and ontology of chemical entities of biological interest. It is widely used as a source of identifiers to facilitate unambiguous reference to chemical entities within biological models, databases, ontologies and literature. ChEBI contains a wealth of chemical data, covering over 46,500 distinct chemical entities, and related data such as chemical formula, charge, molecular mass, structure, synonyms and links to external databases. Furthermore, ChEBI is an ontology, and thus provides meaningful links between chemical entities. Unlike many other resources, ChEBI is fully human-curated, providing a reliable, non-redundant collection of chemical entities and related data. While ChEBI is supported by a web service for programmatic access and a number of download files, it does not have an API library to facilitate the use of ChEBI and its data in cheminformatics software. To provide this missing functionality, libChEBI, a comprehensive API library for accessing ChEBI data, is introduced. libChEBI is available in Java, Python and MATLAB versions from http://github.com/libChEBI, and provides full programmatic access to all data held within the ChEBI database through a simple and documented API. libChEBI is reliant upon the (automated) download and regular update of flat files that are held locally. As such, libChEBI can be embedded in both on- and off-line software applications. libChEBI allows better support of ChEBI and its data in the development of new cheminformatics software. Covering three key programming languages, it allows for the entirety of the ChEBI database to be accessed easily and quickly through a simple API. All code is open access and freely available.

With Interest It Comes To...Unconscionable Clauses in Sales Contracts. A Student's Lesson Plan [and] A Teacher's Lesson Plan [and] A Lawyer's Lesson Plan.

Science.gov (United States)

Howard, Estelle; And Others

One of a series of secondary level teaching units presenting case studies with pro and con analysis of particular legal problems, the document presents a student's lesson plan, a teacher's lesson plan, and a lawyer's lesson plan on unconscionable clauses in sales contracts. The unit acquaints students with the operation of sales contracts and…

The curative management of synchronous rectal and prostate cancer

Science.gov (United States)

Kavanagh, Dara O; Martin, Joseph; Small, Cormac; Joyce, Myles R; Faul, Clare M; Kelly, Paul J; O'Riordain, Michael; Gillham, Charles M; Armstrong, John G; Salib, Osama; McNamara, Deborah A; McVey, Gerard; O'Neill, Brian D P

2016-01-01

Objective: Neoadjuvant “long-course” chemoradiation is considered a standard of care in locally advanced rectal cancer. In addition to prostatectomy, external beam radiotherapy and brachytherapy with or without androgen suppression (AS) are well established in prostate cancer management. A retrospective review of ten cases was completed to explore the feasibility and safety of applying these standards in patients with dual pathology. To our knowledge, this is the largest case series of synchronous rectal and prostate cancers treated with curative intent. Methods: Eligible patients had synchronous histologically proven locally advanced rectal cancer (defined as cT3-4Nx; cTxN1-2) and non-metastatic prostate cancer (pelvic nodal disease permissible). Curative treatment was delivered to both sites simultaneously. Follow-up was as per institutional guidelines. Acute and late toxicities were reviewed, and a literature search performed. Results: Pelvic external beam radiotherapy (RT) 45–50.4 Gy was delivered concurrent with 5-fluorouracil (5FU). Prostate total dose ranged from 70.0 to 79.2 Gy. No acute toxicities occurred, excluding AS-induced erectile dysfunction. Nine patients proceeded to surgery, and one was managed expectantly. Three relapsed with metastatic colorectal cancer, two with metastatic prostate cancer. Five patients have no evidence of recurrence, and four remain alive with metastatic disease. With a median follow-up of 2.2 years (range 1.2–6.3 years), two significant late toxicities occurred; G3 proctitis in a patient receiving palliative bevacizumab and a G3 anastomotic stricture precluding stoma reversal. Conclusion: Patients proceeding to synchronous radical treatment of both primary sites should receive 45–50.4 Gy pelvic RT with infusional 5FU. Prostate dose escalation should be given with due consideration to the potential impact of prostate cancer on patient survival, as increasing dose may result in significant late morbidity

Extending the Reach of IGSN Beyond Earth: Implementing IGSN Registration to Link NASA's Apollo Lunar Samples and their Data

Science.gov (United States)

Todd, N. S.

2016-12-01

The rock and soil samples returned from the Apollo missions from 1969-72 have supported 46 years of research leading to advances in our understanding of the formation and evolution of the inner Solar System. NASA has been engaged in several initiatives that aim to restore, digitize, and make available to the public existing published and unpublished research data for the Apollo samples. One of these initiatives is a collaboration with IEDA (Interdisciplinary Earth Data Alliance) to develop MoonDB, a lunar geochemical database modeled after PetDB. In support of this initiative, NASA has adopted the use of IGSN (International Geo Sample Number) to generate persistent, unique identifiers for lunar samples that scientists can use when publishing research data. To facilitate the IGSN registration of the original 2,200 samples and over 120,000 subdivided samples, NASA has developed an application that retrieves sample metadata from the Lunar Curation Database and uses the SESAR API to automate the generation of IGSNs and registration of samples into SESAR (System for Earth Sample Registration). This presentation will describe the work done by NASA to map existing sample metadata to the IGSN metadata and integrate the IGSN registration process into the sample curation workflow, the lessons learned from this effort, and how this work can be extended in the future to help deal with the registration of large numbers of samples.

The French initiative for scientific cores virtual curating : a user-oriented integrated approach

Science.gov (United States)

Pignol, Cécile; Godinho, Elodie; Galabertier, Bruno; Caillo, Arnaud; Bernardet, Karim; Augustin, Laurent; Crouzet, Christian; Billy, Isabelle; Teste, Gregory; Moreno, Eva; Tosello, Vanessa; Crosta, Xavier; Chappellaz, Jérome; Calzas, Michel; Rousseau, Denis-Didier; Arnaud, Fabien

2016-04-01

Managing scientific data is probably one the most challenging issue in modern science. The question is made even more sensitive with the need of preserving and managing high value fragile geological sam-ples: cores. Large international scientific programs, such as IODP or ICDP are leading an intense effort to solve this problem and propose detailed high standard work- and dataflows thorough core handling and curating. However most results derived from rather small-scale research programs in which data and sample management is generally managed only locally - when it is … The national excellence equipment program (Equipex) CLIMCOR aims at developing French facilities for coring and drilling investigations. It concerns indiscriminately ice, marine and continental samples. As part of this initiative, we initiated a reflexion about core curating and associated coring-data management. The aim of the project is to conserve all metadata from fieldwork in an integrated cyber-environment which will evolve toward laboratory-acquired data storage in a near future. In that aim, our demarche was conducted through an close relationship with field operators as well laboratory core curators in order to propose user-oriented solutions. The national core curating initiative currently proposes a single web portal in which all scientifics teams can store their field data. For legacy samples, this will requires the establishment of a dedicated core lists with associated metadata. For forthcoming samples, we propose a mobile application, under Android environment to capture technical and scientific metadata on the field. This application is linked with a unique coring tools library and is adapted to most coring devices (gravity, drilling, percussion, etc...) including multiple sections and holes coring operations. Those field data can be uploaded automatically to the national portal, but also referenced through international standards or persistent identifiers (IGSN, ORCID and INSPIRE

Lessons learned related to packaging and transportation

International Nuclear Information System (INIS)

Wallen, C.

1995-01-01

The use of lessons learned as a tool for learning from past experiences is well established, especially by many organizations within the nuclear industry. Every person has, at some time, used the principles of lessons learned to adopt good work practices based on their own experiences or the experiences of others. Lessons learned can also help to avoid the recurrence of adverse practices, which is often an area that most lessons-learned programs tend to focus on. This paper will discuss how lessons learned relate to packaging and transportation issues and events experienced at Department of Energy (DOE) facilities. It will also discuss the role performed by the Office of Nuclear and Facility Safety's Office of Operating Experience Analysis and Feedback in disseminating lessons learned and operating experience feedback to the DOE complex. The central concept of lessons learned is that any organization should be able to learn from its own experiences and events. In addition, organizations should implement methodologies to scan external environments for lessons learned, to analyze and determine the relevance of lessons learned, and to bring about the necessary changes learned from these experiences. With increased concerns toward facility safety, the importance of utilizing the lessons-learned principles and the establishment of lessons-learned programs can not be overstated

TBC2health: a database of experimentally validated health-beneficial effects of tea bioactive compounds.

Science.gov (United States)

Zhang, Shihua; Xuan, Hongdong; Zhang, Liang; Fu, Sicong; Wang, Yijun; Yang, Hua; Tai, Yuling; Song, Youhong; Zhang, Jinsong; Ho, Chi-Tang; Li, Shaowen; Wan, Xiaochun

2017-09-01

Tea is one of the most consumed beverages in the world. Considerable studies show the exceptional health benefits (e.g. antioxidation, cancer prevention) of tea owing to its various bioactive components. However, data from these extensively published papers had not been made available in a central database. To lay a foundation in improving the understanding of healthy tea functions, we established a TBC2health database that currently documents 1338 relationships between 497 tea bioactive compounds and 206 diseases (or phenotypes) manually culled from over 300 published articles. Each entry in TBC2health contains comprehensive information about a bioactive relationship that can be accessed in three aspects: (i) compound information, (ii) disease (or phenotype) information and (iii) evidence and reference. Using the curated bioactive relationships, a bipartite network was reconstructed and the corresponding network (or sub-network) visualization and topological analyses are provided for users. This database has a user-friendly interface for entry browse, search and download. In addition, TBC2health provides a submission page and several useful tools (e.g. BLAST, molecular docking) to facilitate use of the database. Consequently, TBC2health can serve as a valuable bioinformatics platform for the exploration of beneficial effects of tea on human health. TBC2health is freely available at http://camellia.ahau.edu.cn/TBC2health. © The Author 2016. Published by Oxford University Press.

GDR (Genome Database for Rosaceae: integrated web resources for Rosaceae genomics and genetics research

Directory of Open Access Journals (Sweden)

Ficklin Stephen

2004-09-01

Full Text Available Abstract Background Peach is being developed as a model organism for Rosaceae, an economically important family that includes fruits and ornamental plants such as apple, pear, strawberry, cherry, almond and rose. The genomics and genetics data of peach can play a significant role in the gene discovery and the genetic understanding of related species. The effective utilization of these peach resources, however, requires the development of an integrated and centralized database with associated analysis tools. Description The Genome Database for Rosaceae (GDR is a curated and integrated web-based relational database. GDR contains comprehensive data of the genetically anchored peach physical map, an annotated peach EST database, Rosaceae maps and markers and all publicly available Rosaceae sequences. Annotations of ESTs include contig assembly, putative function, simple sequence repeats, and anchored position to the peach physical map where applicable. Our integrated map viewer provides graphical interface to the genetic, transcriptome and physical mapping information. ESTs, BACs and markers can be queried by various categories and the search result sites are linked to the integrated map viewer or to the WebFPC physical map sites. In addition to browsing and querying the database, users can compare their sequences with the annotated GDR sequences via a dedicated sequence similarity server running either the BLAST or FASTA algorithm. To demonstrate the utility of the integrated and fully annotated database and analysis tools, we describe a case study where we anchored Rosaceae sequences to the peach physical and genetic map by sequence similarity. Conclusions The GDR has been initiated to meet the major deficiency in Rosaceae genomics and genetics research, namely a centralized web database and bioinformatics tools for data storage, analysis and exchange. GDR can be accessed at http://www.genome.clemson.edu/gdr/.

GDR (Genome Database for Rosaceae): integrated web resources for Rosaceae genomics and genetics research.

Science.gov (United States)

Jung, Sook; Jesudurai, Christopher; Staton, Margaret; Du, Zhidian; Ficklin, Stephen; Cho, Ilhyung; Abbott, Albert; Tomkins, Jeffrey; Main, Dorrie

2004-09-09

Peach is being developed as a model organism for Rosaceae, an economically important family that includes fruits and ornamental plants such as apple, pear, strawberry, cherry, almond and rose. The genomics and genetics data of peach can play a significant role in the gene discovery and the genetic understanding of related species. The effective utilization of these peach resources, however, requires the development of an integrated and centralized database with associated analysis tools. The Genome Database for Rosaceae (GDR) is a curated and integrated web-based relational database. GDR contains comprehensive data of the genetically anchored peach physical map, an annotated peach EST database, Rosaceae maps and markers and all publicly available Rosaceae sequences. Annotations of ESTs include contig assembly, putative function, simple sequence repeats, and anchored position to the peach physical map where applicable. Our integrated map viewer provides graphical interface to the genetic, transcriptome and physical mapping information. ESTs, BACs and markers can be queried by various categories and the search result sites are linked to the integrated map viewer or to the WebFPC physical map sites. In addition to browsing and querying the database, users can compare their sequences with the annotated GDR sequences via a dedicated sequence similarity server running either the BLAST or FASTA algorithm. To demonstrate the utility of the integrated and fully annotated database and analysis tools, we describe a case study where we anchored Rosaceae sequences to the peach physical and genetic map by sequence similarity. The GDR has been initiated to meet the major deficiency in Rosaceae genomics and genetics research, namely a centralized web database and bioinformatics tools for data storage, analysis and exchange. GDR can be accessed at http://www.genome.clemson.edu/gdr/.

Curative Radiation Therapy for T2N0M0

International Nuclear Information System (INIS)

Park, In Kyu; Kim, Jae Choel

1995-01-01

Purpose : Surgery is the treatment of choice for resectable non-small cell lung cancer. For patients who are medically unable to tolerate a surgical resection or who refuse surgery, radiation therapy is an acceptable alternative. A retrospective analysis of patients with stage I non-small cell lung cancer treated with curative radiation therapy was performed to determine the results of curative radiation therapy and patterns of failure, and to identify factors that may influence survival. Materials and Methods : From 1986 through 1993, 39 patients with T2N0M0 non-small cell lung cancer were treated with curative radiation therapy at department of radiation oncology, Kyungpook national university hospital All patients were not candidates for surgical resection because of either patient refusal (16 patients), poor pulmonary function (12 patients), old age (7 patients), poor performance (2 patients) or coexisting medical disease (2 patients). Median age of patients was 67 years. Histologic cell type was squamous cell carcinoma in 1. All patients were treated with megavoltage irradiation and radiation dose raged from 5000cGy to 6150 cGy with a median dose of 600cGy. The median follow-up was 17 months with a range of 4 to 82 months. Survival was measured from the date therapy initiated. Results : The overall survival rate for entire patients was 40.6% at 2 years and 27.7% at 3 years, with a median survival time of 21 months he disease-free survival at 2 and 3 years was 51.7% and 25.8%, respectively. Of evaluable 20 Patients with complete response, 15 Patients were considered to have failed. Of these, 13 patients showed local failure and 2 patients failed distantly. Response to treatment (p=0.0001), tumor size (p=0.0019) and age p=0.0247) were favorably associated with overall survival. Only age was predictive for disease-free survival (p=0.0452). Conclusion : Radiation therapy is an effective treatment for small (less than 3 cm) tumors, and should be offered as an

Lessons for Teaching Art Criticism.

Science.gov (United States)

Barrett, Terry, Ed.; Clark, Gilbert, Ed.

This collection of lessons is meant to be a practical guide to help teachers engage children in art criticism. The lessons generally follow a similar format. Most suggest an age group but may be modified for use with younger or older students. Several authors suggest variations and extensions for lessons that include studio activities. A broad…

"Frankenstein." [Lesson Plan].

Science.gov (United States)

Simon, Melanie

Based on Mary Shelley's novel "Frankenstein," this lesson plan presents activities designed to help students understand that active readers interpret a novel (its characters, plot, setting, and theme) in different ways; and the great literature can be and has been adapted in many ways over time. The main activity of the lesson involves students…

Phagocytosis: history's lessons.

Science.gov (United States)

Garg, Manish; Chandawarkar, Rajiv Y

2013-01-01

The assimilation of lessons from the past is an essential component of education for scientists of tomorrow. These lessons are not easy to find. History books on science are few and usually highly dramatized and biographies of scientists tend to exaggerate the pomp of scientific discovery. Both underplay the hard and laborious work that is integral to any scientific pursuit. Here we illustrate one such example. A century ago, the Nobel Prize in Medicine was awarded to two scientists: Ilya Metchnikoff, a Russian zoologist, for the discovery ofphagocytosis-a cell-mediated ingestion ofmicrobes; and Paul Ehrlich, a distinguished physician-scientist, for discovering a highly antigen-specific serum-derived antibody-based immune defense. These two diametrically opposing views of the host-pathogen interaction set the stage for a strife that led to seminal advancements in immunology. Mirrored in this journey are important lessons for scientists today--ubiquitously as applicable to modern scientific life as they were a century ago. This commentaryhighlights these lessons--a fitting centenary to a well-deserved recognition.

Outcome and prognostic factors following curative-intent surgery for oral tumours in dogs: 234 cases (2004 to 2014).

Science.gov (United States)

Sarowitz, B N; Davis, G J; Kim, S

2017-03-01

To describe the long-term outcomes and prognostic factors associated with curative-intent surgery for oral tumours in a large series of dogs. Retrospective review of records for dogs with oral tumours treated with curative-intent surgery. Data collected included signalment, weight, surgical procedure, lymph node staging results, computed tomography results, tumour size, histopathology results including margin evaluation, complications, adjunctive therapies, local recurrence or metastasis, date and cause of death and owner satisfaction. Median cause-specific survival was shortest for malignant melanoma (206 days) and osteosarcoma (209 days). Local recurrence rate was highest for fibrosarcoma (54·2%) and distant metastatic rate was highest for malignant melanoma (30%). Curative-intent surgery resulted in complete surgical margins in 85·2% of cases. Results suggest tumour type, completeness of excision, tumour size, and age may affect disease-free interval and cause-specific survival. Fibrosarcoma had a higher risk of recurrence compared to other tumour types. © 2017 British Small Animal Veterinary Association.

Hepatoprotective and curative properties of Kombucha tea against carbon tetrachloride-induced toxicity.

Science.gov (United States)

Murugesan, G S; Sathishkumar, M; Jayabalan, R; Binupriya, A R; Swaminathan, K; Yun, S E

2009-04-01

Kombucha tea (KT) is sugared black tea fermented with a symbiotic culture of acetic acid bacteria and yeasts, which is said to be tea fungus. KT is claimed to have various beneficial effects on human health, but there is very little scientific evidence available in the literature. In the present study, KT along with black tea (BT) and black tea manufactured with tea fungus enzymes (enzyme-processed tea, ET) was evaluated for hepatoprotective and curative properties against CCl4-induced toxicity, using male albino rats as an experimental model by analyzing aspartate transaminase, alanine transaminase, and alkaline phosphatase in plasma and malondialdehyde content in plasma and liver tissues. Histopathological analysis of liver tissue was also included. Results showed that BT, ET, and KT have the potential to revert the CCl4-induced hepatotoxicity. Among the three types of teas tried, KT was found to be more efficient than BT and ET. Antioxidant molecules produced during the fermentation period could be the reason for the efficient hepatoprotective and curative properties of KT against CCI4-induced hepatotoxicity.

The Degradome database: mammalian proteases and diseases of proteolysis.

Science.gov (United States)

Quesada, Víctor; Ordóñez, Gonzalo R; Sánchez, Luis M; Puente, Xose S; López-Otín, Carlos

2009-01-01

The degradome is defined as the complete set of proteases present in an organism. The recent availability of whole genomic sequences from multiple organisms has led us to predict the contents of the degradomes of several mammalian species. To ensure the fidelity of these predictions, our methods have included manual curation of individual sequences and, when necessary, direct cloning and sequencing experiments. The results of these studies in human, chimpanzee, mouse and rat have been incorporated into the Degradome database, which can be accessed through a web interface at http://degradome.uniovi.es. The annotations about each individual protease can be retrieved by browsing catalytic classes and families or by searching specific terms. This web site also provides detailed information about genetic diseases of proteolysis, a growing field of great importance for multiple users. Finally, the user can find additional information about protease structures, protease inhibitors, ancillary domains of proteases and differences between mammalian degradomes.

Trafkintu: seed curators defending food sovereignty

Directory of Open Access Journals (Sweden)

Nastassja Nicole Mancilla Ivaca

2014-10-01

Full Text Available This paper examines the resurgence of Trafkintu, an ancient Mapuche ritual of seed trade; now as a folk-communication practice of resistance, against neoliberal transformations in farming that threaten food sovereignty of rural communities in southern Chile. Drawing onparticipant observation and semi-structured interviews with peasant and Mapuche women involved in these practices, we show that seed curators women act as agents that revalue the localness [lo local] through a process of resignification of Trafkintu, this time linking it tofood self-sufficiency. In addition, they build networks between indigenous and peasant communities as a resistance strategy. However, this resurgence of Trafkintu becomes ambivalent as its new symbolic expression is being appropriated by local mainstreampoliticians, for electoral purposes, to promote an image of 'concern about popular culture'. That is, a tool of resistance, on the one hand, and a kind of political folk-marketing, on the other.

Strict follow-up programme including CT and (18) F-FDG-PET after curative surgery for colorectal cancer

DEFF Research Database (Denmark)

Sørensen, N F; Jensen, A B; Wille-Jørgensen, P

2010-01-01

carcinogenic embryonic antigen (CEA), chest X-ray, abdominal ultrasound (US), computed tomography (CT) and (18) F-FDG positron emission tomography (FDG-PET). Method  A cohort of 132 patients, treated by surgery with curative intent for CRC, was included. Patients were followed prospectively with scheduled...... controls at 3, 6, 12 and 24 months after curative surgery. CEA, chest X-ray, US, CT and FDG-PET supplemented by clinical examination. The end-point was recurrence. Sensitivity and specificity was estimated 2 years after surgery. Results  Of the 132 patients included in the study, 25 experienced recurrence...

Community Intelligence in Knowledge Curation: An Application to Managing Scientific Nomenclature

OpenAIRE

Dai, Lin; Xu, Chao; Tian, Ming; Sang, Jian; Zou, Dong; Li, Ang; Liu, Guocheng; Chen, Fei; Wu, Jiayan; Xiao, Jingfa; Wang, Xumin; Yu, Jun; Zhang, Zhang

2013-01-01

Harnessing community intelligence in knowledge curation bears significant promise in dealing with communication and education in the flood of scientific knowledge. As knowledge is accumulated at ever-faster rates, scientific nomenclature, a particular kind of knowledge, is concurrently generated in all kinds of fields. Since nomenclature is a system of terms used to name things in a particular discipline, accurate translation of scientific nomenclature in different languages is of critical im...

The role of endobroncial irradiation as a curative therapy

International Nuclear Information System (INIS)

Fuwa, Nobukazu; Ito, Yoshiyuki; Kato, Eriko; Kamata, Minoru; Morita, Kozo; Kikuchi, Yuzo.

1997-01-01

Endobronchial irradiation for lung cancer has primarily been used in cases of local progression or recurrence. Although its use for palliation of symptoms has been well evaluated, its role in treatment for cure is still unknown. We would like to report on the role of endobronchial irradiation as a curative therapy based on our clinical experience (long time survivors). Forty-one patients treated with endobronchial irradiation using low dose rate 192Iridium between February 1987 and December 1993 were made available for study. Of these, 17 were chest X-P negative cancer, 13 were post operative recurrent cancer, 7 were advanced cancer and 4 were tracheal cancer, respectively. The dose of endobronchial irradiation using an applicator with spacer was 5 to 7 Gy per session, administered either once or twice a week. External irradiation was administered except one case. Local recurrence was observed in two cases of chest X-P negative cancer, three cases of post operative cancer and five cases of advanced cancer. More than three years survivors were observed in 6 cases of chest X-P negative cancer, 5 cases of post operative cancer and one case of tracheal cancer. Complications due to endobronchial irradiation were seen in 2 cases, one case was pulmonary hemorrage and the other was shallow ulceration of the bronchus. It was shown that chest X-P negative lung cancer and part of post operative recurrent cancer could be cured by endobronchial irradiation. This technique is considered to be useful for not only palliative therapy but curative therapy as well. (author)

Astrolabe: Curating, Linking, and Computing Astronomy’s Dark Data

Science.gov (United States)

Heidorn, P. Bryan; Stahlman, Gretchen R.; Steffen, Julie

2018-05-01

Where appropriate repositories are not available to support all relevant astronomical data products, data can fall into darkness: unseen and unavailable for future reference and reuse. Some data in this category are legacy or old data, but newer data sets are also often uncurated and could remain dark. This paper provides a description of the design motivation and development of Astrolabe, a cyberinfrastructure project that addresses a set of community recommendations for locating and ensuring the long-term curation of dark or otherwise at-risk data and integrated computing. This paper also describes the outcomes of the series of community workshops that informed creation of Astrolabe. According to participants in these workshops, much astronomical dark data currently exist that are not curated elsewhere, as well as software that can only be executed by a few individuals and therefore becomes unusable because of changes in computing platforms. Astronomical research questions and challenges would be better addressed with integrated data and computational resources that fall outside the scope of existing observatory and space mission projects. As a solution, the design of the Astrolabe system is aimed at developing new resources for management of astronomical data. The project is based in CyVerse cyberinfrastructure technology and is a collaboration between the University of Arizona and the American Astronomical Society. Overall, the project aims to support open access to research data by leveraging existing cyberinfrastructure resources and promoting scientific discovery by making potentially useful data available to the astronomical community, in a computable format.

Social Media Selves: College Students' Curation of Self and Others through Facebook

Science.gov (United States)

Kasch, David Michael

2013-01-01

This qualitative study used cyber-ethnography and grounded theory to explore the ways in which 35 undergraduate students crafted and refined self-presentations on the social network site Facebook. Findings included the identification of two unique forms of self-presentation that students enacted: a "curated self" and a "commodified…

Pattern of failure in 5001 patients treated for glottic squamous cell carcinoma with curative intent - A population based study from the DAHANCA group

DEFF Research Database (Denmark)

Lyhne, Nina Munk; Johansen, Jørgen; Kristensen, Claus A

2016-01-01