WorldWideScience

Sample records for annotation tool utilising

  1. Algal functional annotation tool

    Energy Technology Data Exchange (ETDEWEB)

    2012-07-12

    Abstract BACKGROUND: Progress in genome sequencing is proceeding at an exponential pace, and several new algal genomes are becoming available every year. One of the challenges facing the community is the association of protein sequences encoded in the genomes with biological function. While most genome assembly projects generate annotations for predicted protein sequences, they are usually limited and integrate functional terms from a limited number of databases. Another challenge is the use of annotations to interpret large lists of 'interesting' genes generated by genome-scale datasets. Previously, these gene lists had to be analyzed across several independent biological databases, often on a gene-by-gene basis. In contrast, several annotation databases, such as DAVID, integrate data from multiple functional databases and reveal underlying biological themes of large gene lists. While several such databases have been constructed for animals, none is currently available for the study of algae. Due to renewed interest in algae as potential sources of biofuels and the emergence of multiple algal genome sequences, a significant need has arisen for such a database to process the growing compendiums of algal genomic data. DESCRIPTION: The Algal Functional Annotation Tool is a web-based comprehensive analysis suite integrating annotation data from several pathway, ontology, and protein family databases. The current version provides annotation for the model alga Chlamydomonas reinhardtii, and in the future will include additional genomes. The site allows users to interpret large gene lists by identifying associated functional terms, and their enrichment. Additionally, expression data for several experimental conditions were compiled and analyzed to provide an expression-based enrichment search. A tool to search for functionally-related genes based on gene expression across these conditions is also provided. Other features include dynamic visualization of genes

  2. Algal functional annotation tool

    Energy Technology Data Exchange (ETDEWEB)

    Lopez, D. [UCLA; Casero, D. [UCLA; Cokus, S. J. [UCLA; Merchant, S. S. [UCLA; Pellegrini, M. [UCLA

    2012-07-01

    The Algal Functional Annotation Tool is a web-based comprehensive analysis suite integrating annotation data from several pathway, ontology, and protein family databases. The current version provides annotation for the model alga Chlamydomonas reinhardtii, and in the future will include additional genomes. The site allows users to interpret large gene lists by identifying associated functional terms, and their enrichment. Additionally, expression data for several experimental conditions were compiled and analyzed to provide an expression-based enrichment search. A tool to search for functionally-related genes based on gene expression across these conditions is also provided. Other features include dynamic visualization of genes on KEGG pathway maps and batch gene identifier conversion.

  3. Creating Annotation Tools with the Annotation Graph Toolkit

    OpenAIRE

    Maeda, Kazuaki; Bird, Steven; Ma, Xiaoyi; Lee, Haejoong

    2002-01-01

    The Annotation Graph Toolkit is a collection of software supporting the development of annotation tools based on the annotation graph model. The toolkit includes application programming interfaces for manipulating annotation graph data and for importing data from other formats. There are interfaces for the scripting languages Tcl and Python, a database interface, specialized graphical user interfaces for a variety of annotation tasks, and several sample applications. This paper describes all ...

  4. BEACON: automated tool for Bacterial GEnome Annotation ComparisON

    KAUST Repository

    Kalkatawi, Manal Matoq Saeed

    2015-08-18

    Background Genome annotation is one way of summarizing the existing knowledge about genomic characteristics of an organism. There has been an increased interest during the last several decades in computer-based structural and functional genome annotation. Many methods for this purpose have been developed for eukaryotes and prokaryotes. Our study focuses on comparison of functional annotations of prokaryotic genomes. To the best of our knowledge there is no fully automated system for detailed comparison of functional genome annotations generated by different annotation methods (AMs). Results The presence of many AMs and development of new ones introduce needs to: a/ compare different annotations for a single genome, and b/ generate annotation by combining individual ones. To address these issues we developed an Automated Tool for Bacterial GEnome Annotation ComparisON (BEACON) that benefits both AM developers and annotation analysers. BEACON provides detailed comparison of gene function annotations of prokaryotic genomes obtained by different AMs and generates extended annotations through combination of individual ones. For the illustration of BEACON’s utility, we provide a comparison analysis of multiple different annotations generated for four genomes and show on these examples that the extended annotation can increase the number of genes annotated by putative functions up to 27 %, while the number of genes without any function assignment is reduced. Conclusions We developed BEACON, a fast tool for an automated and a systematic comparison of different annotations of single genomes. The extended annotation assigns putative functions to many genes with unknown functions. BEACON is available under GNU General Public License version 3.0 and is accessible at: http://www.cbrc.kaust.edu.sa/BEACON/

  5. FolksAnnotation: A Semantic Metadata Tool for Annotating Learning Resources Using Folksonomies and Domain Ontologies

    OpenAIRE

    Hend S. Al-Khalifa; Davis, Hugh C.

    2006-01-01

    There are many resources on the Web which are suitable for educational purposes. Unfortunately the task of identifying suitable resources for a particular educational purpose is difficult as they have not typically been annotated with educational metadata. However, many resources have now been annotated in an unstructured manner within contemporary social bookmaking services. This paper describes a novel tool called ‘FolksAnnotation’ that creates annotations with educational semantics from th...

  6. The GATO gene annotation tool for research laboratories

    Directory of Open Access Journals (Sweden)

    A. Fujita

    2005-11-01

    Full Text Available Large-scale genome projects have generated a rapidly increasing number of DNA sequences. Therefore, development of computational methods to rapidly analyze these sequences is essential for progress in genomic research. Here we present an automatic annotation system for preliminary analysis of DNA sequences. The gene annotation tool (GATO is a Bioinformatics pipeline designed to facilitate routine functional annotation and easy access to annotated genes. It was designed in view of the frequent need of genomic researchers to access data pertaining to a common set of genes. In the GATO system, annotation is generated by querying some of the Web-accessible resources and the information is stored in a local database, which keeps a record of all previous annotation results. GATO may be accessed from everywhere through the internet or may be run locally if a large number of sequences are going to be annotated. It is implemented in PHP and Perl and may be run on any suitable Web server. Usually, installation and application of annotation systems require experience and are time consuming, but GATO is simple and practical, allowing anyone with basic skills in informatics to access it without any special training. GATO can be downloaded at [http://mariwork.iq.usp.br/gato/]. Minimum computer free space required is 2 MB.

  7. The GATO gene annotation tool for research laboratories.

    Science.gov (United States)

    Fujita, A; Massirer, K B; Durham, A M; Ferreira, C E; Sogayar, M C

    2005-11-01

    Large-scale genome projects have generated a rapidly increasing number of DNA sequences. Therefore, development of computational methods to rapidly analyze these sequences is essential for progress in genomic research. Here we present an automatic annotation system for preliminary analysis of DNA sequences. The gene annotation tool (GATO) is a Bioinformatics pipeline designed to facilitate routine functional annotation and easy access to annotated genes. It was designed in view of the frequent need of genomic researchers to access data pertaining to a common set of genes. In the GATO system, annotation is generated by querying some of the Web-accessible resources and the information is stored in a local database, which keeps a record of all previous annotation results. GATO may be accessed from everywhere through the internet or may be run locally if a large number of sequences are going to be annotated. It is implemented in PHP and Perl and may be run on any suitable Web server. Usually, installation and application of annotation systems require experience and are time consuming, but GATO is simple and practical, allowing anyone with basic skills in informatics to access it without any special training. GATO can be downloaded at [http://mariwork.iq.usp.br/gato/]. Minimum computer free space required is 2 MB. PMID:16258624

  8. The Challenges of Blended Learning Using a Media Annotation Tool

    Science.gov (United States)

    Douglas, Kathy A.; Lang, Josephine; Colasante, Meg

    2014-01-01

    Blended learning has been evolving as an important approach to learning and teaching in tertiary education. This approach incorporates learning in both online and face-to-face modes and promotes deep learning by incorporating the best of both approaches. An innovation in blended learning is the use of an online media annotation tool (MAT) in…

  9. SmashCommunity: A metagenomic annotation and analysis tool

    DEFF Research Database (Denmark)

    Arumugam, Manimozhiyan; Harrington, Eoghan D; Foerstner, Konrad U;

    2010-01-01

    SUMMARY: SmashCommunity is a stand-alone metagenomic annotation and analysis pipeline suitable for data from Sanger and 454 sequencing technologies. It supports state-of-the-art software for essential metagenomic tasks such as assembly and gene prediction. It provides tools to estimate...... the quantitative phylogenetic and functional compositions of metagenomes, to compare compositions of multiple metagenomes and to produce intuitive visual representations of such analyses. AVAILABILITY: SmashCommunity is freely available at http://www.bork.embl.de/software/smash CONTACT: bork@embl.de....

  10. Construction et utilisation de modèles à base de connaissance pour l’annotation sémantique des images

    OpenAIRE

    Bannour, Hichem

    2013-01-01

    Cette thèse propose une nouvelle méthodologie pour la construction et l’utilisation de modèles à base de connaissances pour l'annotation automatique d'images. Plus précisément, nous proposons dans un premier lieu des approches pour la construction automatique de modèles de connaissances explicites et structurés, à savoir des hiérarchies sémantiques et des ontologies multimédia adaptées pour l'annotation d'images. Ainsi, nous proposons une approche pour la construction automatique de hiérarchi...

  11. Software tool for researching annotations of proteins: open-source protein annotation software with data visualization.

    Science.gov (United States)

    Bhatia, Vivek N; Perlman, David H; Costello, Catherine E; McComb, Mark E

    2009-12-01

    In order that biological meaning may be derived and testable hypotheses may be built from proteomics experiments, assignments of proteins identified by mass spectrometry or other techniques must be supplemented with additional notation, such as information on known protein functions, protein-protein interactions, or biological pathway associations. Collecting, organizing, and interpreting this data often requires the input of experts in the biological field of study, in addition to the time-consuming search for and compilation of information from online protein databases. Furthermore, visualizing this bulk of information can be challenging due to the limited availability of easy-to-use and freely available tools for this process. In response to these constraints, we have undertaken the design of software to automate annotation and visualization of proteomics data in order to accelerate the pace of research. Here we present the Software Tool for Researching Annotations of Proteins (STRAP), a user-friendly, open-source C# application. STRAP automatically obtains gene ontology (GO) terms associated with proteins in a proteomics results ID list using the freely accessible UniProtKB and EBI GOA databases. Summarized in an easy-to-navigate tabular format, STRAP results include meta-information on the protein in addition to complementary GO terminology. Additionally, this information can be edited by the user so that in-house expertise on particular proteins may be integrated into the larger data set. STRAP provides a sortable tabular view for all terms, as well as graphical representations of GO-term association data in pie charts (biological process, cellular component, and molecular function) and bar charts (cross comparison of sample sets) to aid in the interpretation of large data sets and differential analyses experiments. Furthermore, proteins of interest may be exported as a unique FASTA-formatted file to allow for customizable re-searching of mass spectrometry

  12. ePIANNO: ePIgenomics ANNOtation tool.

    Science.gov (United States)

    Liu, Chia-Hsin; Ho, Bing-Ching; Chen, Chun-Ling; Chang, Ya-Hsuan; Hsu, Yi-Chiung; Li, Yu-Cheng; Yuan, Shin-Sheng; Huang, Yi-Huan; Chang, Chi-Sheng; Li, Ker-Chau; Chen, Hsuan-Yu

    2016-01-01

    Recently, with the development of next generation sequencing (NGS), the combination of chromatin immunoprecipitation (ChIP) and NGS, namely ChIP-seq, has become a powerful technique to capture potential genomic binding sites of regulatory factors, histone modifications and chromatin accessible regions. For most researchers, additional information including genomic variations on the TF binding site, allele frequency of variation between different populations, variation associated disease, and other neighbour TF binding sites are essential to generate a proper hypothesis or a meaningful conclusion. Many ChIP-seq datasets had been deposited on the public domain to help researchers make new discoveries. However, researches are often intimidated by the complexity of data structure and largeness of data volume. Such information would be more useful if they could be combined or downloaded with ChIP-seq data. To meet such demands, we built a webtool: ePIgenomic ANNOtation tool (ePIANNO, http://epianno.stat.sinica.edu.tw/index.html). ePIANNO is a web server that combines SNP information of populations (1000 Genomes Project) and gene-disease association information of GWAS (NHGRI) with ChIP-seq (hmChIP, ENCODE, and ROADMAP epigenomics) data. ePIANNO has a user-friendly website interface allowing researchers to explore, navigate, and extract data quickly. We use two examples to demonstrate how users could use functions of ePIANNO webserver to explore useful information about TF related genomic variants. Users could use our query functions to search target regions, transcription factors, or annotations. ePIANNO may help users to generate hypothesis or explore potential biological functions for their studies. PMID:26859295

  13. ePIANNO: ePIgenomics ANNOtation tool.

    Directory of Open Access Journals (Sweden)

    Chia-Hsin Liu

    Full Text Available Recently, with the development of next generation sequencing (NGS, the combination of chromatin immunoprecipitation (ChIP and NGS, namely ChIP-seq, has become a powerful technique to capture potential genomic binding sites of regulatory factors, histone modifications and chromatin accessible regions. For most researchers, additional information including genomic variations on the TF binding site, allele frequency of variation between different populations, variation associated disease, and other neighbour TF binding sites are essential to generate a proper hypothesis or a meaningful conclusion. Many ChIP-seq datasets had been deposited on the public domain to help researchers make new discoveries. However, researches are often intimidated by the complexity of data structure and largeness of data volume. Such information would be more useful if they could be combined or downloaded with ChIP-seq data. To meet such demands, we built a webtool: ePIgenomic ANNOtation tool (ePIANNO, http://epianno.stat.sinica.edu.tw/index.html. ePIANNO is a web server that combines SNP information of populations (1000 Genomes Project and gene-disease association information of GWAS (NHGRI with ChIP-seq (hmChIP, ENCODE, and ROADMAP epigenomics data. ePIANNO has a user-friendly website interface allowing researchers to explore, navigate, and extract data quickly. We use two examples to demonstrate how users could use functions of ePIANNO webserver to explore useful information about TF related genomic variants. Users could use our query functions to search target regions, transcription factors, or annotations. ePIANNO may help users to generate hypothesis or explore potential biological functions for their studies.

  14. A Case Study of Using a Social Annotation Tool to Support Collaboratively Learning

    Science.gov (United States)

    Gao, Fei

    2013-01-01

    The purpose of the study was to understand student interaction and learning supported by a collaboratively social annotation tool--Diigo. The researcher examined through a case study how students participated and interacted when learning an online text with the social annotation tool--Diigo, and how they perceived their experience. The findings…

  15. Construction et utilisation de la sémantique dans le cadre de l'annotation automatique d'images

    OpenAIRE

    Millet, Christophe

    2008-01-01

    L'annotation automatique d'images est un domaine du traitement d'images permettant d'associer automatiquement des mots-clés ou du texte à des images à partir de leur contenu afin de pouvoir ensuite rechercher des images par requête textuelle. L'annotation automatique d'images cherche à combler les lacunes des deux autres approches actuelles permettant la recherche d'images à partir de requête textuelle. La première consiste à annoter manuellement les images, ce qui n'est plus envisageable ave...

  16. Collaborative Design of an Image Annotation Tool for Oceanographic Imaging Systems

    Science.gov (United States)

    Futrelle, J.; York, A.

    2012-12-01

    We present a design for a web-based image annotation interface developed to assist in supervised classification of organisms and substrate for habitat assessment from multiple, heterogeneous oceanographic imaging systems. The interface enables human image annotators to count, identify, and measure targets and classify substrate in a variety of kinds of imagery including benthic surveys and imaging flow cytometry. These annotations are then used to build training sets for supervised classification algorithms for purposes of characterizing community structure and habitat assessment. The Ocean Imaging Informatics team at WHOI used the Tetherless World Constellation's collaborative design methodology to develop shared formal information model and system design that applies to a variety of image annotation use cases. Because the information model represents consensus between researchers with differing instrumentation and science needs, it assists with rapid prototyping and establishes a baseline against which existing and forthcoming image annotation tools can be evaluated. A technology review suggested that there are few general-purpose image annotation tools suitable for annotation of high-volume oceanographic imagery. Most tools require too many steps for operations that must be repeated thousands of times, and/or lack critical features such as display of instrument metadata, QA/QC, and management of annotator tasks. While some of these problems are user interface limitations, others suggest that existing tools are missing critically important concepts. For example, QA/QC appears in our information model as an "activity stream" associated with each image annotation, consisting of events indicating review status, specific image quality issues, etc. The model also includes "identification modes" that contextualize annotations according to the annotator's assigned task, assisting both with interpreting annotations and with providing contextual user interface shortcuts

  17. Utilisation of Electrochemical Deposition as a Tool for Manufactuing of Micro Components

    DEFF Research Database (Denmark)

    Tang, Peter Torben; Jensen, Jens Dahl

    2003-01-01

    Throughout the evolution of microelectronics, the electrochemical deposition technique has played a vital role in manufacturing of printed circuit boards (PCB´s),in deposition of materials for packaging processes such as flip-chip bonding and recently also in fabrication of interconnects for ultra...... large scale integrated (ULSI) circuits. During the last 5 to 10 years electrochemical deposition has also achieved attention as a tool for manufacturing of micro electromechanical systems (MEMS), microfluidic and optical systems (creating inserts for the injection moulding of polymer optics...... or microfluidic systems) and many other areas within the field of micro systems technology (MST). The present paper describes some applications for which electrodeposition of various metals have been utilised for manufacturing of MEMS and modern interconnect components....

  18. A Novel Visualization Tool for Manual Annotation when Building Large Speech Corpora

    Institute of Scientific and Technical Information of China (English)

    2006-01-01

    A novel visualized sound description, called sound dendrogram is proposed to make manual annotation easier when building large speech corpora. It is a lattice structure built from a group of "seed regions" and through an iterative procedure of mergence. A simple but reliable extraction method of "seed regions" and advanced distance metric are adopted to construct the sound dendrogram, so that it can present speech's structure character ranging from coarse to fine in a visualized way. Tests show that all phonemic boundaries are contained in the lattice structure of sound dendrogram and very easy to identify. Sound dendrogram can be a powerful assistant tool during the process of speech corpora's manual annotation.

  19. AnnTools: a comprehensive and versatile annotation toolkit for genomic variants

    OpenAIRE

    Makarov, Vladimir; O'Grady, Tina; Cai, Guiqing; Lihm, Jayon; Buxbaum, Joseph D; Yoon, Seungtai

    2012-01-01

    Summary: AnnTools is a versatile bioinformatics application designed for comprehensive annotation of a full spectrum of human genome variation: novel and known single-nucleotide substitutions (SNP/SNV), short insertions/deletions (INDEL) and structural variants/copy number variation (SV/CNV). The variants are interpreted by interrogating data compiled from 15 constantly updated sources. In addition to detailed functional characterization of the coding variants, AnnTools searches for overlaps ...

  20. iNGS: a prototype tool for genome interpretation and annotation

    OpenAIRE

    Navas-Delgado, Ismael; García Godoy, María Jesús; Arjona-Pulido, Fátima; Castillo-Castillo, Trinidad; Ramos-Ostio, Ana Isabel; Ifantes Díaz, Sarai; Medina García, Ana; Aldana-Montes, José F.

    2013-01-01

    Currently, clinical interpretation of whole-genome NGS genetic findings are very low-throughput because of a lack of computational tools/software. The current bottleneck of whole-genome and whole-exome sequencing projects is in structured data management and sophisticated computational analysis of experimental data. In this work, we have started designing a platform for integrating, in a first step, existing analysis tools and adding annotations from public databases to the findings of these ...

  1. Ratsnake: A Versatile Image Annotation Tool with Application to Computer-Aided Diagnosis

    Directory of Open Access Journals (Sweden)

    D. K. Iakovidis

    2014-01-01

    Full Text Available Image segmentation and annotation are key components of image-based medical computer-aided diagnosis (CAD systems. In this paper we present Ratsnake, a publicly available generic image annotation tool providing annotation efficiency, semantic awareness, versatility, and extensibility, features that can be exploited to transform it into an effective CAD system. In order to demonstrate this unique capability, we present its novel application for the evaluation and quantification of salient objects and structures of interest in kidney biopsy images. Accurate annotation identifying and quantifying such structures in microscopy images can provide an estimation of pathogenesis in obstructive nephropathy, which is a rather common disease with severe implication in children and infants. However a tool for detecting and quantifying the disease is not yet available. A machine learning-based approach, which utilizes prior domain knowledge and textural image features, is considered for the generation of an image force field customizing the presented tool for automatic evaluation of kidney biopsy images. The experimental evaluation of the proposed application of Ratsnake demonstrates its efficiency and effectiveness and promises its wide applicability across a variety of medical imaging domains.

  2. SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation

    DEFF Research Database (Denmark)

    Panitz, Frank; Stengaard, Henrik; Hornshoj, Henrik;

    2007-01-01

    MOTIVATION: Single nucleotide polymorphisms (SNPs) analysis is an important means to study genetic variation. A fast and cost-efficient approach to identify large numbers of novel candidates is the SNP mining of large scale sequencing projects. The increasing availability of sequence trace data in...... public repositories makes it feasible to evaluate SNP predictions on the DNA chromatogram level. MAVIANT, a platform-independent Multipurpose Alignment VIewing and Annotation Tool, provides DNA chromatogram and alignment views and facilitates evaluation of predictions. In addition, it supports direct...... manual annotation, which is immediately accessible and can be easily shared with external collaborators. RESULTS: Large-scale SNP mining of polymorphisms bases on porcine EST sequences yielded more than 7900 candidate SNPs in coding regions (cSNPs), which were annotated relative to the human genome. Non...

  3. Algal Functional Annotation Tool: a web-based analysis suite to functionally interpret large gene lists using integrated annotation and expression data

    Directory of Open Access Journals (Sweden)

    Merchant Sabeeha S

    2011-07-01

    Full Text Available Abstract Background Progress in genome sequencing is proceeding at an exponential pace, and several new algal genomes are becoming available every year. One of the challenges facing the community is the association of protein sequences encoded in the genomes with biological function. While most genome assembly projects generate annotations for predicted protein sequences, they are usually limited and integrate functional terms from a limited number of databases. Another challenge is the use of annotations to interpret large lists of 'interesting' genes generated by genome-scale datasets. Previously, these gene lists had to be analyzed across several independent biological databases, often on a gene-by-gene basis. In contrast, several annotation databases, such as DAVID, integrate data from multiple functional databases and reveal underlying biological themes of large gene lists. While several such databases have been constructed for animals, none is currently available for the study of algae. Due to renewed interest in algae as potential sources of biofuels and the emergence of multiple algal genome sequences, a significant need has arisen for such a database to process the growing compendiums of algal genomic data. Description The Algal Functional Annotation Tool is a web-based comprehensive analysis suite integrating annotation data from several pathway, ontology, and protein family databases. The current version provides annotation for the model alga Chlamydomonas reinhardtii, and in the future will include additional genomes. The site allows users to interpret large gene lists by identifying associated functional terms, and their enrichment. Additionally, expression data for several experimental conditions were compiled and analyzed to provide an expression-based enrichment search. A tool to search for functionally-related genes based on gene expression across these conditions is also provided. Other features include dynamic visualization of

  4. PFAAT version 2.0 : A tool for editing, annotating, and analyzing multiple sequence alignments

    OpenAIRE

    Somaroo Shyamal; Wang Yaoyu E; Hong Eun-Jong; Ocano Marco; Mathur Vidhya; Dana Paul H; Caffrey Daniel R; Caffrey Brian E; Potluri Shobha; Huang Enoch S

    2007-01-01

    Abstract Background By virtue of their shared ancestry, homologous sequences are similar in their structure and function. Consequently, multiple sequence alignments are routinely used to identify trends that relate to function. This type of analysis is particularly productive when it is combined with structural and phylogenetic analysis. Results Here we describe the release of PFAAT version 2.0, a tool for editing, analyzing, and annotating multiple sequence alignments. Support for multiple a...

  5. Djinn Lite: a tool for customised gene transcript modelling, annotation-data enrichment and exploration

    Directory of Open Access Journals (Sweden)

    Van Dyk Derek

    2006-01-01

    Full Text Available Abstract Background There is an ever increasing rate of data made available on genetic variation, transcriptomes and proteomes. Similarly, a growing variety of bioinformatic programs are becoming available from many diverse sources, designed to identify a myriad of sequence patterns considered to have potential biological importance within inter-genic regions, genes, transcripts, and proteins. However, biologists require easy to use, uncomplicated tools to integrate this information, visualise and print gene annotations. Integrating this information usually requires considerable informatics skills, and comprehensive knowledge of the data format to make full use of this information. Tools are needed to explore gene model variants by allowing users the ability to create alternative transcript models using novel combinations of exons not necessarily represented in current database deposits of mRNA/cDNA sequences. Results Djinn Lite is designed to be an intuitive program for storing and visually exploring of custom annotations relating to a eukaryotic gene sequence and its modelled gene products. In particular, it is helpful in developing hypothesis regarding alternate splicing of transcripts by allowing the construction of model transcripts and inspection of their resulting translations. It facilitates the ability to view a gene and its gene products in one synchronised graphical view, allowing one to drill down into sequence related data. Colour highlighting of selected sequences and added annotations further supports exploration, visualisation of sequence regions and motifs known or predicted to be biologically significant. Conclusion Gene annotating remains an ongoing and challengingtask that will continue as gene structures, gene transcription repertoires, disease loci, protein products and their interactions become moreprecisely defined. Djinn Lite offers an accessible interface to help accumulate, enrich, and individualise sequence

  6. cDNA2Genome: A tool for mapping and annotating cDNAs

    Directory of Open Access Journals (Sweden)

    Suhai Sandor

    2003-09-01

    Full Text Available Abstract Background In the last years several high-throughput cDNA sequencing projects have been funded worldwide with the aim of identifying and characterizing the structure of complete novel human transcripts. However some of these cDNAs are error prone due to frameshifts and stop codon errors caused by low sequence quality, or to cloning of truncated inserts, among other reasons. Therefore, accurate CDS prediction from these sequences first require the identification of potentially problematic cDNAs in order to speed up the posterior annotation process. Results cDNA2Genome is an application for the automatic high-throughput mapping and characterization of cDNAs. It utilizes current annotation data and the most up to date databases, especially in the case of ESTs and mRNAs in conjunction with a vast number of approaches to gene prediction in order to perform a comprehensive assessment of the cDNA exon-intron structure. The final result of cDNA2Genome is an XML file containing all relevant information obtained in the process. This XML output can easily be used for further analysis such us program pipelines, or the integration of results into databases. The web interface to cDNA2Genome also presents this data in HTML, where the annotation is additionally shown in a graphical form. cDNA2Genome has been implemented under the W3H task framework which allows the combination of bioinformatics tools in tailor-made analysis task flows as well as the sequential or parallel computation of many sequences for large-scale analysis. Conclusions cDNA2Genome represents a new versatile and easily extensible approach to the automated mapping and annotation of human cDNAs. The underlying approach allows sequential or parallel computation of sequences for high-throughput analysis of cDNAs.

  7. The Annotation, Mapping, Expression and Network (AMEN suite of tools for molecular systems biology

    Directory of Open Access Journals (Sweden)

    Primig Michael

    2008-02-01

    Full Text Available Abstract Background High-throughput genome biological experiments yield large and multifaceted datasets that require flexible and user-friendly analysis tools to facilitate their interpretation by life scientists. Many solutions currently exist, but they are often limited to specific steps in the complex process of data management and analysis and some require extensive informatics skills to be installed and run efficiently. Results We developed the Annotation, Mapping, Expression and Network (AMEN software as a stand-alone, unified suite of tools that enables biological and medical researchers with basic bioinformatics training to manage and explore genome annotation, chromosomal mapping, protein-protein interaction, expression profiling and proteomics data. The current version provides modules for (i uploading and pre-processing data from microarray expression profiling experiments, (ii detecting groups of significantly co-expressed genes, and (iii searching for enrichment of functional annotations within those groups. Moreover, the user interface is designed to simultaneously visualize several types of data such as protein-protein interaction networks in conjunction with expression profiles and cellular co-localization patterns. We have successfully applied the program to interpret expression profiling data from budding yeast, rodents and human. Conclusion AMEN is an innovative solution for molecular systems biological data analysis freely available under the GNU license. The program is available via a website at the Sourceforge portal which includes a user guide with concrete examples, links to external databases and helpful comments to implement additional functionalities. We emphasize that AMEN will continue to be developed and maintained by our laboratory because it has proven to be extremely useful for our genome biological research program.

  8. XRate: a fast prototyping, training and annotation tool for phylo-grammars

    Directory of Open Access Journals (Sweden)

    Kosiol Carolin

    2006-10-01

    Full Text Available Abstract Background Recent years have seen the emergence of genome annotation methods based on the phylo-grammar, a probabilistic model combining continuous-time Markov chains and stochastic grammars. Previously, phylo-grammars have required considerable effort to implement, limiting their adoption by computational biologists. Results We have developed an open source software tool, xrate, for working with reversible, irreversible or parametric substitution models combined with stochastic context-free grammars. xrate efficiently estimates maximum-likelihood parameters and phylogenetic trees using a novel "phylo-EM" algorithm that we describe. The grammar is specified in an external configuration file, allowing users to design new grammars, estimate rate parameters from training data and annotate multiple sequence alignments without the need to recompile code from source. We have used xrate to measure codon substitution rates and predict protein and RNA secondary structures. Conclusion Our results demonstrate that xrate estimates biologically meaningful rates and makes predictions whose accuracy is comparable to that of more specialized tools.

  9. The Halden viewer: a tool for virtual walkthrough, annotation, radiation visualisation, and dose evaluation

    International Nuclear Information System (INIS)

    The Halden Viewer is a software tool that can be used to interactively walk through and annotate 3D models of environments while visualising radiation dose-rate data. Paths can be defined through the environment and graphs can be plotted showing the dose-rate and accumulated dose of a human moving along the paths. Typical users include radiation protection staff, staff involved in maintenance and training activities, and managers. This report comprises of a foreword documenting the history of the Halden Viewer and the Halden Viewer User Manual. The user manual contains an overview of the tool, a tutorial, and reference information. The version of the Halden Viewer described in this report is release 2.0. (Author)

  10. Snat: a SNP annotation tool for bovine by integrating various sources of genomic information

    Directory of Open Access Journals (Sweden)

    Liu Jian-Feng

    2011-10-01

    Full Text Available Abstract Background Most recently, with maturing of bovine genome sequencing and high throughput SNP genotyping technologies, a large number of significant SNPs associated with economic important traits can be identified by genome-wide association studies (GWAS. To further determine true association findings in GWAS, the common strategy is to sift out most promising SNPs for follow-up replication studies. Hence it is crucial to explore the functional significance of the candidate SNPs in order to screen and select the potential functional ones. To systematically prioritize these statistically significant SNPs and facilitate follow-up replication studies, we developed a bovine SNP annotation tool (Snat based on a web interface. Results With Snat, various sources of genomic information are integrated and retrieved from several leading online databases, including SNP information from dbSNP, gene information from Entrez Gene, protein features from UniProt, linkage information from AnimalQTLdb, conserved elements from UCSC Genome Browser Database and gene functions from Gene Ontology (GO, KEGG PATHWAY and Online Mendelian Inheritance in Animals (OMIA. Snat provides two different applications, including a CGI-based web utility and a command-line version, to access the integrated database, target any single nucleotide loci of interest and perform multi-level functional annotations. For further validation of the practical significance of our study, SNPs involved in two commercial bovine SNP chips, i.e., the Affymetrix Bovine 10K chip array and the Illumina 50K chip array, have been annotated by Snat, and the corresponding outputs can be directly downloaded from Snat website. Furthermore, a real dataset involving 20 identified SNPs associated with milk yield in our recent GWAS was employed to demonstrate the practical significance of Snat. Conclusions To our best knowledge, Snat is one of first tools focusing on SNP annotation for livestock. Snat confers

  11. Cross-species and cross-platform gene expression studies with the Bioconductor-compliant R package 'annotationTools'

    Directory of Open Access Journals (Sweden)

    Luthi-Carter Ruth

    2008-01-01

    Full Text Available Abstract Background The variety of DNA microarray formats and datasets presently available offers an unprecedented opportunity to perform insightful comparisons of heterogeneous data. Cross-species studies, in particular, have the power of identifying conserved, functionally important molecular processes. Validation of discoveries can now often be performed in readily available public data which frequently requires cross-platform studies. Cross-platform and cross-species analyses require matching probes on different microarray formats. This can be achieved using the information in microarray annotations and additional molecular biology databases, such as orthology databases. Although annotations and other biological information are stored using modern database models (e.g. relational, they are very often distributed and shared as tables in text files, i.e. flat file databases. This common flat database format thus provides a simple and robust solution to flexibly integrate various sources of information and a basis for the combined analysis of heterogeneous gene expression profiles. Results We provide annotationTools, a Bioconductor-compliant R package to annotate microarray experiments and integrate heterogeneous gene expression profiles using annotation and other molecular biology information available as flat file databases. First, annotationTools contains a specialized set of functions for mining this widely used database format in a systematic manner. It thus offers a straightforward solution for annotating microarray experiments. Second, building on these basic functions and relying on the combination of information from several databases, it provides tools to easily perform cross-species analyses of gene expression data. Here, we present two example applications of annotationTools that are of direct relevance for the analysis of heterogeneous gene expression profiles, namely a cross-platform mapping of probes and a cross-species mapping

  12. A-MADMAN: Annotation-based microarray data meta-analysis tool

    Directory of Open Access Journals (Sweden)

    Romualdi Chiara

    2009-06-01

    Full Text Available Abstract Background Publicly available datasets of microarray gene expression signals represent an unprecedented opportunity for extracting genomic relevant information and validating biological hypotheses. However, the exploitation of this exceptionally rich mine of information is still hampered by the lack of appropriate computational tools, able to overcome the critical issues raised by meta-analysis. Results This work presents A-MADMAN, an open source web application which allows the retrieval, annotation, organization and meta-analysis of gene expression datasets obtained from Gene Expression Omnibus. A-MADMAN addresses and resolves several open issues in the meta-analysis of gene expression data. Conclusion A-MADMAN allows i the batch retrieval from Gene Expression Omnibus and the local organization of raw data files and of any related meta-information, ii the re-annotation of samples to fix incomplete, or otherwise inadequate, metadata and to create user-defined batches of data, iii the integrative analysis of data obtained from different Affymetrix platforms through custom chip definition files and meta-normalization. Software and documentation are available on-line at http://compgen.bio.unipd.it/bioinfo/amadman/.

  13. Rapid manufacturing of vacuum forming components utilising reconfigurable screw pin tooling

    OpenAIRE

    Wang, Zhijian

    2010-01-01

    Current market trends are moving from large quantity production towards small batch production and mass customization. This has led to the high demand for the flexibility and adaptability of manufacturing technology and systems. Several reconfigurable pin type tooling systems have been proposed and developed to satisfy such demands. However, these reconfigurable tooling systems still suffer from several drawbacks, including difficulties associated with positioning and locking the pins and ...

  14. The discrepancies in the results of bioinformatics tools for genomic structural annotation

    Science.gov (United States)

    Pawełkowicz, Magdalena; Nowak, Robert; Osipowski, Paweł; Rymuszka, Jacek; Świerkula, Katarzyna; Wojcieszek, Michał; Przybecki, Zbigniew

    2014-11-01

    A major focus of sequencing project is to identify genes in genomes. However it is necessary to define the variety of genes and the criteria for identifying them. In this work we present discrepancies and dependencies from the application of different bioinformatic programs for structural annotation performed on the cucumber data set from Polish Consortium of Cucumber Genome Sequencing. We use Fgenesh, GenScan and GeneMark to automated structural annotation, the results have been compared to reference annotation.

  15. SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals.

    Science.gov (United States)

    Nikolaichik, Yevgeny; Damienikan, Aliaksandr U

    2016-01-01

    The majority of bacterial genome annotations are currently automated and based on a 'gene by gene' approach. Regulatory signals and operon structures are rarely taken into account which often results in incomplete and even incorrect gene function assignments. Here we present SigmoID, a cross-platform (OS X, Linux and Windows) open-source application aiming at simplifying the identification of transcription regulatory sites (promoters, transcription factor binding sites and terminators) in bacterial genomes and providing assistance in correcting annotations in accordance with regulatory information. SigmoID combines a user-friendly graphical interface to well known command line tools with a genome browser for visualising regulatory elements in genomic context. Integrated access to online databases with regulatory information (RegPrecise and RegulonDB) and web-based search engines speeds up genome analysis and simplifies correction of genome annotation. We demonstrate some features of SigmoID by constructing a series of regulatory protein binding site profiles for two groups of bacteria: Soft Rot Enterobacteriaceae (Pectobacterium and Dickeya spp.) and Pseudomonas spp. Furthermore, we inferred over 900 transcription factor binding sites and alternative sigma factor promoters in the annotated genome of Pectobacterium atrosepticum. These regulatory signals control putative transcription units covering about 40% of the P. atrosepticum chromosome. Reviewing the annotation in cases where it didn't fit with regulatory information allowed us to correct product and gene names for over 300 loci. PMID:27257541

  16. SigmoID: a user-friendly tool for improving bacterial genome annotation through analysis of transcription control signals

    Science.gov (United States)

    Damienikan, Aliaksandr U.

    2016-01-01

    The majority of bacterial genome annotations are currently automated and based on a ‘gene by gene’ approach. Regulatory signals and operon structures are rarely taken into account which often results in incomplete and even incorrect gene function assignments. Here we present SigmoID, a cross-platform (OS X, Linux and Windows) open-source application aiming at simplifying the identification of transcription regulatory sites (promoters, transcription factor binding sites and terminators) in bacterial genomes and providing assistance in correcting annotations in accordance with regulatory information. SigmoID combines a user-friendly graphical interface to well known command line tools with a genome browser for visualising regulatory elements in genomic context. Integrated access to online databases with regulatory information (RegPrecise and RegulonDB) and web-based search engines speeds up genome analysis and simplifies correction of genome annotation. We demonstrate some features of SigmoID by constructing a series of regulatory protein binding site profiles for two groups of bacteria: Soft Rot Enterobacteriaceae (Pectobacterium and Dickeya spp.) and Pseudomonas spp. Furthermore, we inferred over 900 transcription factor binding sites and alternative sigma factor promoters in the annotated genome of Pectobacterium atrosepticum. These regulatory signals control putative transcription units covering about 40% of the P. atrosepticum chromosome. Reviewing the annotation in cases where it didn’t fit with regulatory information allowed us to correct product and gene names for over 300 loci. PMID:27257541

  17. DNA-binding protein prediction using plant specific support vector machines: validation and application of a new genome annotation tool.

    Science.gov (United States)

    Motion, Graham B; Howden, Andrew J M; Huitema, Edgar; Jones, Susan

    2015-12-15

    There are currently 151 plants with draft genomes available but levels of functional annotation for putative protein products are low. Therefore, accurate computational predictions are essential to annotate genomes in the first instance, and to provide focus for the more costly and time consuming functional assays that follow. DNA-binding proteins are an important class of proteins that require annotation, but current computational methods are not applicable for genome wide predictions in plant species. Here, we explore the use of species and lineage specific models for the prediction of DNA-binding proteins in plants. We show that a species specific support vector machine model based on Arabidopsis sequence data is more accurate (accuracy 81%) than a generic model (74%), and based on this we develop a plant specific model for predicting DNA-binding proteins. We apply this model to the tomato proteome and demonstrate its ability to perform accurate high-throughput prediction of DNA-binding proteins. In doing so, we have annotated 36 currently uncharacterised proteins by assigning a putative DNA-binding function. Our model is publically available and we propose it be used in combination with existing tools to help increase annotation levels of DNA-binding proteins encoded in plant genomes. PMID:26304539

  18. VariOtator, a Software Tool for Variation Annotation with the Variation Ontology.

    Science.gov (United States)

    Schaafsma, Gerard C P; Vihinen, Mauno

    2016-04-01

    The Variation Ontology (VariO) is used for describing and annotating types, effects, consequences, and mechanisms of variations. To facilitate easy and consistent annotations, the online application VariOtator was developed. For variation type annotations, VariOtator is fully automated, accepting variant descriptions in Human Genome Variation Society (HGVS) format, and generating VariO terms, either with or without full lineage, that is, all parent terms. When a coding DNA variant description with a reference sequence is provided, VariOtator checks the description first with Mutalyzer and then generates the predicted RNA and protein descriptions with their respective VariO annotations. For the other sublevels, function, structure, and property, annotations cannot be automated, and VariOtator generates annotation based on provided details. For VariO terms relating to structure and property, one can use attribute terms as modifiers and evidence code terms for annotating experimental evidence. There is an online batch version, and stand-alone batch versions to be used with a Leiden Open Variation Database (LOVD) download file. A SOAP Web service allows client programs to access VariOtator programmatically. Thus, systematic variation effect and type annotations can be efficiently generated to allow easy use and integration of variations and their consequences. PMID:26773573

  19. An automated annotation tool for genomic DNA sequences using GeneScan and BLAST

    Indian Academy of Sciences (India)

    Andrew M. Lynn; Chakresh Kumar Jain; K. Kosalai; Pranjan Barman; Nupur Thakur; Harish Batra; Alok Bhattacharya

    2001-04-01

    Genomic sequence data are often available well before the annotated sequence is published. We present a method for analysis of genomic DNA to identify coding sequences using the GeneScan algorithm and characterize these resultant sequences by BLAST. The routines are used to develop a system for automated annotation of genome DNA sequences.

  20. MADAP, a flexible clustering tool for the interpretation of one-dimensional genome annotation data.

    Science.gov (United States)

    Schmid, Christoph D; Sengstag, Thierry; Bucher, Philipp; Delorenzi, Mauro

    2007-07-01

    A recurring task in the analysis of mass genome annotation data from high-throughput technologies is the identification of peaks or clusters in a noisy signal profile. Examples of such applications are the definition of promoters on the basis of transcription start site profiles, the mapping of transcription factor binding sites based on ChIP-chip data and the identification of quantitative trait loci (QTL) from whole genome SNP profiles. Input to such an analysis is a set of genome coordinates associated with counts or intensities. The output consists of a discrete number of peaks with respective volumes, extensions and center positions. We have developed for this purpose a flexible one-dimensional clustering tool, called MADAP, which we make available as a web server and as standalone program. A set of parameters enables the user to customize the procedure to a specific problem. The web server, which returns results in textual and graphical form, is useful for small to medium-scale applications, as well as for evaluation and parameter tuning in view of large-scale applications, requiring a local installation. The program written in C++ can be freely downloaded from ftp://ftp.epd.unil.ch/pub/software/unix/madap. The MADAP web server can be accessed at http://www.isrec.isb-sib.ch/madap/. PMID:17526516

  1. Documenting Problem-Solving Knowledge: Proposed Annotation Design Guidelines and their Application to Spreadsheet Tools

    CERN Document Server

    Dinmore, Matthew

    2009-01-01

    End-user programmers create software to solve problems, yet the problem-solving knowledge generated in the process often remains tacit within the software artifact. One approach to exposing this knowledge is to enable the end-user to annotate the artifact as they create and use it. A 3-level model of annotation is presented and guidelines are proposed for the design of end-user programming environments supporting the explicit and literate annotation levels. These guidelines are then applied to the spreadsheet end-user programming paradigm.

  2. Kinome Render: a stand-alone and web-accessible tool to annotate the human protein kinome tree

    Directory of Open Access Journals (Sweden)

    Matthieu Chartier

    2013-08-01

    Full Text Available Human protein kinases play fundamental roles mediating the majority of signal transduction pathways in eukaryotic cells as well as a multitude of other processes involved in metabolism, cell-cycle regulation, cellular shape, motility, differentiation and apoptosis. The human protein kinome contains 518 members. Most studies that focus on the human kinome require, at some point, the visualization of large amounts of data. The visualization of such data within the framework of a phylogenetic tree may help identify key relationships between different protein kinases in view of their evolutionary distance and the information used to annotate the kinome tree. For example, studies that focus on the promiscuity of kinase inhibitors can benefit from the annotations to depict binding affinities across kinase groups. Images involving the mapping of information into the kinome tree are common. However, producing such figures manually can be a long arduous process prone to errors. To circumvent this issue, we have developed a web-based tool called Kinome Render (KR that produces customized annotations on the human kinome tree. KR allows the creation and automatic overlay of customizable text or shape-based annotations of different sizes and colors on the human kinome tree. The web interface can be accessed at: http://bcb.med.usherbrooke.ca/kinomerender. A stand-alone version is also available and can be run locally.

  3. DeAnnIso: a tool for online detection and annotation of isomiRs from small RNA sequencing data.

    Science.gov (United States)

    Zhang, Yuanwei; Zang, Qiguang; Zhang, Huan; Ban, Rongjun; Yang, Yifan; Iqbal, Furhan; Li, Ao; Shi, Qinghua

    2016-07-01

    Small RNA (sRNA) Sequencing technology has revealed that microRNAs (miRNAs) are capable of exhibiting frequent variations from their canonical sequences, generating multiple variants: the isoforms of miRNAs (isomiRs). However, integrated tool to precisely detect and systematically annotate isomiRs from sRNA sequencing data is still in great demand. Here, we present an online tool, DeAnnIso (Detection and Annotation of IsomiRs from sRNA sequencing data). DeAnnIso can detect all the isomiRs in an uploaded sample, and can extract the differentially expressing isomiRs from paired or multiple samples. Once the isomiRs detection is accomplished, detailed annotation information, including isomiRs expression, isomiRs classification, SNPs in miRNAs and tissue specific isomiR expression are provided to users. Furthermore, DeAnnIso provides a comprehensive module of target analysis and enrichment analysis for the selected isomiRs. Taken together, DeAnnIso is convenient for users to screen for isomiRs of their interest and useful for further functional studies. The server is implemented in PHP + Perl + R and available to all users for free at: http://mcg.ustc.edu.cn/bsc/deanniso/ and http://mcg2.ustc.edu.cn/bsc/deanniso/. PMID:27179030

  4. SNP mining porcine ESTs with MAVIANT, a novel tool for SNP evaluation and annotation

    DEFF Research Database (Denmark)

    Panitz, Frank; Stengaard, Henrik; Hornshoj, Henrik; Gorodkin, Jan; Hedegaard, Jakob; Cirera, Susanne; Thomsen, Bo; Madsen, Lone B.; Hoj, Anette; Vingborg, Rikke K.; Zahn, Bujie; Wang, Xuegang; Wang, Xuefei; Wernersson, Rasmus; Jørgensen, Claus B.; Scheibye-Knudsen, Karsten; Arvin, Troels; Lumholdt, Steen; Sawera, Milena; Green, Trine; Nielsen, Bente J.; Havgaard, Jakob H.; Brunak, Søren; Fredholm, Merete; Bendixen, Christian

    MOTIVATION: Single nucleotide polymorphisms (SNPs) analysis is an important means to study genetic variation. A fast and cost-efficient approach to identify large numbers of novel candidates is the SNP mining of large scale sequencing projects. The increasing availability of sequence trace data in...... manual annotation, which is immediately accessible and can be easily shared with external collaborators. RESULTS: Large-scale SNP mining of polymorphisms bases on porcine EST sequences yielded more than 7900 candidate SNPs in coding regions (cSNPs), which were annotated relative to the human genome. Non......-synonymous SNPs were analyzed for their potential effect on the protein structure/function using the PolyPhen and SIFT prediction programs. Predicted SNPs and annotations are stored in a web-based database. Using MAVIANT SNPs can visually be verified based on the DNA sequencing traces. A subset of candidate SNPs...

  5. An informatics supported web-based data annotation and query tool to expedite translational research for head and neck malignancies

    Directory of Open Access Journals (Sweden)

    Ridge-Hetrick Jennifer

    2009-11-01

    Full Text Available Abstract Background The Specialized Program of Research Excellence (SPORE in Head and Neck Cancer neoplasm virtual biorepository is a bioinformatics-supported system to incorporate data from various clinical, pathological, and molecular systems into a single architecture based on a set of common data elements (CDEs that provides semantic and syntactic interoperability of data sets. Results The various components of this annotation tool include the Development of Common Data Elements (CDEs that are derived from College of American Pathologists (CAP Checklist and North American Association of Central Cancer Registries (NAACR standards. The Data Entry Tool is a portable and flexible Oracle-based data entry device, which is an easily mastered web-based tool. The Data Query Tool helps investigators and researchers to search de-identified information within the warehouse/resource through a "point and click" interface, thus enabling only the selected data elements to be essentially copied into a data mart using a multi dimensional model from the warehouse's relational structure. The SPORE Head and Neck Neoplasm Database contains multimodal datasets that are accessible to investigators via an easy to use query tool. The database currently holds 6553 cases and 10607 tumor accessions. Among these, there are 965 metastatic, 4227 primary, 1369 recurrent, and 483 new primary cases. The data disclosure is strictly regulated by user's authorization. Conclusion The SPORE Head and Neck Neoplasm Virtual Biorepository is a robust translational biomedical informatics tool that can facilitate basic science, clinical, and translational research. The Data Query Tool acts as a central source providing a mechanism for researchers to efficiently find clinically annotated datasets and biospecimens that are relevant to their research areas. The tool protects patient privacy by revealing only de-identified data in accordance with regulations and approvals of the IRB and

  6. An informatics supported web-based data annotation and query tool to expedite translational research for head and neck malignancies

    International Nuclear Information System (INIS)

    The Specialized Program of Research Excellence (SPORE) in Head and Neck Cancer neoplasm virtual biorepository is a bioinformatics-supported system to incorporate data from various clinical, pathological, and molecular systems into a single architecture based on a set of common data elements (CDEs) that provides semantic and syntactic interoperability of data sets. The various components of this annotation tool include the Development of Common Data Elements (CDEs) that are derived from College of American Pathologists (CAP) Checklist and North American Association of Central Cancer Registries (NAACR) standards. The Data Entry Tool is a portable and flexible Oracle-based data entry device, which is an easily mastered web-based tool. The Data Query Tool helps investigators and researchers to search de-identified information within the warehouse/resource through a 'point and click' interface, thus enabling only the selected data elements to be essentially copied into a data mart using a multi dimensional model from the warehouse's relational structure. The SPORE Head and Neck Neoplasm Database contains multimodal datasets that are accessible to investigators via an easy to use query tool. The database currently holds 6553 cases and 10607 tumor accessions. Among these, there are 965 metastatic, 4227 primary, 1369 recurrent, and 483 new primary cases. The data disclosure is strictly regulated by user's authorization. The SPORE Head and Neck Neoplasm Virtual Biorepository is a robust translational biomedical informatics tool that can facilitate basic science, clinical, and translational research. The Data Query Tool acts as a central source providing a mechanism for researchers to efficiently find clinically annotated datasets and biospecimens that are relevant to their research areas. The tool protects patient privacy by revealing only de-identified data in accordance with regulations and approvals of the IRB and scientific review committee

  7. Adding Value to Large Multimedia Collections through Annotation Technologies and Tools: Serving Communities of Interest.

    Science.gov (United States)

    Shabajee, Paul; Miller, Libby; Dingley, Andy

    A group of research projects based at HP-Labs Bristol, the University of Bristol (England) and ARKive (a new large multimedia database project focused on the worlds biodiversity based in the United Kingdom) are working to develop a flexible model for the indexing of multimedia collections that allows users to annotate content utilizing extensible…

  8. Prototype of annotation tools for microscopic digital images on Android devices

    Science.gov (United States)

    Muhimmah, I.; Nugraha, D. DC

    2016-01-01

    Reading a slide under a microscope manually is very complicated. An expert may spend 3-4 hours to read a single slide. Moreover, the intra- and inter-observer variability is known to be high. This prototype was developed to simplify the slide-reading process on Android devices in order to accelerate the reading process and generate more accurate information.The prototype allows users to annotate the boundaries of an object. Moreover, the proposed prototype has successfully reconstructed multiple object boundaries into simple closed curves from a limited amount of user input.Thecoordinates of the annotated objects are stored in a text file (*.txt) that can be usedfor further analysis.The prototype's performance with respect to time and memory usage are included.

  9. SNPsnap: a Web-based tool for identification and annotation of matched SNPs

    DEFF Research Database (Denmark)

    Pers, Tune Hannes; Timshel, Pascal; Hirschhorn, Joel N.

    2015-01-01

    Summary : An important computational step following genome-wide association studies (GWAS) is to assess whether disease or trait-associated single-nucleotide polymorphisms (SNPs) enrich for particular biological annotations. SNP-based enrichment analysis needs to account for biases such as co......-localization of GWAS signals to gene-dense and high linkage disequilibrium (LD) regions, and correlations of gene size, location and function. The SNPsnap Web server enables SNP-based enrichment analysis by providing matched sets of SNPs that can be used to calibrate background expectations. Specifically, SNPsnap...... efficiently identifies sets of randomly drawn SNPs that are matched to a set of query SNPs based on allele frequency, number of SNPs in LD, distance to nearest gene and gene density. Availability and implementation : SNPsnap server is available at http://www.broadinstitute.org/mpg/snpsnap/. Contact: joelh...

  10. Virtual Ribosome - a comprehensive DNA translation tool with support for integration of sequence feature annotation

    DEFF Research Database (Denmark)

    Wernersson, Rasmus

    2006-01-01

    Virtual Ribosome is a DNA translation tool with two areas of focus. ( i) Providing a strong translation tool in its own right, with an integrated ORF finder, full support for the IUPAC degenerate DNA alphabet and all translation tables defined by the NCBI taxonomy group, including the use of...

  11. TreeQ-VISTA: An Interactive Tree Visualization Tool withFunctional Annotation Query Capabilities

    Energy Technology Data Exchange (ETDEWEB)

    Gu, Shengyin; Anderson, Iain; Kunin, Victor; Cipriano, Michael; Minovitsky, Simon; Weber, Gunther; Amenta, Nina; Hamann, Bernd; Dubchak,Inna

    2007-05-07

    Summary: We describe a general multiplatform exploratorytool called TreeQ-Vista, designed for presenting functional annotationsin a phylogenetic context. Traits, such as phenotypic and genomicproperties, are interactively queried from a relational database with auser-friendly interface which provides a set of tools for users with orwithout SQL knowledge. The query results are projected onto aphylogenetic tree and can be displayed in multiple color groups. A richset of browsing, grouping and query tools are provided to facilitatetrait exploration, comparison and analysis.Availability: The program,detailed tutorial and examples are available online athttp://genome-test.lbl.gov/vista/TreeQVista.

  12. Pegasus: a comprehensive annotation and prediction tool for detection of driver gene fusions in cancer

    OpenAIRE

    Abate, Francesco; Zairis, Sakellarios; Ficarra, Elisa; Acquaviva, Andrea; Wiggins, Chris H.; Frattini, Veronique; Lasorella, Anna; Iavarone, Antonio; Inghirami, Giorgio; Rabadan, Raul

    2014-01-01

    Background The extraordinary success of imatinib in the treatment of BCR-ABL1 associated cancers underscores the need to identify novel functional gene fusions in cancer. RNA sequencing offers a genome-wide view of expressed transcripts, uncovering biologically functional gene fusions. Although several bioinformatics tools are already available for the detection of putative fusion transcripts, candidate event lists are plagued with non-functional read-through events, reverse transcriptase tem...

  13. A-MADMAN: Annotation-based microarray data meta-analysis tool

    OpenAIRE

    Romualdi Chiara; Risso Davide; Ferrari Francesco; Coppe Alessandro; Bisognin Andrea; Bicciato Silvio; Bortoluzzi Stefania

    2009-01-01

    Abstract Background Publicly available datasets of microarray gene expression signals represent an unprecedented opportunity for extracting genomic relevant information and validating biological hypotheses. However, the exploitation of this exceptionally rich mine of information is still hampered by the lack of appropriate computational tools, able to overcome the critical issues raised by meta-analysis. Results This work presents A-MADMAN, an open source web application which allows the retr...

  14. High accuracy mass spectrometry analysis as a tool to verify and improve gene annotation using Mycobacterium tuberculosis as an example

    Directory of Open Access Journals (Sweden)

    Prasad Swati

    2008-07-01

    Full Text Available Abstract Background While the genomic annotations of diverse lineages of the Mycobacterium tuberculosis complex are available, divergences between gene prediction methods are still a challenge for unbiased protein dataset generation. M. tuberculosis gene annotation is an example, where the most used datasets from two independent institutions (Sanger Institute and Institute of Genomic Research-TIGR differ up to 12% in the number of annotated open reading frames, and 46% of the genes contained in both annotations have different start codons. Such differences emphasize the importance of the identification of the sequence of protein products to validate each gene annotation including its sequence coding area. Results With this objective, we submitted a culture filtrate sample from M. tuberculosis to a high-accuracy LTQ-Orbitrap mass spectrometer analysis and applied refined N-terminal prediction to perform comparison of two gene annotations. From a total of 449 proteins identified from the MS data, we validated 35 tryptic peptides that were specific to one of the two datasets, representing 24 different proteins. From those, 5 proteins were only annotated in the Sanger database. In the remaining proteins, the observed differences were due to differences in annotation of transcriptional start sites. Conclusion Our results indicate that, even in a less complex sample likely to represent only 10% of the bacterial proteome, we were still able to detect major differences between different gene annotation approaches. This gives hope that high-throughput proteomics techniques can be used to improve and validate gene annotations, and in particular for verification of high-throughput, automatic gene annotations.

  15. PageMan: An interactive ontology tool to generate, display, and annotate overview graphs for profiling experiments

    Directory of Open Access Journals (Sweden)

    Hannah Matthew A

    2006-12-01

    Full Text Available Abstract Background Microarray technology has become a widely accepted and standardized tool in biology. The first microarray data analysis programs were developed to support pair-wise comparison. However, as microarray experiments have become more routine, large scale experiments have become more common, which investigate multiple time points or sets of mutants or transgenics. To extract biological information from such high-throughput expression data, it is necessary to develop efficient analytical platforms, which combine manually curated gene ontologies with efficient visualization and navigation tools. Currently, most tools focus on a few limited biological aspects, rather than offering a holistic, integrated analysis. Results Here we introduce PageMan, a multiplatform, user-friendly, and stand-alone software tool that annotates, investigates, and condenses high-throughput microarray data in the context of functional ontologies. It includes a GUI tool to transform different ontologies into a suitable format, enabling the user to compare and choose between different ontologies. It is equipped with several statistical modules for data analysis, including over-representation analysis and Wilcoxon statistical testing. Results are exported in a graphical format for direct use, or for further editing in graphics programs. PageMan provides a fast overview of single treatments, allows genome-level responses to be compared across several microarray experiments covering, for example, stress responses at multiple time points. This aids in searching for trait-specific changes in pathways using mutants or transgenics, analyzing development time-courses, and comparison between species. In a case study, we analyze the results of publicly available microarrays of multiple cold stress experiments using PageMan, and compare the results to a previously published meta-analysis. PageMan offers a complete user's guide, a web-based over-representation analysis as

  16. MetaRNA-Seq: An Interactive Tool to Browse and Annotate Metadata from RNA-Seq Studies

    Directory of Open Access Journals (Sweden)

    Pankaj Kumar

    2015-01-01

    Full Text Available The number of RNA-Seq studies has grown in recent years. The design of RNA-Seq studies varies from very simple (e.g., two-condition case-control to very complicated (e.g., time series involving multiple samples at each time point with separate drug treatments. Most of these publically available RNA-Seq studies are deposited in NCBI databases, but their metadata are scattered throughout four different databases: Sequence Read Archive (SRA, Biosample, Bioprojects, and Gene Expression Omnibus (GEO. Although the NCBI web interface is able to provide all of the metadata information, it often requires significant effort to retrieve study- or project-level information by traversing through multiple hyperlinks and going to another page. Moreover, project- and study-level metadata lack manual or automatic curation by categories, such as disease type, time series, case-control, or replicate type, which are vital to comprehending any RNA-Seq study. Here we describe “MetaRNA-Seq,” a new tool for interactively browsing, searching, and annotating RNA-Seq metadata with the capability of semiautomatic curation at the study level.

  17. The role of market failure in the utilisation of quality management services by the tooling industry / Shawn Cunningham

    OpenAIRE

    Cunningham, Shawn

    2009-01-01

    The primary objective of this research is to identify the determinants of market failure that affect transactions between the tool, die and mould making industry and Quality Management service providers within the Nelson Mandela Bay area. A literature review of market failure, the service economy and the evolution of donors' interventions in business service markets was conducted. It provided valuable insights into the identification of issues that could indicate whether a market was performi...

  18. Annotated English

    CERN Document Server

    Hernandez-Orallo, Jose

    2010-01-01

    This document presents Annotated English, a system of diacritical symbols which turns English pronunciation into a precise and unambiguous process. The annotations are defined and located in such a way that the original English text is not altered (not even a letter), thus allowing for a consistent reading and learning of the English language with and without annotations. The annotations are based on a set of general rules that make the frequency of annotations not dramatically high. This makes the reader easily associate annotations with exceptions, and makes it possible to shape, internalise and consolidate some rules for the English language which otherwise are weakened by the enormous amount of exceptions in English pronunciation. The advantages of this annotation system are manifold. Any existing text can be annotated without a significant increase in size. This means that we can get an annotated version of any document or book with the same number of pages and fontsize. Since no letter is affected, the ...

  19. maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination

    Directory of Open Access Journals (Sweden)

    Nashar Karim

    2005-11-01

    Full Text Available Abstract Background maxdLoad2 is a relational database schema and Java® application for microarray experimental annotation and storage. It is compliant with all standards for microarray meta-data capture; including the specification of what data should be recorded, extensive use of standard ontologies and support for data exchange formats. The output from maxdLoad2 is of a form acceptable for submission to the ArrayExpress microarray repository at the European Bioinformatics Institute. maxdBrowse is a PHP web-application that makes contents of maxdLoad2 databases accessible via web-browser, the command-line and web-service environments. It thus acts as both a dissemination and data-mining tool. Results maxdLoad2 presents an easy-to-use interface to an underlying relational database and provides a full complement of facilities for browsing, searching and editing. There is a tree-based visualization of data connectivity and the ability to explore the links between any pair of data elements, irrespective of how many intermediate links lie between them. Its principle novel features are: • the flexibility of the meta-data that can be captured, • the tools provided for importing data from spreadsheets and other tabular representations, • the tools provided for the automatic creation of structured documents, • the ability to browse and access the data via web and web-services interfaces. Within maxdLoad2 it is very straightforward to customise the meta-data that is being captured or change the definitions of the meta-data. These meta-data definitions are stored within the database itself allowing client software to connect properly to a modified database without having to be specially configured. The meta-data definitions (configuration file can also be centralized allowing changes made in response to revisions of standards or terminologies to be propagated to clients without user intervention. maxdBrowse is hosted on a web-server and presents

  20. Computing human image annotation.

    Science.gov (United States)

    Channin, David S; Mongkolwat, Pattanasak; Kleper, Vladimir; Rubin, Daniel L

    2009-01-01

    An image annotation is the explanatory or descriptive information about the pixel data of an image that is generated by a human (or machine) observer. An image markup is the graphical symbols placed over the image to depict an annotation. In the majority of current, clinical and research imaging practice, markup is captured in proprietary formats and annotations are referenced only in free text radiology reports. This makes these annotations difficult to query, retrieve and compute upon, hampering their integration into other data mining and analysis efforts. This paper describes the National Cancer Institute's Cancer Biomedical Informatics Grid's (caBIG) Annotation and Image Markup (AIM) project, focusing on how to use AIM to query for annotations. The AIM project delivers an information model for image annotation and markup. The model uses controlled terminologies for important concepts. All of the classes and attributes of the model have been harmonized with the other models and common data elements in use at the National Cancer Institute. The project also delivers XML schemata necessary to instantiate AIMs in XML as well as a software application for translating AIM XML into DICOM S/R and HL7 CDA. Large collections of AIM annotations can be built and then queried as Grid or Web services. Using the tools of the AIM project, image annotations and their markup can be captured and stored in human and machine readable formats. This enables the inclusion of human image observation and inference as part of larger data mining and analysis activities. PMID:19964202

  1. Interactive tree of life (iTOL) v3: an online tool for the display and annotation of phylogenetic and other trees

    OpenAIRE

    Letunic, I.; Bork, P.

    2016-01-01

    Interactive Tree Of Life (http://itol.embl.de) is a web-based tool for the display, manipulation and annotation of phylogenetic trees. It is freely available and open to everyone. The current version was completely redesigned and rewritten, utilizing current web technologies for speedy and streamlined processing. Numerous new features were introduced and several new data types are now supported. Trees with up to 100,000 leaves can now be efficiently displayed. Full interactive control over pr...

  2. Assessing similarity analysis of chromatographic fingerprints of Cyclopia subternata extracts as potential screening tool for in vitro glucose utilisation.

    Science.gov (United States)

    Schulze, Alexandra E; De Beer, Dalene; Mazibuko, Sithandiwe E; Muller, Christo J F; Roux, Candice; Willenburg, Elize L; Nyunaï, Nyemb; Louw, Johan; Manley, Marena; Joubert, Elizabeth

    2016-01-01

    Similarity analysis of the phenolic fingerprints of a large number of aqueous extracts of Cyclopia subternata, obtained by high-performance liquid chromatography (HPLC), was evaluated as a potential tool to screen extracts for relative bioactivity. The assessment was based on the (dis)similarity of their fingerprints to that of a reference active extract of C. subternata, proven to enhance glucose uptake in vitro and in vivo. In vitro testing of extracts, selected as being most similar (n = 5; r ≥ 0.962) and most dissimilar (n = 5; r ≤ 0.688) to the reference active extract, showed that no clear pattern in terms of relative glucose uptake efficacy in C2C12 myocytes emerged, irrespective of the dose. Some of the most dissimilar extracts had higher glucose-lowering activity than the reference active extract. Principal component analysis revealed the major compounds responsible for the most variation within the chromatographic fingerprints, as mangiferin, isomangiferin, iriflophenone-3-C-β-D-glucoside-4-O-β-D-glucoside, iriflophenone-3-C-β-D-glucoside, scolymoside, and phloretin-3',5'-di-C-β-D-glucoside. Quantitative analysis of the selected extracts showed that the most dissimilar extracts contained the highest mangiferin and isomangiferin levels, whilst the most similar extracts had the highest scolymoside content. These compounds demonstrated similar glucose uptake efficacy in C2C12 myocytes. It can be concluded that (dis)similarity of chromatographic fingerprints of extracts of unknown activity to that of a proven bioactive extract does not necessarily translate to lower or higher bioactivity. PMID:26542834

  3. SENTIMENT ANALYSIS OF DOCUMENT BASED ON ANNOTATION

    Directory of Open Access Journals (Sweden)

    Archana Shukla

    2011-11-01

    Full Text Available I present a tool which tells the quality of document or its usefulness based on annotations. Annotation mayinclude comments, notes, observation, highlights, underline, explanation, question or help etc. commentsare used for evaluative purpose while others are used for summarization or for expansion also. Furtherthese comments may be on another annotation. Such annotations are referred as meta-annotation. Allannotation may not get equal weightage. My tool considered highlights, underline as well as comments toinfer the collective sentiment of annotators. Collective sentiments of annotators are classified as positive,negative, objectivity. My tool computes collective sentiment of annotations in two manners. It counts all theannotation present on the documents as well as it also computes sentiment scores of all annotation whichincludes comments to obtain the collective sentiments about the document or to judge the quality ofdocument. I demonstrate the use of tool on research paper.

  4. Un modèle d'annotation sémantique centré sur les utilisateurs de documents scientifiques: cas d'utilisation dans les études genre

    OpenAIRE

    Falquet, Gilles; De Ribaupierre, Hélène

    2014-01-01

    Lors de recherche de documents, les scientifiques ont des objectifs précis en tête. Nous avons mené des interviews auprès de scientifiques pour comprendre plus précisément comment ils recherchaient leurs informations et travaillaient avec les documents trouvés. Nous avons observé que les scientifiques recherchent leurs informations dans des éléments de discours précis, et non pas toujours dans le document en entier. A partir de cela, nous avons créé un modèle d'annotation prenant en compte ce...

  5. maxdLoad2 and maxdBrowse: standards-compliant tools for microarray experimental annotation, data management and dissemination

    OpenAIRE

    Nashar Karim; Wood A Joseph; Hulme Helen; Hayes Andrew; Morrison Norman; Velarde Giles; Wilson Michael; Hancock David; Kell Douglas B; Brass Andy

    2005-01-01

    Abstract Background maxdLoad2 is a relational database schema and Java® application for microarray experimental annotation and storage. It is compliant with all standards for microarray meta-data capture; including the specification of what data should be recorded, extensive use of standard ontologies and support for data exchange formats. The output from maxdLoad2 is of a form acceptable for submission to the ArrayExpress microarray repository at the European Bioinformatics Institute. maxdBr...

  6. Methods and software tools for mitochondrial genome assembly and annotation%线粒体基因组数据的分析方法和软件

    Institute of Scientific and Technical Information of China (English)

    李雪娟; 杨婧; 王俊红; 任倩俐; 李霞; 黄原

    2013-01-01

    With the increasing popularity of mitochondrial genome studies, the correct assembly and annotation of genomes are the basis of all subsequent research into a species. Here we describe the protocols using Staden Package software to assemble and annotate the mitochondrial genome, along with other commonly used software, such as ContigExpress, DNAMAN, DNASTAR, BioEdit and Sequencher. In addition, methods for the use of different software packages (including DOGMA.MOSAS.MITOS.GOBASE.OGRe.MitoZoa.tRNAscan-SE.ARWEN.BLAST and MiTFi) to annotate mitochondrial genomic protein-coding genes, rRNA, tRNA and the A +T region are briefly introduced. Finally, application of MEGAS software to analyze the composition of mitochondrial genomes, Sequin software to submit sequences to GenBank, and mitochondrial genome data visualization tools ( CG view. MTviz and OGDRAW) are also briefly introduced.%线粒体基因组的研究已经普及,其正确的拼接和注释是所有后续研究的基础.本文以Staden Package软件为主介绍了拼接和注释的线粒体基因组的方法,同时介绍了其他常用的拼接软件ContigExpress、DNAMAN、DNASTAR、BioEdit和Sequencher,以及利用不同软件(包括DOGMA、MOSAS、MITOS、GOBASE、OGRe、MitoZoa、tRNAscan-SE、ARWEN、BLAST和MiTFi等)对线粒体基因组中的蛋白质编码基因、rRNA、tRNA和A+T富集区进行注释的方法,最后介绍了利用MEGA5软件分析线粒体基因组的组成、Sequin软件提交序列和线粒体基因组数据绘图工具(CG view、MTviz和OGDRAW).

  7. Collaborative Movie Annotation

    Science.gov (United States)

    Zad, Damon Daylamani; Agius, Harry

    In this paper, we focus on metadata for self-created movies like those found on YouTube and Google Video, the duration of which are increasing in line with falling upload restrictions. While simple tags may have been sufficient for most purposes for traditionally very short video footage that contains a relatively small amount of semantic content, this is not the case for movies of longer duration which embody more intricate semantics. Creating metadata is a time-consuming process that takes a great deal of individual effort; however, this effort can be greatly reduced by harnessing the power of Web 2.0 communities to create, update and maintain it. Consequently, we consider the annotation of movies within Web 2.0 environments, such that users create and share that metadata collaboratively and propose an architecture for collaborative movie annotation. This architecture arises from the results of an empirical experiment where metadata creation tools, YouTube and an MPEG-7 modelling tool, were used by users to create movie metadata. The next section discusses related work in the areas of collaborative retrieval and tagging. Then, we describe the experiments that were undertaken on a sample of 50 users. Next, the results are presented which provide some insight into how users interact with existing tools and systems for annotating movies. Based on these results, the paper then develops an architecture for collaborative movie annotation.

  8. TAPDANCE: An automated tool to identify and annotate transposon insertion CISs and associations between CISs from next generation sequence data

    Directory of Open Access Journals (Sweden)

    Sarver Aaron L

    2012-06-01

    Full Text Available Abstract Background Next generation sequencing approaches applied to the analyses of transposon insertion junction fragments generated in high throughput forward genetic screens has created the need for clear informatics and statistical approaches to deal with the massive amount of data currently being generated. Previous approaches utilized to 1 map junction fragments within the genome and 2 identify Common Insertion Sites (CISs within the genome are not practical due to the volume of data generated by current sequencing technologies. Previous approaches applied to this problem also required significant manual annotation. Results We describe Transposon Annotation Poisson Distribution Association Network Connectivity Environment (TAPDANCE software, which automates the identification of CISs within transposon junction fragment insertion data. Starting with barcoded sequence data, the software identifies and trims sequences and maps putative genomic sequence to a reference genome using the bowtie short read mapper. Poisson distribution statistics are then applied to assess and rank genomic regions showing significant enrichment for transposon insertion. Novel methods of counting insertions are used to ensure that the results presented have the expected characteristics of informative CISs. A persistent mySQL database is generated and utilized to keep track of sequences, mappings and common insertion sites. Additionally, associations between phenotypes and CISs are also identified using Fisher’s exact test with multiple testing correction. In a case study using previously published data we show that the TAPDANCE software identifies CISs as previously described, prioritizes them based on p-value, allows holistic visualization of the data within genome browser software and identifies relationships present in the structure of the data. Conclusions The TAPDANCE process is fully automated, performs similarly to previous labor intensive approaches

  9. Annotated Answer Set Programming

    OpenAIRE

    Straccia, Umberto

    2005-01-01

    We present Annotated Answer Set Programming, that extends the ex pressive power of disjunctive logic programming with annotation terms, taken from the generalized annotated logic programming framework.

  10. Annotated Videography.

    Science.gov (United States)

    United States Holocaust Memorial Museum, Washington, DC.

    This annotated list of 43 videotapes recommended for classroom use addresses various themes for teaching about the Holocaust, including: (1) overviews of the Holocaust; (2) life before the Holocaust; (3) propaganda; (4) racism, anti-Semitism; (5) "enemies of the state"; (6) ghettos; (7) camps; (8) genocide; (9) rescue; (10) resistance; (11)…

  11. Manual Annotation of Translational Equivalence The Blinker Project

    CERN Document Server

    Melamed, I D

    1998-01-01

    Bilingual annotators were paid to link roughly sixteen thousand corresponding words between on-line versions of the Bible in modern French and modern English. These annotations are freely available to the research community from http://www.cis.upenn.edu/~melamed . The annotations can be used for several purposes. First, they can be used as a standard data set for developing and testing translation lexicons and statistical translation models. Second, researchers in lexical semantics will be able to mine the annotations for insights about cross-linguistic lexicalization patterns. Third, the annotations can be used in research into certain recently proposed methods for monolingual word-sense disambiguation. This paper describes the annotated texts, the specially-designed annotation tool, and the strategies employed to increase the consistency of the annotations. The annotation process was repeated five times by different annotators. Inter-annotator agreement rates indicate that the annotations are reasonably rel...

  12. Pattern of Smartphones Utilisation among Engineering Undergraduates

    Directory of Open Access Journals (Sweden)

    Muliati Sedek

    2014-04-01

    Full Text Available The smartphones ownership among the undergraduates in Malaysia was recorded as high. However, little was known about its utilization patterns, thus, the focus of this research was to determine the utilisation patterns of smartphones based on the National Education Technology Standard for Students (NETS.S among engineering undergraduates in Malaysia. This study was based on a quantitative research and the population comprised undergraduates from four Malaysian Technical Universities. A total of 400 questionnaires were analyzed. Based on the results, the undergraduates’ utilisation level of smartphones for communication and collaboration tool was at a high level. Meanwhile, utilisation for operations and concepts tool and research and information fluency tool were at moderate level. Finally, smartphones utilisation as digital citizenship tool and critical thinking, problem solving and creativity tool were both at a low level. Hence, more training and workshops should be given to the students in order to encourage them to fully utilise smartphones in enhancing the higher order thinking skills.

  13. Modeling Loosely Annotated Images with Imagined Annotations

    CERN Document Server

    Tang, Hong; Chen, Yunhao

    2008-01-01

    In this paper, we present an approach to learning latent semantic analysis models from loosely annotated images for automatic image annotation and indexing. The given annotation in training images is loose due to: (1) ambiguous correspondences between visual features and annotated keywords; (2) incomplete lists of annotated keywords. The second reason motivates us to enrich the incomplete annotation in a simple way before learning topic models. In particular, some imagined keywords are poured into the incomplete annotation through measuring similarity between keywords. Then, both given and imagined annotations are used to learning probabilistic topic models for automatically annotating new images. We conduct experiments on a typical Corel dataset of images and loose annotations, and compare the proposed method with state-of-the-art discrete annotation methods (using a set of discrete blobs to represent an image). The proposed method improves word-driven probability Latent Semantic Analysis (PLSA-words) up to ...

  14. Gene Ontology annotations and resources.

    Science.gov (United States)

    Blake, J A; Dolan, M; Drabkin, H; Hill, D P; Li, Ni; Sitnikov, D; Bridges, S; Burgess, S; Buza, T; McCarthy, F; Peddinti, D; Pillai, L; Carbon, S; Dietze, H; Ireland, A; Lewis, S E; Mungall, C J; Gaudet, P; Chrisholm, R L; Fey, P; Kibbe, W A; Basu, S; Siegele, D A; McIntosh, B K; Renfro, D P; Zweifel, A E; Hu, J C; Brown, N H; Tweedie, S; Alam-Faruque, Y; Apweiler, R; Auchinchloss, A; Axelsen, K; Bely, B; Blatter, M -C; Bonilla, C; Bouguerleret, L; Boutet, E; Breuza, L; Bridge, A; Chan, W M; Chavali, G; Coudert, E; Dimmer, E; Estreicher, A; Famiglietti, L; Feuermann, M; Gos, A; Gruaz-Gumowski, N; Hieta, R; Hinz, C; Hulo, C; Huntley, R; James, J; Jungo, F; Keller, G; Laiho, K; Legge, D; Lemercier, P; Lieberherr, D; Magrane, M; Martin, M J; Masson, P; Mutowo-Muellenet, P; O'Donovan, C; Pedruzzi, I; Pichler, K; Poggioli, D; Porras Millán, P; Poux, S; Rivoire, C; Roechert, B; Sawford, T; Schneider, M; Stutz, A; Sundaram, S; Tognolli, M; Xenarios, I; Foulgar, R; Lomax, J; Roncaglia, P; Khodiyar, V K; Lovering, R C; Talmud, P J; Chibucos, M; Giglio, M Gwinn; Chang, H -Y; Hunter, S; McAnulla, C; Mitchell, A; Sangrador, A; Stephan, R; Harris, M A; Oliver, S G; Rutherford, K; Wood, V; Bahler, J; Lock, A; Kersey, P J; McDowall, D M; Staines, D M; Dwinell, M; Shimoyama, M; Laulederkind, S; Hayman, T; Wang, S -J; Petri, V; Lowry, T; D'Eustachio, P; Matthews, L; Balakrishnan, R; Binkley, G; Cherry, J M; Costanzo, M C; Dwight, S S; Engel, S R; Fisk, D G; Hitz, B C; Hong, E L; Karra, K; Miyasato, S R; Nash, R S; Park, J; Skrzypek, M S; Weng, S; Wong, E D; Berardini, T Z; Huala, E; Mi, H; Thomas, P D; Chan, J; Kishore, R; Sternberg, P; Van Auken, K; Howe, D; Westerfield, M

    2013-01-01

    The Gene Ontology (GO) Consortium (GOC, http://www.geneontology.org) is a community-based bioinformatics resource that classifies gene product function through the use of structured, controlled vocabularies. Over the past year, the GOC has implemented several processes to increase the quantity, quality and specificity of GO annotations. First, the number of manual, literature-based annotations has grown at an increasing rate. Second, as a result of a new 'phylogenetic annotation' process, manually reviewed, homology-based annotations are becoming available for a broad range of species. Third, the quality of GO annotations has been improved through a streamlined process for, and automated quality checks of, GO annotations deposited by different annotation groups. Fourth, the consistency and correctness of the ontology itself has increased by using automated reasoning tools. Finally, the GO has been expanded not only to cover new areas of biology through focused interaction with experts, but also to capture greater specificity in all areas of the ontology using tools for adding new combinatorial terms. The GOC works closely with other ontology developers to support integrated use of terminologies. The GOC supports its user community through the use of e-mail lists, social media and web-based resources. PMID:23161678

  15. Data federation in the Biomedical Informatics Research Network: tools for semantic annotation and query of distributed multiscale brain data.

    Science.gov (United States)

    Bug, William; Astahkov, Vadim; Boline, Jyl; Fennema-Notestine, Christine; Grethe, Jeffrey S; Gupta, Amarnath; Kennedy, David N; Rubin, Daniel L; Sanders, Brian; Turner, Jessica A; Martone, Maryann E

    2008-01-01

    The broadly defined mission of the Biomedical Informatics Research Network (BIRN, www.nbirn.net) is to better understand the causes human disease and the specific ways in which animal models inform that understanding. To construct the community-wide infrastructure for gathering, organizing and managing this knowledge, BIRN is developing a federated architecture for linking multiple databases across sites contributing data and knowledge. Navigating across these distributed data sources requires a shared semantic scheme and supporting software framework to actively link the disparate repositories. At the core of this knowledge organization is BIRNLex, a formally-represented ontology facilitating data exchange. Source curators enable database interoperability by mapping their schema and data to BIRNLex semantic classes thereby providing a means to cast BIRNLex-based queries against specific data sources in the federation. We will illustrate use of the source registration, term mapping, and query tools. PMID:18999211

  16. Annotation sémantique par classification

    OpenAIRE

    Toussaint, Yannick; Tenier, Sylvain

    2007-01-01

    Les systèmes actuels d'annotation sémantique exploitent peu les connaissances du domaine et fonctionnent essentiellement du texte vers l'ontologie. Pourtant, il est fréquent qu'un élément dans une page doive être annoté par un concept parce que certains autres éléments de cette même page sont annotés par d'autres concepts. Cet article propose une méthode d'annotation prenant en compte cette dépendance entre concepts, exprimée dans une ontologie sous forme de concepts définis. L'utilisation de...

  17. Annotated bibliography

    International Nuclear Information System (INIS)

    Under a cooperative agreement with the U.S. Department of Energy's Office of Science and Technology, Waste Policy Institute (WPI) is conducting a five-year research project to develop a research-based approach for integrating communication products in stakeholder involvement related to innovative technology. As part of the research, WPI developed this annotated bibliography which contains almost 100 citations of articles/books/resources involving topics related to communication and public involvement aspects of deploying innovative cleanup technology. To compile the bibliography, WPI performed on-line literature searches (e.g., Dialog, International Association of Business Communicators Public Relations Society of America, Chemical Manufacturers Association, etc.), consulted past years proceedings of major environmental waste cleanup conferences (e.g., Waste Management), networked with professional colleagues and DOE sites to gather reports or case studies, and received input during the August 1996 Research Design Team meeting held to discuss the project's research methodology. Articles were selected for annotation based upon their perceived usefulness to the broad range of public involvement and communication practitioners

  18. Project Aloha:indexing, highlighting and annotation

    OpenAIRE

    Fallahkhair, Sanaz; Kennedy, Ian

    2010-01-01

    Lifelong learning requires many skills that are often not taught or are poorly taught. Such skills include speed reading, critical analysis, creative thinking, active reading and even a “little” skill like annotation. There are many ways that readers annotate. A short classification of some ways that reader may annotate includes underlining, using coloured highlighters, interlinear notes, marginal notes, and disassociated notes. This paper presents an investigation into the use of a tool for ...

  19. NCBI prokaryotic genome annotation pipeline.

    Science.gov (United States)

    Tatusova, Tatiana; DiCuccio, Michael; Badretdin, Azat; Chetvernin, Vyacheslav; Nawrocki, Eric P; Zaslavsky, Leonid; Lomsadze, Alexandre; Pruitt, Kim D; Borodovsky, Mark; Ostell, James

    2016-08-19

    Recent technological advances have opened unprecedented opportunities for large-scale sequencing and analysis of populations of pathogenic species in disease outbreaks, as well as for large-scale diversity studies aimed at expanding our knowledge across the whole domain of prokaryotes. To meet the challenge of timely interpretation of structure, function and meaning of this vast genetic information, a comprehensive approach to automatic genome annotation is critically needed. In collaboration with Georgia Tech, NCBI has developed a new approach to genome annotation that combines alignment based methods with methods of predicting protein-coding and RNA genes and other functional elements directly from sequence. A new gene finding tool, GeneMarkS+, uses the combined evidence of protein and RNA placement by homology as an initial map of annotation to generate and modify ab initio gene predictions across the whole genome. Thus, the new NCBI's Prokaryotic Genome Annotation Pipeline (PGAP) relies more on sequence similarity when confident comparative data are available, while it relies more on statistical predictions in the absence of external evidence. The pipeline provides a framework for generation and analysis of annotation on the full breadth of prokaryotic taxonomy. For additional information on PGAP see https://www.ncbi.nlm.nih.gov/genome/annotation_prok/ and the NCBI Handbook, https://www.ncbi.nlm.nih.gov/books/NBK174280/. PMID:27342282

  20. Automatic annotation of head velocity and acceleration in Anvil

    DEFF Research Database (Denmark)

    Jongejan, Bart

    2012-01-01

    We describe an automatic face tracker plugin for the ANVIL annotation tool. The face tracker produces data for velocity and for acceleration in two dimensions. We compare the annotations generated by the face tracking algorithm with independently made manual annotations for head movements. The...

  1. Students' Perceptions of the Usefulness of an E-Book with Annotative and Sharing Capabilities as a Tool for Learning: A Case Study

    Science.gov (United States)

    Lim, Ee-Lon; Hew, Khe Foon

    2014-01-01

    E-books offer a range of benefits to both educators and students, including ease of accessibility and searching capabilities. However, the majority of current e-books are repository-cum-delivery platforms of textual information. Hitherto, there is a lack of empirical research that examines e-books with annotative and sharing capabilities. This…

  2. Facilitating functional annotation of chicken microarray data

    Directory of Open Access Journals (Sweden)

    Gresham Cathy R

    2009-10-01

    Full Text Available Abstract Background Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. The Affymetrix GenChip chicken genome array, one of the biggest arrays that serve as a key research tool for the study of chicken functional genomics, is among the few arrays that link gene products to Gene Ontology (GO. However the GO annotation data presented by Affymetrix is incomplete, for example, they do not show references linked to manually annotated functions. In addition, there is no tool that facilitates microarray researchers to directly retrieve functional annotations for their datasets from the annotated arrays. This costs researchers amount of time in searching multiple GO databases for functional information. Results We have improved the breadth of functional annotations of the gene products associated with probesets on the Affymetrix chicken genome array by 45% and the quality of annotation by 14%. We have also identified the most significant diseases and disorders, different types of genes, and known drug targets represented on Affymetrix chicken genome array. To facilitate functional annotation of other arrays and microarray experimental datasets we developed an Array GO Mapper (AGOM tool to help researchers to quickly retrieve corresponding functional information for their dataset. Conclusion Results from this study will directly facilitate annotation of other chicken arrays and microarray experimental datasets. Researchers will be able to quickly model their microarray dataset into more reliable biological functional information by using AGOM tool. The disease, disorders, gene types and drug targets revealed in the study will allow researchers to learn more about how genes function in complex biological systems and may lead to new drug discovery and development of therapies. The GO annotation data generated will be available for public use via AgBase website and

  3. Services for annotation of biomedical text

    OpenAIRE

    Hakenberg, Jörg

    2008-01-01

    Motivation: Text mining in the biomedical domain in recent years has focused on the development of tools for recognizing named entities and extracting relations. Such research resulted from the need for such tools as basic components for more advanced solutions. Named entity recognition, entity mention normalization, and relationship extraction now have reached a stage where they perform comparably to human annotators (considering inter--annotator agreement, measured in many studies to be aro...

  4. Learning Object Annotation for Agricultural Learning Repositories

    OpenAIRE

    Ebner, Hannes; Manouselis, Nikos; Palmér, Matthias; Enoksson, Fredrik; Palavitsinis, Nikos; Kastrantas, Kostas; Naeve, Ambjörn

    2009-01-01

    This paper introduces a Web-based tool that has been developed to facilitate learning object annotation in agricultural learning repositories with IEEE LOM-compliant metadata. More specifically, it presents how an application profile of the IEEE LOM standard has been developed for the description of learning objects on organic agriculture and agroecology. Then, it describes the design and prototype development of the Organic.Edunet repository tool: a Web-based for annotating learning objects ...

  5. AnnaBot: A Static Verifier for Java Annotation Usage

    OpenAIRE

    Ian Darwin

    2010-01-01

    This paper describes AnnaBot, one of the first tools to verify correct use of Annotation-based metadata in the Java programming language. These Annotations are a standard Java 5 mechanism used to attach metadata to types, methods, or fields without using an external configuration file. A binary representation of the Annotation becomes part of the compiled “.class” file, for inspection by another component or library at runtime. Java Annotations were introduced into the Java language in 2004 a...

  6. Annotation des Bulletins de Santé du Végétal

    OpenAIRE

    Roussey, C.; Bernard, S.

    2015-01-01

    / Dans cet article nous décrivons les différents schémas d’annotation envisagés pour annoter des bulletins agricoles disponibles sur le web. Notre but est de publier aussi sur le web de données les annotations manuelles permettant le catalogage des bulletins mais aussi les index utilisables par un système de recherche d’information sémantique.

  7. Annotation des Bulletins de Santé du Végétal

    OpenAIRE

    Roussey, C.; Bernard, S.

    2015-01-01

    Dans cet article nous décrivons les différents schémas d'annotation envisagés pour annoter des bulletins agricoles disponibles sur le web. Notre but est de publier aussi sur le web de données les annotations manuelles permettant le catalogage des bulletins mais aussi les index utilisables par un système de recherche d'information sémantique.

  8. Interlinking Multimedia Annotations

    OpenAIRE

    Li, Yunjia; Wald, Mike; Wills, Gary

    2011-01-01

    With the fast growth of multimedia sharing and annotating applications on the Web, there is an increasing research interests in semantic annotations of multimedia. However, applying linked data principles in multimedia annotations is a relatively new topic, especially when annotations are related to media fragments. This paper, therefore, discusses this problem and further breaks it down into three fundamental sub-questions: 1) choosing media fragment URIs 2) Dereferencing media fragment URIs...

  9. COFECO: composite function annotation enriched by protein complex data

    OpenAIRE

    Sun, Choong-Hyun; Kim, Min-Sung; Han, Youngwoong; Yi, Gwan-Su

    2009-01-01

    COFECO is a web-based tool for a composite annotation of protein complexes, KEGG pathways and Gene Ontology (GO) terms within a class of genes and their orthologs under study. Widely used functional enrichment tools using GO and KEGG pathways create large list of annotations that make it difficult to derive consolidated information and often include over-generalized terms. The interrelationship of annotation terms can be more clearly delineated by integrating the information of physically int...

  10. IIS--Integrated Interactome System: a web-based platform for the annotation, analysis and visualization of protein-metabolite-gene-drug interactions by integrating a variety of data sources and tools.

    Directory of Open Access Journals (Sweden)

    Marcelo Falsarella Carazzolle

    Full Text Available High-throughput screening of physical, genetic and chemical-genetic interactions brings important perspectives in the Systems Biology field, as the analysis of these interactions provides new insights into protein/gene function, cellular metabolic variations and the validation of therapeutic targets and drug design. However, such analysis depends on a pipeline connecting different tools that can automatically integrate data from diverse sources and result in a more comprehensive dataset that can be properly interpreted.We describe here the Integrated Interactome System (IIS, an integrative platform with a web-based interface for the annotation, analysis and visualization of the interaction profiles of proteins/genes, metabolites and drugs of interest. IIS works in four connected modules: (i Submission module, which receives raw data derived from Sanger sequencing (e.g. two-hybrid system; (ii Search module, which enables the user to search for the processed reads to be assembled into contigs/singlets, or for lists of proteins/genes, metabolites and drugs of interest, and add them to the project; (iii Annotation module, which assigns annotations from several databases for the contigs/singlets or lists of proteins/genes, generating tables with automatic annotation that can be manually curated; and (iv Interactome module, which maps the contigs/singlets or the uploaded lists to entries in our integrated database, building networks that gather novel identified interactions, protein and metabolite expression/concentration levels, subcellular localization and computed topological metrics, GO biological processes and KEGG pathways enrichment. This module generates a XGMML file that can be imported into Cytoscape or be visualized directly on the web.We have developed IIS by the integration of diverse databases following the need of appropriate tools for a systematic analysis of physical, genetic and chemical-genetic interactions. IIS was validated with

  11. Facilitating functional annotation of chicken microarray data

    OpenAIRE

    Buza, Teresia J; Kumar, Ranjit; Gresham, Cathy R; Burgess, Shane C.; McCarthy, Fiona M

    2009-01-01

    Modeling results from chicken microarray studies is challenging for researchers due to little functional annotation associated with these arrays. The Affymetrix GenChip chicken genome array, one of the biggest arrays that serve as a key research tool for the study of chicken functional genomics, is among the few arrays that link gene products to Gene Ontology (GO). However the GO annotation data presented by Affymetrix is incomplete, for example, they do not show references linked to manually...

  12. Annotations for Intersection Typechecking

    Directory of Open Access Journals (Sweden)

    Joshua Dunfield

    2013-07-01

    Full Text Available In functional programming languages, the classic form of annotation is a single type constraint on a term. Intersection types add complications: a single term may have to be checked several times against different types, in different contexts, requiring annotation with several types. Moreover, it is useful (in some systems, necessary to indicate the context in which each such type is to be used. This paper explores the technical design space of annotations in systems with intersection types. Earlier work (Dunfield and Pfenning 2004 introduced contextual typing annotations, which we now tease apart into more elementary mechanisms: a "right hand" annotation (the standard form, a "left hand" annotation (the context in which a right-hand annotation is to be used, a merge that allows for multiple annotations, and an existential binder for index variables. The most novel element is the left-hand annotation, which guards terms (and right-hand annotations with a judgment that must follow from the current context.

  13. Annotated Stack Trees

    OpenAIRE

    Hague, Matthew; Penelle, Vincent

    2015-01-01

    Annotated pushdown automata provide an automaton model of higher-order recursion schemes, which may in turn be used to model higher-order programs for the purposes of verification. We study Ground Annotated Stack Tree Rewrite Systems -- a tree rewrite system where each node is labelled by the configuration of an annotated pushdown automaton. This allows the modelling of fork and join constructs in higher-order programs and is a generalisation of higher-order stack trees recently introduced by...

  14. Annotation Graphs and Servers and Multi-Modal Resources: Infrastructure for Interdisciplinary Education, Research and Development

    OpenAIRE

    Cieri, Christopher; Bird, Steven

    2002-01-01

    Annotation graphs and annotation servers offer infrastructure to support the analysis of human language resources in the form of time-series data such as text, audio and video. This paper outlines areas of common need among empirical linguists and computational linguists. After reviewing examples of data and tools used or under development for each of several areas, it proposes a common framework for future tool development, data annotation and resource sharing based upon annotation graphs an...

  15. Bioinformatics Assisted Gene Discovery and Annotation of Human Genome

    Institute of Scientific and Technical Information of China (English)

    2002-01-01

    As the sequencing stage of human genome project is near the end, the work has begun for discovering novel genes from genome sequences and annotating their biological functions. Here are reviewed current major bioinformatics tools and technologies available for large scale gene discovery and annotation from human genome sequences. Some ideas about possible future development are also provided.

  16. Personnalisation de Syst\\`emes OLAP Annot\\'es

    CERN Document Server

    Jerbi, Houssem; Ravat, Franck; Teste, Olivier

    2010-01-01

    This paper deals with personalization of annotated OLAP systems. Data constellation is extended to support annotations and user preferences. Annotations reflect the decision-maker experience whereas user preferences enable users to focus on the most interesting data. User preferences allow annotated contextual recommendations helping the decision-maker during his/her multidimensional navigations.

  17. Introduction to annotated logics foundations for paracomplete and paraconsistent reasoning

    CERN Document Server

    Abe, Jair Minoro; Nakamatsu, Kazumi

    2015-01-01

    This book is written as an introduction to annotated logics. It provides logical foundations for annotated logics, discusses some interesting applications of these logics and also includes the authors' contributions to annotated logics. The central idea of the book is to show how annotated logic can be applied as a tool to solve problems of technology and of applied science. The book will be of interest to pure and applied logicians, philosophers, and computer scientists as a monograph on a kind of paraconsistent logic. But, the layman will also take profit from its reading.

  18. On Anomalies in Annotation Systems

    CERN Document Server

    Brust, Matthias R

    2007-01-01

    Today's computer-based annotation systems implement a wide range of functionalities that often go beyond those available in traditional paper-and-pencil annotations. Conceptually, annotation systems are based on thoroughly investigated psycho-sociological and pedagogical learning theories. They offer a huge diversity of annotation types that can be placed in textual as well as in multimedia format. Additionally, annotations can be published or shared with a group of interested parties via well-organized repositories. Although highly sophisticated annotation systems exist both conceptually as well as technologically, we still observe that their acceptance is somewhat limited. In this paper, we argue that nowadays annotation systems suffer from several fundamental problems that are inherent in the traditional paper-and-pencil annotation paradigm. As a solution, we propose to shift the annotation paradigm for the implementation of annotation system.

  19. Semantic annotation of mutable data.

    Directory of Open Access Journals (Sweden)

    Robert A Morris

    Full Text Available Electronic annotation of scientific data is very similar to annotation of documents. Both types of annotation amplify the original object, add related knowledge to it, and dispute or support assertions in it. In each case, annotation is a framework for discourse about the original object, and, in each case, an annotation needs to clearly identify its scope and its own terminology. However, electronic annotation of data differs from annotation of documents: the content of the annotations, including expectations and supporting evidence, is more often shared among members of networks. Any consequent actions taken by the holders of the annotated data could be shared as well. But even those current annotation systems that admit data as their subject often make it difficult or impossible to annotate at fine-enough granularity to use the results in this way for data quality control. We address these kinds of issues by offering simple extensions to an existing annotation ontology and describe how the results support an interest-based distribution of annotations. We are using the result to design and deploy a platform that supports annotation services overlaid on networks of distributed data, with particular application to data quality control. Our initial instance supports a set of natural science collection metadata services. An important application is the support for data quality control and provision of missing data. A previous proof of concept demonstrated such use based on data annotations modeled with XML-Schema.

  20. SEWS : an web-based server for evaluating syntactic annotation tools SEWS : un serveur d’évaluation orienté Web pour la syntaxe

    Directory of Open Access Journals (Sweden)

    Olivier Hamon

    2009-06-01

    Full Text Available Examples of Automated Evaluation platforms deployed as Web server are currently very rare and often underestimated. Time and, effort savings, faster system improvement, com- mon paradigm of evaluation for a community, the benefits offered by such services are plentiful. In this paper, we present a platform for evaluating automatically parsers and we comment on its deployment during an evaluation campaign. First, we draw up a state-of-the-art for plat- forms used in evaluation of NLP systems, then we present the tools available for Web server deployment. Next, we describe our platform and its deployment in the PASSAGE project as a Web server. Finally we show the interest of generalizing such service to other NLP domains.

  1. Utilisation of thorium in reactors

    Science.gov (United States)

    Anantharaman, K.; Shivakumar, V.; Saha, D.

    2008-12-01

    India's nuclear programme envisages a large-scale utilisation of thorium, as it has limited deposits of uranium but vast deposits of thorium. The large-scale utilisation of thorium requires the adoption of closed fuel cycle. The stable nature of thoria and the radiological issues associated with thoria poses challenges in the adoption of a closed fuel cycle. A thorium fuel based Advanced Heavy Water Reactor (AHWR) is being planned to provide impetus to development of technologies for the closed thorium fuel cycle. Thoria fuel has been loaded in Indian reactors and test irradiations have been carried out with (Th-Pu) MOX fuel. Irradiated thorium assemblies have been reprocessed and the separated 233U fuel has been used for test reactor KAMINI. The paper highlights the Indian experience with the use of thorium and brings out various issues associated with the thorium cycle.

  2. Apollo2Go: a web service adapter for the Apollo genome viewer to enable distributed genome annotation

    OpenAIRE

    Mayer Klaus FX; Spannagl Manuel; Ernst Rebecca; Klee Kathrin

    2007-01-01

    Abstract Background Apollo, a genome annotation viewer and editor, has become a widely used genome annotation and visualization tool for distributed genome annotation projects. When using Apollo for annotation, database updates are carried out by uploading intermediate annotation files into the respective database. This non-direct database upload is laborious and evokes problems of data synchronicity. Results To overcome these limitations we extended the Apollo data adapter with a generic, co...

  3. GELATO and SAGE: An Integrated Framework for MS Annotation

    OpenAIRE

    AlJadda, Khalifeh; Ranzinger, Rene; Porterfield, Melody; Weatherly, Brent; Korayem, Mohammed; Miller, John A.; Rasheed, Khaled; Kochut, Krys J; York, William S.

    2015-01-01

    Several algorithms and tools have been developed to (semi) automate the process of glycan identification by interpreting Mass Spectrometric data. However, each has limitations when annotating MSn data with thousands of MS spectra using uncurated public databases. Moreover, the existing tools are not designed to manage MSn data where n > 2. We propose a novel software package to automate the annotation of tandem MS data. This software consists of two major components. The first, is a free, sem...

  4. EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genome

    Directory of Open Access Journals (Sweden)

    Hamilton John P

    2007-10-01

    Full Text Available Abstract Background Despite the improvements of tools for automated annotation of genome sequences, manual curation at the structural and functional level can provide an increased level of refinement to genome annotation. The Institute for Genomic Research Rice Genome Annotation (hereafter named the Osa1 Genome Annotation is the product of an automated pipeline and, for this reason, will benefit from the input of biologists with expertise in rice and/or particular gene families. Leveraging knowledge from a dispersed community of scientists is a demonstrated way of improving a genome annotation. This requires tools that facilitate 1 the submission of gene annotation to an annotation project, 2 the review of the submitted models by project annotators, and 3 the incorporation of the submitted models in the ongoing annotation effort. Results We have developed the Eukaryotic Community Annotation Package (EuCAP, an annotation tool, and have applied it to the rice genome. The primary level of curation by community annotators (CA has been the annotation of gene families. Annotation can be submitted by email or through the EuCAP Web Tool. The CA models are aligned to the rice pseudomolecules and the coordinates of these alignments, along with functional annotation, are stored in the MySQL EuCAP Gene Model database. Web pages displaying the alignments of the CA models to the Osa1 Genome models are automatically generated from the EuCAP Gene Model database. The alignments are reviewed by the project annotators (PAs in the context of experimental evidence. Upon approval by the PAs, the CA models, along with the corresponding functional annotations, are integrated into the Osa1 Genome Annotation. The CA annotations, grouped by family, are displayed on the Community Annotation pages of the project website http://rice.tigr.org, as well as in the Community Annotation track of the Genome Browser. Conclusion We have applied EuCAP to rice. As of July 2007, the

  5. EuCAP, a Eukaryotic Community Annotation Package, and its application to the rice genome

    OpenAIRE

    Hamilton John P; Campbell Matthew; Thibaud-Nissen Françoise; Zhu Wei; Buell C

    2007-01-01

    Abstract Background Despite the improvements of tools for automated annotation of genome sequences, manual curation at the structural and functional level can provide an increased level of refinement to genome annotation. The Institute for Genomic Research Rice Genome Annotation (hereafter named the Osa1 Genome Annotation) is the product of an automated pipeline and, for this reason, will benefit from the input of biologists with expertise in rice and/or particular gene families. Leveraging k...

  6. Aspekte der bioinformatischen Analyse und Annotation des Genoms von Rhodopirellula baltica

    OpenAIRE

    Teeling, Hanno

    2004-01-01

    This thesis focuses on the bioinformatic analysis and annotation of the genome of the marine planctomycete Rhodopirellula baltica. A comprehensive bioinformatic pipeline was set up and established that comprises gene prediction, annotation and visualization tools. Considerable effort was put into the manual annotation process.The annotation of the genome of Rhodopirellula baltica revealed that this organism is specialized on the aerobic degradation of complex carbohydrates. Its genome harbors...

  7. Automated analysis and annotation of basketball video

    Science.gov (United States)

    Saur, Drew D.; Tan, Yap-Peng; Kulkarni, Sanjeev R.; Ramadge, Peter J.

    1997-01-01

    Automated analysis and annotation of video sequences are important for digital video libraries, content-based video browsing and data mining projects. A successful video annotation system should provide users with useful video content summary in a reasonable processing time. Given the wide variety of video genres available today, automatically extracting meaningful video content for annotation still remains hard by using current available techniques. However, a wide range video has inherent structure such that some prior knowledge about the video content can be exploited to improve our understanding of the high-level video semantic content. In this paper, we develop tools and techniques for analyzing structured video by using the low-level information available directly from MPEG compressed video. Being able to work directly in the video compressed domain can greatly reduce the processing time and enhance storage efficiency. As a testbed, we have developed a basketball annotation system which combines the low-level information extracted from MPEG stream with the prior knowledge of basketball video structure to provide high level content analysis, annotation and browsing for events such as wide- angle and close-up views, fast breaks, steals, potential shots, number of possessions and possession times. We expect our approach can also be extended to structured video in other domains.

  8. Evaluating techniques for metagenome annotation using simulated sequence data.

    Science.gov (United States)

    Randle-Boggis, Richard J; Helgason, Thorunn; Sapp, Melanie; Ashton, Peter D

    2016-07-01

    The advent of next-generation sequencing has allowed huge amounts of DNA sequence data to be produced, advancing the capabilities of microbial ecosystem studies. The current challenge is to identify from which microorganisms and genes the DNA originated. Several tools and databases are available for annotating DNA sequences. The tools, databases and parameters used can have a significant impact on the results: naïve choice of these factors can result in a false representation of community composition and function. We use a simulated metagenome to show how different parameters affect annotation accuracy by evaluating the sequence annotation performances of MEGAN, MG-RAST, One Codex and Megablast. This simulated metagenome allowed the recovery of known organism and function abundances to be quantitatively evaluated, which is not possible for environmental metagenomes. The performance of each program and database varied, e.g. One Codex correctly annotated many sequences at the genus level, whereas MG-RAST RefSeq produced many false positive annotations. This effect decreased as the taxonomic level investigated increased. Selecting more stringent parameters decreases the annotation sensitivity, but increases precision. Ultimately, there is a trade-off between taxonomic resolution and annotation accuracy. These results should be considered when annotating metagenomes and interpreting results from previous studies. PMID:27162180

  9. SNAD: sequence name annotation-based designer

    Directory of Open Access Journals (Sweden)

    Gorbalenya Alexander E

    2009-08-01

    Full Text Available Abstract Background A growing diversity of biological data is tagged with unique identifiers (UIDs associated with polynucleotides and proteins to ensure efficient computer-mediated data storage, maintenance, and processing. These identifiers, which are not informative for most people, are often substituted by biologically meaningful names in various presentations to facilitate utilization and dissemination of sequence-based knowledge. This substitution is commonly done manually that may be a tedious exercise prone to mistakes and omissions. Results Here we introduce SNAD (Sequence Name Annotation-based Designer that mediates automatic conversion of sequence UIDs (associated with multiple alignment or phylogenetic tree, or supplied as plain text list into biologically meaningful names and acronyms. This conversion is directed by precompiled or user-defined templates that exploit wealth of annotation available in cognate entries of external databases. Using examples, we demonstrate how this tool can be used to generate names for practical purposes, particularly in virology. Conclusion A tool for controllable annotation-based conversion of sequence UIDs into biologically meaningful names and acronyms has been developed and placed into service, fostering links between quality of sequence annotation, and efficiency of communication and knowledge dissemination among researchers.

  10. Annotated bibliography traceability

    NARCIS (Netherlands)

    Narain, G.

    2006-01-01

    This annotated bibliography contains summaries of articles and chapters of books, which are relevant to traceability. After each summary there is a part about the relevancy of the paper for the LEI project. The aim of the LEI-project is to gain insight in several aspects of traceability in order to

  11. Annotation: The Savant Syndrome

    Science.gov (United States)

    Heaton, Pamela; Wallace, Gregory L.

    2004-01-01

    Background: Whilst interest has focused on the origin and nature of the savant syndrome for over a century, it is only within the past two decades that empirical group studies have been carried out. Methods: The following annotation briefly reviews relevant research and also attempts to address outstanding issues in this research area.…

  12. Semantator: annotating clinical narratives with semantic web ontologies.

    Science.gov (United States)

    Song, Dezhao; Chute, Christopher G; Tao, Cui

    2012-01-01

    To facilitate clinical research, clinical data needs to be stored in a machine processable and understandable way. Manual annotating clinical data is time consuming. Automatic approaches (e.g., Natural Language Processing systems) have been adopted to convert such data into structured formats; however, the quality of such automatically extracted data may not always be satisfying. In this paper, we propose Semantator, a semi-automatic tool for document annotation with Semantic Web ontologies. With a loaded free text document and an ontology, Semantator supports the creation/deletion of ontology instances for any document fragment, linking/disconnecting instances with the properties in the ontology, and also enables automatic annotation by connecting to the NCBO annotator and cTAKES. By representing annotations in Semantic Web standards, Semantator supports reasoning based upon the underlying semantics of the owl:disjointWith and owl:equivalentClass predicates. We present discussions based on user experiences of using Semantator. PMID:22779043

  13. Improving microbial genome annotations in an integrated database context.

    Directory of Open Access Journals (Sweden)

    I-Min A Chen

    Full Text Available Effective comparative analysis of microbial genomes requires a consistent and complete view of biological data. Consistency regards the biological coherence of annotations, while completeness regards the extent and coverage of functional characterization for genomes. We have developed tools that allow scientists to assess and improve the consistency and completeness of microbial genome annotations in the context of the Integrated Microbial Genomes (IMG family of systems. All publicly available microbial genomes are characterized in IMG using different functional annotation and pathway resources, thus providing a comprehensive framework for identifying and resolving annotation discrepancies. A rule based system for predicting phenotypes in IMG provides a powerful mechanism for validating functional annotations, whereby the phenotypic traits of an organism are inferred based on the presence of certain metabolic reactions and pathways and compared to experimentally observed phenotypes. The IMG family of systems are available at http://img.jgi.doe.gov/.

  14. Coal ash utilisation in India

    International Nuclear Information System (INIS)

    Coal based thermal power stations have been the major source of power generation in our country in the past and would continue for decades to come. In India, thermal generation which contributes about 72% of the overall power generation of 2,45,000 MU (1989-90) is the main source of power and mainly based on coal firing. Total ash generation in India presently is to the tune of 38 million tonnes per annum. India is fourth in the world as far as coal ash generation is concerned. USSR is first, (100 million tonnes), then come USA (45 million tonnes) and China (41 million tonnes). The basic problem of thermal power station fired with high ash content coal is the generation of huge quantity of coal ash which would pose serious environmental and other related problems. The present paper analyses the extensive scope of utilisation of coal ash and enlightens the strategies to be adopted to overcome the related problems for proper utilisation of coal ash. (author). 9 tabs

  15. Reducing Risky Security Behaviours: Utilising Affective Feedback to Educate Users

    Directory of Open Access Journals (Sweden)

    Lynsay A. Shepherd

    2014-11-01

    Full Text Available Despite the number of tools created to help end-users reduce risky security behaviours, users are still falling victim to online attacks. This paper proposes a browser extension utilising affective feedback to provide warnings on detection of risky behaviour. The paper provides an overview of behaviour considered to be risky, explaining potential threats users may face online. Existing tools developed to reduce risky security behaviours in end-users have been compared, discussing the success rates of various methodologies. Ongoing research is described which attempts to educate users regarding the risks and consequences of poor security behaviour by providing the appropriate feedback on the automatic recognition of risky behaviour. The paper concludes that a solution utilising a browser extension is a suitable method of monitoring potentially risky security behaviour. Ultimately, future work seeks to implement an affective feedback mechanism within the browser extension with the aim of improving security awareness.

  16. Bovine Genome Database: supporting community annotation and analysis of the Bos taurus genome

    Directory of Open Access Journals (Sweden)

    Childs Kevin L

    2010-11-01

    Full Text Available Abstract Background A goal of the Bovine Genome Database (BGD; http://BovineGenome.org has been to support the Bovine Genome Sequencing and Analysis Consortium (BGSAC in the annotation and analysis of the bovine genome. We were faced with several challenges, including the need to maintain consistent quality despite diversity in annotation expertise in the research community, the need to maintain consistent data formats, and the need to minimize the potential duplication of annotation effort. With new sequencing technologies allowing many more eukaryotic genomes to be sequenced, the demand for collaborative annotation is likely to increase. Here we present our approach, challenges and solutions facilitating a large distributed annotation project. Results and Discussion BGD has provided annotation tools that supported 147 members of the BGSAC in contributing 3,871 gene models over a fifteen-week period, and these annotations have been integrated into the bovine Official Gene Set. Our approach has been to provide an annotation system, which includes a BLAST site, multiple genome browsers, an annotation portal, and the Apollo Annotation Editor configured to connect directly to our Chado database. In addition to implementing and integrating components of the annotation system, we have performed computational analyses to create gene evidence tracks and a consensus gene set, which can be viewed on individual gene pages at BGD. Conclusions We have provided annotation tools that alleviate challenges associated with distributed annotation. Our system provides a consistent set of data to all annotators and eliminates the need for annotators to format data. Involving the bovine research community in genome annotation has allowed us to leverage expertise in various areas of bovine biology to provide biological insight into the genome sequence.

  17. TESAURVAI: Extraction, Annotation and Term Organization Tool

    OpenAIRE

    Cardeñosa Lera, Jesús; Gallardo Pérez, Carolina; Maldonado Martínez, Ángeles

    2008-01-01

    Each concrete field of disciplinary or thematic specializations makes use of its own terminology. The compilation, definition, and organization of terms used in a given domain are a basic task, because it becomes the base for the constitution of specialized terminology resources of great usefulness. Thesauri are a type of terminological resource of increasing relevance at the present time; frequently used in the recovery and localization of information in digital environments. The hierarchic ...

  18. Deburring: an annotated bibliography. Volume V

    International Nuclear Information System (INIS)

    An annotated summary of 204 articles and publications on burrs, burr prevention and deburring is presented. Thirty-seven deburring processes are listed. Entries cited include English, Russian, French, Japanese and German language articles. Entries are indexed by deburring processes, author, and language. Indexes also indicate which references discuss equipment and tooling, how to use a process, economics, burr properties, and how to design to minimize burr problems. Research studies are identified as are the materials deburred

  19. Functional annotation and ENU

    OpenAIRE

    Gunn, Teresa M.

    2012-01-01

    Functional annotation of every gene in the mouse genome is a herculean task that requires a multifaceted approach. Many large-scale initiatives are contributing to this undertaking. The International Knockout Mouse Consortium (IKMC) plans to mutate every protein-coding gene, using a combination of gene trapping and gene targeting in embryonic stem cells. Many other groups are performing using the chemical mutagen ethylnitrosourea (ENU) or transpon-based systems to induce mutations, screening ...

  20. Ontological Annotation with WordNet

    Energy Technology Data Exchange (ETDEWEB)

    Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.; Chappell, Alan R.; Whitney, Paul D.; Posse, Christian; Paulson, Patrick R.; Baddeley, Bob; Hohimer, Ryan E.; White, Amanda M.

    2006-06-06

    Semantic Web applications require robust and accurate annotation tools that are capable of automating the assignment of ontological classes to words in naturally occurring text (ontological annotation). Most current ontologies do not include rich lexical databases and are therefore not easily integrated with word sense disambiguation algorithms that are needed to automate ontological annotation. WordNet provides a potentially ideal solution to this problem as it offers a highly structured lexical conceptual representation that has been extensively used to develop word sense disambiguation algorithms. However, WordNet has not been designed as an ontology, and while it can be easily turned into one, the result of doing this would present users with serious practical limitations due to the great number of concepts (synonym sets) it contains. Moreover, mapping WordNet to an existing ontology may be difficult and requires substantial labor. We propose to overcome these limitations by developing an analytical platform that (1) provides a WordNet-based ontology offering a manageable and yet comprehensive set of concept classes, (2) leverages the lexical richness of WordNet to give an extensive characterization of concept class in terms of lexical instances, and (3) integrates a class recognition algorithm that automates the assignment of concept classes to words in naturally occurring text. The ensuing framework makes available an ontological annotation platform that can be effectively integrated with intelligence analysis systems to facilitate evidence marshaling and sustain the creation and validation of inference models.

  1. Automating Ontological Annotation with WordNet

    Energy Technology Data Exchange (ETDEWEB)

    Sanfilippo, Antonio P.; Tratz, Stephen C.; Gregory, Michelle L.; Chappell, Alan R.; Whitney, Paul D.; Posse, Christian; Paulson, Patrick R.; Baddeley, Bob L.; Hohimer, Ryan E.; White, Amanda M.

    2006-01-22

    Semantic Web applications require robust and accurate annotation tools that are capable of automating the assignment of ontological classes to words in naturally occurring text (ontological annotation). Most current ontologies do not include rich lexical databases and are therefore not easily integrated with word sense disambiguation algorithms that are needed to automate ontological annotation. WordNet provides a potentially ideal solution to this problem as it offers a highly structured lexical conceptual representation that has been extensively used to develop word sense disambiguation algorithms. However, WordNet has not been designed as an ontology, and while it can be easily turned into one, the result of doing this would present users with serious practical limitations due to the great number of concepts (synonym sets) it contains. Moreover, mapping WordNet to an existing ontology may be difficult and requires substantial labor. We propose to overcome these limitations by developing an analytical platform that (1) provides a WordNet-based ontology offering a manageable and yet comprehensive set of concept classes, (2) leverages the lexical richness of WordNet to give an extensive characterization of concept class in terms of lexical instances, and (3) integrates a class recognition algorithm that automates the assignment of concept classes to words in naturally occurring text. The ensuing framework makes available an ontological annotation platform that can be effectively integrated with intelligence analysis systems to facilitate evidence marshaling and sustain the creation and validation of inference models.

  2. Wearable cameras for real-time activity annotation

    OpenAIRE

    Zhou, Jiang; Duane, Aaron; Albatal, Rami; Gurrin, Cathal; Johansen, Dag

    2015-01-01

    Google Glass has potential to be a real-time data capture and annotation tool. With professional sports as a use-case, we present a platform which helps a football coach capture and annotate interesting events using Google Glass. In our implementation, an interesting event is indicated by a predefined hand gesture or motion, and our platform can automatically detect these gestures in a video without training any classifier. Three event detectors are examined and our experiment shows that the ...

  3. The car parking used as control tool of individual motor traffic. Good practices of european towns; Le stationnement utilise comme outil de regulation des deplacements individuels motorises. Bonnes pratiques de villes europeennes

    Energy Technology Data Exchange (ETDEWEB)

    Cahn, M.; Vallar, J.P.

    2001-07-01

    This study aims to identify and present significant actions of european towns in the domain of local parking policy as a control tool of motor traffic. Some cases are presented to illustrate the study and six axis of actions have been identified: parking restriction measures to protect the town center and encourage people to use other transport systems; urban areas regulations; initiatives in little towns; tariffs of parking; assistance to disabled persons and actions realized in outlying areas. (A.L.B.)

  4. Pertinent Discussions Toward Modeling the Social Edition: Annotated Bibliographies

    NARCIS (Netherlands)

    R. Siemens; M. Timney; C. Leitch; C. Koolen; A. Garnett

    2012-01-01

    The two annotated bibliographies present in this publication document and feature pertinent discussions toward the activity of modeling the social edition, first exploring reading devices, tools and social media issues and, second, social networking tools for professional readers in the Humanities.

  5. Utilisation of chemically treated coal

    International Nuclear Information System (INIS)

    The numerous application of coal with high content of humic substances are known. They are used in many branches of industry. The complex study of the composition of coal from upper Nitra mines has directed research to its application in the field of ecology and agriculture. The effective sorption layers of this coal and their humic acids can trap a broad spectrum of toxic harmful substances present in industrial wastes, particularly heavy metals. A major source of humic acids is coal - the most abundant and predominant product of plant residue coalification. All ranks of coal contain humic acids but lignite from Novaky deposit represents the most easily available and concentrated from of humic acids. The possibilities of utilisation of humic acids to remove heavy metals from waste waters was studied. The residual concentrations of the investigated metals in the aqueous phase were determined by AAs. From the results follows that the samples of coals humic acids can be used for the heavy metal removal from metal solutions and the real acid mine water. Oxidised coal with high content of humic acids and nitrogen is used in agriculture as fertilizer. Humic acids are active component in coal and can help to utilize almost quantitatively nitrogen in soil. The humic substances block and stabilize toxic metal residues already present in soil. (author)

  6. Predicting word sense annotation agreement

    DEFF Research Database (Denmark)

    Martinez Alonso, Hector; Johannsen, Anders Trærup; Lopez de Lacalle, Oier;

    2015-01-01

    High agreement is a common objective when annotating data for word senses. However, a number of factors make perfect agreement impossible, e.g. the limitations of the sense inventories, the difficulty of the examples or the interpretation preferences of the annotations. Estimating potential...... agreement is thus a relevant task to supplement the evaluation of sense annotations. In this article we propose two methods to predict agreement on word-annotation instances. We experiment with a continuous representation and a three-way discretization of observed agreement. In spite of the difficulty of...

  7. The Ensembl gene annotation system.

    Science.gov (United States)

    Aken, Bronwen L; Ayling, Sarah; Barrell, Daniel; Clarke, Laura; Curwen, Valery; Fairley, Susan; Fernandez Banet, Julio; Billis, Konstantinos; García Girón, Carlos; Hourlier, Thibaut; Howe, Kevin; Kähäri, Andreas; Kokocinski, Felix; Martin, Fergal J; Murphy, Daniel N; Nag, Rishi; Ruffier, Magali; Schuster, Michael; Tang, Y Amy; Vogel, Jan-Hinnerk; White, Simon; Zadissa, Amonida; Flicek, Paul; Searle, Stephen M J

    2016-01-01

    The Ensembl gene annotation system has been used to annotate over 70 different vertebrate species across a wide range of genome projects. Furthermore, it generates the automatic alignment-based annotation for the human and mouse GENCODE gene sets. The system is based on the alignment of biological sequences, including cDNAs, proteins and RNA-seq reads, to the target genome in order to construct candidate transcript models. Careful assessment and filtering of these candidate transcripts ultimately leads to the final gene set, which is made available on the Ensembl website. Here, we describe the annotation process in detail.Database URL: http://www.ensembl.org/index.html. PMID:27337980

  8. A proteogenomic update to Yersinia: enhancing genome annotation

    Directory of Open Access Journals (Sweden)

    Huang Shih-Ting

    2010-08-01

    Full Text Available Abstract Background Modern biomedical research depends on a complete and accurate proteome. With the widespread adoption of new sequencing technologies, genome sequences are generated at a near exponential rate, diminishing the time and effort that can be invested in genome annotation. The resulting gene set contains numerous errors in even the most basic form of annotation: the primary structure of the proteins. Results The application of experimental proteomics data to genome annotation, called proteogenomics, can quickly and efficiently discover misannotations, yielding a more accurate and complete genome annotation. We present a comprehensive proteogenomic analysis of the plague bacterium, Yersinia pestis KIM. We discover non-annotated genes, correct protein boundaries, remove spuriously annotated ORFs, and make major advances towards accurate identification of signal peptides. Finally, we apply our data to 21 other Yersinia genomes, correcting and enhancing their annotations. Conclusions In total, 141 gene models were altered and have been updated in RefSeq and Genbank, which can be accessed seamlessly through any NCBI tool (e.g. blast or downloaded directly. Along with the improved gene models we discover new, more accurate means of identifying signal peptides in proteomics data.

  9. The caBIG annotation and image Markup project.

    Science.gov (United States)

    Channin, David S; Mongkolwat, Pattanasak; Kleper, Vladimir; Sepukar, Kastubh; Rubin, Daniel L

    2010-04-01

    Image annotation and markup are at the core of medical interpretation in both the clinical and the research setting. Digital medical images are managed with the DICOM standard format. While DICOM contains a large amount of meta-data about whom, where, and how the image was acquired, DICOM says little about the content or meaning of the pixel data. An image annotation is the explanatory or descriptive information about the pixel data of an image that is generated by a human or machine observer. An image markup is the graphical symbols placed over the image to depict an annotation. While DICOM is the standard for medical image acquisition, manipulation, transmission, storage, and display, there are no standards for image annotation and markup. Many systems expect annotation to be reported verbally, while markups are stored in graphical overlays or proprietary formats. This makes it difficult to extract and compute with both of them. The goal of the Annotation and Image Markup (AIM) project is to develop a mechanism, for modeling, capturing, and serializing image annotation and markup data that can be adopted as a standard by the medical imaging community. The AIM project produces both human- and machine-readable artifacts. This paper describes the AIM information model, schemas, software libraries, and tools so as to prepare researchers and developers for their use of AIM. PMID:19294468

  10. GIFtS: annotation landscape analysis with GeneCards

    Directory of Open Access Journals (Sweden)

    Dalah Irina

    2009-10-01

    Full Text Available Abstract Background Gene annotation is a pivotal component in computational genomics, encompassing prediction of gene function, expression analysis, and sequence scrutiny. Hence, quantitative measures of the annotation landscape constitute a pertinent bioinformatics tool. GeneCards® is a gene-centric compendium of rich annotative information for over 50,000 human gene entries, building upon 68 data sources, including Gene Ontology (GO, pathways, interactions, phenotypes, publications and many more. Results We present the GeneCards Inferred Functionality Score (GIFtS which allows a quantitative assessment of a gene's annotation status, by exploiting the unique wealth and diversity of GeneCards information. The GIFtS tool, linked from the GeneCards home page, facilitates browsing the human genome by searching for the annotation level of a specified gene, retrieving a list of genes within a specified range of GIFtS value, obtaining random genes with a specific GIFtS value, and experimenting with the GIFtS weighting algorithm for a variety of annotation categories. The bimodal shape of the GIFtS distribution suggests a division of the human gene repertoire into two main groups: the high-GIFtS peak consists almost entirely of protein-coding genes; the low-GIFtS peak consists of genes from all of the categories. Cluster analysis of GIFtS annotation vectors provides the classification of gene groups by detailed positioning in the annotation arena. GIFtS also provide measures which enable the evaluation of the databases that serve as GeneCards sources. An inverse correlation is found (for GIFtS>25 between the number of genes annotated by each source, and the average GIFtS value of genes associated with that source. Three typical source prototypes are revealed by their GIFtS distribution: genome-wide sources, sources comprising mainly highly annotated genes, and sources comprising mainly poorly annotated genes. The degree of accumulated knowledge for a

  11. Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine.

    Science.gov (United States)

    Elsik, Christine G; Tayal, Aditi; Diesh, Colin M; Unni, Deepak R; Emery, Marianne L; Nguyen, Hung N; Hagen, Darren E

    2016-01-01

    We report an update of the Hymenoptera Genome Database (HGD) (http://HymenopteraGenome.org), a model organism database for insect species of the order Hymenoptera (ants, bees and wasps). HGD maintains genomic data for 9 bee species, 10 ant species and 1 wasp, including the versions of genome and annotation data sets published by the genome sequencing consortiums and those provided by NCBI. A new data-mining warehouse, HymenopteraMine, based on the InterMine data warehousing system, integrates the genome data with data from external sources and facilitates cross-species analyses based on orthology. New genome browsers and annotation tools based on JBrowse/WebApollo provide easy genome navigation, and viewing of high throughput sequence data sets and can be used for collaborative genome annotation. All of the genomes and annotation data sets are combined into a single BLAST server that allows users to select and combine sequence data sets to search. PMID:26578564

  12. Collaborative Semantic Annotation of Images : Ontology-Based Model

    Directory of Open Access Journals (Sweden)

    Damien E. ZOMAHOUN

    2015-12-01

    Full Text Available In the quest for models that could help to represen t the meaning of images, some approaches have used contextual knowledge by building semantic hierarchi es. Others have resorted to the integration of imag es analysis improvement knowledge and images interpret ation using ontologies. The images are often annotated with a set of keywords (or ontologies, w hose relevance remains highly subjective and relate d to only one interpretation (one annotator. However , an image can get many associated semantics because annotators can interpret it differently. Th e purpose of this paper is to propose a collaborati ve annotation system that brings out the meaning of im ages from the different interpretations of annotato rs. The different works carried out in this paper lead to a semantic model of an image, i.e. the different means that a picture may have. This method relies o n the different tools of the Semantic Web, especial ly ontologies.

  13. MimoSA: a system for minimotif annotation

    Directory of Open Access Journals (Sweden)

    Kundeti Vamsi

    2010-06-01

    Full Text Available Abstract Background Minimotifs are short peptide sequences within one protein, which are recognized by other proteins or molecules. While there are now several minimotif databases, they are incomplete. There are reports of many minimotifs in the primary literature, which have yet to be annotated, while entirely novel minimotifs continue to be published on a weekly basis. Our recently proposed function and sequence syntax for minimotifs enables us to build a general tool that will facilitate structured annotation and management of minimotif data from the biomedical literature. Results We have built the MimoSA application for minimotif annotation. The application supports management of the Minimotif Miner database, literature tracking, and annotation of new minimotifs. MimoSA enables the visualization, organization, selection and editing functions of minimotifs and their attributes in the MnM database. For the literature components, Mimosa provides paper status tracking and scoring of papers for annotation through a freely available machine learning approach, which is based on word correlation. The paper scoring algorithm is also available as a separate program, TextMine. Form-driven annotation of minimotif attributes enables entry of new minimotifs into the MnM database. Several supporting features increase the efficiency of annotation. The layered architecture of MimoSA allows for extensibility by separating the functions of paper scoring, minimotif visualization, and database management. MimoSA is readily adaptable to other annotation efforts that manually curate literature into a MySQL database. Conclusions MimoSA is an extensible application that facilitates minimotif annotation and integrates with the Minimotif Miner database. We have built MimoSA as an application that integrates dynamic abstract scoring with a high performance relational model of minimotif syntax. MimoSA's TextMine, an efficient paper-scoring algorithm, can be used to

  14. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.

    Science.gov (United States)

    Gaudet, Pascale; Livstone, Michael S; Lewis, Suzanna E; Thomas, Paul D

    2011-09-01

    The goal of the Gene Ontology (GO) project is to provide a uniform way to describe the functions of gene products from organisms across all kingdoms of life and thereby enable analysis of genomic data. Protein annotations are either based on experiments or predicted from protein sequences. Since most sequences have not been experimentally characterized, most available annotations need to be based on predictions. To make as accurate inferences as possible, the GO Consortium's Reference Genome Project is using an explicit evolutionary framework to infer annotations of proteins from a broad set of genomes from experimental annotations in a semi-automated manner. Most components in the pipeline, such as selection of sequences, building multiple sequence alignments and phylogenetic trees, retrieving experimental annotations and depositing inferred annotations, are fully automated. However, the most crucial step in our pipeline relies on software-assisted curation by an expert biologist. This curation tool, Phylogenetic Annotation and INference Tool (PAINT) helps curators to infer annotations among members of a protein family. PAINT allows curators to make precise assertions as to when functions were gained and lost during evolution and record the evidence (e.g. experimentally supported GO annotations and phylogenetic information including orthology) for those assertions. In this article, we describe how we use PAINT to infer protein function in a phylogenetic context with emphasis on its strengths, limitations and guidelines. We also discuss specific examples showing how PAINT annotations compare with those generated by other highly used homology-based methods. PMID:21873635

  15. USING FACEBOOK AS A TEACHING TOOL IN TEACHING FRENCH: EXAMPLE OF UNIVERSITY OF MERSIN / UTILISATION DE FACEBOOK COMME OUTIL DIDACTIQUE EN ENSEIGNEMENT DU FRANÇAIS: EXEMPLE D’UNIVERSITE DE MERSIN

    Directory of Open Access Journals (Sweden)

    Erdinç ASLAN

    2016-06-01

    Full Text Available This study is performed to show the effects of Facebook in French language instruction as a tool. It seeks to analyze the activities of using Facebook in a position of learning French. To conduct this study, we set up a Facebook group with 23 students in French Preparatory Program and three teachers who lead the program in the Department of Translation and Interpreting, Faculty of Letters and Sciences, University of Mersin, in the study period 2014-2015 fall semester. This closed group, teachers shared topics of their courses, images, writings, videos and they want their students to answer to their questions in the group. The students are also participated to the activities making comments under the sharing, giving answers to asked questions, making themselves sharing on this platform. The course announcements were also shared in the group. Moreover, in the current application portion exemplary, extracts the students' work were made anonymous to protect the right to privacy. For the protection of the names and photos profiles have hidden. In the period of the application, the observation technique was used. At the end of the application a student survey was submitted as part of the copy of this study. For the analysis of survey data the content analysis technique was used.

  16. LocusTrack: Integrated visualization of GWAS results and genomic annotation

    OpenAIRE

    Cuellar-Partida, Gabriel; Renteria, Miguel E.; Macgregor, Stuart

    2015-01-01

    Background Genome-wide association studies (GWAS) are an important tool for the mapping of complex traits and diseases. Visual inspection of genomic annotations may be used to generate insights into the biological mechanisms underlying GWAS-identified loci. Results We developed LocusTrack, a web-based application that annotates and creates plots of regional GWAS results and incorporates user-specified tracks that display annotations such as linkage disequilibrium (LD), phylogenetic conservati...

  17. ProteomeCommons.org Collaborative Annotation and Project Management Resource Integrated With the Tranche Repository

    OpenAIRE

    Hill, James A.; Smith, Bryan E.; Papoulias, Panagiotis G.; Andrews, Philip C.

    2010-01-01

    ProteomeCommons.org has implemented a resource that incorporates concepts of Web 2.0 social networking for collaborative annotation of data sets placed in the Tranche repository. The annotation tools are part of a project management resource that is effective for individual laboratories or large distributed groups. The creation of the resource was motivated by the need for a way to encourage annotation of data sets with high accuracy and compliance rates. The system is designed to respond to ...

  18. Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

    Energy Technology Data Exchange (ETDEWEB)

    Haas, B J; Salzberg, S L; Zhu, W; Pertea, M; Allen, J E; Orvis, J; White, O; Buell, C R; Wortman, J R

    2007-12-10

    EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

  19. Integrating and annotating the interactome using the MiMI plugin for cytoscape

    OpenAIRE

    Gao, Jing; Ade, Alex S; Tarcea, V. Glenn; Weymouth, Terry E.; Mirel, Barbara R.; Jagadish, H.V.; States, David J.

    2008-01-01

    Summary: The MiMI molecular interaction repository integrates data from multiple sources, resolves interactions to standard gene names and symbols, links to annotation data from GO, MeSH and PubMed and normalizes the descriptions of interaction type. Here, we describe a Cytoscape plugin that retrieves interaction and annotation data from MiMI and links out to multiple data sources and tools. Community annotation of the interactome is supported.

  20. Collective dynamics of social annotation

    CERN Document Server

    Cattuto, Ciro; Baldassarri, Andrea; Schehr, G; Loreto, Vittorio

    2009-01-01

    The enormous increase of popularity and use of the WWW has led in the recent years to important changes in the ways people communicate. An interesting example of this fact is provided by the now very popular social annotation systems, through which users annotate resources (such as web pages or digital photographs) with text keywords dubbed tags. Understanding the rich emerging structures resulting from the uncoordinated actions of users calls for an interdisciplinary effort. In particular concepts borrowed from statistical physics, such as random walks, and the complex networks framework, can effectively contribute to the mathematical modeling of social annotation systems. Here we show that the process of social annotation can be seen as a collective but uncoordinated exploration of an underlying semantic space, pictured as a graph, through a series of random walks. This modeling framework reproduces several aspects, so far unexplained, of social annotation, among which the peculiar growth of the size of the...

  1. Annotation of Regular Polysemy

    DEFF Research Database (Denmark)

    Martinez Alonso, Hector

    Regular polysemy has received a lot of attention from the theory of lexical semantics and from computational linguistics. However, there is no consensus on how to represent the sense of underspecified examples at the token level, namely when annotating or disambiguating senses of metonymic words...... like “London” (Location/Organization) or “cup” (Container/Content). The goal of this dissertation is to assess whether metonymic sense underspecification justifies incorporating a third sense into our sense inventories, thereby treating the underspecified sense as independent from the literal and...... metonymic. We have conducted an analysis in English, Danish and Spanish. Later on, we have tried to replicate the human judgments by means of unsupervised and semi-supervised sense prediction. The automatic sense-prediction systems have been unable to find empiric evidence for the underspecified sense, even...

  2. Utilisation of biofuels in CHP system

    International Nuclear Information System (INIS)

    The paper deals with possibilities of utilisation of biogas for energy purposes by combined production of electric power and heat. As a example of like this cogeneration units the urban waste water treatment Lucenec is given. (authors)

  3. IMG ER: A System for Microbial Genome Annotation Expert Review and Curation

    Energy Technology Data Exchange (ETDEWEB)

    Markowitz, Victor M.; Mavromatis, Konstantinos; Ivanova, Natalia N.; Chen, I-Min A.; Chu, Ken; Kyrpides, Nikos C.

    2009-05-25

    A rapidly increasing number of microbial genomes are sequenced by organizations worldwide and are eventually included into various public genome data resources. The quality of the annotations depends largely on the original dataset providers, with erroneous or incomplete annotations often carried over into the public resources and difficult to correct. We have developed an Expert Review (ER) version of the Integrated Microbial Genomes (IMG) system, with the goal of supporting systematic and efficient revision of microbial genome annotations. IMG ER provides tools for the review and curation of annotations of both new and publicly available microbial genomes within IMG's rich integrated genome framework. New genome datasets are included into IMG ER prior to their public release either with their native annotations or with annotations generated by IMG ER's annotation pipeline. IMG ER tools allow addressing annotation problems detected with IMG's comparative analysis tools, such as genes missed by gene prediction pipelines or genes without an associated function. Over the past year, IMG ER was used for improving the annotations of about 150 microbial genomes.

  4. Model and Interoperability using Meta Data Annotations

    Science.gov (United States)

    David, O.

    2011-12-01

    Software frameworks and architectures are in need for meta data to efficiently support model integration. Modelers have to know the context of a model, often stepping into modeling semantics and auxiliary information usually not provided in a concise structure and universal format, consumable by a range of (modeling) tools. XML often seems the obvious solution for capturing meta data, but its wide adoption to facilitate model interoperability is limited by XML schema fragmentation, complexity, and verbosity outside of a data-automation process. Ontologies seem to overcome those shortcomings, however the practical significance of their use remains to be demonstrated. OMS version 3 took a different approach for meta data representation. The fundamental building block of a modular model in OMS is a software component representing a single physical process, calibration method, or data access approach. Here, programing language features known as Annotations or Attributes were adopted. Within other (non-modeling) frameworks it has been observed that annotations lead to cleaner and leaner application code. Framework-supported model integration, traditionally accomplished using Application Programming Interfaces (API) calls is now achieved using descriptive code annotations. Fully annotated components for various hydrological and Ag-system models now provide information directly for (i) model assembly and building, (ii) data flow analysis for implicit multi-threading or visualization, (iii) automated and comprehensive model documentation of component dependencies, physical data properties, (iv) automated model and component testing, calibration, and optimization, and (v) automated audit-traceability to account for all model resources leading to a particular simulation result. Such a non-invasive methodology leads to models and modeling components with only minimal dependencies on the modeling framework but a strong reference to its originating code. Since models and

  5. Utilisation of the buffy coat technique and an antibody-detection ELISA as tools for assessing the impact of trypanosomosis on health and productivity of N'Dama cattle

    International Nuclear Information System (INIS)

    The buffy coat technique (BCT), a parasitological test, and an indirect antibody ELISA (Ab-ELISA) were used to detect trypanosome infections in blood and serum samples, respectively, collected on N'Dama cattle exposed to natural high tsetse challenge. These two diagnostic tools were also utilized to assess trypanosomal status in sequentially collected blood and serum samples from two groups composed of 5 N'Dama cattle each experimentally challenged with Trypanosoma congolense and T. vivax, In both studies, packed red cell volume (PCV) and live weight were measured. The specificity of the Ab-ELISA was computed by testing approximately 70 serum samples obtained from a cattle population kept under zero tsetse challenge. The specificity was found to be 95.8% for T. vivax and 97. 1 % for T. congolense. In the field study, 3.9% (12/310) of blood samples was parasitologically positive. In corresponding serum samples the prevalence of positive trypanosome sero-reactors was 54.8% (170/310). However, antibodies against trypanosomes persisted in serum when blood samples were no longer parasitologically positive. In both blood and serum samples, T. vivax was found to be the main infecting species. The sensitivity of the Ab-ELISA for T. vivax was 81.8%. Due to the extremely low numbers of T. congolense infection (only one), as detected by BCT, the sensitivity for that trypanosome species was not computed. In the experimentally challenged cattle, 80% (24/30) and 33.3% (10/30) of blood samples were BCT positive for T. congolense and T. vivax, respectively. Antibodies in corresponding sera were present in 69% (20/29) and 96.3% (26/27) of animals challenged with T. congolense and T. vivax, respectively. The serological assay for T. congolense antibody detection exhibited high cross-reactivity with T. vivax antigens, as assessed in sera collected from T. vivax infected animals. In the field study, cattle showing the presence of antibodies against T. congolense and/or T. vivax had

  6. AGeS: A Software System for Microbial Genome Sequence Annotation

    Science.gov (United States)

    Kumar, Kamal; Desai, Valmik; Cheng, Li; Khitrov, Maxim; Grover, Deepak; Satya, Ravi Vijaya; Yu, Chenggang; Zavaljevski, Nela; Reifman, Jaques

    2011-01-01

    Background The annotation of genomes from next-generation sequencing platforms needs to be rapid, high-throughput, and fully integrated and automated. Although a few Web-based annotation services have recently become available, they may not be the best solution for researchers that need to annotate a large number of genomes, possibly including proprietary data, and store them locally for further analysis. To address this need, we developed a standalone software application, the Annotation of microbial Genome Sequences (AGeS) system, which incorporates publicly available and in-house-developed bioinformatics tools and databases, many of which are parallelized for high-throughput performance. Methodology The AGeS system supports three main capabilities. The first is the storage of input contig sequences and the resulting annotation data in a central, customized database. The second is the annotation of microbial genomes using an integrated software pipeline, which first analyzes contigs from high-throughput sequencing by locating genomic regions that code for proteins, RNA, and other genomic elements through the Do-It-Yourself Annotation (DIYA) framework. The identified protein-coding regions are then functionally annotated using the in-house-developed Pipeline for Protein Annotation (PIPA). The third capability is the visualization of annotated sequences using GBrowse. To date, we have implemented these capabilities for bacterial genomes. AGeS was evaluated by comparing its genome annotations with those provided by three other methods. Our results indicate that the software tools integrated into AGeS provide annotations that are in general agreement with those provided by the compared methods. This is demonstrated by a >94% overlap in the number of identified genes, a significant number of identical annotated features, and a >90% agreement in enzyme function predictions. PMID:21408217

  7. Web Annotation and Threaded Forum: How Did Learners Use the Two Environments in an Online Discussion?

    Science.gov (United States)

    Sun, Yanyan; Gao, Fei

    2014-01-01

    Web annotation is a Web 2.0 technology that allows learners to work collaboratively on web pages or electronic documents. This study explored the use of Web annotation as an online discussion tool by comparing it to a traditional threaded discussion forum. Ten graduate students participated in the study. Participants had access to both a Web…

  8. Semantic annotation of biological concepts interplaying microbial cellular responses

    Directory of Open Access Journals (Sweden)

    Carreira Rafael

    2011-11-01

    Full Text Available Abstract Background Automated extraction systems have become a time saving necessity in Systems Biology. Considerable human effort is needed to model, analyse and simulate biological networks. Thus, one of the challenges posed to Biomedical Text Mining tools is that of learning to recognise a wide variety of biological concepts with different functional roles to assist in these processes. Results Here, we present a novel corpus concerning the integrated cellular responses to nutrient starvation in the model-organism Escherichia coli. Our corpus is a unique resource in that it annotates biomedical concepts that play a functional role in expression, regulation and metabolism. Namely, it includes annotations for genetic information carriers (genes and DNA, RNA molecules, proteins (transcription factors, enzymes and transporters, small metabolites, physiological states and laboratory techniques. The corpus consists of 130 full-text papers with a total of 59043 annotations for 3649 different biomedical concepts; the two dominant classes are genes (highest number of unique concepts and compounds (most frequently annotated concepts, whereas other important cellular concepts such as proteins account for no more than 10% of the annotated concepts. Conclusions To the best of our knowledge, a corpus that details such a wide range of biological concepts has never been presented to the text mining community. The inter-annotator agreement statistics provide evidence of the importance of a consolidated background when dealing with such complex descriptions, the ambiguities naturally arising from the terminology and their impact for modelling purposes. Availability is granted for the full-text corpora of 130 freely accessible documents, the annotation scheme and the annotation guidelines. Also, we include a corpus of 340 abstracts.

  9. The GOA database in 2009--an integrated Gene Ontology Annotation resource.

    Science.gov (United States)

    Barrell, Daniel; Dimmer, Emily; Huntley, Rachael P; Binns, David; O'Donovan, Claire; Apweiler, Rolf

    2009-01-01

    The Gene Ontology Annotation (GOA) project at the EBI (http://www.ebi.ac.uk/goa) provides high-quality electronic and manual associations (annotations) of Gene Ontology (GO) terms to UniProt Knowledgebase (UniProtKB) entries. Annotations created by the project are collated with annotations from external databases to provide an extensive, publicly available GO annotation resource. Currently covering over 160 000 taxa, with greater than 32 million annotations, GOA remains the largest and most comprehensive open-source contributor to the GO Consortium (GOC) project. Over the last five years, the group has augmented the number and coverage of their electronic pipelines and a number of new manual annotation projects and collaborations now further enhance this resource. A range of files facilitate the download of annotations for particular species, and GO term information and associated annotations can also be viewed and downloaded from the newly developed GOA QuickGO tool (http://www.ebi.ac.uk/QuickGO), which allows users to precisely tailor their annotation set. PMID:18957448

  10. Analysing Temporally Annotated Corpora with CAVaT

    CERN Document Server

    Derczynski, Leon

    2012-01-01

    We present CAVaT, a tool that performs Corpus Analysis and Validation for TimeML. CAVaT is an open source, modular checking utility for statistical analysis of features specific to temporally-annotated natural language corpora. It provides reporting, highlights salient links between a variety of general and time-specific linguistic features, and also validates a temporal annotation to ensure that it is logically consistent and sufficiently annotated. Uniquely, CAVaT provides analysis specific to TimeML-annotated temporal information. TimeML is a standard for annotating temporal information in natural language text. In this paper, we present the reporting part of CAVaT, and then its error-checking ability, including the workings of several novel TimeML document verification methods. This is followed by the execution of some example tasks using the tool to show relations between times, events, signals and links. We also demonstrate inconsistencies in a TimeML corpus (TimeBank) that have been detected with CAVaT...

  11. Combined evidence annotation of transposable elements in genome sequences.

    Directory of Open Access Journals (Sweden)

    Hadi Quesneville

    2005-07-01

    Full Text Available Transposable elements (TEs are mobile, repetitive sequences that make up significant fractions of metazoan genomes. Despite their near ubiquity and importance in genome and chromosome biology, most efforts to annotate TEs in genome sequences rely on the results of a single computational program, RepeatMasker. In contrast, recent advances in gene annotation indicate that high-quality gene models can be produced from combining multiple independent sources of computational evidence. To elevate the quality of TE annotations to a level comparable to that of gene models, we have developed a combined evidence-model TE annotation pipeline, analogous to systems used for gene annotation, by integrating results from multiple homology-based and de novo TE identification methods. As proof of principle, we have annotated "TE models" in Drosophila melanogaster Release 4 genomic sequences using the combined computational evidence derived from RepeatMasker, BLASTER, TBLASTX, all-by-all BLASTN, RECON, TE-HMM and the previous Release 3.1 annotation. Our system is designed for use with the Apollo genome annotation tool, allowing automatic results to be curated manually to produce reliable annotations. The euchromatic TE fraction of D. melanogaster is now estimated at 5.3% (cf. 3.86% in Release 3.1, and we found a substantially higher number of TEs (n = 6,013 than previously identified (n = 1,572. Most of the new TEs derive from small fragments of a few hundred nucleotides long and highly abundant families not previously annotated (e.g., INE-1. We also estimated that 518 TE copies (8.6% are inserted into at least one other TE, forming a nest of elements. The pipeline allows rapid and thorough annotation of even the most complex TE models, including highly deleted and/or nested elements such as those often found in heterochromatic sequences. Our pipeline can be easily adapted to other genome sequences, such as those of the D. melanogaster heterochromatin or other

  12. Sequence-based feature prediction and annotation of proteins

    DEFF Research Database (Denmark)

    Juncker, Agnieszka; Jensen, Lars J.; Pierleoni, Andrea; Bernsel, Andreas; Tress, Michael L.; Bork, Peer; Von Heijne, Gunnar; Valencia, Alfonso; A Ouzounis, Christos; Casadio, Rita; Brunak, Søren

    2009-01-01

    A recent trend in computational methods for annotation of protein function is that many prediction tools are combined in complex workflows and pipelines to facilitate the analysis of feature combinations, for example, the entire repertoire of kinase-binding motifs in the human proteome....

  13. Protein function annotation by homology-based inference

    OpenAIRE

    Loewenstein, Yaniv; Raimondo, Domenico; Redfern, Oliver C.; Watson, James; Frishman, Dmitrij; Linial, Michal; Orengo, Christine; Thornton, Janet; Tramontano, Anna

    2009-01-01

    With many genomes now sequenced, computational annotation methods to characterize genes and proteins from their sequence are increasingly important. The BioSapiens Network has developed tools to address all stages of this process, and here we review progress in the automated prediction of protein function based on protein sequence and structure.

  14. Gender and Health Care Utilisation in Pakistan

    OpenAIRE

    Syed Mubashir Ali

    2000-01-01

    This study is undertaken to test whether or not there exists gender bias in health care utilisation of sick children in Pakistan. Overall, the results are encouraging, as medical consultation has been sought for by a very high proportion (79 percent) of sick children. Moreover, there do not appear to be significant differences by gender in health care utilisation, be it curative or preventive. This is so in spite of the fact that many studies on various gender-related issues in Pakistan have ...

  15. Knowledge Representation and Management. From Ontology to Annotation

    Science.gov (United States)

    Darmoni, S.J.

    2015-01-01

    Summary Objective To summarize the best papers in the field of Knowledge Representation and Management (KRM). Methods A comprehensive review of medical informatics literature was performed to select some of the most interesting papers of KRM published in 2014. Results Four articles were selected, two focused on annotation and information retrieval using an ontology. The two others focused mainly on ontologies, one dealing with the usage of a temporal ontology in order to analyze the content of narrative document, one describing a methodology for building multilingual ontologies. Conclusion Semantic models began to show their efficiency, coupled with annotation tools. PMID:26293860

  16. Enhancing Cloud Resource Utilisation using Statistical Analysis

    Directory of Open Access Journals (Sweden)

    Sijin He

    2014-04-01

    Full Text Available Resource provisioning based on virtual machine (VM has been widely accepted and adopted in cloud computing environments. A key problem resulting from using static scheduling approaches for allocating VMs on different physical machines (PMs is that resources tend to be not fully utilised. Although some existing cloud reconfiguration algorithms have been developed to address the problem, they normally result in high migration costs and low resource utilisation due to ignoring the multi-dimensional characteristics of VMs and PMs. In this paper we present and evaluate a new algorithm for improving resource utilisation for cloud providers. By using a multivariate probabilistic model, our algorithm selects suitable PMs for VM re-allocation which are then used to generate a reconfiguration plan. We also describe two heuristics metrics which can be used in the algorithm to capture the multi-dimensional characteristics of VMs and PMs. By combining these two heuristics metrics in our experiments, we observed that our approach improves the resource utilisation level by around 8% for cloud providers, such as IC Cloud, which accept user-defined VM configurations and 14% for providers, such as Amazon EC2, which only provide limited types of VM configurations.

  17. Energetic utilisation of biomass in Hungary

    International Nuclear Information System (INIS)

    Energetic utilisation of biomass has been known since prehistoric times and was only pushed into the background by the technological developments of the last century. The energy crisis and, more recently, environmental problems have now brought it back to the fore, and efforts are being made worldwide to find modern technical applications for biomass and contribute to its advance. (orig.)

  18. Construction of an annotated corpus to support biomedical information extraction

    Directory of Open Access Journals (Sweden)

    McNaught John

    2009-10-01

    Full Text Available Abstract Background Information Extraction (IE is a component of text mining that facilitates knowledge discovery by automatically locating instances of interesting biomedical events from huge document collections. As events are usually centred on verbs and nominalised verbs, understanding the syntactic and semantic behaviour of these words is highly important. Corpora annotated with information concerning this behaviour can constitute a valuable resource in the training of IE components and resources. Results We have defined a new scheme for annotating sentence-bound gene regulation events, centred on both verbs and nominalised verbs. For each event instance, all participants (arguments in the same sentence are identified and assigned a semantic role from a rich set of 13 roles tailored to biomedical research articles, together with a biological concept type linked to the Gene Regulation Ontology. To our knowledge, our scheme is unique within the biomedical field in terms of the range of event arguments identified. Using the scheme, we have created the Gene Regulation Event Corpus (GREC, consisting of 240 MEDLINE abstracts, in which events relating to gene regulation and expression have been annotated by biologists. A novel method of evaluating various different facets of the annotation task showed that average inter-annotator agreement rates fall within the range of 66% - 90%. Conclusion The GREC is a unique resource within the biomedical field, in that it annotates not only core relationships between entities, but also a range of other important details about these relationships, e.g., location, temporal, manner and environmental conditions. As such, it is specifically designed to support bio-specific tool and resource development. It has already been used to acquire semantic frames for inclusion within the BioLexicon (a lexical, terminological resource to aid biomedical text mining. Initial experiments have also shown that the corpus may

  19. Collective dynamics of social annotation.

    Science.gov (United States)

    Cattuto, Ciro; Barrat, Alain; Baldassarri, Andrea; Schehr, Gregory; Loreto, Vittorio

    2009-06-30

    The enormous increase of popularity and use of the worldwide web has led in the recent years to important changes in the ways people communicate. An interesting example of this fact is provided by the now very popular social annotation systems, through which users annotate resources (such as web pages or digital photographs) with keywords known as "tags." Understanding the rich emergent structures resulting from the uncoordinated actions of users calls for an interdisciplinary effort. In particular concepts borrowed from statistical physics, such as random walks (RWs), and complex networks theory, can effectively contribute to the mathematical modeling of social annotation systems. Here, we show that the process of social annotation can be seen as a collective but uncoordinated exploration of an underlying semantic space, pictured as a graph, through a series of RWs. This modeling framework reproduces several aspects, thus far unexplained, of social annotation, among which are the peculiar growth of the size of the vocabulary used by the community and its complex network structure that represents an externalization of semantic structures grounded in cognition and that are typically hard to access. PMID:19506244

  20. ProSAT+: visualizing sequence annotations on 3D structure.

    Science.gov (United States)

    Stank, Antonia; Richter, Stefan; Wade, Rebecca C

    2016-08-01

    PRO: tein S: tructure A: nnotation T: ool-plus (ProSAT(+)) is a new web server for mapping protein sequence annotations onto a protein structure and visualizing them simultaneously with the structure. ProSAT(+) incorporates many of the features of the preceding ProSAT and ProSAT2 tools but also provides new options for the visualization and sharing of protein annotations. Data are extracted from the UniProt KnowledgeBase, the RCSB PDB and the PDBe SIFTS resource, and visualization is performed using JSmol. User-defined sequence annotations can be added directly to the URL, thus enabling visualization and easy data sharing. ProSAT(+) is available at http://prosat.h-its.org. PMID:27284084

  1. Apollo2Go: a web service adapter for the Apollo genome viewer to enable distributed genome annotation

    Directory of Open Access Journals (Sweden)

    Mayer Klaus FX

    2007-08-01

    Full Text Available Abstract Background Apollo, a genome annotation viewer and editor, has become a widely used genome annotation and visualization tool for distributed genome annotation projects. When using Apollo for annotation, database updates are carried out by uploading intermediate annotation files into the respective database. This non-direct database upload is laborious and evokes problems of data synchronicity. Results To overcome these limitations we extended the Apollo data adapter with a generic, configurable web service client that is able to retrieve annotation data in a GAME-XML-formatted string and pass it on to Apollo's internal input routine. Conclusion This Apollo web service adapter, Apollo2Go, simplifies the data exchange in distributed projects and aims to render the annotation process more comfortable. The Apollo2Go software is freely available from ftp://ftpmips.gsf.de/plants/apollo_webservice.

  2. Assessment of community-submitted ontology annotations from a novel database-journal partnership.

    Science.gov (United States)

    Berardini, Tanya Z; Li, Donghui; Muller, Robert; Chetty, Raymond; Ploetz, Larry; Singh, Shanker; Wensel, April; Huala, Eva

    2012-01-01

    As the scientific literature grows, leading to an increasing volume of published experimental data, so does the need to access and analyze this data using computational tools. The most commonly used method to convert published experimental data on gene function into controlled vocabulary annotations relies on a professional curator, employed by a model organism database or a more general resource such as UniProt, to read published articles and compose annotation statements based on the articles' contents. A more cost-effective and scalable approach capable of capturing gene function data across the whole range of biological research organisms in computable form is urgently needed. We have analyzed a set of ontology annotations generated through collaborations between the Arabidopsis Information Resource and several plant science journals. Analysis of the submissions entered using the online submission tool shows that most community annotations were well supported and the ontology terms chosen were at an appropriate level of specificity. Of the 503 individual annotations that were submitted, 97% were approved and community submissions captured 72% of all possible annotations. This new method for capturing experimental results in a computable form provides a cost-effective way to greatly increase the available body of annotations without sacrificing annotation quality. Database URL: www.arabidopsis.org. PMID:22859749

  3. Vcfanno: fast, flexible annotation of genetic variants.

    Science.gov (United States)

    Pedersen, Brent S; Layer, Ryan M; Quinlan, Aaron R

    2016-01-01

    The integration of genome annotations is critical to the identification of genetic variants that are relevant to studies of disease or other traits. However, comprehensive variant annotation with diverse file formats is difficult with existing methods. Here we describe vcfanno, which flexibly extracts and summarizes attributes from multiple annotation files and integrates the annotations within the INFO column of the original VCF file. By leveraging a parallel "chromosome sweeping" algorithm, we demonstrate substantial performance gains by annotating ~85,000 variants per second with 50 attributes from 17 commonly used genome annotation resources. Vcfanno is available at https://github.com/brentp/vcfanno under the MIT license. PMID:27250555

  4. Comparing functional annotation analyses with Catmap

    Directory of Open Access Journals (Sweden)

    Krogh Morten

    2004-12-01

    Full Text Available Abstract Background Ranked gene lists from microarray experiments are usually analysed by assigning significance to predefined gene categories, e.g., based on functional annotations. Tools performing such analyses are often restricted to a category score based on a cutoff in the ranked list and a significance calculation based on random gene permutations as null hypothesis. Results We analysed three publicly available data sets, in each of which samples were divided in two classes and genes ranked according to their correlation to class labels. We developed a program, Catmap (available for download at http://bioinfo.thep.lu.se/Catmap, to compare different scores and null hypotheses in gene category analysis, using Gene Ontology annotations for category definition. When a cutoff-based score was used, results depended strongly on the choice of cutoff, introducing an arbitrariness in the analysis. Comparing results using random gene permutations and random sample permutations, respectively, we found that the assigned significance of a category depended strongly on the choice of null hypothesis. Compared to sample label permutations, gene permutations gave much smaller p-values for large categories with many coexpressed genes. Conclusions In gene category analyses of ranked gene lists, a cutoff independent score is preferable. The choice of null hypothesis is very important; random gene permutations does not work well as an approximation to sample label permutations.

  5. Intégration de raisonnements automatiques dans le système d'annotation MemoNote

    OpenAIRE

    Mokeddem, Hakim; Desmoulins, Cyrille

    2012-01-01

    Les raisonnements automatiques dans les EIAH basés sur les ontologies reposent le plus souvent sur des algorithmes ad hoc du fait des langages de représentations utilisés. Cet article développe autour de l'exemple du logiciel d'annotation MemoNote, les avantages de l'utilisation des technologies standards du web sémantique pour permettre des raisonnements sur les ontologies. A partir des limites de la version MemoNote actuelle basée sur le langage des Frames, l'utilisation d'une représentatio...

  6. Using Semantic Annotation for Mining Privacy and Security Requirements from European Union Directives

    OpenAIRE

    Guarda, Paolo; Kiyavitskaya, Nadzeya; Zannone, Nicola

    2008-01-01

    The increasing complexity of software systems and growing demand for regulations compliance require effective methods and tools to support requirements analysts activities. In order to facilitate alignment of software system requirements and regulations, systematic methods and tools automating regulations analysis must be developed. This work explores applicability of the semantic annotation tool Cerno to mining of rights and obligations from European privacy directives.

  7. Increased health care utilisation in international adoptees

    DEFF Research Database (Denmark)

    Graff, Heidi Jeannet; Siersma, Volkert Dirk; Kragstrup, Jakob;

    2015-01-01

    Introduction: Several studies have documented thatinternational adoptees have an increased occurrence ofhealth problems and contacts to the health-care systemafter arriving to their new country of residence. This maybe explained by pre-adoption adversities, especially for theperiod immediately...... after adoption. Our study aimed to theassess health-care utilisation of international adoptees inprimary and secondary care for somatic and psychiatricdiagnoses in a late post-adoption period. Is there an increaseduse of the health-care system in this period, evenwhen increased morbidity in the group...... of internationaladoptees is taken into consideration? Methods: This was a Danish register-based cohort studyexamining health-care utilisation in a multivariable two-partmodel. The prevalence of selected outcomes and the quantityof use were assessed in a late (year three, four and five)post-adoption period. The cohort...

  8. Systems Theory and Communication. Annotated Bibliography.

    Science.gov (United States)

    Covington, William G., Jr.

    This annotated bibliography presents annotations of 31 books and journal articles dealing with systems theory and its relation to organizational communication, marketing, information theory, and cybernetics. Materials were published between 1963 and 1992 and are listed alphabetically by author. (RS)

  9. International Standard for a Linguistic Annotation Framework

    CERN Document Server

    Romary, Laurent

    2004-01-01

    This paper describes the Linguistic Annotation Framework under development within ISO TC37 SC4 WG1. The Linguistic Annotation Framework is intended to serve as a basis for harmonizing existing language resources as well as developing new ones.

  10. Annotated Bibliography, Grades K-6.

    Science.gov (United States)

    Massachusetts Dept. of Education, Boston. Bureau of Nutrition Education and School Food Services.

    This annotated bibliography on nutrition is for the use of teachers at the elementary grade level. It contains a list of books suitable for reading about nutrition and foods for pupils from kindergarten through the sixth grade. Films and audiovisual presentations for classroom use are also listed. The names and addresses from which these materials…

  11. Annotating Coloured Petri Nets

    DEFF Research Database (Denmark)

    Lindstrøm, Bo; Wells, Lisa Marie

    2002-01-01

    Coloured Petri nets (CP-nets) can be used for several fundamentally different purposes like functional analysis, performance analysis, and visualisation. To be able to use the corresponding tool extensions and libraries it is sometimes necessary to include extra auxiliary information in the CP......-net. An example of such auxiliary information is a counter which is associated with a token to be able to do performance analysis. Modifying colour sets and arc inscriptions in a CP-net to support a specific use may lead to creation of several slightly different CP-nets – only to support the different...... uses of the same basic CP-net. One solution to this problem is that the auxiliary information is not integrated into colour sets and arc inscriptions of a CP-net, but is kept separately. This makes it easy to disable this auxiliary information if a CP-net is to be used for another purpose. This paper...

  12. Enhancing Graduate Attributes Utilising Social Media

    OpenAIRE

    Bates, Eric; Hinch, Peter

    2014-01-01

    The objective of this research was to ascertain the usefulness of utilising social media to enhance graduate attributes. This study was conducted during one semester and concentrated on one aspect of graduate attributes which were interview skills. Two videos were scripted, shot and edited that focused on interviews from the perspective of both the interviewer and the interviewee. These videos were incorporated into workshops with first year and second year level 8 undergraduate students. Pre...

  13. Utilising intrinsic robustness in agricultural production systems

    OpenAIRE

    Napel, ten, H.M.Th.D.; Bianchi, F.J.J.A.; Bestman, M.W.P.

    2006-01-01

    This paper explores the potential of utilising robust crops and livestock for improving sustainability of agriculture. Two approaches for dealing with unwanted fluctuations that may influence agricultural production, such as diseases and pests, are discussed. The prevailing approach, which we call the ‘Control Model’, is to protect crops and livestock from disturbances as much as possible, to regain balance with monitoring and intervention and to look for add-on solutions only. There are a nu...

  14. Concept annotation in the CRAFT corpus

    OpenAIRE

    Bada Michael; Eckert Miriam; Evans Donald; Garcia Kristin; Shipley Krista; Sitnikov Dmitry; Baumgartner William A; Cohen K; Verspoor Karin; Blake Judith A; Hunter Lawrence E

    2012-01-01

    Abstract Background Manually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text. Results This paper presents the concept annotations of the Colorado Richly Annotated Full-Text (CRAFT) Corpus, a collection of 97 full-length, open-access biomedical journal articles that have been annotated both semantically and syntactically to serve as a research resource for the biomedical natural-language-processing (NLP) community. CRA...

  15. Annotating images by mining image search results

    NARCIS (Netherlands)

    X.J. Wang; L. Zhang; X. Li; W.Y. Ma

    2008-01-01

    Although it has been studied for years by the computer vision and machine learning communities, image annotation is still far from practical. In this paper, we propose a novel attempt at model-free image annotation, which is a data-driven approach that annotates images by mining their search results

  16. Eight questions about semantic web annotations

    OpenAIRE

    Euzenat, Jérôme

    2002-01-01

    Improving information retrieval is annotation¹s central goal. However, without sufficient planning, annotation - especially when running a robot and attaching automatically extracted content - risks producing incoherent information. The author recommends answering eight questions before you annotate. He provides a practical application of this approach, and discusses applying the questions to other systems.

  17. Annotation and Classification of Argumentative Writing Revisions

    Science.gov (United States)

    Zhang, Fan; Litman, Diane

    2015-01-01

    This paper explores the annotation and classification of students' revision behaviors in argumentative writing. A sentence-level revision schema is proposed to capture why and how students make revisions. Based on the proposed schema, a small corpus of student essays and revisions was annotated. Studies show that manual annotation is reliable with…

  18. Genome re-annotation: a wiki solution?

    OpenAIRE

    Salzberg, Steven L.

    2007-01-01

    The annotation of most genomes becomes outdated over time, owing in part to our ever-improving knowledge of genomes and in part to improvements in bioinformatics software. Unfortunately, annotation is rarely if ever updated and resources to support routine reannotation are scarce. Wiki software, which would allow many scientists to edit each genome's annotation, offers one possible solution.

  19. Applied bioinformatics: Genome annotation and transcriptome analysis

    DEFF Research Database (Denmark)

    Gupta, Vikas

    Next generation sequencing (NGS) has revolutionized the field of genomics and its wide range of applications has resulted in the genome-wide analysis of hundreds of species and the development of thousands of computational tools. This thesis represents my work on NGS analysis of four species, Lotus...... japonicus (Lotus), Vaccinium corymbosum (blueberry), Stegodyphus mimosarum (spider) and Trifolium occidentale (clover). From a bioinformatics data analysis perspective, my work can be divided into three parts; genome annotation, small RNA, and gene expression analysis. Lotus is a legume of significant...... agricultural and biological importance. Its capacity to form symbiotic relationships with rhizobia and microrrhizal fungi has fascinated researchers for years. Lotus has a small genome of approximately 470 Mb and a short life cycle of 2 to 3 months, which has made Lotus a model legume plant for many molecular...

  20. 3D annotation and manipulation of medical anatomical structures

    Science.gov (United States)

    Vitanovski, Dime; Schaller, Christian; Hahn, Dieter; Daum, Volker; Hornegger, Joachim

    2009-02-01

    Although the medical scanners are rapidly moving towards a three-dimensional paradigm, the manipulation and annotation/labeling of the acquired data is still performed in a standard 2D environment. Editing and annotation of three-dimensional medical structures is currently a complex task and rather time-consuming, as it is carried out in 2D projections of the original object. A major problem in 2D annotation is the depth ambiguity, which requires 3D landmarks to be identified and localized in at least two of the cutting planes. Operating directly in a three-dimensional space enables the implicit consideration of the full 3D local context, which significantly increases accuracy and speed. A three-dimensional environment is as well more natural optimizing the user's comfort and acceptance. The 3D annotation environment requires the three-dimensional manipulation device and display. By means of two novel and advanced technologies, Wii Nintendo Controller and Philips 3D WoWvx display, we define an appropriate 3D annotation tool and a suitable 3D visualization monitor. We define non-coplanar setting of four Infrared LEDs with a known and exact position, which are tracked by the Wii and from which we compute the pose of the device by applying a standard pose estimation algorithm. The novel 3D renderer developed by Philips uses either the Z-value of a 3D volume, or it computes the depth information out of a 2D image, to provide a real 3D experience without having some special glasses. Within this paper we present a new framework for manipulation and annotation of medical landmarks directly in three-dimensional volume.

  1. Ontology Based Document Annotation: Trends and Open Research Problems

    OpenAIRE

    Corcho, Oscar

    2006-01-01

    Metadata is used to describe documents and applications, improving information seeking and retrieval and its understanding and use. Metadata can be expressed in a wide variety of vocabularies and languages, and can be created and maintained with a variety of tools. Ontology based annotation refers to the process of creating metadata using ontologies as their vocabularies. We present similarities and differences with respect to other approaches for metadata creation, and describe languages and...

  2. ONEMercury: Towards Automatic Annotation of Earth Science Metadata

    Science.gov (United States)

    Tuarob, S.; Pouchard, L. C.; Noy, N.; Horsburgh, J. S.; Palanisamy, G.

    2012-12-01

    Earth sciences have become more data-intensive, requiring access to heterogeneous data collected from multiple places, times, and thematic scales. For example, research on climate change may involve exploring and analyzing observational data such as the migration of animals and temperature shifts across the earth, as well as various model-observation inter-comparison studies. Recently, DataONE, a federated data network built to facilitate access to and preservation of environmental and ecological data, has come to exist. ONEMercury has recently been implemented as part of the DataONE project to serve as a portal for discovering and accessing environmental and observational data across the globe. ONEMercury harvests metadata from the data hosted by multiple data repositories and makes it searchable via a common search interface built upon cutting edge search engine technology, allowing users to interact with the system, intelligently filter the search results on the fly, and fetch the data from distributed data sources. Linking data from heterogeneous sources always has a cost. A problem that ONEMercury faces is the different levels of annotation in the harvested metadata records. Poorly annotated records tend to be missed during the search process as they lack meaningful keywords. Furthermore, such records would not be compatible with the advanced search functionality offered by ONEMercury as the interface requires a metadata record be semantically annotated. The explosion of the number of metadata records harvested from an increasing number of data repositories makes it impossible to annotate the harvested records manually, urging the need for a tool capable of automatically annotating poorly curated metadata records. In this paper, we propose a topic-model (TM) based approach for automatic metadata annotation. Our approach mines topics in the set of well annotated records and suggests keywords for poorly annotated records based on topic similarity. We utilize the

  3. RNAspace.org: An integrated environment for the prediction, annotation, and analysis of ncRNA

    OpenAIRE

    Cros, Marie-Josee; de Monte, Antoine; Mariette, Jérôme; Bardou, Philippe; Grenier-Boley, Benjamin; Gautheret, Daniel

    2011-01-01

    The annotation of noncoding RNA genes remains a major bottleneck in genome sequencing projects. Most genome sequences released today still come with sets of tRNAs and rRNAs as the only annotated RNA elements, ignoring hundreds of other RNA families. We have developed a web environment that is dedicated to noncoding RNA (ncRNA) prediction, annotation, and analysis and allows users to run a variety of tools in an integrated and flexible manner. This environment offers complementary ncRNA gene f...

  4. Werkzeuge zur Annotation diachroner Korpora

    OpenAIRE

    Burghardt, Manuel; Wolff, Christian

    2009-01-01

    Wir diskutieren zunächst die Problematik der (syntaktischen) Annotation diachroner Korpora und stellen anschließend eine Evaluationsstudie vor, bei der mehr als 50 Annotationswerkzeuge und -frameworks vor dem Hintergrund eines funktionalen und software-ergonomischen Anforderungsprofils nach dem Qualitätsmodell von ISO/IEC 9126-1:2001 (Software engineering – Product quality – Part 1: Quality model) und ISO/IEC 25000:2005 (Software Engineering – Software product Quality Requirements and Evaluat...

  5. Utilisation of magnets to enhance gastrointestinalendoscopy

    Institute of Scientific and Technical Information of China (English)

    2015-01-01

    Methods to assess, access and treat pathology withinthe gastrointestinal tract continue to evolve with videoendoscopy replacing radiology as the gold standard.Whilst endoscope technology develops further with theadvent of newer higher resolution chips, an array ofadjuncts has been developed to enhance endoscopy inother ways; most notable is the use of magnets. Magnetsare utilised in many areas, ranging from endoscopictraining, lesion resection, aiding manoeuvrability ofcapsule endoscopes, to assisting in easy placement oftubes for nutritional feeding. Some of these are still at anexperimental stage, whilst others are being increasinglyincorporated in our everyday practice.

  6. Utilising inorganic nanocarriers for gene delivery.

    Science.gov (United States)

    Loh, Xian Jun; Lee, Tung-Chun; Dou, Qingqing; Deen, G Roshan

    2016-01-01

    The delivery of genetic materials into cells to elicit cellular responses has been extensively studied by biomaterials scientists globally. Many materials such as lipids, peptides, viruses, synthetically modified cationic polymers and certain inorganic nanomaterials could be used to complex the negatively charged plasmids and deliver the formed package into cells. The recent literature on the delivery of genetic materials utilising inorganic nanoparticles is carefully examined in this review. We have picked out the most relevant references and concisely summarised the findings with illustrated examples. We further propose alternative approaches and suggest future pathways towards the practical use of multifunctional nanocarriers. PMID:26484365

  7. High-performance web services for querying gene and variant annotation

    OpenAIRE

    Xin, Jiwen; Mark, Adam; Afrasiabi, Cyrus; Tsueng, Ginger; Juchler, Moritz; Gopal, Nikhil; Stupp, Gregory S.; Putman, Timothy E.; Ainscough, Benjamin J.; Griffith, Obi L.; Torkamani, Ali; Whetzel, Patricia L.; Mungall, Christopher J.; Mooney, Sean D; Su, Andrew I

    2016-01-01

    Efficient tools for data management and integration are essential for many aspects of high-throughput biology. In particular, annotations of genes and human genetic variants are commonly used but highly fragmented across many resources. Here, we describe MyGene.info and MyVariant.info, high-performance web services for querying gene and variant annotation information. These web services are currently accessed more than three million times permonth. They also demonstrate a generalizable cloud-...

  8. Recent improvements to the SMART domain-based sequence annotation resource

    OpenAIRE

    Letunic, I.; Goodstadt, L.; Dickens, N.J.; Doerks, T.; Schultz, J; R. Mott; Ciccarelli, F.; Copley, R. R.; Ponting, C. P.; Bork, P.

    2002-01-01

    SMART (Simple Modular Architecture Research Tool, http://smart.embl-heidelberg.de) is a web-based resource used for the annotation of protein domains and the analysis of domain architectures, with particular emphasis on mobile eukaryotic domains. Extensive annotation for each domain family is available, providing information relating to function, subcellular localization, phyletic distribution and tertiary structure. The January 2002 release has added more than 200 hand-curated domain models....

  9. Report on the Third Workshop on Exploiting Semantic Annotations in Information Retrieval (ESAIR)

    OpenAIRE

    Kamps, Jaap; Karlgren, Jussi; Schenkel, Ralf

    2011-01-01

    There is an increasing amount of structure on the Web as a result of modern Web lan- guages, user tagging and annotation, and emerging robust NLP tools. These meaningful, semantic, annotations hold the promise to significantly enhance information access, by en- hancing the depth of analysis of today’s systems. Currently, we have only started exploring the possibilities and only begin to understand how these valuable semantic cues can be put to fruitful use. The workshop had an interactive for...

  10. Report on the Third Workshop on Exploiting Semantic Annotations in Information Retrieval (ESAIR), Toronto, Canada

    OpenAIRE

    Kamps, Jaap; Karlgren, Jussi; Schenkel, Ralf

    2011-01-01

    There is an increasing amount of structure on the Web as a result of modern Web lan- guages, user tagging and annotation, and emerging robust NLP tools. These meaningful, semantic, annotations hold the promise to significantly enhance information access, by en- hancing the depth of analysis of today?s systems. Currently, we have only started exploring the possibilities and only begin to understand how these valuable semantic cues can be put to fruitful use. The workshop had an interactive for...

  11. D4.5 Final Report on the Corpus Acquisition & Annotation subsystem and its components

    OpenAIRE

    Prokopidis, Prokopis; Papavassiliou, Vassilis; Toral, Antonio; Poch Riera, Marc; Frontini, Francesca; Rubino, Francesco; Thurmair, Gregor

    2012-01-01

    PANACEA WP4 targets the creation of a Corpus Acquisition and Annotation (CAA) subsystem for the acquisition and processing of monolingual and bilingual language resources (LRs). The CAA subsystem consists of tools that have been integrated as web services in the PANACEA platform of LR production. D4.2 Initial functional prototype and documentation in T13 and D4.4 Report on the revised Corpus Acquisition & Annotation subsystem and its components in T23 provided initial and updated documentatio...

  12. Final Report on the Corpus Acquisition & Annotation subsystem and its components

    OpenAIRE

    Prokopidis, Prokopis; Papavassiliou, Vassilis; Toral, Antonio; Poch, Marc; Frontini, Francesca; Rubino, Francesco; Thurmair, Gregor

    2012-01-01

    PANACEA WP4 targets the creation of a Corpus Acquisition and Annotation (CAA) subsystem for the acquisition and processing of monolingual and bilingual language resources (LRs). The CAA subsystem consists of tools that have been integrated as web services in the PANACEA platform of LR production. D4.2 Initial functional prototype and documentation in T13 and D4.4 Report on the revised Corpus Acquisition & Annotation subsystem and its components in T23 provided initial and updated documenta...

  13. AphidBase: A centralized bioinformatic resource for annotation of the pea aphid genome

    OpenAIRE

    Legeai, Fabrice; Shigenobu, Shuji; Gauthier, Jean-Pierre; Colbourne, John; Rispe, Claude; Collin, Olivier; Richards, Stephen; Wilson, Alex C. C.; Tagu, Denis

    2010-01-01

    AphidBase is a centralized bioinformatic resource that was developed to facilitate community annotation of the pea aphid genome by the International Aphid Genomics Consortium (IAGC). The AphidBase Information System designed to organize and distribute genomic data and annotations for a large international community was constructed using open source software tools from the Generic Model Organism Database (GMOD). The system includes Apollo and GBrowse utilities as well as a wiki, blast search c...

  14. Annotation an effective device for student feedback: a critical review of the literature.

    Science.gov (United States)

    Ball, Elaine C

    2010-05-01

    The paper examines hand-written annotation, its many features, difficulties and strengths as a feedback tool. It extends and clarifies what modest evidence is in the public domain and offers an evaluation of how to use annotation effectively in the support of student feedback [Marshall, C.M., 1998a. The Future of Annotation in a Digital (paper) World. Presented at the 35th Annual GLSLIS Clinic: Successes and Failures of Digital Libraries, June 20-24, University of Illinois at Urbana-Champaign, March 24, pp. 1-20; Marshall, C.M., 1998b. Toward an ecology of hypertext annotation. Hypertext. In: Proceedings of the Ninth ACM Conference on Hypertext and Hypermedia, June 20-24, Pittsburgh Pennsylvania, US, pp. 40-49; Wolfe, J.L., Nuewirth, C.M., 2001. From the margins to the centre: the future of annotation. Journal of Business and Technical Communication, 15(3), 333-371; Diyanni, R., 2002. One Hundred Great Essays. Addison-Wesley, New York; Wolfe, J.L., 2002. Marginal pedagogy: how annotated texts affect writing-from-source texts. Written Communication, 19(2), 297-333; Liu, K., 2006. Annotation as an index to critical writing. Urban Education, 41, 192-207; Feito, A., Donahue, P., 2008. Minding the gap annotation as preparation for discussion. Arts and Humanities in Higher Education, 7(3), 295-307; Ball, E., 2009. A participatory action research study on handwritten annotation feedback and its impact on staff and students. Systemic Practice and Action Research, 22(2), 111-124; Ball, E., Franks, H., McGrath, M., Leigh, J., 2009. Annotation is a valuable tool to enhance learning and assessment in student essays. Nurse Education Today, 29(3), 284-291]. Although a significant number of studies examine annotation, this is largely related to on-line tools and computer mediated communication and not hand-written annotation as comment, phrase or sign written on the student essay to provide critique. Little systematic research has been conducted to consider how this latter form

  15. Re-annotation of genome microbial CoDing-Sequences: finding new genes and inaccurately annotated genes

    Directory of Open Access Journals (Sweden)

    Danchin Antoine

    2002-02-01

    Full Text Available Abstract Background Analysis of any newly sequenced bacterial genome starts with the identification of protein-coding genes. Despite the accumulation of multiple complete genome sequences, which provide useful comparisons with close relatives among other organisms during the annotation process, accurate gene prediction remains quite difficult. A major reason for this situation is that genes are tightly packed in prokaryotes, resulting in frequent overlap. Thus, detection of translation initiation sites and/or selection of the correct coding regions remain difficult unless appropriate biological knowledge (about the structure of a gene is imbedded in the approach. Results We have developed a new program that automatically identifies biologically significant candidate genes in a bacterial genome. Twenty-six complete prokaryotic genomes were analyzed using this tool, and the accuracy of gene finding was assessed by comparison with existing annotations. This analysis revealed that, despite the enormous effort of genome program annotators, a small but not negligible number of genes annotated within the framework of sequencing projects are likely to be partially inaccurate or plainly wrong. Moreover, the analysis of several putative new genes shows that, as expected, many short genes have escaped annotation. In most cases, these new genes revealed frameshifts that could be either artifacts or genuine frameshifts. Some entirely unexpected new genes have also been identified. This allowed us to get a more complete picture of prokaryotic genomes. The results of this procedure are progressively integrated into the SWISS-PROT reference databank. Conclusions The results described in the present study show that our procedure is very satisfactory in terms of gene finding accuracy. Except in few cases, discrepancies between our results and annotations provided by individual authors can be accounted for by the nature of each annotation process or by specific

  16. Needle custom search recall-oriented search on the web using semantic annotations

    NARCIS (Netherlands)

    Kaptein, R.; Koot, G.; Huis in 't Veld, M.A.A.; Broek, E.L. van den

    2014-01-01

    Web search engines are optimized for early precision, which makes it difficult to perform recall-oriented tasks using these search engines. In this article, we present our tool Needle Custom Search. This tool exploits semantic annotations of Web search results and, thereby, increase the efficiency o

  17. Needle custom search: recall-oriented search on the Web using semantic annotations

    NARCIS (Netherlands)

    Kaptein, Rianne; Koot, Gijs; Huis in 't Veld, Mirjam A.A.; Broek, van den Egon L.; Rijke, de Maarten; Kenter, Tom; Vries, de Arjen P.; Zhai, Chen Xiang; Jong, de Franciska; Radinsky, Kira; Hofmann, Katja

    2014-01-01

    Web search engines are optimized for early precision, which makes it difficult to perform recall-oriented tasks using these search engines. In this article, we present our tool Needle Custom Search. This tool exploits semantic annotations of Web search results and, thereby, increase the efficiency o

  18. Needle Custom Search : Recall-oriented search on the web using semantic annotations

    NARCIS (Netherlands)

    Kaptein, Rianne; Koot, Gijs; Huis in 't Veld, Mirjam A.A.; van den Broek, Egon L.

    2014-01-01

    Web search engines are optimized for early precision, which makes it difficult to perform recall-oriented tasks using these search engines. In this article, we present our tool Needle Custom Search. This tool exploits semantic annotations of Web search results and, thereby, increase the efficiency o

  19. Omics data management and annotation.

    Science.gov (United States)

    Harel, Arye; Dalah, Irina; Pietrokovski, Shmuel; Safran, Marilyn; Lancet, Doron

    2011-01-01

    Technological Omics breakthroughs, including next generation sequencing, bring avalanches of data which need to undergo effective data management to ensure integrity, security, and maximal knowledge-gleaning. Data management system requirements include flexible input formats, diverse data entry mechanisms and views, user friendliness, attention to standards, hardware and software platform definition, as well as robustness. Relevant solutions elaborated by the scientific community include Laboratory Information Management Systems (LIMS) and standardization protocols facilitating data sharing and managing. In project planning, special consideration has to be made when choosing relevant Omics annotation sources, since many of them overlap and require sophisticated integration heuristics. The data modeling step defines and categorizes the data into objects (e.g., genes, articles, disorders) and creates an application flow. A data storage/warehouse mechanism must be selected, such as file-based systems and relational databases, the latter typically used for larger projects. Omics project life cycle considerations must include the definition and deployment of new versions, incorporating either full or partial updates. Finally, quality assurance (QA) procedures must validate data and feature integrity, as well as system performance expectations. We illustrate these data management principles with examples from the life cycle of the GeneCards Omics project (http://www.genecards.org), a comprehensive, widely used compendium of annotative information about human genes. For example, the GeneCards infrastructure has recently been changed from text files to a relational database, enabling better organization and views of the growing data. Omics data handling benefits from the wealth of Web-based information, the vast amount of public domain software, increasingly affordable hardware, and effective use of data management and annotation principles as outlined in this chapter

  20. Automatic Multilevel Medical Image Annotation and Retrieval

    OpenAIRE

    Mueen, A.; Zainuddin, R.; Baba, M. Sapiyan

    2007-01-01

    Image retrieval at the semantic level mostly depends on image annotation or image classification. Image annotation performance largely depends on three issues: (1) automatic image feature extraction; (2) a semantic image concept modeling; (3) algorithm for semantic image annotation. To address first issue, multilevel features are extracted to construct the feature vector, which represents the contents of the image. To address second issue, domain-dependent concept hierarchy is constructed for...

  1. Essential marketing tools

    OpenAIRE

    Potter, Ned

    2012-01-01

    This chapter from The Library Marketing Toolkit introduces several essential tools which every library needs as part of their marketing toolkit. These include developing the library website (including mobile version), utilising word-of-mouth promotion, obtaining and interpreting user feedback, perfecting the elevator pitch, and signs and displays. It includes case studies from David Lee King, and Aaron Tay, Rebecca Jones.

  2. Knowledge Annotation maknig implicit knowledge explicit

    CERN Document Server

    Dingli, Alexiei

    2011-01-01

    Did you ever read something on a book, felt the need to comment, took up a pencil and scribbled something on the books' text'? If you did, you just annotated a book. But that process has now become something fundamental and revolutionary in these days of computing. Annotation is all about adding further information to text, pictures, movies and even to physical objects. In practice, anything which can be identified either virtually or physically can be annotated. In this book, we will delve into what makes annotations, and analyse their significance for the future evolutions of the web. We wil

  3. Waste and dust utilisation in shaft furnaces

    Energy Technology Data Exchange (ETDEWEB)

    Senk, D.; Babich, A.; Gudenau, H.W. [Rhein Westfal TH Aachen, Aachen (Germany)

    2005-07-01

    Wastes and dusts from steel industry, non-ferrous metallurgy and other branches can be utilised e.g. in agglomeration processes (sintering, pelletising or briquetting) and by injection into shaft furnaces. This paper deals with the second way. Combustion and reduction behaviour of iron- and carbon-rich metallurgical dusts and sludges containing lead, zinc and alkali as well as other wastes with and without pulverised coal (PC) has been studied when injecting into shaft furnaces. Following shaft furnaces have been examined: blast furnace, cupola furnace, OxiCup furnace and imperial-smelting furnace. Investigations have been done at laboratory and industrial scale. Some dusts and wastes under certain conditions can be not only reused but can also improve combustion efficiency at the tuyeres as well as furnace performance and productivity.

  4. Climate impact from peat utilisation in Sweden

    International Nuclear Information System (INIS)

    The climate impact from the use of peat for energy production in Sweden has been evaluated in terms of contribution to atmospheric radiative forcing. This was done by attempting to answer the question 'What will be the climate impact if one would use 1 m2 of mire for peat extraction during 20 years?'. Two different methods of after-treatment were studied: afforestation and restoration of wetland. The climate impact from a peatland - wetland energy scenario and a peatland - forestry energy scenario was compared to the climate impact from coal, natural gas and forest residues. Sensitivity analyses were performed to evaluate which parameters that are important to take into consideration in order to minimize the climate impact from peat utilisation

  5. Restauro-G: A Rapid Genome Re-Annotation System for Comparative Genomics

    Institute of Scientific and Technical Information of China (English)

    Satoshi Tamaki; Kazuharu Arakawa; Nobuaki Kono; Masaru Tomita

    2007-01-01

    Annotations of complete genome sequences submitted directly from sequencing projects are diverse in terms of annotation strategies and update frequencies. These inconsistencies make comparative studies difficult. To allow rapid data preparation of a large number of complete genomes, automation and speed are important for genome re-annotation. Here we introduce an open-source rapid genome re-annotation software system, Restauro-G, specialized for bacterial genomes. Restauro-G re-annotates a genome by similarity searches utilizing the BLAST-Like Alignment Tool, referring to protein databases such as UniProt KB, NCBI nr, NCBI COGs, Pfam, and PSORTb. Re-annotation by Restauro-G achieved over 98% accuracy for most bacterial chromosomes in comparison with the original manually curated annotation of EMBL releases. Restauro-G was developed in the generic bioinformatics workbench G-language Genome Analysis Environment and is distributed at http://restauro-g.iab.keio.ac.jp/ under the GNU General Public License.

  6. Estimating the annotation error rate of curated GO database sequence annotations

    Directory of Open Access Journals (Sweden)

    Brown Alfred L

    2007-05-01

    Full Text Available Abstract Background Annotations that describe the function of sequences are enormously important to researchers during laboratory investigations and when making computational inferences. However, there has been little investigation into the data quality of sequence function annotations. Here we have developed a new method of estimating the error rate of curated sequence annotations, and applied this to the Gene Ontology (GO sequence database (GOSeqLite. This method involved artificially adding errors to sequence annotations at known rates, and used regression to model the impact on the precision of annotations based on BLAST matched sequences. Results We estimated the error rate of curated GO sequence annotations in the GOSeqLite database (March 2006 at between 28% and 30%. Annotations made without use of sequence similarity based methods (non-ISS had an estimated error rate of between 13% and 18%. Annotations made with the use of sequence similarity methodology (ISS had an estimated error rate of 49%. Conclusion While the overall error rate is reasonably low, it would be prudent to treat all ISS annotations with caution. Electronic annotators that use ISS annotations as the basis of predictions are likely to have higher false prediction rates, and for this reason designers of these systems should consider avoiding ISS annotations where possible. Electronic annotators that use ISS annotations to make predictions should be viewed sceptically. We recommend that curators thoroughly review ISS annotations before accepting them as valid. Overall, users of curated sequence annotations from the GO database should feel assured that they are using a comparatively high quality source of information.

  7. SVA: software for annotating and visualizing sequenced human genomes

    Science.gov (United States)

    Ge, Dongliang; Ruzzo, Elizabeth K.; Shianna, Kevin V.; He, Min; Pelak, Kimberly; Heinzen, Erin L.; Need, Anna C.; Cirulli, Elizabeth T.; Maia, Jessica M.; Dickson, Samuel P.; Zhu, Mingfu; Singh, Abanish; Allen, Andrew S.; Goldstein, David B.

    2011-01-01

    Summary: Here we present Sequence Variant Analyzer (SVA), a software tool that assigns a predicted biological function to variants identified in next-generation sequencing studies and provides a browser to visualize the variants in their genomic contexts. SVA also provides for flexible interaction with software implementing variant association tests allowing users to consider both the bioinformatic annotation of identified variants and the strength of their associations with studied traits. We illustrate the annotation features of SVA using two simple examples of sequenced genomes that harbor Mendelian mutations. Availability and implementation: Freely available on the web at http://www.svaproject.org. Contact: d.ge@duke.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:21624899

  8. Automatic extraction of gene ontology annotation and its correlation with clusters in protein networks

    Directory of Open Access Journals (Sweden)

    Mazo Ilya

    2007-07-01

    Full Text Available Abstract Background Uncovering cellular roles of a protein is a task of tremendous importance and complexity that requires dedicated experimental work as well as often sophisticated data mining and processing tools. Protein functions, often referred to as its annotations, are believed to manifest themselves through topology of the networks of inter-proteins interactions. In particular, there is a growing body of evidence that proteins performing the same function are more likely to interact with each other than with proteins with other functions. However, since functional annotation and protein network topology are often studied separately, the direct relationship between them has not been comprehensively demonstrated. In addition to having the general biological significance, such demonstration would further validate the data extraction and processing methods used to compose protein annotation and protein-protein interactions datasets. Results We developed a method for automatic extraction of protein functional annotation from scientific text based on the Natural Language Processing (NLP technology. For the protein annotation extracted from the entire PubMed, we evaluated the precision and recall rates, and compared the performance of the automatic extraction technology to that of manual curation used in public Gene Ontology (GO annotation. In the second part of our presentation, we reported a large-scale investigation into the correspondence between communities in the literature-based protein networks and GO annotation groups of functionally related proteins. We found a comprehensive two-way match: proteins within biological annotation groups form significantly denser linked network clusters than expected by chance and, conversely, densely linked network communities exhibit a pronounced non-random overlap with GO groups. We also expanded the publicly available GO biological process annotation using the relations extracted by our NLP technology

  9. The consequences of introducing stochasticity in nutrient utilisation models: the case of phosphorus utilisation by pigs.

    Science.gov (United States)

    Symeou, V; Leinonen, I; Kyriazakis, I

    2016-02-14

    Simulation models of nutrient utilisation ignore that variation in pig system components can influence the predicted mean and variance of the performance of a group of pigs. The objective of this study was to develop a methodology to investigate how variation in feed composition would (a) affect the outputs of a nutrient utilisation model and (b) interact with variation that arises from the traits of individual pigs. We used a P intake and utilisation model to address these characteristics. Introduction of stochasticity gave rise to a number of methodological challenges--for example, how to generate variation in both feed composition and pigs and account for correlations between ingredients when modelling variation associated with feed mixing efficiency. Introducing variation in feed composition and pig phenotype resulted in moderate decreases in mean digested, retained and excreted P predicted for a population of pigs and an increase in their associated CV. A lower percentage of pigs in the population were predicted to meet their requirements during the feeding period considered, by comparison with the no-variation scenario. Variation in feed ingredient composition contributed more to performance variation than variation due to mixing efficiency. When variations in both feed composition and pig traits were considered, it was the former rather than the latter that had the dominant influence on variability in pig performance. The developed framework emphasises the consequences of random variability on the predictions of nutrient utilisation models. Such consequences will have a significant impact on decisions about management strategies such as feeding that are subject to variation. PMID:26608351

  10. Semantic annotation of requirements for automatic UML class diagram generation

    Directory of Open Access Journals (Sweden)

    Soumaya Amdouni

    2011-05-01

    Full Text Available The increasing complexity of software engineering requires effective methods and tools to support requirements analysts' activities. While much of a company's knowledge can be found in text repositories, current content management systems have limited capabilities for structuring and interpreting documents. In this context, we propose a tool for transforming text documents describing users' requirements to an UML model. The presented tool uses Natural Language Processing (NLP and semantic rules to generate an UML class diagram. The main contribution of our tool is to provide assistance to designers facilitating the transition from a textual description of user requirements to their UML diagrams based on GATE (General Architecture of Text by formulating necessary rules that generate new semantic annotations.

  11. The surplus value of semantic annotations

    NARCIS (Netherlands)

    M. Marx

    2010-01-01

    We compare the costs of semantic annotation of textual documents to its benefits for information processing tasks. Semantic annotation can improve the performance of retrieval tasks and facilitates an improved search experience through faceted search, focused retrieval, better document summaries, an

  12. Towards an event annotated corpus of Polish

    Directory of Open Access Journals (Sweden)

    Michał Marcińczuk

    2015-12-01

    Full Text Available Towards an event annotated corpus of PolishThe paper presents a typology of events built on the basis of TimeML specification adapted to Polish language. Some changes were introduced to the definition of the event categories and a motivation for event categorization was formulated. The event annotation task is presented on two levels – ontology level (language independent and text mentions (language dependant. The various types of event mentions in Polish text are discussed. A procedure for annotation of event mentions in Polish texts is presented and evaluated. In the evaluation a randomly selected set of documents from the Corpus of Wrocław University of Technology (called KPWr was annotated by two linguists and the annotator agreement was calculated. The evaluation was done in two iterations. After the first evaluation we revised and improved the annotation procedure. The second evaluation showed a significant improvement of the agreement between annotators. The current work was focused on annotation and categorisation of event mentions in text. The future work will be focused on description of event with a set of attributes, arguments and relations.

  13. DIMA – Annotation guidelines for German intonation

    DEFF Research Database (Denmark)

    Kügler, Frank; Smolibocki, Bernadett; Arnold, Denis;

    2015-01-01

    easier since German intonation is currently annotated according to different models. To this end, we aim to provide guidelines that are easy to learn. The guidelines were evaluated running an inter-annotator reliability study on three different speech styles (read speech, monologue and dialogue...

  14. Creating Gaze Annotations in Head Mounted Displays

    DEFF Research Database (Denmark)

    Mardanbeigi, Diako; Qvarfordt, Pernilla

    To facilitate distributed communication in mobile settings, we developed GazeNote for creating and sharing gaze annotations in head mounted displays (HMDs). With gaze annotations it possible to point out objects of interest within an image and add a verbal description. To create an annota- tion, ...

  15. Crowdsourcing and annotating NER for Twitter #drift

    DEFF Research Database (Denmark)

    Fromreide, Hege; Hovy, Dirk; Søgaard, Anders

    2014-01-01

    We present two new NER datasets for Twitter; a manually annotated set of 1,467 tweets (kappa=0.942) and a set of 2,975 expert-corrected, crowdsourced NER annotated tweets from the dataset described in Finin et al. (2010). In our experiments with these datasets, we observe two important points: (a...

  16. Annotation of regular polysemy and underspecification

    DEFF Research Database (Denmark)

    Martínez Alonso, Héctor; Pedersen, Bolette Sandford; Bel, Núria

    2013-01-01

    We present the result of an annotation task on regular polysemy for a series of seman- tic classes or dot types in English, Dan- ish and Spanish. This article describes the annotation process, the results in terms of inter-encoder agreement, and the sense distributions obtained with two methods...

  17. Harnessing Collaborative Annotations on Online Formative Assessments

    Science.gov (United States)

    Lin, Jian-Wei; Lai, Yuan-Cheng

    2013-01-01

    This paper harnesses collaborative annotations by students as learning feedback on online formative assessments to improve the learning achievements of students. Through the developed Web platform, students can conduct formative assessments, collaboratively annotate, and review historical records in a convenient way, while teachers can generate…

  18. Concept annotation in the CRAFT corpus

    Directory of Open Access Journals (Sweden)

    Bada Michael

    2012-07-01

    Full Text Available Abstract Background Manually annotated corpora are critical for the training and evaluation of automated methods to identify concepts in biomedical text. Results This paper presents the concept annotations of the Colorado Richly Annotated Full-Text (CRAFT Corpus, a collection of 97 full-length, open-access biomedical journal articles that have been annotated both semantically and syntactically to serve as a research resource for the biomedical natural-language-processing (NLP community. CRAFT identifies all mentions of nearly all concepts from nine prominent biomedical ontologies and terminologies: the Cell Type Ontology, the Chemical Entities of Biological Interest ontology, the NCBI Taxonomy, the Protein Ontology, the Sequence Ontology, the entries of the Entrez Gene database, and the three subontologies of the Gene Ontology. The first public release includes the annotations for 67 of the 97 articles, reserving two sets of 15 articles for future text-mining competitions (after which these too will be released. Concept annotations were created based on a single set of guidelines, which has enabled us to achieve consistently high interannotator agreement. Conclusions As the initial 67-article release contains more than 560,000 tokens (and the full set more than 790,000 tokens, our corpus is among the largest gold-standard annotated biomedical corpora. Unlike most others, the journal articles that comprise the corpus are drawn from diverse biomedical disciplines and are marked up in their entirety. Additionally, with a concept-annotation count of nearly 100,000 in the 67-article subset (and more than 140,000 in the full collection, the scale of conceptual markup is also among the largest of comparable corpora. The concept annotations of the CRAFT Corpus have the potential to significantly advance biomedical text mining by providing a high-quality gold standard for NLP systems. The corpus, annotation guidelines, and other associated resources are

  19. The GOA database: Gene Ontology annotation updates for 2015

    OpenAIRE

    Huntley, Rachael P; Sawford, Tony; Mutowo-Meullenet, Prudence; Shypitsyna, Aleksandra; Bonilla, Carlos; Martin, Maria J.; O'Donovan, Claire

    2014-01-01

    The Gene Ontology Annotation (GOA) resource (http://www.ebi.ac.uk/GOA) provides evidence-based Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB). Manual annotations provided by UniProt curators are supplemented by manual and automatic annotations from model organism databases and specialist annotation groups. GOA currently supplies 368 million GO annotations to almost 54 million proteins in more than 480 000 taxonomic groups. The resource now provides annotat...

  20. Utilisation of Estonian energy wood resources

    Energy Technology Data Exchange (ETDEWEB)

    Muiste, P.; Tullus, H.; Uri, V. [Estonian Agricultural University, Tartu (Estonia)

    1996-12-31

    In the end of the Soviet period in the 1980s, a long-term energy programme for Estonia was worked out. The energy system was planned to be based on nuclear power and the share of domestic alternative sources of energy was low. The situation has greatly changed after the re-establishment of the Estonian independence, and now wood and peat fuels play an important role in the energy system. Energy consumption in Estonia decreased during the period 1970-1993, but this process has less influenced the consumption of domestic renewable fuels - peat and wood. It means that the share of these fuels has grown. The investment on substitution of imported fossil fuels and on conversion of boiler plants from fossil fuels to domestic fuels has reached the level of USD 100 million. The perspectives of the wood energy depend mainly on two factors; the resources and the price of wood energy compared with other fuels. The situation in wood market influences both the possible quantities and the price. It is typical that the quickly growing cost of labour power in Estonia is greatly affecting the price of energy wood. Though the price level of fuel peat and wood chips is lower than the world market price today, the conditions for using biofuels could be more favourable, if higher environmental fees were introduced. In conjunction with increasing utilisation of biofuels it is important to evaluate possible emissions or removal of greenhouse gases from Estonian forests 3 refs.

  1. Utilisation of Estonian energy wood resources

    International Nuclear Information System (INIS)

    In the end of the Soviet period in the 1980s, a long-term energy programme for Estonia was worked out. The energy system was planned to be based on nuclear power and the share of domestic alternative sources of energy was low. The situation has greatly changed after the re-establishment of the Estonian independence, and now wood and peat fuels play an important role in the energy system. Energy consumption in Estonia decreased during the period 1970-1993, but this process has less influenced the consumption of domestic renewable fuels - peat and wood. It means that the share of these fuels has grown. The investment on substitution of imported fossil fuels and on conversion of boiler plants from fossil fuels to domestic fuels has reached the level of USD 100 million. The perspectives of the wood energy depend mainly on two factors; the resources and the price of wood energy compared with other fuels. The situation in wood market influences both the possible quantities and the price. It is typical that the quickly growing cost of labour power in Estonia is greatly affecting the price of energy wood. Though the price level of fuel peat and wood chips is lower than the world market price today, the conditions for using biofuels could be more favourable, if higher environmental fees were introduced. In conjunction with increasing utilisation of biofuels it is important to evaluate possible emissions or removal of greenhouse gases from Estonian forests 3 refs

  2. Incorporating evolution of transcription factor binding sites into annotated alignments

    Indian Academy of Sciences (India)

    Abha S Bais; Steffen Grossmann; Martin Vingron

    2007-08-01

    Identifying transcription factor binding sites (TFBSs) is essential to elucidate putative regulatory mechanisms. A common strategy is to combine cross-species conservation with single sequence TFBS annotation to yield ``conserved TFBSs”. Most current methods in this field adopt a multi-step approach that segregates the two aspects. Again, it is widely accepted that the evolutionary dynamics of binding sites differ from those of the surrounding sequence. Hence, it is desirable to have an approach that explicitly takes this factor into account. Although a plethora of approaches have been proposed for the prediction of conserved TFBSs, very few explicitly model TFBS evolutionary properties, while additionally being multi-step. Recently, we introduced a novel approach to simultaneously align and annotate conserved TFBSs in a pair of sequences. Building upon the standard Smith-Waterman algorithm for local alignments, SimAnn introduces additional states for profiles to output extended alignments or annotated alignments. That is, alignments with parts annotated as gaplessly aligned TFBSs (pair-profile hits) are generated. Moreover, the pair-profile related parameters are derived in a sound statistical framework. In this article, we extend this approach to explicitly incorporate evolution of binding sites in the SimAnn framework. We demonstrate the extension in the theoretical derivations through two position-specific evolutionary models, previously used for modelling TFBS evolution. In a simulated setting, we provide a proof of concept that the approach works given the underlying assumptions, as compared to the original work. Finally, using a real dataset of experimentally verified binding sites in human-mouse sequence pairs, we compare the new approach (eSimAnn) to an existing multi-step tool that also considers TFBS evolution. Although it is widely accepted that binding sites evolve differently from the surrounding sequences, most comparative TFBS identification

  3. Computational annotation of genes differentially expressed along olive fruit development

    Directory of Open Access Journals (Sweden)

    Martinelli Federico

    2009-10-01

    Full Text Available Abstract Background Olea europaea L. is a traditional tree crop of the Mediterranean basin with a worldwide economical high impact. Differently from other fruit tree species, little is known about the physiological and molecular basis of the olive fruit development and a few sequences of genes and gene products are available for olive in public databases. This study deals with the identification of large sets of differentially expressed genes in developing olive fruits and the subsequent computational annotation by means of different software. Results mRNA from fruits of the cv. Leccino sampled at three different stages [i.e., initial fruit set (stage 1, completed pit hardening (stage 2 and veraison (stage 3] was used for the identification of differentially expressed genes putatively involved in main processes along fruit development. Four subtractive hybridization libraries were constructed: forward and reverse between stage 1 and 2 (libraries A and B, and 2 and 3 (libraries C and D. All sequenced clones (1,132 in total were analyzed through BlastX against non-redundant NCBI databases and about 60% of them showed similarity to known proteins. A total of 89 out of 642 differentially expressed unique sequences was further investigated by Real-Time PCR, showing a validation of the SSH results as high as 69%. Library-specific cDNA repertories were annotated according to the three main vocabularies of the gene ontology (GO: cellular component, biological process and molecular function. BlastX analysis, GO terms mapping and annotation analysis were performed using the Blast2GO software, a research tool designed with the main purpose of enabling GO based data mining on sequence sets for which no GO annotation is yet available. Bioinformatic analysis pointed out a significantly different distribution of the annotated sequences for each GO category, when comparing the three fruit developmental stages. The olive fruit-specific transcriptome dataset was

  4. A Common XML-based Framework for Syntactic Annotations

    CERN Document Server

    Ide, Nancy; Erjavec, Tomaz

    2009-01-01

    It is widely recognized that the proliferation of annotation schemes runs counter to the need to re-use language resources, and that standards for linguistic annotation are becoming increasingly mandatory. To answer this need, we have developed a framework comprised of an abstract model for a variety of different annotation types (e.g., morpho-syntactic tagging, syntactic annotation, co-reference annotation, etc.), which can be instantiated in different ways depending on the annotator's approach and goals. In this paper we provide an overview of the framework, demonstrate its applicability to syntactic annotation, and show how it can contribute to comparative evaluation of parser output and diverse syntactic annotation schemes.

  5. Linking Disparate Datasets of the Earth Sciences with the SemantEco Annotator

    Science.gov (United States)

    Seyed, P.; Chastain, K.; McGuinness, D. L.

    2013-12-01

    library of vocabularies to assist the user in locating terms to describe observed entities, their properties, and relationships. The Annotator leverages vocabulary definitions of these concepts to guide the user in describing data in a logically consistent manner. The vocabularies made available through the Annotator are open, as is the Annotator itself. We have taken a step towards making semantic annotation/translation of data more accessible. Our vision for the Annotator is as a tool that can be integrated into a semantic data 'workbench' environment, which would allow semantic annotation of a variety of data formats, using standard vocabularies. These vocabularies involved enable search for similar datasets, and integration with any semantically-enabled applications for analysis and visualization.

  6. Context-Aware Service Utilisation in the Clouds and Energy Conservation

    CERN Document Server

    Kiani, Saad Liaquat; Antonopoulos, Nick; Knappmeyer, Michael; Baker, Nigel; McClatchey, Richard

    2012-01-01

    Ubiquitous computing environments are characterised by smart, interconnected artefacts embedded in our physical world that are projected to provide useful services to human inhabitants unobtrusively. Mobile devices are becoming the primary tools of human interaction with these embedded artefacts and utilisation of services available in smart computing environments such as clouds. Advancements in capabilities of mobile devices allow a number of user and environment related context consumers to be hosted on these devices. Without a coordinating component, these context consumers and providers are a potential burden on device resources; specifically the effect of uncoordinated computation and communication with cloud-enabled services can negatively impact the battery life. Therefore energy conservation is a major concern in realising the collaboration and utilisation of mobile device based context-aware applications and cloud based services. This paper presents the concept of a context-brokering component to aid...

  7. Annotating Cancer Variants and Anti-Cancer Therapeutics in Reactome

    International Nuclear Information System (INIS)

    Reactome describes biological pathways as chemical reactions that closely mirror the actual physical interactions that occur in the cell. Recent extensions of our data model accommodate the annotation of cancer and other disease processes. First, we have extended our class of protein modifications to accommodate annotation of changes in amino acid sequence and the formation of fusion proteins to describe the proteins involved in disease processes. Second, we have added a disease attribute to reaction, pathway, and physical entity classes that uses disease ontology terms. To support the graphical representation of “cancer” pathways, we have adapted our Pathway Browser to display disease variants and events in a way that allows comparison with the wild type pathway, and shows connections between perturbations in cancer and other biological pathways. The curation of pathways associated with cancer, coupled with our efforts to create other disease-specific pathways, will interoperate with our existing pathway and network analysis tools. Using the Epidermal Growth Factor Receptor (EGFR) signaling pathway as an example, we show how Reactome annotates and presents the altered biological behavior of EGFR variants due to their altered kinase and ligand-binding properties, and the mode of action and specificity of anti-cancer therapeutics

  8. Video annotations of Mexican nature in a collaborative environment

    Science.gov (United States)

    Oropesa Morales, Lester Arturo; Montoya Obeso, Abraham; Hernández García, Rosaura; Cocolán Almeda, Sara Ivonne; García Vázquez, Mireya Saraí; Benois-Pineau, Jenny; Zamudio Fuentes, Luis Miguel; Martinez Nuño, Jesús A.; Ramírez Acosta, Alejandro Alvaro

    2015-09-01

    Multimedia content production and storage in repositories are now an increasingly widespread practice. Indexing concepts for search in multimedia libraries are very useful for users of the repositories. However the search tools of content-based retrieval and automatic video tagging, still do not have great consistency. Regardless of how these systems are implemented, it is of vital importance to possess lots of videos that have concepts tagged with ground truth (training and testing sets). This paper describes a novel methodology to make complex annotations on video resources through ELAN software. The concepts are annotated and related to Mexican nature in a High Level Features (HLF) from development set of TRECVID 2014 in a collaborative environment. Based on this set, each nature concept observed is tagged on each video shot using concepts of the TRECVid 2014 dataset. We also propose new concepts, -like tropical settings, urban scenes, actions, events, weather, places for name a few. We also propose specific concepts that best describe video content of Mexican culture. We have been careful to get the database tagged with concepts of nature and ground truth. It is evident that a collaborative environment is more suitable for annotation of concepts related to ground truth and nature. As a result a Mexican nature database was built. It also is the basis for testing and training sets to automatically classify new multimedia content of Mexican nature.

  9. A Method for Producing Reminiscence Videos by Using Photo Annotations

    Science.gov (United States)

    Kuwahara, Noriaki; Kuwabara, Kazuhiro; Abe, Shinji; Susami, Kenji; Yasuda, Kiyoshi

    Providing good home-based care to people with dementia is becoming an important issue as the size of the elderly population increases. One of the main problems in providing such care is that it must be constantly provided without interruption, and this puts a great burden on caregivers, who are often family members. Networked Interaction Therapy is the name we call our methods designed to relieve the stress of people suffering from dementia as well as that of their family members. This therapy aims to provide a system that interacts with people with dementia by utilizing various engaging stimuli. One such stimulus is a reminiscence video created from old photo albums, which is a promising way to hold a dementia sufferer's attention for a long time. In this paper, we present an authoring tool to assist in the production of a reminiscence video by using photo annotations. We conducted interviews with several video creators on how they used photo annotations such as date, title and subject of photos when they produced the reminiscence videos. According to the creators' comments, we have defined an ontology for representing the creators' knowledge of how to add visual effects to a reminiscence video. Subsequently, we developed an authoring tool that automatically produces a reminiscence video from the annotated photos. Subjective evaluation of the quality of reminiscence videos produced with our tool indicates that they give impressions similar to those produced by creators using conventional video editing software. The effectiveness of presenting such a video to people with dementia is also discussed.

  10. Making web annotations persistent over time

    Energy Technology Data Exchange (ETDEWEB)

    Sanderson, Robert [Los Alamos National Laboratory; Van De Sompel, Herbert [Los Alamos National Laboratory

    2010-01-01

    As Digital Libraries (DL) become more aligned with the web architecture, their functional components need to be fundamentally rethought in terms of URIs and HTTP. Annotation, a core scholarly activity enabled by many DL solutions, exhibits a clearly unacceptable characteristic when existing models are applied to the web: due to the representations of web resources changing over time, an annotation made about a web resource today may no longer be relevant to the representation that is served from that same resource tomorrow. We assume the existence of archived versions of resources, and combine the temporal features of the emerging Open Annotation data model with the capability offered by the Memento framework that allows seamless navigation from the URI of a resource to archived versions of that resource, and arrive at a solution that provides guarantees regarding the persistence of web annotations over time. More specifically, we provide theoretical solutions and proof-of-concept experimental evaluations for two problems: reconstructing an existing annotation so that the correct archived version is displayed for all resources involved in the annotation, and retrieving all annotations that involve a given archived version of a web resource.

  11. Effective Utilisation of Waste Glass in Concrete

    Directory of Open Access Journals (Sweden)

    Sameer Shaikh

    2015-12-01

    Full Text Available Glass is a widely used product throughout the world; it is versatile, durable and reliable. The uses of glass ranges drastically, therefore waste glass is discarded, stockpiled or land filled. About million tons of waste glass is generated and around large percent of this glass is disposed of in landfills. This pattern has influenced environmental organizations to pressure the professional community to lower the amount of glass being discarded as well as find use to the non-recycled glass in new applications. In relation, the recycling of waste glass as a component in concrete gives waste glass a sustainable alternative to land filling and therefore makes it economically viable.The proposed study of utilising waste glass powder(GLP in concrete as partial replacement of cement as well as the use of crushed glass particles(CGP retained on 1.18mm & 2.36mm IS sieve as a partial replacement to sand, which offers important benefits related to strength of concrete as well as it is eco-friendly. Recycling of mixed-colour waste glass possesses major problems for municipalities, and this problem can be greatly eliminated by re-using waste glass as sand/cement replacement in concrete. Moreover, re-using waste materials in construction can reduce the demand on the sources of primary materials.In this project the attempts have been made to partially replace the cement as well as sand by waste glass powder and crushed glass particles with equal combination by 5% interval up to 20% replacement and observe its effect on the strength of concrete after 7 days and 28 days of curing.

  12. Hydrogen from coal: Production and utilisation technologies

    International Nuclear Information System (INIS)

    Although coal may be viewed as a dirty fuel due to its high greenhouse emissions when combusted, a strong case can be made for coal to be a major world source of clean H2 energy. Apart from the fact that resources of coal will outlast oil and natural gas by centuries, there is a shift towards developing environmentally benign coal technologies, which can lead to high energy conversion efficiencies and low air pollution emissions as compared to conventional coal fired power generation plant. There are currently several world research and industrial development projects in the areas of Integrated Gasification Combined Cycles (IGCC) and Integrated Gasification Fuel Cell (IGFC) systems. In such systems, there is a need to integrate complex unit operations including gasifiers, gas separation and cleaning units, water gas shift reactors, turbines, heat exchangers, steam generators and fuel cells. IGFC systems tested in the USA, Europe and Japan employing gasifiers (Texaco, Lurgi and Eagle) and fuel cells have resulted in energy conversions at efficiency of 47.5% (HHV) which is much higher than the 30-35% efficiency of conventional coal fired power generation. Solid oxide fuel cells (SOFC) and molten carbonate fuel cells (MCFC) are the front runners in energy production from coal gases. These fuel cells can operate at high temperatures and are robust to gas poisoning impurities. IGCC and IGFC technologies are expensive and currently economically uncompetitive as compared to established and mature power generation technology. However, further efficiency and technology improvements coupled with world pressures on limitation of greenhouse gases and other gaseous pollutants could make IGCC/IGFC technically and economically viable for hydrogen production and utilisation in clean and environmentally benign energy systems. (author)

  13. BioSAVE: Display of scored annotation within a sequence context

    Directory of Open Access Journals (Sweden)

    Adryan Boris

    2008-03-01

    Full Text Available Abstract Background Visualization of sequence annotation is a common feature in many bioinformatics tools. For many applications it is desirable to restrict the display of such annotation according to a score cutoff, as biological interpretation can be difficult in the presence of the entire data. Unfortunately, many visualisation solutions are somewhat static in the way they handle such score cutoffs. Results We present BioSAVE, a sequence annotation viewer with on-the-fly selection of visualisation thresholds for each feature. BioSAVE is a versatile OS X program for visual display of scored features (annotation within a sequence context. The program reads sequence and additional supplementary annotation data (e.g., position weight matrix matches, conservation scores, structural domains from a variety of commonly used file formats and displays them graphically. Onscreen controls then allow for live customisation of these graphics, including on-the-fly selection of visualisation thresholds for each feature. Conclusion Possible applications of the program include display of transcription factor binding sites in a genomic context or the visualisation of structural domain assignments in protein sequences and many more. The dynamic visualisation of these annotations is useful, e.g., for the determination of cutoff values of predicted features to match experimental data. Program, source code and exemplary files are freely available at the BioSAVE homepage.

  14. EXTRACT: interactive extraction of environment metadata and term suggestion for metagenomic sample annotation.

    Science.gov (United States)

    Pafilis, Evangelos; Buttigieg, Pier Luigi; Ferrell, Barbra; Pereira, Emiliano; Schnetzer, Julia; Arvanitidis, Christos; Jensen, Lars Juhl

    2016-01-01

    The microbial and molecular ecology research communities have made substantial progress on developing standards for annotating samples with environment metadata. However, sample manual annotation is a highly labor intensive process and requires familiarity with the terminologies used. We have therefore developed an interactive annotation tool, EXTRACT, which helps curators identify and extract standard-compliant terms for annotation of metagenomic records and other samples. Behind its web-based user interface, the system combines published methods for named entity recognition of environment, organism, tissue and disease terms. The evaluators in the BioCreative V Interactive Annotation Task found the system to be intuitive, useful, well documented and sufficiently accurate to be helpful in spotting relevant text passages and extracting organism and environment terms. Comparison of fully manual and text-mining-assisted curation revealed that EXTRACT speeds up annotation by 15-25% and helps curators to detect terms that would otherwise have been missed. Database URL: https://extract.hcmr.gr/. PMID:26896844

  15. PANDA: pathway and annotation explorer for visualizing and interpreting gene-centric data

    Directory of Open Access Journals (Sweden)

    Steven N. Hart

    2015-05-01

    Full Text Available Objective. Bringing together genomics, transcriptomics, proteomics, and other -omics technologies is an important step towards developing highly personalized medicine. However, instrumentation has advances far beyond expectations and now we are able to generate data faster than it can be interpreted. Materials and Methods. We have developed PANDA (Pathway AND Annotation Explorer, a visualization tool that integrates gene-level annotation in the context of biological pathways to help interpret complex data from disparate sources. PANDA is a web-based application that displays data in the context of well-studied pathways like KEGG, BioCarta, and PharmGKB. PANDA represents data/annotations as icons in the graph while maintaining the other data elements (i.e., other columns for the table of annotations. Custom pathways from underrepresented diseases can be imported when existing data sources are inadequate. PANDA also allows sharing annotations among collaborators. Results. In our first use case, we show how easy it is to view supplemental data from a manuscript in the context of a user’s own data. Another use-case is provided describing how PANDA was leveraged to design a treatment strategy from the somatic variants found in the tumor of a patient with metastatic sarcomatoid renal cell carcinoma. Conclusion. PANDA facilitates the interpretation of gene-centric annotations by visually integrating this information with context of biological pathways. The application can be downloaded or used directly from our website: http://bioinformaticstools.mayo.edu/research/panda-viewer/.

  16. Annotating user-defined abstractions for optimization

    Energy Technology Data Exchange (ETDEWEB)

    Quinlan, D; Schordan, M; Vuduc, R; Yi, Q

    2005-12-05

    This paper discusses the features of an annotation language that we believe to be essential for optimizing user-defined abstractions. These features should capture semantics of function, data, and object-oriented abstractions, express abstraction equivalence (e.g., a class represents an array abstraction), and permit extension of traditional compiler optimizations to user-defined abstractions. Our future work will include developing a comprehensive annotation language for describing the semantics of general object-oriented abstractions, as well as automatically verifying and inferring the annotated semantics.

  17. HBVRegDB: Annotation, comparison, detection and visualization of regulatory elements in hepatitis B virus sequences

    Directory of Open Access Journals (Sweden)

    Firth Andrew E

    2007-12-01

    Full Text Available Abstract Background The many Hepadnaviridae sequences available have widely varied functional annotation. The genomes are very compact (~3.2 kb but contain multiple layers of functional regulatory elements in addition to coding regions. Key regions are subject to purifying selection, as mutations in these regions will produce non-functional viruses. Results These genomic sequences have been organized into a structured database to facilitate research at the molecular level. HBVRegDB is a comparative genomic analysis tool with an integrated underlying sequence database. The database contains genomic sequence data from representative viruses. In addition to INSDC and RefSeq annotation, HBVRegDB also contains expert and systematically calculated annotations (e.g. promoters and comparative genome analysis results (e.g. blastn, tblastx. It also contains analyses based on curated HBV alignments. Information about conserved regions – including primary conservation (e.g. CDS-Plotcon and RNA secondary structure predictions (e.g. Alidot – is integrated into the database. A large amount of data is graphically presented using the GBrowse (Generic Genome Browser adapted for analysis of viral genomes. Flexible query access is provided based on any annotated genomic feature. Novel regulatory motifs can be found by analysing the annotated sequences. Conclusion HBVRegDB serves as a knowledge database and as a comparative genomic analysis tool for molecular biologists investigating HBV. It is publicly available and complementary to other viral and HBV focused datasets and tools http://hbvregdb.otago.ac.nz. The availability of multiple and highly annotated sequences of viral genomes in one database combined with comparative analysis tools facilitates detection of novel genomic elements.

  18. New in protein structure and function annotation: hotspots, single nucleotide polymorphisms and the 'Deep Web'.

    Science.gov (United States)

    Bromberg, Yana; Yachdav, Guy; Ofran, Yanay; Schneider, Reinhard; Rost, Burkhard

    2009-05-01

    The rapidly increasing quantity of protein sequence data continues to widen the gap between available sequences and annotations. Comparative modeling suggests some aspects of the 3D structures of approximately half of all known proteins; homology- and network-based inferences annotate some aspect of function for a similar fraction of the proteome. For most known protein sequences, however, there is detailed knowledge about neither their function nor their structure. Comprehensive efforts towards the expert curation of sequence annotations have failed to meet the demand of the rapidly increasing number of available sequences. Only the automated prediction of protein function in the absence of homology can close the gap between available sequences and annotations in the foreseeable future. This review focuses on two novel methods for automated annotation, and briefly presents an outlook on how modern web software may revolutionize the field of protein sequence annotation. First, predictions of protein binding sites and functional hotspots, and the evolution of these into the most successful type of prediction of protein function from sequence will be discussed. Second, a new tool, comprehensive in silico mutagenesis, which contributes important novel predictions of function and at the same time prepares for the onset of the next sequencing revolution, will be described. While these two new sub-fields of protein prediction represent the breakthroughs that have been achieved methodologically, it will then be argued that a different development might further change the way biomedical researchers benefit from annotations: modern web software can connect the worldwide web in any browser with the 'Deep Web' (ie, proprietary data resources). The availability of this direct connection, and the resulting access to a wealth of data, may impact drug discovery and development more than any existing method that contributes to protein annotation. PMID:19396742

  19. Annotated bibliography of uranium in Australia, 1970-1987

    International Nuclear Information System (INIS)

    The bibliography contains 845 separate numbered items which deal with uranium mining in Australia during the period 1970-1987, which it was feasible to annotate, which are publicly available, and which are not of a highly technical nature. The bibliography is not restricted to material originating in Australia. The items are organised into nine major subject areas on the basis of their principal subject matter, with cross references being added in cases where more than one subject area is dealt with. The nine sections deal with the development and structure of the Australian uranium industry; the uranium debate; uranium policies; uranium and Aborigines; economic issues; domestic processing and utilisation of Australian uranium; environmental issues; nuclear proliferation and safeguards; and the major individual uranium projects. The bibliography is preceded by a chapter on its scope, organisation and sources and by an overview providing background information on the nuclear fuel cycle, uranium in Australia and Australian uranium policy and is followed by an author index

  20. Usability and satisfaction in multimedia annotation tools for MOOCs

    OpenAIRE

    Juan José Monedero Moya; Daniel Cebrián Robles; Philip Desenne

    2015-01-01

    The worldwide boom in digital video may be one of the reasons behind the exponential growth of MOOC courses. The evaluation of a MOOC requires a great degree of multimedia and collaborative interaction. Given that videos are one of the main elements in these courses, it would be interesting to work on innovations that would allow users to interact with multimedia and collaborative activities within the videos. This paper is part of a collaboration project whose main objective is ...

  1. Meteor showers an annotated catalog

    CERN Document Server

    Kronk, Gary W

    2014-01-01

    Meteor showers are among the most spectacular celestial events that may be observed by the naked eye, and have been the object of fascination throughout human history. In “Meteor Showers: An Annotated Catalog,” the interested observer can access detailed research on over 100 annual and periodic meteor streams in order to capitalize on these majestic spectacles. Each meteor shower entry includes details of their discovery, important observations and orbits, and gives a full picture of duration, location in the sky, and expected hourly rates. Armed with a fuller understanding, the amateur observer can better view and appreciate the shower of their choice. The original book, published in 1988, has been updated with over 25 years of research in this new and improved edition. Almost every meteor shower study is expanded, with some original minor showers being dropped while new ones are added. The book also includes breakthroughs in the study of meteor showers, such as accurate predictions of outbursts as well ...

  2. SASL: A Semantic Annotation System for Literature

    Science.gov (United States)

    Yuan, Pingpeng; Wang, Guoyin; Zhang, Qin; Jin, Hai

    Due to ambiguity, search engines for scientific literatures may not return right search results. One efficient solution to the problems is to automatically annotate literatures and attach the semantic information to them. Generally, semantic annotation requires identifying entities before attaching semantic information to them. However, due to abbreviation and other reasons, it is very difficult to identify entities correctly. The paper presents a Semantic Annotation System for Literature (SASL), which utilizes Wikipedia as knowledge base to annotate literatures. SASL mainly attaches semantic to terminology, academic institutions, conferences, and journals etc. Many of them are usually abbreviations, which induces ambiguity. Here, SASL uses regular expressions to extract the mapping between full name of entities and their abbreviation. Since full names of several entities may map to a single abbreviation, SASL introduces Hidden Markov Model to implement name disambiguation. Finally, the paper presents the experimental results, which confirm SASL a good performance.

  3. Modeling Social Annotation: a Bayesian Approach

    CERN Document Server

    Plangprasopchok, Anon

    2008-01-01

    Collaborative tagging systems, such as del.icio.us, CiteULike, and others, allow users to annotate objects, e.g., Web pages or scientific papers, with descriptive labels called tags. The social annotations, contributed by thousands of users, can potentially be used to infer categorical knowledge, classify documents or recommend new relevant information. Traditional text inference methods do not make best use of socially-generated data, since they do not take into account variations in individual users' perspectives and vocabulary. In a previous work, we introduced a simple probabilistic model that takes interests of individual annotators into account in order to find hidden topics of annotated objects. Unfortunately, our proposed approach had a number of shortcomings, including overfitting, local maxima and the requirement to specify values for some parameters. In this paper we address these shortcomings in two ways. First, we extend the model to a fully Bayesian framework. Second, we describe an infinite ver...

  4. GRADUATE AND PROFESSIONAL EDUCATION, AN ANNOTATED BIBLIOGRAPHY.

    Science.gov (United States)

    HEISS, ANN M.; AND OTHERS

    THIS ANNOTATED BIBLIOGRAPHY CONTAINS REFERENCES TO GENERAL GRADUATE EDUCATION AND TO EDUCATION FOR THE FOLLOWING PROFESSIONAL FIELDS--ARCHITECTURE, BUSINESS, CLINICAL PSYCHOLOGY, DENTISTRY, ENGINEERING, LAW, LIBRARY SCIENCE, MEDICINE, NURSING, SOCIAL WORK, TEACHING, AND THEOLOGY. (HW)

  5. Generation of silver standard concept annotations from biomedical texts with special relevance to phenotypes.

    Directory of Open Access Journals (Sweden)

    Anika Oellrich

    Full Text Available Electronic health records and scientific articles possess differing linguistic characteristics that may impact the performance of natural language processing tools developed for one or the other. In this paper, we investigate the performance of four extant concept recognition tools: the clinical Text Analysis and Knowledge Extraction System (cTAKES, the National Center for Biomedical Ontology (NCBO Annotator, the Biomedical Concept Annotation System (BeCAS and MetaMap. Each of the four concept recognition systems is applied to four different corpora: the i2b2 corpus of clinical documents, a PubMed corpus of Medline abstracts, a clinical trails corpus and the ShARe/CLEF corpus. In addition, we assess the individual system performances with respect to one gold standard annotation set, available for the ShARe/CLEF corpus. Furthermore, we built a silver standard annotation set from the individual systems' output and assess the quality as well as the contribution of individual systems to the quality of the silver standard. Our results demonstrate that mainly the NCBO annotator and cTAKES contribute to the silver standard corpora (F1-measures in the range of 21% to 74% and their quality (best F1-measure of 33%, independent from the type of text investigated. While BeCAS and MetaMap can contribute to the precision of silver standard annotations (precision of up to 42%, the F1-measure drops when combined with NCBO Annotator and cTAKES due to a low recall. In conclusion, the performances of individual systems need to be improved independently from the text types, and the leveraging strategies to best take advantage of individual systems' annotations need to be revised. The textual content of the PubMed corpus, accession numbers for the clinical trials corpus, and assigned annotations of the four concept recognition systems as well as the generated silver standard annotation sets are available from http://purl.org/phenotype/resources. The textual content

  6. Generation of silver standard concept annotations from biomedical texts with special relevance to phenotypes.

    Science.gov (United States)

    Oellrich, Anika; Collier, Nigel; Smedley, Damian; Groza, Tudor

    2015-01-01

    Electronic health records and scientific articles possess differing linguistic characteristics that may impact the performance of natural language processing tools developed for one or the other. In this paper, we investigate the performance of four extant concept recognition tools: the clinical Text Analysis and Knowledge Extraction System (cTAKES), the National Center for Biomedical Ontology (NCBO) Annotator, the Biomedical Concept Annotation System (BeCAS) and MetaMap. Each of the four concept recognition systems is applied to four different corpora: the i2b2 corpus of clinical documents, a PubMed corpus of Medline abstracts, a clinical trails corpus and the ShARe/CLEF corpus. In addition, we assess the individual system performances with respect to one gold standard annotation set, available for the ShARe/CLEF corpus. Furthermore, we built a silver standard annotation set from the individual systems' output and assess the quality as well as the contribution of individual systems to the quality of the silver standard. Our results demonstrate that mainly the NCBO annotator and cTAKES contribute to the silver standard corpora (F1-measures in the range of 21% to 74%) and their quality (best F1-measure of 33%), independent from the type of text investigated. While BeCAS and MetaMap can contribute to the precision of silver standard annotations (precision of up to 42%), the F1-measure drops when combined with NCBO Annotator and cTAKES due to a low recall. In conclusion, the performances of individual systems need to be improved independently from the text types, and the leveraging strategies to best take advantage of individual systems' annotations need to be revised. The textual content of the PubMed corpus, accession numbers for the clinical trials corpus, and assigned annotations of the four concept recognition systems as well as the generated silver standard annotation sets are available from http://purl.org/phenotype/resources. The textual content of the Sh

  7. Functional annotation of 2D protein maps: The GelMap portal

    Directory of Open Access Journals (Sweden)

    Hans-Peter eBraun

    2012-05-01

    Full Text Available In classical proteome analyses, final experimental data are (a images of 2D protein separations obtained by gel electrophoresis and (b corresponding lists of proteins which were identified by mass spectrometry (MS. For data annotation, software tools were developed which allow to link protein identity data directly to 2D gels (clickable gels. GelMap is a new online software tool to annotate 2D protein maps. It allows (i functional annotation of all identified proteins according to biological categories defined by the user, e.g. subcellular localization, metabolic pathway, or assignment to a protein complex and (ii annotation of several proteins per analyzed protein spot according to MS primary data. Options to differentially display proteins of functional categories offer new opportunities for data evaluation. For instance, if used for the annotation of 2D Blue native / SDS gels, GelMap allows identifying protein complexes of low abundance. A web portal has been established for presentation and evaluation of protein identity data related to 2D gels and is freely accessible at http://www.gelmap.de/.

  8. Capacity Utilisation of Vehicles for Road Freight Transport

    DEFF Research Database (Denmark)

    Kveiborg, Ole; Abate, Megersa Abera

    Purpose This chapter discusses a central aspect of freight transport – capacity utilisation with a link to empty running of commercial freight vehicles. Methodology/approach The paper provides an overview of the literature on these topics and groups the contributions into two segments according to...... their analytical approach and origin of research. Findings The first approach looks at utilisation based on economic theories such as the firms’ objective to maximise profitability and considers how various firm and haul (market) characteristics influence utilisation. The second approach stems from the...... transport modelling literature and its main aim is analysing vehicle movement and usage in transport demand modelling context. A strand of this second group of contributions is the modelling of trip-chain and its implication on the level of capacity utilisation. Research limitations The review is not a...

  9. Optimal radiotherapy utilisation rate in developing countries: An IAEA study

    International Nuclear Information System (INIS)

    Optimal radiotherapy utilisation rate (RTU) is the proportion of all cancer cases that should receive radiotherapy. Optimal RTU was estimated for 9 Middle Income Countries as part of a larger IAEA project to better understand RTU and stage distribution

  10. Multimedia Annotations on the Semantic Web

    OpenAIRE

    Stamou, G.; Ossenbruggen, J.R.; Pan, J; Schreiber, A.T.

    2006-01-01

    Multimedia in all forms (images, video, graphics, music, speech) is exploding on the Web. The content needs to be annotated and indexed to enable effective search and retrieval. However, recent standards and best practices for multimedia metadata don't provide semantically rich descriptions of multimedia content. On the other hand, the World Wide Web Consortium's (W3C's) Semantic Web effort has been making great progress in advancing techniques for annotating semantics of Web resources. To br...

  11. Fluid Annotations in a Open World

    DEFF Research Database (Denmark)

    Zellweger, Polle Trescott; Bouvin, Niels Olof; Jehøj, Henning;

    2001-01-01

    Fluid Documents use animated typographical changes to provide a novel and appealing user experience for hypertext browsing and for viewing document annotations in context. This paper describes an effort to broaden the utility of Fluid Documents by using the open hypermedia Arakne Environment to l...... layer fluid annotations and links on top of abitrary HTML pages on the World Wide Web. Changes to both Fluid Documents and Arakne are required....

  12. Instantiation of relations for semantic annotation

    OpenAIRE

    Tenier, Sylvain; Toussaint, Yannick; Napoli, Amedeo; Polanco, Xavier

    2006-01-01

    This paper presents a methodology for the semantic annotation of web pages with individuals of a domain ontology. While most semantic annotation systems can recognize knowledge units, they usually do not establish explicit relations between them. The method presented identifies the individuals which should be related among the whole set of individuals and codes them as role instances within an OWL ontology. This is done by using a correspondence between the tree structure of a web page and th...

  13. Instructions for Temporal Annotation of Scheduling Dialogs

    OpenAIRE

    O'Hara, Tom; Wiebe, Janyce; Payne, Karen

    1997-01-01

    Human annotation of natural language facilitates standardized evaluation of natural language processing systems and supports automated feature extraction. This document consists of instructions for annotating the temporal information in scheduling dialogs, dialogs in which the participants schedule a meeting with one another. Task-oriented dialogs, such as these are, would arise in many useful applications, for instance, automated information providers and automated phone operators. Explicit ...

  14. DIMA – Annotation guidelines for German intonation

    OpenAIRE

    Kügler, Frank; Smolibocki, Bernadett; Arnold, Denis; Baumann, Stefan; Braun, Bettina; Grice, Martine; Jannedy, Stefanie; Michalsky, Jan; Niebuhr, Oliver; Peters, Jörg; Ritter, Simon; Röhr, Christine T.; Schweitzer, Antje; Schweitzer, Katrin; Wagner, Petra

    2015-01-01

    This paper presents newly developed guidelines for prosodic annotation of German as a consensus system agreed upon by German intonologists. The DIMA system is rooted in the framework of autosegmental-metrical phonology. One important goal of the consensus is to make exchanging data between groups easier since German intonation is currently annotated according to different models. To this end, we aim to provide guidelines that are easy to learn. The guidelines were e...

  15. Annotating Honorifics Denoting Social Ranking of Referents

    OpenAIRE

    Nariyama, Shigeko; Nakaiwa, Hiromi; Siegel, Melanie

    2011-01-01

    This paper proposes an annotating scheme that encodes honorifics (respectful words). Honorifics are used extensively in Japanese, reflecting the social relationship (e.g. social ranks and age) of the referents. This referential information is vital for resolving zero pronouns and improving machine translation outputs. Annotating honorifics is a complex task that involves identifying a predicate with honorifics, assigning ranks to referents of the predicate, calibrating the ranks, and co...

  16. MannDB: A microbial annotation database for protein characterization

    Energy Technology Data Exchange (ETDEWEB)

    Zhou, C; Lam, M; Smith, J; Zemla, A; Dyer, M; Kuczmarski, T; Vitalis, E; Slezak, T

    2006-05-19

    MannDB was created to meet a need for rapid, comprehensive automated protein sequence analyses to support selection of proteins suitable as targets for driving the development of reagents for pathogen or protein toxin detection. Because a large number of open-source tools were needed, it was necessary to produce a software system to scale the computations for whole-proteome analysis. Thus, we built a fully automated system for executing software tools and for storage, integration, and display of automated protein sequence analysis and annotation data. MannDB is a relational database that organizes data resulting from fully automated, high-throughput protein-sequence analyses using open-source tools. Types of analyses provided include predictions of cleavage, chemical properties, classification, features, functional assignment, post-translational modifications, motifs, antigenicity, and secondary structure. Proteomes (lists of hypothetical and known proteins) are downloaded and parsed from Genbank and then inserted into MannDB, and annotations from SwissProt are downloaded when identifiers are found in the Genbank entry or when identical sequences are identified. Currently 36 open-source tools are run against MannDB protein sequences either on local systems or by means of batch submission to external servers. In addition, BLAST against protein entries in MvirDB, our database of microbial virulence factors, is performed. A web client browser enables viewing of computational results and downloaded annotations, and a query tool enables structured and free-text search capabilities. When available, links to external databases, including MvirDB, are provided. MannDB contains whole-proteome analyses for at least one representative organism from each category of biological threat organism listed by APHIS, CDC, HHS, NIAID, USDA, USFDA, and WHO. MannDB comprises a large number of genomes and comprehensive protein sequence analyses representing organisms listed as high

  17. A community-curated consensual annotation that is continuously updated: the Bacillus subtilis centred wiki SubtiWiki.

    OpenAIRE

    Flórez, Lope A.; Roppel, Sebastian F.; Schmeisky, Arne G.; Lammers, Christoph R.; Stülke, Jörg

    2009-01-01

    Bacillus subtilis is the model organism for Gram-positive bacteria, with a large amount of publications on all aspects of its biology. To facilitate genome annotation and the collection of comprehensive information on B. subtilis, we created SubtiWiki as a community-oriented annotation tool for information retrieval and continuous maintenance. The wiki is focused on the needs and requirements of scientists doing experimental work. This has implications for the design of the interface and for ...

  18. FeatureViewer, a BioJS component for visualization of position-based annotations in protein sequences

    OpenAIRE

    Leyla Garcia; Guy Yachdav; Maria-Jesus Martin

    2014-01-01

    Summary: FeatureViewer is a BioJS component that lays out, maps, orients, and renders position-based annotations for protein sequences. This component is highly flexible and customizable, allowing the presentation of annotations by rows, all centered, or distributed in non-overlapping tracks. It uses either lines or shapes for sites and rectangles for regions. The result is a powerful visualization tool that can be easily integrated into web applications as well as documents as it provides an...

  19. Report on the Fifth Workshop on Exploiting Semantic Annotations in Information Retrieval (ESAIR’12) : CIKM WORKSHOP REPORT

    OpenAIRE

    Kamps, Jaap; Karlgren, Jussi; Mika, Peter; Murdock, Vanessa

    2013-01-01

    There is an increasing amount of structure on the web as a result of modern web lan- guages, user tagging and annotation, emerging robust NLP tools, and an ever growing volume of linked data. These meaningful, semantic, annotations hold the promise to significantly en- hance information access, by enhancing the depth of analysis of today’s systems. Currently, we have only started exploring the possibilities and only begin to understand how these valu- able semantic cues can be put to fruitful...

  20. Medicare and Private and Public Medical Practice: Utilisation and Substitution

    OpenAIRE

    Duhs, L.A.

    1994-01-01

    The Commonwealth Government is currently undertaking a review of various issues in the health sector. A recently published study by John Deeble has analysed expenditures, utilisation, workforce issues etc. under Australia’s current health insurance arrangements (Medicare) for the provision of medical services remunerated on a fee-for-service basis. This study has highlighted increased utilisation of services as a major “management issue”. It is demonstrated here that the data on which these c...

  1. Renewable hydrogen utilisation for the production of methanol.

    OpenAIRE

    Galindo, Cifre P; Badr, Ossama

    2007-01-01

    Electrolytic hydrogen production is an efficient way of storing renewable energy generated electricity and securing the contribution of renewables in the future electricity supply. The use of this hydrogen for the production of methanol results in a liquid fuel that can be utilised directly with minor changes in the existing infrastructure. To utilise the renewable generated hydrogen for production of renewable methanol, a sustainable carbon source is needed. This carbon can...

  2. SETIS Magazine - Carbon Capture Utilisation and Storage issue

    OpenAIRE

    TZIMAS Evangelos; PEREZ FORTES MARIA DEL MAR

    2016-01-01

    The SETIS magazine aims at delivering timely information and analysis on the state of play of energy technologies, related research and innovation efforts in support of the implementation of the European Strategic Energy Technology Plan (SET-Plan). The current issue is dedicated to Carbon Capture Utilisation and Storage. The editorial for the Carbon Capture Utilisation and Storage issue is provided by A.SPIRE Executive Director Loredana Ghinea. The issue also includes contributions by:...

  3. Related Documents Search Using User Created Annotations

    Directory of Open Access Journals (Sweden)

    Jakub Sevcech

    2013-01-01

    Full Text Available We often use various services for creating bookmarks,tags, highlights and other types of annotations while surf-ing the Internet or when reading electronic documentsas well. These services allows us to create a number oftypes of annotation that we are commonly creating intoprinted documents. Annotations attached to electronicdocuments however can be used for other purposes suchas navigation support, text summarization etc. We pro-posed a method for searching related documents to cur-rently studied document using annotations created by thedocument reader as indicators of user's interest in par-ticular parts of the document. The method is based onspreading activation in text transformed into graph. Forevaluation we created a service called Annota, which al-lows users to insert various types of annotations into webpages and PDF documents displayed in the web browser.We analyzed properties of various types of annotations in-serted by users of Annota into documents. Based on thesewe evaluated our method by simulation and we comparedit against commonly used TF-IDF based method.

  4. JGI Plant Genomics Gene Annotation Pipeline

    Energy Technology Data Exchange (ETDEWEB)

    Shu, Shengqiang; Rokhsar, Dan; Goodstein, David; Hayes, David; Mitros, Therese

    2014-07-14

    Plant genomes vary in size and are highly complex with a high amount of repeats, genome duplication and tandem duplication. Gene encodes a wealth of information useful in studying organism and it is critical to have high quality and stable gene annotation. Thanks to advancement of sequencing technology, many plant species genomes have been sequenced and transcriptomes are also sequenced. To use these vastly large amounts of sequence data to make gene annotation or re-annotation in a timely fashion, an automatic pipeline is needed. JGI plant genomics gene annotation pipeline, called integrated gene call (IGC), is our effort toward this aim with aid of a RNA-seq transcriptome assembly pipeline. It utilizes several gene predictors based on homolog peptides and transcript ORFs. See Methods for detail. Here we present genome annotation of JGI flagship green plants produced by this pipeline plus Arabidopsis and rice except for chlamy which is done by a third party. The genome annotations of these species and others are used in our gene family build pipeline and accessible via JGI Phytozome portal whose URL and front page snapshot are shown below.

  5. An annotation based approach to support design communication

    CERN Document Server

    Hisarciklilar, Onur

    2007-01-01

    The aim of this paper is to propose an approach based on the concept of annotation for supporting design communication. In this paper, we describe a co-operative design case study where we analyse some annotation practices, mainly focused on design minutes recorded during project reviews. We point out specific requirements concerning annotation needs. Based on these requirements, we propose an annotation model, inspired from the Speech Act Theory (SAT) to support communication in a 3D digital environment. We define two types of annotations in the engineering design context, locutionary and illocutionary annotations. The annotations we describe in this paper are materialised by a set of digital artefacts, which have a semantic dimension allowing express/record elements of technical justifications, traces of contradictory debates, etc. In this paper, we first clarify the semantic annotation concept, and we define general properties of annotations in the engineering design context, and the role of annotations in...

  6. The Annotation of RNA Motifs

    Directory of Open Access Journals (Sweden)

    Eric Westhof

    2006-04-01

    Full Text Available The recent deluge of new RNA structures, including complete atomic-resolution views of both subunits of the ribosome, has on the one hand literally overwhelmed our individual abilities to comprehend the diversity of RNA structure, and on the other hand presented us with new opportunities for comprehensive use of RNA sequences for comparative genetic, evolutionary and phylogenetic studies. Two concepts are key to understanding RNA structure: hierarchical organization of global structure and isostericity of local interactions. Global structure changes extremely slowly, as it relies on conserved long-range tertiary interactions. Tertiary RNA–RNA and quaternary RNA–protein interactions are mediated by RNA motifs, defined as recurrent and ordered arrays of non-Watson–Crick base-pairs. A single RNA motif comprises a family of sequences, all of which can fold into the same three-dimensional structure and can mediate the same interaction(s. The chemistry and geometry of base pairing constrain the evolution of motifs in such a way that random mutations that occur within motifs are accepted or rejected insofar as they can mediate a similar ordered array of interactions. The steps involved in the analysis and annotation of RNA motifs in 3D structures are: (a decomposition of each motif into non-Watson–Crick base-pairs; (b geometric classification of each basepair; (c identification of isosteric substitutions for each basepair by comparison to isostericity matrices; (d alignment of homologous sequences using the isostericity matrices to identify corresponding positions in the crystal structure; (e acceptance or rejection of the null hypothesis that the motif is conserved.

  7. GOAnnotator: linking protein GO annotations to evidence text

    OpenAIRE

    Couto, Francisco M.; Silva, Mário J.; Lee, Vivian; Dimmer, Emily; Camon, Evelyn; Apweiler, Rolf; Kirsch, Harald; Rebholz-Schuhmann, Dietrich

    2006-01-01

    Background Annotation of proteins with gene ontology (GO) terms is ongoing work and a complex task. Manual GO annotation is precise and precious, but it is time-consuming. Therefore, instead of curated annotations most of the proteins come with uncurated annotations, which have been generated automatically. Text-mining systems that use literature for automatic annotation have been proposed but they do not satisfy the high quality expectations of curators. Results In this paper we describe an ...

  8. Web Database Query Interface Annotation Based on User Collaboration

    Institute of Scientific and Technical Information of China (English)

    LIU Wei; LIN Can; MENG Xiaofeng

    2006-01-01

    A vision based query interface annotation method is used to relate attributes and form elements in form-based web query interfaces, this method can reach accuracy of 82%.And a user participation method is used to tune the result; user can answer "yes" or "no" for existing annotations, or manually annotate form elements.Mass feedback is added to the annotation algorithm to produce more accurate result.By this approach, query interface annotation can reach a perfect accuracy.

  9. Versatile annotation and publication quality visualization of protein complexes using POLYVIEW-3D

    Directory of Open Access Journals (Sweden)

    Meller Jaroslaw

    2007-08-01

    Full Text Available Abstract Background Macromolecular visualization as well as automated structural and functional annotation tools play an increasingly important role in the post-genomic era, contributing significantly towards the understanding of molecular systems and processes. For example, three dimensional (3D models help in exploring protein active sites and functional hot spots that can be targeted in drug design. Automated annotation and visualization pipelines can also reveal other functionally important attributes of macromolecules. These goals are dependent on the availability of advanced tools that integrate better the existing databases, annotation servers and other resources with state-of-the-art rendering programs. Results We present a new tool for protein structure analysis, with the focus on annotation and visualization of protein complexes, which is an extension of our previously developed POLYVIEW web server. By integrating the web technology with state-of-the-art software for macromolecular visualization, such as the PyMol program, POLYVIEW-3D enables combining versatile structural and functional annotations with a simple web-based interface for creating publication quality structure rendering, as well as animated images for Powerpoint™, web sites and other electronic resources. The service is platform independent and no plug-ins are required. Several examples of how POLYVIEW-3D can be used for structural and functional analysis in the context of protein-protein interactions are presented to illustrate the available annotation options. Conclusion POLYVIEW-3D server features the PyMol image rendering that provides detailed and high quality presentation of macromolecular structures, with an easy to use web-based interface. POLYVIEW-3D also provides a wide array of options for automated structural and functional analysis of proteins and their complexes. Thus, the POLYVIEW-3D server may become an important resource for researches and educators in

  10. Eliciting the Functional Taxonomy from protein annotations and taxa.

    Science.gov (United States)

    Falda, Marco; Lavezzo, Enrico; Fontana, Paolo; Bianco, Luca; Berselli, Michele; Formentin, Elide; Toppo, Stefano

    2016-01-01

    The advances of omics technologies have triggered the production of an enormous volume of data coming from thousands of species. Meanwhile, joint international efforts like the Gene Ontology (GO) consortium have worked to provide functional information for a vast amount of proteins. With these data available, we have developed FunTaxIS, a tool that is the first attempt to infer functional taxonomy (i.e. how functions are distributed over taxa) combining functional and taxonomic information. FunTaxIS is able to define a taxon specific functional space by exploiting annotation frequencies in order to establish if a function can or cannot be used to annotate a certain species. The tool generates constraints between GO terms and taxa and then propagates these relations over the taxonomic tree and the GO graph. Since these constraints nearly cover the whole taxonomy, it is possible to obtain the mapping of a function over the taxonomy. FunTaxIS can be used to make functional comparative analyses among taxa, to detect improper associations between taxa and functions, and to discover how functional knowledge is either distributed or missing. A benchmark test set based on six different model species has been devised to get useful insights on the generated taxonomic rules. PMID:27534507

  11. Annotated chemical patent corpus: a gold standard for text mining.

    Directory of Open Access Journals (Sweden)

    Saber A Akhondi

    Full Text Available Exploring the chemical and biological space covered by patent applications is crucial in early-stage medicinal chemistry activities. Patent analysis can provide understanding of compound prior art, novelty checking, validation of biological assays, and identification of new starting points for chemical exploration. Extracting chemical and biological entities from patents through manual extraction by expert curators can take substantial amount of time and resources. Text mining methods can help to ease this process. To validate the performance of such methods, a manually annotated patent corpus is essential. In this study we have produced a large gold standard chemical patent corpus. We developed annotation guidelines and selected 200 full patents from the World Intellectual Property Organization, United States Patent and Trademark Office, and European Patent Office. The patents were pre-annotated automatically and made available to four independent annotator groups each consisting of two to ten annotators. The annotators marked chemicals in different subclasses, diseases, targets, and modes of action. Spelling mistakes and spurious line break due to optical character recognition errors were also annotated. A subset of 47 patents was annotated by at least three annotator groups, from which harmonized annotations and inter-annotator agreement scores were derived. One group annotated the full set. The patent corpus includes 400,125 annotations for the full set and 36,537 annotations for the harmonized set. All patents and annotated entities are publicly available at www.biosemantics.org.

  12. Annotation en rôles sémantiques du français en domaine spécifique

    OpenAIRE

    Pradet, Quentin

    2015-01-01

    Cette thèse de Traitement Automatique des Langues a pour objectif l'annotation automatique en rôles sémantiques du français en domaine spécifique. Cette tâche désambiguïse le sens des prédicats d'un texte et annote les syntagmes liés avec des rôles sémantiques tels qu'Agent, Patient ou Destination. Elle aide de nombreuses applications dans les domaines où des corpus annotés existent, mais est difficile à utiliser quand ce n'est pas le cas. Nous avons d'abord évalué sur le corpus FrameNet une ...

  13. A Cross-cultural Corpus of Annotated Verbal and Nonverbal Behaviors in Receptionist Encounters

    CERN Document Server

    Makatchev, Maxim; Sakr, Majd

    2012-01-01

    We present the first annotated corpus of nonverbal behaviors in receptionist interactions, and the first nonverbal corpus (excluding the original video and audio data) of service encounters freely available online. Native speakers of American English and Arabic participated in a naturalistic role play at reception desks of university buildings in Doha, Qatar and Pittsburgh, USA. Their manually annotated nonverbal behaviors include gaze direction, hand and head gestures, torso positions, and facial expressions. We discuss possible uses of the corpus and envision it to become a useful tool for the human-robot interaction community.

  14. Gene Ontology annotations at SGD: new data sources and annotation methods.

    Science.gov (United States)

    Hong, Eurie L; Balakrishnan, Rama; Dong, Qing; Christie, Karen R; Park, Julie; Binkley, Gail; Costanzo, Maria C; Dwight, Selina S; Engel, Stacia R; Fisk, Dianna G; Hirschman, Jodi E; Hitz, Benjamin C; Krieger, Cynthia J; Livstone, Michael S; Miyasato, Stuart R; Nash, Robert S; Oughtred, Rose; Skrzypek, Marek S; Weng, Shuai; Wong, Edith D; Zhu, Kathy K; Dolinski, Kara; Botstein, David; Cherry, J Michael

    2008-01-01

    The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) collects and organizes biological information about the chromosomal features and gene products of the budding yeast Saccharomyces cerevisiae. Although published data from traditional experimental methods are the primary sources of evidence supporting Gene Ontology (GO) annotations for a gene product, high-throughput experiments and computational predictions can also provide valuable insights in the absence of an extensive body of literature. Therefore, GO annotations available at SGD now include high-throughput data as well as computational predictions provided by the GO Annotation Project (GOA UniProt; http://www.ebi.ac.uk/GOA/). Because the annotation method used to assign GO annotations varies by data source, GO resources at SGD have been modified to distinguish data sources and annotation methods. In addition to providing information for genes that have not been experimentally characterized, GO annotations from independent sources can be compared to those made by SGD to help keep the literature-based GO annotations current. PMID:17982175

  15. Fast and accurate semantic annotation of bioassays exploiting a hybrid of machine learning and user confirmation.

    Science.gov (United States)

    Clark, Alex M; Bunin, Barry A; Litterman, Nadia K; Schürer, Stephan C; Visser, Ubbo

    2014-01-01

    Bioinformatics and computer aided drug design rely on the curation of a large number of protocols for biological assays that measure the ability of potential drugs to achieve a therapeutic effect. These assay protocols are generally published by scientists in the form of plain text, which needs to be more precisely annotated in order to be useful to software methods. We have developed a pragmatic approach to describing assays according to the semantic definitions of the BioAssay Ontology (BAO) project, using a hybrid of machine learning based on natural language processing, and a simplified user interface designed to help scientists curate their data with minimum effort. We have carried out this work based on the premise that pure machine learning is insufficiently accurate, and that expecting scientists to find the time to annotate their protocols manually is unrealistic. By combining these approaches, we have created an effective prototype for which annotation of bioassay text within the domain of the training set can be accomplished very quickly. Well-trained annotations require single-click user approval, while annotations from outside the training set domain can be identified using the search feature of a well-designed user interface, and subsequently used to improve the underlying models. By drastically reducing the time required for scientists to annotate their assays, we can realistically advocate for semantic annotation to become a standard part of the publication process. Once even a small proportion of the public body of bioassay data is marked up, bioinformatics researchers can begin to construct sophisticated and useful searching and analysis algorithms that will provide a diverse and powerful set of tools for drug discovery researchers. PMID:25165633

  16. MPEG-7 based video annotation and browsing

    Science.gov (United States)

    Hoeynck, Michael; Auweiler, Thorsten; Wellhausen, Jens

    2003-11-01

    The huge amount of multimedia data produced worldwide requires annotation in order to enable universal content access and to provide content-based search-and-retrieval functionalities. Since manual video annotation can be time consuming, automatic annotation systems are required. We review recent approaches to content-based indexing and annotation of videos for different kind of sports and describe our approach to automatic annotation of equestrian sports videos. We especially concentrate on MPEG-7 based feature extraction and content description, where we apply different visual descriptors for cut detection. Further, we extract the temporal positions of single obstacles on the course by analyzing MPEG-7 edge information. Having determined single shot positions as well as the visual highlights, the information is jointly stored with meta-textual information in an MPEG-7 description scheme. Based on this information, we generate content summaries which can be utilized in a user-interface in order to provide content-based access to the video stream, but further for media browsing on a streaming server.

  17. A norm utilisation for scarce hospital resources: Evidence from operating rooms in a Dutch university hospital

    NARCIS (Netherlands)

    Houdenhoven, van Mark; Hans, Erwin W.; Klein, Jan; Wullink, Gerhard; Kazemier, Geert

    2007-01-01

    Background: Utilisation of operating rooms is high on the agenda of hospital managers and researchers. Many efforts in the area of maximising the utilisation have been focussed on finding the holy grail of 100% utilisation. The utilisation that can be realised, however, depends on the patient mix an

  18. Studying Oogenesis in a Non-model Organism Using Transcriptomics: Assembling, Annotating, and Analyzing Your Data.

    Science.gov (United States)

    Carter, Jean-Michel; Gibbs, Melanie; Breuker, Casper J

    2016-01-01

    This chapter provides a guide to processing and analyzing RNA-Seq data in a non-model organism. This approach was implemented for studying oogenesis in the Speckled Wood Butterfly Pararge aegeria. We focus in particular on how to perform a more informative primary annotation of your non-model organism by implementing our multi-BLAST annotation strategy. We also provide a general guide to other essential steps in the next-generation sequencing analysis workflow. Before undertaking these methods, we recommend you familiarize yourself with command line usage and fundamental concepts of database handling. Most of the operations in the primary annotation pipeline can be performed in Galaxy (or equivalent standalone versions of the tools) and through the use of common database operations (e.g. to remove duplicates) but other equivalent programs and/or custom scripts can be implemented for further automation. PMID:27557578

  19. Ontology-Based Annotation of Multimedia Language Data for the Semantic Web

    CERN Document Server

    Chebotko, Artem; Fotouhi, Farshad; Aristar, Anthony

    2009-01-01

    There is an increasing interest and effort in preserving and documenting endangered languages. Language data are valuable only when they are well-cataloged, indexed and searchable. Many language data, particularly those of lesser-spoken languages, are collected as audio and video recordings. While multimedia data provide more channels and dimensions to describe a language's function, and gives a better presentation of the cultural system associated with the language of that community, they are not text-based or structured (in binary format), and their semantics is implicit in their content. The content is thus easy for a human being to understand, but difficult for computers to interpret. Hence, there is a great need for a powerful and user-friendly system to annotate multimedia data with text-based, well-structured and searchable metadata. This chapter describes an ontology-based multimedia annotation tool, OntoELAN, that enables annotation of language multimedia data with a linguistic ontology.

  20. GLASS MELTING PHENOMENA, THEIR ORDERING AND MELTING SPACE UTILISATION

    Directory of Open Access Journals (Sweden)

    Němec L.

    2013-12-01

    Full Text Available Four aspects of effective glass melting have been defined – namely the fast kinetics of partial melting phenomena, a consideration of the melting phenomena ordering, high utilisation of the melting space, and effective utilisation of the supplied energy. The relations were defined for the specific melting performance and specific energy consumption of the glass melting process which involve the four mentioned aspects of the process and indicate the potentials of effective melting. The quantity “space utilisation” has been treated in more detail as an aspect not considered in practice till this time. The space utilisation was quantitatively defined and its values have been determined for the industrial melting facility by mathematical modelling. The definitions of the specific melting performance and specific energy consumption have been used for assessment of the potential impact of a controlled melt flow and high space utilisation on the melting process efficiency on the industrial scale. The results have shown that even the partial control of the melt flow, leading to the partial increase of the space utilisation, may considerably increase the melting performance, whereas a decrease of the specific energy consumption was determined to be between 10 - 15 %.

  1. Critical Assessment of Function Annotation Meeting, 2011

    Energy Technology Data Exchange (ETDEWEB)

    Friedberg, Iddo

    2015-01-21

    The Critical Assessment of Function Annotation meeting was held July 14-15, 2011 at the Austria Conference Center in Vienna, Austria. There were 73 registered delegates at the meeting. We thank the DOE for this award. It helped us organize and support a scientific meeting AFP 2011 as a special interest group (SIG) meeting associated with the ISMB 2011 conference. The conference was held in Vienna, Austria, in July 2011. The AFP SIG was held on July 15-16, 2011 (immediately preceding the conference). The meeting consisted of two components, the first being a series of talks (invited and contributed) and discussion sections dedicated to protein function research, with an emphasis on the theory and practice of computational methods utilized in functional annotation. The second component provided a large-scale assessment of computational methods through participation in the Critical Assessment of Functional Annotation (CAFA).

  2. Graph Annotations in Modeling Complex Network Topologies

    CERN Document Server

    Dimitropoulos, Xenofontas; Vahdat, Amin; Riley, George

    2007-01-01

    The coarsest approximation of the structure of a complex network, such as the Internet, is a simple undirected unweighted graph. This approximation, however, loses too much detail. In reality, objects represented by vertices and edges in such a graph possess some non-trivial internal structure that varies across and differentiates among distinct types of links or nodes. In this work, we abstract such additional information as network annotations. We introduce a network topology modeling framework that treats annotations as an extended correlation profile of a network. Assuming we have this profile measured for a given network, we present an algorithm to rescale it in order to construct networks of varying size that still reproduce the original measured annotation profile. Using this methodology, we accurately capture the network properties essential for realistic simulations of network applications and protocols, or any other simulations involving complex network topologies, including modeling and simulation ...

  3. Knowledge-based reasoning to annotate noncoding RNA using multi-agent system.

    Science.gov (United States)

    Arruda, Wosley C; Souza, Daniel S; Ralha, Célia G; Walter, Maria Emilia M T; Raiol, Tainá; Brigido, Marcelo M; Stadler, Peter F

    2015-12-01

    Noncoding RNAs (ncRNAs) have been focus of intense research over the last few years. Since characteristics and signals of ncRNAs are not entirely known, researchers use different computational tools together with their biological knowledge to predict putative ncRNAs. In this context, this work presents ncRNA-Agents, a multi-agent system to annotate ncRNAs based on the output of different tools, using inference rules to simulate biologists' reasoning. Experiments with data from the fungus Saccharomyces cerevisiae allowed to measure the performance of ncRNA-Agents, with better sensibility, when compared to Infernal, a widely used tool for annotating ncRNA. Besides, data of the Schizosaccharomyces pombe and Paracoccidioides brasiliensis fungi identified novel putative ncRNAs, which demonstrated the usefulness of our approach. NcRNA-Agents can be be found at: http://www.biomol.unb.br/ncrna-agents. PMID:26223200

  4. An Annotated Dataset of 14 Meat Images

    DEFF Research Database (Denmark)

    Stegmann, Mikkel Bille

    2002-01-01

    This note describes a dataset consisting of 14 annotated images of meat. Points of correspondence are placed on each image. As such, the dataset can be readily used for building statistical models of shape. Further, format specifications and terms of use are given.......This note describes a dataset consisting of 14 annotated images of meat. Points of correspondence are placed on each image. As such, the dataset can be readily used for building statistical models of shape. Further, format specifications and terms of use are given....

  5. Software for computing and annotating genomic ranges.

    Directory of Open Access Journals (Sweden)

    Michael Lawrence

    Full Text Available We describe Bioconductor infrastructure for representing and computing on annotated genomic ranges and integrating genomic data with the statistical computing features of R and its extensions. At the core of the infrastructure are three packages: IRanges, GenomicRanges, and GenomicFeatures. These packages provide scalable data structures for representing annotated ranges on the genome, with special support for transcript structures, read alignments and coverage vectors. Computational facilities include efficient algorithms for overlap and nearest neighbor detection, coverage calculation and other range operations. This infrastructure directly supports more than 80 other Bioconductor packages, including those for sequence analysis, differential expression analysis and visualization.

  6. The Phenomenon of Youtubers and their Utilisation in Marketing

    OpenAIRE

    Tauchenová, Kateřina

    2014-01-01

    This master´s thesis is called The Phenomenon of Youtubers and their Utilisation in Marketing. It presents Youtubers as idols of today´s young people and introduces options of utilization of their power for marketing purposes. The first chapter introduces the reader to the general matters of online marketing and offers basic knowledge about this area. The second chapter is dedicated to social networks and their utilisation in marketing field. The third chapter introduces the topic YouTube. It...

  7. Geothermal energy - hydrothermal utilisation of geothermal energy in Germany

    International Nuclear Information System (INIS)

    In this phase of developing and utilisation of geothermal potentials the hydrothermal sector plays a very important role due to its possibilities of supplying heat in the MW-range at any time of day or night or year. The heat is contained in thermal water extracted from depth between 2000 and 2500 m by means of deep drilling. In Germany there are hydrothermal potentials in the South (Rhine Valley) and North. The following article describes the geological, technological and economic aspects of thermal water utilisation for the generation of thermal energy. (orig.)

  8. Utilisation of antibiotic therapy in community practice.

    LENUS (Irish Health Repository)

    McGowan, B

    2008-10-01

    The aim of the study was to identify outpatient antibiotic consumption between Jan 2000 and Dec 2005 through analysis of the HSE-Primary Care Reimbursement Services (PCRS) database as part of the Surveillance of Antimicrobial Resistance in Ireland (SARI) project. Total antibiotic consumption on the PCRS scheme between January 2000 and December 2005 expressed in Defined Daily Dose per 1000 PCRS inhabitants per day increased by 26%. The penicillin group represents the highest consumption accounting for approximately 50% of the total outpatient antibiotic use. Total DIDs for this group increased by 25% between 2000 and 2005. Co-amoxiclav and amoxicillin account for 80% of the total consumption of this group of anti-infectives. With the exception of aminoglycosides and sulfonamides which demonstrated a decrease in DID consumption of 47% and 8% respectively, all other groups of anti-infectives had an increase in DID consumption of greater than 25% during the study period. Antibiotic prescribing data is a valuable tool for assessing public health strategies aiming to optimise antibiotic prescribing.

  9. ASAP: Amplification, sequencing & annotation of plastomes

    Directory of Open Access Journals (Sweden)

    Folta Kevin M

    2005-12-01

    Full Text Available Abstract Background Availability of DNA sequence information is vital for pursuing structural, functional and comparative genomics studies in plastids. Traditionally, the first step in mining the valuable information within a chloroplast genome requires sequencing a chloroplast plasmid library or BAC clones. These activities involve complicated preparatory procedures like chloroplast DNA isolation or identification of the appropriate BAC clones to be sequenced. Rolling circle amplification (RCA is being used currently to amplify the chloroplast genome from purified chloroplast DNA and the resulting products are sheared and cloned prior to sequencing. Herein we present a universal high-throughput, rapid PCR-based technique to amplify, sequence and assemble plastid genome sequence from diverse species in a short time and at reasonable cost from total plant DNA, using the large inverted repeat region from strawberry and peach as proof of concept. The method exploits the highly conserved coding regions or intergenic regions of plastid genes. Using an informatics approach, chloroplast DNA sequence information from 5 available eudicot plastomes was aligned to identify the most conserved regions. Cognate primer pairs were then designed to generate ~1 – 1.2 kb overlapping amplicons from the inverted repeat region in 14 diverse genera. Results 100% coverage of the inverted repeat region was obtained from Arabidopsis, tobacco, orange, strawberry, peach, lettuce, tomato and Amaranthus. Over 80% coverage was obtained from distant species, including Ginkgo, loblolly pine and Equisetum. Sequence from the inverted repeat region of strawberry and peach plastome was obtained, annotated and analyzed. Additionally, a polymorphic region identified from gel electrophoresis was sequenced from tomato and Amaranthus. Sequence analysis revealed large deletions in these species relative to tobacco plastome thus exhibiting the utility of this method for structural and

  10. TOPSAN: a collaborative annotation environment for structural genomics

    Directory of Open Access Journals (Sweden)

    Weekes Dana

    2010-08-01

    Full Text Available Abstract Background Many protein structures determined in high-throughput structural genomics centers, despite their significant novelty and importance, are available only as PDB depositions and are not accompanied by a peer-reviewed manuscript. Because of this they are not accessible by the standard tools of literature searches, remaining underutilized by the broad biological community. Results To address this issue we have developed TOPSAN, The Open Protein Structure Annotation Network, a web-based platform that combines the openness of the wiki model with the quality control of scientific communication. TOPSAN enables research collaborations and scientific dialogue among globally distributed participants, the results of which are reviewed by experts and eventually validated by peer review. The immediate goal of TOPSAN is to harness the combined experience, knowledge, and data from such collaborations in order to enhance the impact of the astonishing number and diversity of structures being determined by structural genomics centers and high-throughput structural biology. Conclusions TOPSAN combines features of automated annotation databases and formal, peer-reviewed scientific research literature, providing an ideal vehicle to bridge a gap between rapidly accumulating data from high-throughput technologies and a much slower pace for its analysis and integration with other, relevant research.

  11. Assembly, Annotation, and Analysis of Multiple Mycorrhizal Fungal Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Initiative Consortium, Mycorrhizal Genomics; Kuo, Alan; Grigoriev, Igor; Kohler, Annegret; Martin, Francis

    2013-03-08

    Mycorrhizal fungi play critical roles in host plant health, soil community structure and chemistry, and carbon and nutrient cycling, all areas of intense interest to the US Dept. of Energy (DOE) Joint Genome Institute (JGI). To this end we are building on our earlier sequencing of the Laccaria bicolor genome by partnering with INRA-Nancy and the mycorrhizal research community in the MGI to sequence and analyze dozens of mycorrhizal genomes of all Basidiomycota and Ascomycota orders and multiple ecological types (ericoid, orchid, and ectomycorrhizal). JGI has developed and deployed high-throughput sequencing techniques, and Assembly, RNASeq, and Annotation Pipelines. In 2012 alone we sequenced, assembled, and annotated 12 draft or improved genomes of mycorrhizae, and predicted ~;;232831 genes and ~;;15011 multigene families, All of this data is publicly available on JGI MycoCosm (http://jgi.doe.gov/fungi/), which provides access to both the genome data and tools with which to analyze the data. Preliminary comparisons of the current total of 14 public mycorrhizal genomes suggest that 1) short secreted proteins potentially involved in symbiosis are more enriched in some orders than in others amongst the mycorrhizal Agaricomycetes, 2) there are wide ranges of numbers of genes involved in certain functional categories, such as signal transduction and post-translational modification, and 3) novel gene families are specific to some ecological types.

  12. Annotation Semantique de Documents Semi-Structurés pour la recherche d'information

    OpenAIRE

    Thiam, Mouhamadou

    2010-01-01

    Le web sémantique est défini par un ensemble de méthodes et de technologies permettant à des agents logiciels de raisonner sur le contenu des ressources du Web. Cette vision du Web dépend de la construction des ontologies et de l'utilisation de métadonnées pour représenter ces ressources. L'objectif de notre travail de thèse est d'annoter sémantiquement des documents balisés et relatifs au même domaine. Ces documents peuvent comporter des parties bien structurées et d'autres textuelles. Nous ...

  13. Annotation et recherche contextuelle des documents multimédias socio-personnels

    OpenAIRE

    Lajmi, Sonia

    2011-01-01

    L’objectif de cette thèse est d’instrumentaliser des moyens, centrés utilisateur, de représentation, d’acquisition, d’enrichissement et d’exploitation des métadonnées décrivant des documents multimédias socio-personnels. Afin d’atteindre cet objectif, nous avons proposé un modèle d’annotation, appelé SeMAT avec une nouvelle vision du contexte de prise de vue. Nous avons proposé d’utiliser des ressources sémantiques externes telles que GeoNames , et Wikipédia pour enrichir automatiquement les ...

  14. Détection de logos pour l'annotation d'images de presse

    OpenAIRE

    Tirilly, Pierre; Claveau, Vincent; Gros, Patrick

    2010-01-01

    Dans cet article, nous proposons une méthode d'annotation d'images tirées d'un corpus d'articles de presse. Pour contourner le problème du fossé sémantique posé par l'utilisation de descripteurs de bas-niveau, nous mettons en relation des indices visuels de haut-niveau extraits des images (présence de logos ou de panneaux) et des indices textuels issus de l'analyse du texte des articles (un sousensemble des entités nommées – noms d'entreprises. . .–). Dans un premier temps, nous proposons un ...

  15. Analysis and comparison of very large metagenomes with fast clustering and functional annotation

    Directory of Open Access Journals (Sweden)

    Li Weizhong

    2009-10-01

    Full Text Available Abstract Background The remarkable advance of metagenomics presents significant new challenges in data analysis. Metagenomic datasets (metagenomes are large collections of sequencing reads from anonymous species within particular environments. Computational analyses for very large metagenomes are extremely time-consuming, and there are often many novel sequences in these metagenomes that are not fully utilized. The number of available metagenomes is rapidly increasing, so fast and efficient metagenome comparison methods are in great demand. Results The new metagenomic data analysis method Rapid Analysis of Multiple Metagenomes with a Clustering and Annotation Pipeline (RAMMCAP was developed using an ultra-fast sequence clustering algorithm, fast protein family annotation tools, and a novel statistical metagenome comparison method that employs a unique graphic interface. RAMMCAP processes extremely large datasets with only moderate computational effort. It identifies raw read clusters and protein clusters that may include novel gene families, and compares metagenomes using clusters or functional annotations calculated by RAMMCAP. In this study, RAMMCAP was applied to the two largest available metagenomic collections, the "Global Ocean Sampling" and the "Metagenomic Profiling of Nine Biomes". Conclusion RAMMCAP is a very fast method that can cluster and annotate one million metagenomic reads in only hundreds of CPU hours. It is available from http://tools.camera.calit2.net/camera/rammcap/.

  16. Developing a Social Media Marketing tool

    OpenAIRE

    Valova, Olga

    2015-01-01

    The objective of the thesis is to develop a better, easier to use social media marketing tool that could be utilised in any business. By understanding and analysing how business uses social media as well as currently available social media marketing tools, design a tool with the maximum amount of features, but with a simple and intuitive User Interface. An agile software development life cycle was used throughout the creation of the tool. Qualitative analysis was used to analyse existing ...

  17. Annotation Method (AM): SE22_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available ether with predicted molecular formulae and putative structures, were provided as metabolite annotations. Comparison with public data...bases was performed. A grading system was introduced to describe the evidence supporting the annotations. ...

  18. Computer systems for annotation of single molecule fragments

    Science.gov (United States)

    Schwartz, David Charles; Severin, Jessica

    2016-07-19

    There are provided computer systems for visualizing and annotating single molecule images. Annotation systems in accordance with this disclosure allow a user to mark and annotate single molecules of interest and their restriction enzyme cut sites thereby determining the restriction fragments of single nucleic acid molecules. The markings and annotations may be automatically generated by the system in certain embodiments and they may be overlaid translucently onto the single molecule images. An image caching system may be implemented in the computer annotation systems to reduce image processing time. The annotation systems include one or more connectors connecting to one or more databases capable of storing single molecule data as well as other biomedical data. Such diverse array of data can be retrieved and used to validate the markings and annotations. The annotation systems may be implemented and deployed over a computer network. They may be ergonomically optimized to facilitate user interactions.

  19. Multicultural Education: A Selected Annotated Bibliography.

    Science.gov (United States)

    Mathieson, Moira B.; Tatis, Rita M.

    This annotated bibliography lists 70 documents dealing with cultural differences and cross-cultural educational problems on the elementary-secondary-collegiate level and does not include material on the economically disadvantaged or inner city problems as such. The first section reports citations drawn from Research in Education and the…

  20. Semantic Annotation to Support Automatic Taxonomy Classification

    DEFF Research Database (Denmark)

    Kim, Sanghee; Ahmed, Saeema; Wallace, Ken

    2006-01-01

    This paper presents a new taxonomy classification method that generates classification criteria from a small number of important sentences identified through semantic annotations, e.g. cause-effect. Rhetorical Structure Theory (RST) is used to discover the semantics (Mann et al. 1988). Specifically...

  1. Reflective Annotations: On Becoming a Scholar

    Science.gov (United States)

    Alexander, Mark; Taylor, Caroline; Greenberger, Scott; Watts, Margie; Balch, Riann

    2012-01-01

    This article presents the authors' reflective annotations on becoming a scholar. This paper begins with a discussion on socialization for teaching, followed by a discussion on socialization for service and sense of belonging. Then, it describes how the doctoral process evolves. Finally, it talks about adult learners who pursue doctoral education.

  2. Annotated Bibliography of EDGE2D Use

    International Nuclear Information System (INIS)

    This annotated bibliography is intended to help EDGE2D users, and particularly new users, find existing published literature that has used EDGE2D. Our idea is that a person can find existing studies which may relate to his intended use, as well as gain ideas about other possible applications by scanning the attached tables

  3. Statistical mechanics of ontology based annotations

    CERN Document Server

    Hoyle, David C

    2016-01-01

    We present a statistical mechanical theory of the process of annotating an object with terms selected from an ontology. The term selection process is formulated as an ideal lattice gas model, but in a highly structured inhomogeneous field. The model enables us to explain patterns recently observed in real-world annotation data sets, in terms of the underlying graph structure of the ontology. By relating the external field strengths to the information content of each node in the ontology graph, the statistical mechanical model also allows us to propose a number of practical metrics for assessing the quality of both the ontology, and the annotations that arise from its use. Using the statistical mechanical formalism we also study an ensemble of ontologies of differing size and complexity; an analysis not readily performed using real data alone. Focusing on regular tree ontology graphs we uncover a rich set of scaling laws describing the growth in the optimal ontology size as the number of objects being annotate...

  4. Statistical mechanics of ontology based annotations

    Science.gov (United States)

    Hoyle, David C.; Brass, Andrew

    2016-01-01

    We present a statistical mechanical theory of the process of annotating an object with terms selected from an ontology. The term selection process is formulated as an ideal lattice gas model, but in a highly structured inhomogeneous field. The model enables us to explain patterns recently observed in real-world annotation data sets, in terms of the underlying graph structure of the ontology. By relating the external field strengths to the information content of each node in the ontology graph, the statistical mechanical model also allows us to propose a number of practical metrics for assessing the quality of both the ontology, and the annotations that arise from its use. Using the statistical mechanical formalism we also study an ensemble of ontologies of differing size and complexity; an analysis not readily performed using real data alone. Focusing on regular tree ontology graphs we uncover a rich set of scaling laws describing the growth in the optimal ontology size as the number of objects being annotated increases. In doing so we provide a further possible measure for assessment of ontologies.

  5. Studies of Scientific Disciplines. An Annotated Bibliography.

    Science.gov (United States)

    Weisz, Diane; Kruytbosch, Carlos

    Provided in this bibliography are annotated lists of social studies of science literature, arranged alphabetically by author in 13 disciplinary areas. These areas include astronomy; general biology; biochemistry and molecular biology; biomedicine; chemistry; earth and space sciences; economics; engineering; mathematics; physics; political science;…

  6. Food Habits: A Selected Annotated Bibliography

    Science.gov (United States)

    Wilson, Christine S.

    1973-01-01

    This is a selective annotated bibliography of material on food habits and factors affecting them, published during the period 1928-1972. References are mainly in English, although a few in European languages are included, and represent information primarily from scholarly and professional journals. Entries are organized by subject and author. (LK)

  7. An Annotated Publications List on Homelessness.

    Science.gov (United States)

    Tutunjian, Beth Ann

    This annotated publications list on homelessness contains citations for 19 publications, most of which deal with problems of alcohol or drug abuse among homeless persons. Citations are listed alphabetically by author and cover the topics of homelessness and alcoholism, drug abuse, public policy, research methodologies, mental illness, alcohol- and…

  8. Law in the Classroom. An Annotated Bibliography.

    Science.gov (United States)

    Carsello, Carmen J.

    An annotated bibliography of some 236 items relevant to discussions of school law, from novels to government-published law and court reports. The material is listed alphabetically by author within each document type (books; periodicals; documents; monographs and special reports; law reports; digests; newsletters; dictionaries, directories, and…

  9. Organizational and Intercultural Communication: An Annotated Bibliography.

    Science.gov (United States)

    Constantinides, Helen; St. Amant, Kirk; Kampf, Connie

    2001-01-01

    Presents a 27-item annotated bibliography that overviews theories of organization from the viewpoint of culture, using five themes of organizational research as a framework. Notes that each section introduces specific theories of international, intercultural, or organizational communication, building upon them through a series of related articles,…

  10. Teleconferencing, an annotated bibliography, volume 3

    Science.gov (United States)

    Shervis, K.

    1971-01-01

    In this annotated and indexed listing of works on teleconferencing, emphasis has been placed upon teleconferencing as real-time, two way audio communication with or without visual aids. However, works on the use of television in two-way or multiway nets, data transmission, regional communications networks and on telecommunications in general are also included.

  11. Kwanzaa: A Selective Annotated Bibliography for Teachers.

    Science.gov (United States)

    Dupree, Sandra K., Comp.; Gillum, Holly A., Comp.

    This annotated bibliography about Kwanzaa, an end-of-the-year holiday that emphasizes an appreciation for the culture of African Americans, aims to provide ready access to information for classroom teachers. Noting that Kwanzaa (celebrated from December 26 to January 1) is an important cultural event, the bibliography states that the festival…

  12. Skin Cancer Education Materials: Selected Annotations.

    Science.gov (United States)

    National Cancer Inst. (NIH), Bethesda, MD.

    This annotated bibliography presents 85 entries on a variety of approaches to cancer education. The entries are grouped under three broad headings, two of which contain smaller sub-divisions. The first heading, Public Education, contains prevention and general information, and non-print materials. The second heading, Professional Education,…

  13. College Students in Transition: An Annotated Bibliography

    Science.gov (United States)

    Foote, Stephanie M., Ed.; Hinkle, Sara M., Ed.; Kranzow, Jeannine, Ed.; Pistilli, Matthew D., Ed.; Miles, LaTonya Rease, Ed.; Simmons, Jannell G., Ed.

    2013-01-01

    The transition from high school to college is an important milestone, but it is only one of many steps in the journey through higher education. This volume is an annotated bibliography of the emerging literature examining the many other transitions students make beyond the first year, including the sophomore year, the transfer experience, and the…

  14. Annotated Bibliography of EDGE2D Use

    Energy Technology Data Exchange (ETDEWEB)

    J.D. Strachan and G. Corrigan

    2005-06-24

    This annotated bibliography is intended to help EDGE2D users, and particularly new users, find existing published literature that has used EDGE2D. Our idea is that a person can find existing studies which may relate to his intended use, as well as gain ideas about other possible applications by scanning the attached tables.

  15. MEETING: Chlamydomonas Annotation Jamboree - October 2003

    Energy Technology Data Exchange (ETDEWEB)

    Grossman, Arthur R

    2007-04-13

    Shotgun sequencing of the nuclear genome of Chlamydomonas reinhardtii (Chlamydomonas throughout) was performed at an approximate 10X coverage by JGI. Roughly half of the genome is now contained on 26 scaffolds, all of which are at least 1.6 Mb, and the coverage of the genome is ~95%. There are now over 200,000 cDNA sequence reads that we have generated as part of the Chlamydomonas genome project (Grossman, 2003; Shrager et al., 2003; Grossman et al. 2007; Merchant et al., 2007); other sequences have also been generated by the Kasuza sequence group (Asamizu et al., 1999; Asamizu et al., 2000) or individual laboratories that have focused on specific genes. Shrager et al. (2003) placed the reads into distinct contigs (an assemblage of reads with overlapping nucleotide sequences), and contigs that group together as part of the same genes have been designated ACEs (assembly of contigs generated from EST information). All of the reads have also been mapped to the Chlamydomonas nuclear genome and the cDNAs and their corresponding genomic sequences have been reassembled, and the resulting assemblage is called an ACEG (an Assembly of contiguous EST sequences supported by genomic sequence) (Jain et al., 2007). Most of the unique genes or ACEGs are also represented by gene models that have been generated by the Joint Genome Institute (JGI, Walnut Creek, CA). These gene models have been placed onto the DNA scaffolds and are presented as a track on the Chlamydomonas genome browser associated with the genome portal (http://genome.jgi-psf.org/Chlre3/Chlre3.home.html). Ultimately, the meeting grant awarded by DOE has helped enormously in the development of an annotation pipeline (a set of guidelines used in the annotation of genes) and resulted in high quality annotation of over 4,000 genes; the annotators were from both Europe and the USA. Some of the people who led the annotation initiative were Arthur Grossman, Olivier Vallon, and Sabeeha Merchant (with many individual

  16. UniProt Tools.

    Science.gov (United States)

    Pundir, Sangya; Martin, Maria J; O'Donovan, Claire

    2016-01-01

    The Universal Protein Resource (UniProt) is a comprehensive resource for protein sequence and annotation data (UniProt Consortium, 2015). The UniProt Web site receives ∼400,000 unique visitors per month and is the primary means to access UniProt. Along with various datasets that you can search, UniProt provides three main tools. These are the 'BLAST' tool for sequence similarity searching, the 'Align' tool for multiple sequence alignment, and the 'Retrieve/ID Mapping' tool for using a list of identifiers to retrieve UniProtKB proteins and to convert database identifiers from UniProt to external databases or vice versa. This unit provides three basic protocols, three alternate protocols, and two support protocols for using UniProt tools. © 2016 by John Wiley & Sons, Inc. PMID:27010333

  17. Classes d'annotation pour l'annotation sémantique

    OpenAIRE

    Tenier, Sylvain; Toussaint, Yannick

    2007-01-01

    Les classes d'annotation constituent une méthode d'annotation sémantique de pages web fondée sur les logiques de descriptions. Elles désignent l'annotation à la fois comme processus et comme résultat de ce processus. Cette approche est motivée par un parallèle entre la structure d'une page web et la sémantique qui lui est associée. Ces deux dimensions de structure et de sémantique sont formalisées en OWL-DL, un langage fondé sur les logiques de descriptions. L'annotation est ensuite traitée c...

  18. Ontology Learning and Semantic Annotation: a Necessary Symbiosis

    OpenAIRE

    Giovannetti, Emiliano; Marchi, Simone; Montemagni, Simonetta; Bartolini, Roberto

    2008-01-01

    Semantic annotation of text requires the dynamic merging of linguistically structured information and a ?world model?, usually represented as a domain-specific ontology. On the other hand, the process of engineering a domain-ontology through semi-automatic ontology learning system requires the availability of a considerable amount of semantically annotated documents. Facing this bootstrapping paradox requires an incremental process of annotation-acquisition-annotation, whereby domain-specific...

  19. SURFACE: a database of protein surface regions for functional annotation

    OpenAIRE

    Ferrè, Fabrizio; Ausiello, Gabriele; Zanzoni, Andreas; Helmer-Citterich, Manuela

    2004-01-01

    The SURFACE (SUrface Residues and Functions Annotated, Compared and Evaluated, URL http://cbm.bio.uniroma2.it/surface/) database is a repository of annotated and compared protein surface regions. SURFACE contains the results of a large-scale protein annotation and local structural comparison project. A non-redundant set of protein chains is used to build a database of protein surface patches, defined as putative surface functional sites. Each patch is annotated with sequence and structure-der...

  20. A unified representation for morphological, syntactic, semantic, and referential annotations

    OpenAIRE

    Hinrichs, Erhard W.; Kübler, Sandra; Naumann, Karin

    2008-01-01

    This paper reports on the SYN-RA (SYNtax-based Reference Annotation) project, an on-going project of annotating German newspaper texts with referential relations. The project has developed an inventory of anaphoric and coreference relations for German in the context of a unified, XML-based annotation scheme for combining morphological, syntactic, semantic, and anaphoric information. The paper discusses how this unified annotation scheme relates to other formats currently discussed in the lite...

  1. Glucose utilisation in the lungs of septic rats

    International Nuclear Information System (INIS)

    Sequestration and degranulation of leucocytes in the pulmonary microcirculation is considered to be a key event in the development of acute respiratory distress syndrome in patients with sepsis. Glucose serves as the main source of energy in activated leucocytes. The aim of this study was to assess whether glucose utilisation in the lungs can be used as an indicator of pulmonary leucocyte accumulation in an experimental model of sepsis of intra-abdominal origin. Sepsis was induced in rats by abdominal implantation of a gelatine capsule containing bacteria and rat colonic contents. Empty gelatine capsules were implanted in control animals. Animals were studied 6 and 12 h after sepsis induction. Glucose utilisation was measured as the tissue uptake of fluorine-18-fluorodeoxyglucose (18FDG) 1 h after intravenous injection of the tracer. Micro-autoradiography was also performed after injection of tritiated deoxyglucose. We found increased uptake of 18FDG in the lungs of septic animals. The uptake also increased with time after sepsis induction. 18FDG uptake in circulating leucocytes was increased in septic animals compared with controls, and micro-autoradiography showed intense accumulation of deoxyglucose in leucocytes in the lungs of septic animals. We conclude that glucose utilisation is increased in the lungs of septic rats. Measurements of pulmonary glucose utilisation as an index of leucocyte metabolic activity may open new possibilities for studies of the pathophysiology of sepsis and for evaluation of therapeutic interventions. (orig.)

  2. Utilisation of medical technology assessment in health policy

    NARCIS (Netherlands)

    van den Heuvel, WJA; Wieringh, R; van den Heuvel, LPM

    1997-01-01

    Objective: To assess the contribution of medical technology assessment (MTA) to health policy decision making, the question has to be answered whether MTA is actually being used in decision-making processes and what factors are related to its utilisation. Design: We investigated recent Dutch policy

  3. CERN un physicien dénonce des utilisations militaires

    CERN Multimedia

    2001-01-01

    André Gsponer, ancien chercheur au CERN, a écrit un rapport qui dénone les utilisations militaires développées par certains Etat, dont l'Irak, sur la base des technologies mises au point au CERN (1 page).

  4. Redirecting Under-Utilised Computer Laboratories into Cluster Computing Facilities

    Science.gov (United States)

    Atkinson, John S.; Spenneman, Dirk H. R.; Cornforth, David

    2005-01-01

    Purpose: To provide administrators at an Australian university with data on the feasibility of redirecting under-utilised computer laboratories facilities into a distributed high performance computing facility. Design/methodology/approach: The individual log-in records for each computer located in the computer laboratories at the university were…

  5. Policy framework for utilisation. A pillar of better accessibility

    International Nuclear Information System (INIS)

    The goals and frameworks for traffic and transport policy for the Netherlands to 2020 are described in the Mobility Document. Whereas government policy previously viewed mobility as a problem or as something permissible, the assumption is now that mobility is a must. Mobility, for people as well as goods, is a prerequisite for society and the economy to function well. The Mobility Document contains ambitious goals to deal with current and anticipated traffic and transport problems: door to door, faster, cleaner and safer. Three interrelated pillars are to help achieve these goals: Building, Pricing and Utilisation. Work is being done on the Building and Pricing pillars; Utilisation is elaborated further in this policy framework. The Policy Framework for Utilisation is an elaboration of the Mobility Document for the 2008-2020 period and aims for faster, cleaner, safer travel from door to door. The purpose of this policy framework is to describe the direction of development of utilisation, in terms of content as well as process, to indicate actions that are required and to provide perspective on the expected effects. The policy framework is in line with current developments or plans, caters to new opportunities (technological and otherwise), encourages the innovative potential of the market and provides room for joint ventures between the government and the market. It will result in actions for the short term and provide direction for activities and developments for the longer term

  6. Improving the Utilisation of Management Information Systems in Secondary Schools

    Science.gov (United States)

    Bosker, R. J.; Branderhorst, E. M.; Visscher, A. J.

    2007-01-01

    Although most secondary schools do use management information systems (MISs), these systems tend not to be used to support higher order managerial activities but are currently primarily used for clerical purposes. This situation is unsatisfactory as MISs fully utilised could offer invaluable support to schools, which are increasingly being granted…

  7. Utilisation du transport en commun chez les immigrants

    OpenAIRE

    Heisz, Andrew; Schellenberg, Grant

    2004-01-01

    Dans cet article, on examine, a l'aide des donnees tirees des recensements de la population de 1996 et de 2001, la probabilite que les immigrants et les personnes nees au Canada utilisent le transport en commun. On discute egalement des repercussions sur les services de transport en commun.

  8. An Integrated Marine Propulsion System Utilising TRIGATM Fuel

    International Nuclear Information System (INIS)

    This paper describes the reactor physics, shielding, thermal hydraulics, reactor dynamics and safety studies conducted to develop a proposed Integrated Marine Propulsion System (IMPS) utilising TRIGATM type uranium zirconium hydride fuel. The study has demonstrated that the IMPS plant is feasible and meets the design safety principles and safety criteria imposed on the study. (authors)

  9. Linking human diseases to animal models using ontology-based phenotype annotation.

    Directory of Open Access Journals (Sweden)

    Nicole L Washington

    2009-11-01

    Full Text Available Scientists and clinicians who study genetic alterations and disease have traditionally described phenotypes in natural language. The considerable variation in these free-text descriptions has posed a hindrance to the important task of identifying candidate genes and models for human diseases and indicates the need for a computationally tractable method to mine data resources for mutant phenotypes. In this study, we tested the hypothesis that ontological annotation of disease phenotypes will facilitate the discovery of new genotype-phenotype relationships within and across species. To describe phenotypes using ontologies, we used an Entity-Quality (EQ methodology, wherein the affected entity (E and how it is affected (Q are recorded using terms from a variety of ontologies. Using this EQ method, we annotated the phenotypes of 11 gene-linked human diseases described in Online Mendelian Inheritance in Man (OMIM. These human annotations were loaded into our Ontology-Based Database (OBD along with other ontology-based phenotype descriptions of mutants from various model organism databases. Phenotypes recorded with this EQ method can be computationally compared based on the hierarchy of terms in the ontologies and the frequency of annotation. We utilized four similarity metrics to compare phenotypes and developed an ontology of homologous and analogous anatomical structures to compare phenotypes between species. Using these tools, we demonstrate that we can identify, through the similarity of the recorded phenotypes, other alleles of the same gene, other members of a signaling pathway, and orthologous genes and pathway members across species. We conclude that EQ-based annotation of phenotypes, in conjunction with a cross-species ontology, and a variety of similarity metrics can identify biologically meaningful similarities between genes by comparing phenotypes alone. This annotation and search method provides a novel and efficient means to identify

  10. SplicingTypesAnno: annotating and quantifying alternative splicing events for RNA-Seq data.

    Science.gov (United States)

    Sun, Xiaoyong; Zuo, Fenghua; Ru, Yuanbin; Guo, Jiqiang; Yan, Xiaoyan; Sablok, Gaurav

    2015-04-01

    Alternative splicing plays a key role in the regulation of the central dogma. Four major types of alternative splicing have been classified as intron retention, exon skipping, alternative 5 splice sites or alternative donor sites, and alternative 3 splice sites or alternative acceptor sites. A few algorithms have been developed to detect splice junctions from RNA-Seq reads. However, there are few tools targeting at the major alternative splicing types at the exon/intron level. This type of analysis may reveal subtle, yet important events of alternative splicing, and thus help gain deeper understanding of the mechanism of alternative splicing. This paper describes a user-friendly R package, extracting, annotating and analyzing alternative splicing types for sequence alignment files from RNA-Seq. SplicingTypesAnno can: (1) provide annotation for major alternative splicing at exon/intron level. By comparing the annotation from GTF/GFF file, it identifies the novel alternative splicing sites; (2) offer a convenient two-level analysis: genome-scale annotation for users with high performance computing environment, and gene-scale annotation for users with personal computers; (3) generate a user-friendly web report and additional BED files for IGV visualization. SplicingTypesAnno is a user-friendly R package for extracting, annotating and analyzing alternative splicing types at exon/intron level for sequence alignment files from RNA-Seq. It is publically available at https://sourceforge.net/projects/splicingtypes/files/ or http://genome.sdau.edu.cn/research/software/SplicingTypesAnno.html. PMID:25720307

  11. VASCo: computation and visualization of annotated protein surface contacts

    Directory of Open Access Journals (Sweden)

    Thallinger Gerhard G

    2009-01-01

    Full Text Available Abstract Background Structural data from crystallographic analyses contain a vast amount of information on protein-protein contacts. Knowledge on protein-protein interactions is essential for understanding many processes in living cells. The methods to investigate these interactions range from genetics to biophysics, crystallography, bioinformatics and computer modeling. Also crystal contact information can be useful to understand biologically relevant protein oligomerisation as they rely in principle on the same physico-chemical interaction forces. Visualization of crystal and biological contact data including different surface properties can help to analyse protein-protein interactions. Results VASCo is a program package for the calculation of protein surface properties and the visualization of annotated surfaces. Special emphasis is laid on protein-protein interactions, which are calculated based on surface point distances. The same approach is used to compare surfaces of two aligned molecules. Molecular properties such as electrostatic potential or hydrophobicity are mapped onto these surface points. Molecular surfaces and the corresponding properties are calculated using well established programs integrated into the package, as well as using custom developed programs. The modular package can easily be extended to include new properties for annotation. The output of the program is most conveniently displayed in PyMOL using a custom-made plug-in. Conclusion VASCo supplements other available protein contact visualisation tools and provides additional information on biological interactions as well as on crystal contacts. The tool provides a unique feature to compare surfaces of two aligned molecules based on point distances and thereby facilitates the visualization and analysis of surface differences.

  12. Annotations and the Collaborative Digital Library: Effects of an Aligned Annotation Interface on Student Argumentation and Reading Strategies

    Science.gov (United States)

    Wolfe, Joanna

    2008-01-01

    Recent research on annotation interfaces provides provocative evidence that anchored, annotation-based discussion environments may lead to better conversations about a text. However, annotation interfaces raise complicated tradeoffs regarding screen real estate and positioning. It is argued that solving this screen real estate problem requires…

  13. Using Hausdorff Distance for New Medical Image Annotation

    CERN Document Server

    Bouslimi, Riadh

    2012-01-01

    Medical images annotation is most of the time a repetitive hard task. Collecting old similar annotations and assigning them to new medical images may not only enhance the annotation process, but also reduce ambiguity caused by repetitive annotations. The goal of this work is to propose an approach based on Hausdorff distance able to compute similarity between a new medical image and old stored images. User has to choose then one of the similar images and annotations related to the selected one are assigned to the new one.

  14. xGDBvm: A Web GUI-Driven Workflow for Annotating Eukaryotic Genomes in the Cloud[OPEN

    Science.gov (United States)

    Merchant, Nirav

    2016-01-01

    Genome-wide annotation of gene structure requires the integration of numerous computational steps. Currently, annotation is arguably best accomplished through collaboration of bioinformatics and domain experts, with broad community involvement. However, such a collaborative approach is not scalable at today’s pace of sequence generation. To address this problem, we developed the xGDBvm software, which uses an intuitive graphical user interface to access a number of common genome analysis and gene structure tools, preconfigured in a self-contained virtual machine image. Once their virtual machine instance is deployed through iPlant’s Atmosphere cloud services, users access the xGDBvm workflow via a unified Web interface to manage inputs, set program parameters, configure links to high-performance computing (HPC) resources, view and manage output, apply analysis and editing tools, or access contextual help. The xGDBvm workflow will mask the genome, compute spliced alignments from transcript and/or protein inputs (locally or on a remote HPC cluster), predict gene structures and gene structure quality, and display output in a public or private genome browser complete with accessory tools. Problematic gene predictions are flagged and can be reannotated using the integrated yrGATE annotation tool. xGDBvm can also be configured to append or replace existing data or load precomputed data. Multiple genomes can be annotated and displayed, and outputs can be archived for sharing or backup. xGDBvm can be adapted to a variety of use cases including de novo genome annotation, reannotation, comparison of different annotations, and training or teaching. PMID:27020957

  15. A Novel Technique to Image Annotation using Neural Network

    Directory of Open Access Journals (Sweden)

    Pankaj Savita

    2013-03-01

    Full Text Available : Automatic annotation of digital pictures is a key technology for managing and retrieving images from large image collection. Traditional image semantics extraction and representation schemes were commonly divided into two categories, namely visual features and text annotations. However, visual feature scheme are difficult to extract and are often semantically inconsistent. On the other hand, the image semantics can be well represented by text annotations. It is also easier to retrieve images according to their annotations. Traditional image annotation techniques are time-consuming and requiring lots of human effort. In this paper we propose Neural Network based a novel approach to the problem of image annotation. These approaches are applied to the Image data set. Our main work is focused on the image annotation by using multilayer perceptron, which exhibits a clear-cut idea on application of multilayer perceptron with special features. MLP Algorithm helps us to discover the concealed relations between image data and annotation data, and annotate image according to such relations. By using this algorithm we can save more memory space, and in case of web applications, transferring of images and download should be fast. This paper reviews 50 image annotation systems using supervised machine learning Techniques to annotate images for image retrieval. Results obtained show that the multi layer perceptron Neural Network classifier outperforms conventional DST Technique.

  16. Automated annotation of microbial proteomes in SWISS-PROT.

    Science.gov (United States)

    Gattiker, Alexandre; Michoud, Karine; Rivoire, Catherine; Auchincloss, Andrea H; Coudert, Elisabeth; Lima, Tania; Kersey, Paul; Pagni, Marco; Sigrist, Christian J A; Lachaize, Corinne; Veuthey, Anne Lise; Gasteiger, Elisabeth; Bairoch, Amos

    2003-02-01

    Large-scale sequencing of prokaryotic genomes demands the automation of certain annotation tasks currently manually performed in the production of the SWISS-PROT protein knowledgebase. The HAMAP project, or 'High-quality Automated and Manual Annotation of microbial Proteomes', aims to integrate manual and automatic annotation methods in order to enhance the speed of the curation process while preserving the quality of the database annotation. Automatic annotation is only applied to entries that belong to manually defined orthologous families and to entries with no identifiable similarities (ORFans). Many checks are enforced in order to prevent the propagation of wrong annotation and to spot problematic cases, which are channelled to manual curation. The results of this annotation are integrated in SWISS-PROT, and a website is provided at http://www.expasy.org/sprot/hamap/. PMID:12798039

  17. Exploring the Relationship between Annotation Use of EFL Learners and Their Learning Styles

    OpenAIRE

    Şakar, Asım

    2015-01-01

    This study explores the relationship between (perceptual and cognitive) learning styles and the use of hypermedia annotations by intermediate EFL learners while reading a hypermedia text. The participants were 44 EFL adult learners studying English for academic purposes. Data were collected through a software tracking tool, a learning styles survey and interviews. Results did not indicate a significant relationship, suggesting that learners with different learning styles had similar patterns ...

  18. Supporting community annotation and user collaboration in the integrated microbial genomes (IMG) system

    OpenAIRE

    I-Min A Chen; Markowitz, Victor M.; Palaniappan, Krishna; Szeto, Ernest; Chu, Ken; Huang, Jinghua; Ratner, Anna; Pillay, Manoj; Hadjithomas, Michalis; Huntemann, Marcel; Mikhailova, Natalia; Ovchinnikova, Galina; Ivanova, Natalia N.; Kyrpides, Nikos C.

    2016-01-01

    Background The exponential growth of genomic data from next generation technologies renders traditional manual expert curation effort unsustainable. Many genomic systems have included community annotation tools to address the problem. Most of these systems adopted a “Wiki-based” approach to take advantage of existing wiki technologies, but encountered obstacles in issues such as usability, authorship recognition, information reliability and incentive for community participation. Results Here,...

  19. Enlight: web-based integration of GWAS results with biological annotations

    OpenAIRE

    Guo, Yunfei; Conti, David V; Kai WANG

    2014-01-01

    Summary: Identifying causal variants remains a key challenge in post-GWAS (genome-wide association study) era, as many GWAS single-nucleotide polymorphisms (SNPs) (including imputed ones) fall into non-coding regions, making it difficult to associate statistical significance with predicted functionality. Therefore, we created a web-based tool, Enlight, which overlays functional annotation information, such as histone modification states, methylation patterns, transcription factor binding site...

  20. Approches statistiques en segmentation : application à la ré-annotation de génome

    OpenAIRE

    Cleynen, Alice

    2013-01-01

    We propose to model the output of transcriptome sequencing technologies (RNA-Seq) using the negative binomial distribution, as well as build segmentation models suited to their study at different biological scales, in the context of these technologies becoming a valuable tool for genome annotation, gene expression analysis, and new-transcript discovery. We develop a fast segmentation algorithm to analyze whole chromosomes series, and we propose two methods for estimating the number of segment...

  1. A Concept Annotation System for Clinical Records

    CERN Document Server

    Kang, Ning; Afzal, Zubair; Singh, Bharat; Schuemie, Martijn J; van Mulligen, Erik M; Kors, Jan A

    2010-01-01

    Unstructured information comprises a valuable source of data in clinical records. For text mining in clinical records, concept extraction is the first step in finding assertions and relationships. This study presents a system developed for the annotation of medical concepts, including medical problems, tests, and treatments, mentioned in clinical records. The system combines six publicly available named entity recognition system into one framework, and uses a simple voting scheme that allows to tune precision and recall of the system to specific needs. The system provides both a web service interface and a UIMA interface which can be easily used by other systems. The system was tested in the fourth i2b2 challenge and achieved an F-score of 82.1% for the concept exact match task, a score which is among the top-ranking systems. To our knowledge, this is the first publicly available clinical record concept annotation system.

  2. Exploiting Social Annotation for Automatic Resource Discovery

    CERN Document Server

    Plangprasopchok, Anon

    2007-01-01

    Information integration applications, such as mediators or mashups, that require access to information resources currently rely on users manually discovering and integrating them in the application. Manual resource discovery is a slow process, requiring the user to sift through results obtained via keyword-based search. Although search methods have advanced to include evidence from document contents, its metadata and the contents and link structure of the referring pages, they still do not adequately cover information sources -- often called ``the hidden Web''-- that dynamically generate documents in response to a query. The recently popular social bookmarking sites, which allow users to annotate and share metadata about various information sources, provide rich evidence for resource discovery. In this paper, we describe a probabilistic model of the user annotation process in a social bookmarking system del.icio.us. We then use the model to automatically find resources relevant to a particular information dom...

  3. CGKB: an annotation knowledge base for cowpea (Vigna unguiculata L. methylation filtered genomic genespace sequences

    Directory of Open Access Journals (Sweden)

    Spraggins Thomas A

    2007-04-01

    Full Text Available Abstract Background Cowpea [Vigna unguiculata (L. Walp.] is one of the most important food and forage legumes in the semi-arid tropics because of its ability to tolerate drought and grow on poor soils. It is cultivated mostly by poor farmers in developing countries, with 80% of production taking place in the dry savannah of tropical West and Central Africa. Cowpea is largely an underexploited crop with relatively little genomic information available for use in applied plant breeding. The goal of the Cowpea Genomics Initiative (CGI, funded by the Kirkhouse Trust, a UK-based charitable organization, is to leverage modern molecular genetic tools for gene discovery and cowpea improvement. One aspect of the initiative is the sequencing of the gene-rich region of the cowpea genome (termed the genespace recovered using methylation filtration technology and providing annotation and analysis of the sequence data. Description CGKB, Cowpea Genespace/Genomics Knowledge Base, is an annotation knowledge base developed under the CGI. The database is based on information derived from 298,848 cowpea genespace sequences (GSS isolated by methylation filtering of genomic DNA. The CGKB consists of three knowledge bases: GSS annotation and comparative genomics knowledge base, GSS enzyme and metabolic pathway knowledge base, and GSS simple sequence repeats (SSRs knowledge base for molecular marker discovery. A homology-based approach was applied for annotations of the GSS, mainly using BLASTX against four public FASTA formatted protein databases (NCBI GenBank Proteins, UniProtKB-Swiss-Prot, UniprotKB-PIR (Protein Information Resource, and UniProtKB-TrEMBL. Comparative genome analysis was done by BLASTX searches of the cowpea GSS against four plant proteomes from Arabidopsis thaliana, Oryza sativa, Medicago truncatula, and Populus trichocarpa. The possible exons and introns on each cowpea GSS were predicted using the HMM-based Genscan gene predication program and the

  4. Semantic Annotation: The Mainstay of Semantic Web

    OpenAIRE

    Slimani, Thabet

    2013-01-01

    Given that semantic Web realization is based on the critical mass of metadata accessibility and the representation of data with formal knowledge, it needs to generate metadata that is specific, easy to understand and well-defined. However, semantic annotation of the web documents is the successful way to make the Semantic Web vision a reality. This paper introduces the Semantic Web and its vision (stack layers) with regard to some concept definitions that helps the understanding of semantic a...

  5. About Certain Semantic Annotation in Parallel Corpora

    OpenAIRE

    Violetta Koseska-Toszewa

    2015-01-01

    About Certain Semantic Annotation in Parallel CorporaThe semantic notation analyzed in this works is contained in the second stream of semantic theories presented here – in the direct approach semantics. We used this stream in our work on the Bulgarian-Polish Contrastive Grammar. Our semantic notation distinguishes quantificational meanings of names and predicates, and indicates aspectual and temporal meanings of verbs. It relies on logical scope-based quantification and on the contemporary t...

  6. Improving gene annotation of complete viral genomes

    OpenAIRE

    Mills, Ryan; Rozanov, Michael; Lomsadze, Alexandre; Tatusova, Tatiana; Borodovsky, Mark

    2003-01-01

    Gene annotation in viruses often relies upon similarity search methods. These methods possess high specificity but some genes may be missed, either those unique to a particular genome or those highly divergent from known homologs. To identify potentially missing viral genes we have analyzed all complete viral genomes currently available in GenBank with a specialized and augmented version of the gene finding program GeneMarkS. In particular, by implementing genome-specific self-training protoc...

  7. Html template system using java annotations

    OpenAIRE

    Speck, Peter

    2007-01-01

    The problems that motivate this project are to (1) solve the lack of separation between html templates and java code when using existing template systems (e.g. embedded language or macros), to (2) solve the lack of scoped declaration of macros and java variables inside template loops, and (3) to solve the lack of validation of template macro definitions at compile time to help finding bugs before the web applications are deployed. Annotations are used as metadata format for...

  8. EFFICIENT VIDEO ANNOTATIONS BY AN IMAGE GROUPS

    OpenAIRE

    K . Mahi balan; K . Rajakumari

    2015-01-01

    Searching desirable events in uncontrolled videos is a challenging task. So, researches mainly focus on obtaining concepts from numerous labelled videos. But it is time consuming and labour expensive to collect a large amount of required labelled videos for training event models under various condition. To avoid this problem, we propose to leverage abundant Web images for videos since Web images contain a rich source of information with many events roughly annotated and taken under various co...

  9. Transcriptome Annotation using Tandem SAGE Tags

    OpenAIRE

    Rivals, Eric; Boureux, Anthony; Lejeune, Mireille; Ottones, Florence; Pecharromàn Pérez, Oscar; Tarhio, Jorma; Pierrat, Fabien; Ruffle, Florence; Commes, Thérèse; Marti, Jacques

    2007-01-01

    Analysis of several million expressed gene signatures (tags) revealed an increasing number of different sequences, largely exceeding that of annotated genes in mammalian genomes. Serial Analysis of Gene Expression (SAGE) can reveal new polyadenylated RNAs transcribed from previously unrecognized chromosomal regions. However, conventional SAGE tags are too short to identify unambiguously unique sites in large genomes. Here, we design a novel strategy with tags anchored on two different restric...

  10. Sustainable utilisation of forest biomass for energy - Possibilities and problems

    DEFF Research Database (Denmark)

    Stupak, I.; Asikainen, A.; Jonsell, M.;

    2007-01-01

    . and other synthesis publications on Sustainable use of forest biomass for energy. Topics are listed and an overview of advantages. disadvantages, and trade-offs between them is given, from the viewpoint of society in general and the forestry or the Nordic and Baltic countries, the paper also...... identifies the extent to which wood for energy is and energy sectors in particular. F included in forest legislation and forest certification standards under the "Programme for the Endorsement of Forest Certification" (PEFC) and the "Forest Stewardship Council" (FSC) schemes. Energy and forest policies at EU...... and national levels, and European PEFC forest standards are analysed. With respect to energy policies, the utilisation of wood for energy is generally supported in forest policies but forest legislation is seldom used as a direct toot to encourage the utilisation of wood for energy. Regulations...

  11. Fuel peat utilisation in Finland: resource use and emissions

    Energy Technology Data Exchange (ETDEWEB)

    Leijting, J.

    1999-11-01

    The aim of the study was to inventorize the emissions and other stressors caused by fuel peat use in Finland. The life cycle approach was used to organise and compile the burdens associated with the fuel peat utilisation sector in the years 1994 and 1995. Fuel peat accounts for about 6.5 % of the total primary energy production in Finland. The study showed that most emissions out into the air occur during combustion of peat in energy plants. The emissions account for about 13 - 14 % of the CO{sub 2} emissions released by fossil fuel utilisation in Finland, for 12 % of the SO{sub 2} for 8 % of the N{sub 2}O and approximately 4 % of the NOR emissions released by anthropogenic sources in Finland. Phosphorus releases into waters contributes for about 0.2 % while nitrogen releases account for 0.3 % in the total anthropogenic discharge in Finland. (orig.) 88 refs.

  12. L'utilisation de sandwichs a materiaux composites

    OpenAIRE

    Remen, W

    1992-01-01

    Cet article passe en revue ce qui a été fait dans le domaine des sandwichs FRP dans l'industrie maritime ces 15 dernières années. Les avantages de la construction en sandwich FRP seront discutés par rapport aux méthodes de production passées et aux applications pour d'autres marchés. Depuis la fin des années soixante, le développement et l'utilisation de matériaux de construction légers et résistants, ainsi que des nouvelles méthodes de construction ont augmenté. L'utilisation de sandwich-pla...

  13. Synthesis, characterisation and microbial utilisation of amorphous polysugars from lactose.

    Science.gov (United States)

    Daines, Alison M; Smart, Zlatka; Sims, Ian M; Tannock, Gerald W; Hinkley, Simon F R

    2015-03-01

    The melt polymerisations of glucose, galactose, xylose and fucose with citric acid, and mixtures of sugars therein are reported. Characterisation of the citric-acid catalysed reaction products indicated similar degrees of branched polymerisation but differences in the overall molecular weight of the polymers produced. The dairy by-product lactose could not be polymerised in a similar fashion but was shown to be readily hydrolysed using microwave radiation and a polymer generated from the melt condensation of the resultant glucose and galactose monosaccharides. A preliminary assessment of the bifido-bacterial utilisation of the lactose-derived polymerised products demonstrated a significantly different growth profile compared to commercially utilised galactooligosaccharides (GOS). PMID:25498629

  14. Self-rated health, chronic diseases and health service utilisation in Hong Kong

    OpenAIRE

    Xu, Fang; 徐方

    2015-01-01

    Introduction Self-rated health (SRH) is a widely used indicator of health service utilisation and reflects self-perceived objective health condition. Poorer non-comparative SRH was shown to be related to higher inpatient and outpatient utilisation in Western and elderly populations. Little is known about how healthcare utilisation relates to SRH in non-Western settings, such as Hong Kong and in adult populations. The association of age- and time- comparative SRH with healthcare utilisation is...

  15. Basic phenomena utilised in aerosol particle measurement techniques; Hiukkasmittaustekniikoiden perusilmioet

    Energy Technology Data Exchange (ETDEWEB)

    Janka, K. [Dekati Oy, Tampere (Finland)

    2006-10-15

    The project deals with development of basic phenomena and mechanism utilised in aerosol particle measurement techniques. The areas under development are: particle-charging techniques, photoelectric charging, particle concentrating using virtual-impactor technique, and optical characterising techniques of particles. Results will be applied on detection techniques of bioaerosol attract, particle emission sensors for diesel exhaust gases, and widening the application areas of existing measurement techniques. (orig.)

  16. IMPROVING THE EFFECTIVENESS AND UTILISATION OF THE INDUSTRIAL ENGINEERING FUNCTION

    OpenAIRE

    Gordon Lister

    2012-01-01

    Research work carried out by the University of Cape Town has examined the following questions:
    - are industrial engineering techniques being used in industry?
    - what are the reasons for not using the various techniques?
    - what factors that can be addressed by industrial engineers, are inhibiting the improvement of manufacturing productivity?
    - are industrial engineers being utilised in the most effective t"ay? Investigations in South African and...

  17. Latent class models for utilisation of health care

    OpenAIRE

    Teresa Bago d’Uva

    2005-01-01

    This paper explores different approaches to econometric modelling of count measures of health care utilisation, with an emphasis on latent class models. A new model is proposed that combines the features of the two most common approaches- the hurdle model and the finite mixture Negative Binomial. Additionally, the panel structure of the data is taken into account. The proposed model is shown to perform better than the existing models for a particular application with data from the RAND Health...

  18. Utilisation by homeless people of acute hospital services in London.

    OpenAIRE

    Black, M E; Scheuer, M A; Victor, C.; Benzeval, M; Gill, M; Judge, K.

    1991-01-01

    OBJECTIVES--To estimate the numbers and distribution of homeless people in London; to quantify the utilisation of acute inpatient services by homeless people in two health authorities; and to predict the total numbers of admissions in homeless people in district health authorities across London. DESIGN--Data were collected from various sources on the distribution of homeless people across London boroughs. All unplanned acute inpatient admissions during November 1990 to relevant hospitals were...

  19. Briquetting of EAF Dust for its Utilisation in Metallurgical Processes

    OpenAIRE

    Magdziarz Aneta; Kuźnia Monika; Bembenek Michał; Gara Paweł; Hryniewicz Marek

    2015-01-01

    Dust generated at an electric arc furnace during steel production industry is still not a solved problem. Electric arc furnace dust (EAF) is a hazardous solid waste. Sintering of well-prepared briquetted mixtures in a shaft furnace is one of possible methods of EAFD utilisation. Simultaneously some metal oxides from exhaust gases can be separated. In this way, various metals are obtained, particularly zinc is recovered. As a result, zinc-free briquettes are received with high iron content whi...

  20. Utilisation of payment instruments at a retail chain in Gauteng

    OpenAIRE

    Adriaan M. Bester; Seugnet Bronkhorst

    2015-01-01

    Purpose: The purpose of this research was to determine the influence of race and income on the preferred payment instrument at pay points in a retail store in Pretoria Gauteng.Problem investigated: The method of payment, as well as the way these payment methods have been utilised, has evolved throughout history. Cash has stayed at the top of the payment instrument deck as a payment choice for the past 10 decades. With the expansion of technology payment instruments evolved to facilitate excha...

  1. Primary care utilisation and workers’ opportunity costs. Evidence from Italy

    OpenAIRE

    De Luca, Giuliana; Ponzo, Michela

    2010-01-01

    This paper analyses the effects of employment condition and work hours on the utilisation of primary care services in Italy. Although the Italian NHS provides free and equitable access to primary care, type of occupation and labour contracts may still deter workers to attend medical appointments. The hypothesis is that the higher the workers’ opportunity cost in terms of earning forgone, the less the demand for General Practitioner (GP) visits. Using survey data provided by the Italian Nation...

  2. Guidelines for the functional annotation of microRNAs using the Gene Ontology

    Science.gov (United States)

    D'Eustachio, Peter; Smith, Jennifer R.; Zampetaki, Anna

    2016-01-01

    MicroRNA regulation of developmental and cellular processes is a relatively new field of study, and the available research data have not been organized to enable its inclusion in pathway and network analysis tools. The association of gene products with terms from the Gene Ontology is an effective method to analyze functional data, but until recently there has been no substantial effort dedicated to applying Gene Ontology terms to microRNAs. Consequently, when performing functional analysis of microRNA data sets, researchers have had to rely instead on the functional annotations associated with the genes encoding microRNA targets. In consultation with experts in the field of microRNA research, we have created comprehensive recommendations for the Gene Ontology curation of microRNAs. This curation manual will enable provision of a high-quality, reliable set of functional annotations for the advancement of microRNA research. Here we describe the key aspects of the work, including development of the Gene Ontology to represent this data, standards for describing the data, and guidelines to support curators making these annotations. The full microRNA curation guidelines are available on the GO Consortium wiki (http://wiki.geneontology.org/index.php/MicroRNA_GO_annotation_manual). PMID:26917558

  3. ASPicDB: a database of annotated transcript and protein variants generated by alternative splicing

    Science.gov (United States)

    Martelli, Pier L.; D’Antonio, Mattia; Bonizzoni, Paola; Castrignanò, Tiziana; D’Erchia, Anna M.; D’Onorio De Meo, Paolo; Fariselli, Piero; Finelli, Michele; Licciulli, Flavio; Mangiulli, Marina; Mignone, Flavio; Pavesi, Giulio; Picardi, Ernesto; Rizzi, Raffaella; Rossi, Ivan; Valletti, Alessio; Zauli, Andrea; Zambelli, Federico; Casadio, Rita; Pesole, Graziano

    2011-01-01

    Alternative splicing is emerging as a major mechanism for the expansion of the transcriptome and proteome diversity, particularly in human and other vertebrates. However, the proportion of alternative transcripts and proteins actually endowed with functional activity is currently highly debated. We present here a new release of ASPicDB which now provides a unique annotation resource of human protein variants generated by alternative splicing. A total of 256 939 protein variants from 17 191 multi-exon genes have been extensively annotated through state of the art machine learning tools providing information of the protein type (globular and transmembrane), localization, presence of PFAM domains, signal peptides, GPI-anchor propeptides, transmembrane and coiled-coil segments. Furthermore, full-length variants can be now specifically selected based on the annotation of CAGE-tags and polyA signal and/or polyA sites, marking transcription initiation and termination sites, respectively. The retrieval can be carried out at gene, transcript, exon, protein or splice site level allowing the selection of data sets fulfilling one or more features settled by the user. The retrieval interface also enables the selection of protein variants showing specific differences in the annotated features. ASPicDB is available at http://www.caspur.it/ASPicDB/. PMID:21051348

  4. Guidelines for the functional annotation of microRNAs using the Gene Ontology.

    Science.gov (United States)

    Huntley, Rachael P; Sitnikov, Dmitry; Orlic-Milacic, Marija; Balakrishnan, Rama; D'Eustachio, Peter; Gillespie, Marc E; Howe, Doug; Kalea, Anastasia Z; Maegdefessel, Lars; Osumi-Sutherland, David; Petri, Victoria; Smith, Jennifer R; Van Auken, Kimberly; Wood, Valerie; Zampetaki, Anna; Mayr, Manuel; Lovering, Ruth C

    2016-05-01

    MicroRNA regulation of developmental and cellular processes is a relatively new field of study, and the available research data have not been organized to enable its inclusion in pathway and network analysis tools. The association of gene products with terms from the Gene Ontology is an effective method to analyze functional data, but until recently there has been no substantial effort dedicated to applying Gene Ontology terms to microRNAs. Consequently, when performing functional analysis of microRNA data sets, researchers have had to rely instead on the functional annotations associated with the genes encoding microRNA targets. In consultation with experts in the field of microRNA research, we have created comprehensive recommendations for the Gene Ontology curation of microRNAs. This curation manual will enable provision of a high-quality, reliable set of functional annotations for the advancement of microRNA research. Here we describe the key aspects of the work, including development of the Gene Ontology to represent this data, standards for describing the data, and guidelines to support curators making these annotations. The full microRNA curation guidelines are available on the GO Consortium wiki (http://wiki.geneontology.org/index.php/MicroRNA_GO_annotation_manual). PMID:26917558

  5. A hybrid system using symbolic and numeric knowledge for the semantic annotation of sulco-gyral anatomy in brain MRI images.

    OpenAIRE

    Mechouche, Ammar; Morandi, Xavier; Golbreich, Christine; Gibaud, Bernard

    2009-01-01

    This paper describes an interactive system for the semantic annotation of brain magnetic resonance images. The system uses both a numerical atlas and symbolic knowledge of brain anatomical structures depicted using the Semantic Web standards. This knowledge is combined with graphical data, automatically extracted from the images by imaging tools. The annotations of parts of gyri and sulci, in a region of interest, rely on constraint satisfaction problem solving and description logics inferenc...

  6. Customer-related knowledge utilisation in the collaborative relationships of professional service organisation

    OpenAIRE

    Nätti, S. (Satu)

    2005-01-01

    Abstract The purpose of this study is to describe customer-related knowledge utilisation in the collaborative relationships of professional service organisations. Within this specific context, knowledge transfer capabilities are emphasised as an important prerequisite in the utilisation process. Effective organisation-level knowledge utilisation is crucial in collaborative relationships of professional service organisations. In order to formulate a coherent service offering across diff...

  7. The GOA database: gene Ontology annotation updates for 2015.

    Science.gov (United States)

    Huntley, Rachael P; Sawford, Tony; Mutowo-Meullenet, Prudence; Shypitsyna, Aleksandra; Bonilla, Carlos; Martin, Maria J; O'Donovan, Claire

    2015-01-01

    The Gene Ontology Annotation (GOA) resource (http://www.ebi.ac.uk/GOA) provides evidence-based Gene Ontology (GO) annotations to proteins in the UniProt Knowledgebase (UniProtKB). Manual annotations provided by UniProt curators are supplemented by manual and automatic annotations from model organism databases and specialist annotation groups. GOA currently supplies 368 million GO annotations to almost 54 million proteins in more than 480,000 taxonomic groups. The resource now provides annotations to five times the number of proteins it did 4 years ago. As a member of the GO Consortium, we adhere to the most up-to-date Consortium-agreed annotation guidelines via the use of quality control checks that ensures that the GOA resource supplies high-quality functional information to proteins from a wide range of species. Annotations from GOA are freely available and are accessible through a powerful web browser as well as a variety of annotation file formats. PMID:25378336

  8. Utilisation-Focused Evaluation of ICT in Education: The Case of DFAQ Consultation Space

    Directory of Open Access Journals (Sweden)

    Irwin Brown

    2004-07-01

    Full Text Available This paper describes an evaluation of a web-based consultation space (a dynamic frequently asked questions environment - DFAQ in which learners consult one another using questions, and in which both the flow of interaction and its artefacts become a resource available to a community of learners. The DFAQ is a special form of a Computer-Mediated-Communication tool specifically developed to facilitate question-based interaction. We argue that education is too complex a social structure to be evaluated using deterministic positivist quantitative approaches. Given the volatility of determining what constitutes value, costs, inputs and outputs and the complexity of dynamics of socialization, a non-deterministic qualitative approach, utilisation-focused evaluation approach is used. Our conclusion is that the DFAQ does contribute to students’ academic performance and frees the lecturer-learner consultation time.

  9. Functional annotation of the human retinal pigment epithelium transcriptome

    Directory of Open Access Journals (Sweden)

    Gorgels Theo GMF

    2009-04-01

    Full Text Available Abstract Background To determine level, variability and functional annotation of gene expression of the human retinal pigment epithelium (RPE, the key tissue involved in retinal diseases like age-related macular degeneration and retinitis pigmentosa. Macular RPE cells from six selected healthy human donor eyes (aged 63–78 years were laser dissected and used for 22k microarray studies (Agilent technologies. Data were analyzed with Rosetta Resolver, the web tool DAVID and Ingenuity software. Results In total, we identified 19,746 array entries with significant expression in the RPE. Gene expression was analyzed according to expression levels, interindividual variability and functionality. A group of highly (n = 2,194 expressed RPE genes showed an overrepresentation of genes of the oxidative phosphorylation, ATP synthesis and ribosome pathways. In the group of moderately expressed genes (n = 8,776 genes of the phosphatidylinositol signaling system and aminosugars metabolism were overrepresented. As expected, the top 10 percent (n = 2,194 of genes with the highest interindividual differences in expression showed functional overrepresentation of the complement cascade, essential in inflammation in age-related macular degeneration, and other signaling pathways. Surprisingly, this same category also includes the genes involved in Bruch's membrane (BM composition. Among the top 10 percent of genes with low interindividual differences, there was an overrepresentation of genes involved in local glycosaminoglycan turnover. Conclusion Our study expands current knowledge of the RPE transcriptome by assigning new genes, and adding data about expression level and interindividual variation. Functional annotation suggests that the RPE has high levels of protein synthesis, strong energy demands, and is exposed to high levels of oxidative stress and a variable degree of inflammation. Our data sheds new light on the molecular composition of BM, adjacent to the

  10. Life cycle assessment of peat utilisation in Finland

    International Nuclear Information System (INIS)

    Environmental issues related to the production of peat and its use in energy generation have been the subject of public debate and research over the past few years in Finland. Peat is both an indigenous and a locally utilised fuel. Finland has no fossil fuel resources, and the transportation distances of imported fuels into Finland are normally long. In Finland the large peat resources can be utilised locally and peat-burning power plants are situated near the peatlands. Peat production and energy conversion methods are being continuously developed to make use of the environmentally and technically best available technology. In Finland peat formation exceeds peat utilisation and an increase in peat utilisation is therefore sustainable. The life cycle assessment concept gives an opportunity to evaluate and improve the environmental quality of peat utilisation options. The study focuses on an inventory analysis, but some of the most common methods of impact assessment with valuation are also included. The study also includes a comparison of fossil fuels and a discussion part. All the calculated results are based on net emissions. The background emissions of natural peatland are subtracted from the emissions of the utilisation phases. Milled peat and sod peat are reported in this study. Horticultural peat is studied simultaneously, but it will be reported later. The Sod Wave, Haku and Tehoturve methods are studied for the production of peat. The power plants of the study are Kempele heating plant and Rauhalahti cogeneration plant. The functional unit is 1 MWh produced total energy. The temporal boundaries vary from 112 to 128 years, depending on the peat production methods used. The restoration time is 100 years in all options. The emissions of greenhouse gases are based on the reports of The Finnish Research Programme on Climate Change. The water emissions are based on control monitoring reports from 1994 and 1995. The water emissions of the restoration phase are

  11. CARMO: a comprehensive annotation platform for functional exploration of rice multi-omics data.

    Science.gov (United States)

    Wang, Jiawei; Qi, Meifang; Liu, Jian; Zhang, Yijing

    2015-07-01

    High-throughput technology is gradually becoming a powerful tool for routine research in rice. Interpretation of biological significance from the huge amount of data is a critical but non-trivial task, especially for rice, for which gene annotations rely heavily on sequence similarity rather than direct experimental evidence. Here we describe the annotation platform for comprehensive annotation of rice multi-omics data (CARMO), which provides multiple web-based analysis tools for in-depth data mining and visualization. The central idea involves systematic integration of 1819 samples from omics studies and diverse sources of functional evidence (15 401 terms), which are further organized into gene sets and higher-level gene modules. In this way, the high-throughput data may easily be compared across studies and platforms, and integration of multiple types of evidence allows biological interpretation from the level of gene functional modules with high confidence. In addition, the functions and pathways for thousands of genes lacking description or validation may be deduced based on concerted expression of genes within the constructed co-expression networks or gene modules. Overall, CARMO provides comprehensive annotations for transcriptomic datasets, epi-genomic modification sites, single nucleotide polymorphisms identified from genome re-sequencing, and the large gene lists derived from these omics studies. Well-organized results, as well as multiple tools for interactive visualization, are available through a user-friendly web interface. Finally, we illustrate how CARMO enables biological insights using four examples, demonstrating that CARMO is a highly useful resource for intensive data mining and hypothesis generation based on rice multi-omics data. CARMO is freely available online (http://bioinfo.sibs.ac.cn/carmo). PMID:26040787

  12. Gene Ontology annotation of the rice blast fungus, Magnaporthe oryzae

    Directory of Open Access Journals (Sweden)

    Deng Jixin

    2009-02-01

    Full Text Available Abstract Background Magnaporthe oryzae, the causal agent of blast disease of rice, is the most destructive disease of rice worldwide. The genome of this fungal pathogen has been sequenced and an automated annotation has recently been updated to Version 6 http://www.broad.mit.edu/annotation/genome/magnaporthe_grisea/MultiDownloads.html. However, a comprehensive manual curation remains to be performed. Gene Ontology (GO annotation is a valuable means of assigning functional information using standardized vocabulary. We report an overview of the GO annotation for Version 5 of M. oryzae genome assembly. Methods A similarity-based (i.e., computational GO annotation with manual review was conducted, which was then integrated with a literature-based GO annotation with computational assistance. For similarity-based GO annotation a stringent reciprocal best hits method was used to identify similarity between predicted proteins of M. oryzae and GO proteins from multiple organisms with published associations to GO terms. Significant alignment pairs were manually reviewed. Functional assignments were further cross-validated with manually reviewed data, conserved domains, or data determined by wet lab experiments. Additionally, biological appropriateness of the functional assignments was manually checked. Results In total, 6,286 proteins received GO term assignment via the homology-based annotation, including 2,870 hypothetical proteins. Literature-based experimental evidence, such as microarray, MPSS, T-DNA insertion mutation, or gene knockout mutation, resulted in 2,810 proteins being annotated with GO terms. Of these, 1,673 proteins were annotated with new terms developed for Plant-Associated Microbe Gene Ontology (PAMGO. In addition, 67 experiment-determined secreted proteins were annotated with PAMGO terms. Integration of the two data sets resulted in 7,412 proteins (57% being annotated with 1,957 distinct and specific GO terms. Unannotated proteins

  13. 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.

  14. LANGUAGE POLICIES AND LANGUAGE EDUCATION IN EAST ASIA:AN ANNOTATED BIBLIOGRAPHY FOR LANGUAGE EDUCATORS, POSTGRADUATE STUDENTS AND RESEARCHERS

    Institute of Scientific and Technical Information of China (English)

    WangHong

    2004-01-01

    This is an annotated bibliography of language policies and language education in East Asia. The book contains abstracts of some 500 papers by researchers from 16 different countries and regions in East Asia. Among them. “Papers on ELT” are recorded and abstracted in most of 16 “country sections”. The book is well organised and is a versatile research tool. It has filled a blank in the field of applied linguistics in a regional purview. For researchers and students in the field of applied linguistics, this annotated bibliography provides an excellent starting point to conceive or design a research project.

  15. Carbohydrate catabolic flexibility in the mammalian intestinal commensal Lactobacillus ruminis revealed by fermentation studies aligned to genome annotations

    LENUS (Irish Health Repository)

    2011-08-30

    Abstract Background Lactobacillus ruminis is a poorly characterized member of the Lactobacillus salivarius clade that is part of the intestinal microbiota of pigs, humans and other mammals. Its variable abundance in human and animals may be linked to historical changes over time and geographical differences in dietary intake of complex carbohydrates. Results In this study, we investigated the ability of nine L. ruminis strains of human and bovine origin to utilize fifty carbohydrates including simple sugars, oligosaccharides, and prebiotic polysaccharides. The growth patterns were compared with metabolic pathways predicted by annotation of a high quality draft genome sequence of ATCC 25644 (human isolate) and the complete genome of ATCC 27782 (bovine isolate). All of the strains tested utilized prebiotics including fructooligosaccharides (FOS), soybean-oligosaccharides (SOS) and 1,3:1,4-β-D-gluco-oligosaccharides to varying degrees. Six strains isolated from humans utilized FOS-enriched inulin, as well as FOS. In contrast, three strains isolated from cows grew poorly in FOS-supplemented medium. In general, carbohydrate utilisation patterns were strain-dependent and also varied depending on the degree of polymerisation or complexity of structure. Six putative operons were identified in the genome of the human isolate ATCC 25644 for the transport and utilisation of the prebiotics FOS, galacto-oligosaccharides (GOS), SOS, and 1,3:1,4-β-D-Gluco-oligosaccharides. One of these comprised a novel FOS utilisation operon with predicted capacity to degrade chicory-derived FOS. However, only three of these operons were identified in the ATCC 27782 genome that might account for the utilisation of only SOS and 1,3:1,4-β-D-Gluco-oligosaccharides. Conclusions This study has provided definitive genome-based evidence to support the fermentation patterns of nine strains of Lactobacillus ruminis, and has linked it to gene distribution patterns in strains from different sources

  16. Vers un système hybride pour l'annotation sémantique d'images IRM du cerveau

    OpenAIRE

    Mechouche, Ammar; Golbreich, Christine; Gibaud, Bernard

    2007-01-01

    National audience Cet article montre l'intérêt de combiner des méthodes numériques et symboliques pour obtenir une annotation sémantique des images IRM du cerveau humain. Il s'agit d'identifier des structures anatomiques du cortex cérébral humain, en utilisant conjointement des connaissances a priori de nature numérique et une ontologie des structures corticales du cerveau représentée en OWL DL, étendue par des règles SWRL. Ces connaissances symboliques a priori représentées dans des langa...

  17. Du texte à la connaissance : annotation sémantique et peuplement d'ontologie appliqués à des artefacts logiciels

    OpenAIRE

    Amardeilh, Florence; Damljanovic, Danica

    2009-01-01

    Les applications logicielles possèdent généralement une courbe d'apprentissage considérable pour les nouveaux développeurs et pour ceux qui souhaitent en intégrer des parties dans leurs propres applications. L'attrait d'utiliser ici une technologie à base de sémantique repose sur son potentiel à associer un réseau de connaissance aux artefacts logiciels existants, structurés ou non. Ceci se traduit notamment par deux étapes clefs, l'annotation sémantique et le peuplement d'ontologie, qui rest...

  18. dcGOR: an R package for analysing ontologies and protein domain annotations.

    Directory of Open Access Journals (Sweden)

    Hai Fang

    2014-10-01

    Full Text Available I introduce an open-source R package 'dcGOR' to provide the bioinformatics community with the ease to analyse ontologies and protein domain annotations, particularly those in the dcGO database. The dcGO is a comprehensive resource for protein domain annotations using a panel of ontologies including Gene Ontology. Although increasing in popularity, this database needs statistical and graphical support to meet its full potential. Moreover, there are no bioinformatics tools specifically designed for domain ontology analysis. As an add-on package built in the R software environment, dcGOR offers a basic infrastructure with great flexibility and functionality. It implements new data structure to represent domains, ontologies, annotations, and all analytical outputs as well. For each ontology, it provides various mining facilities, including: (i domain-based enrichment analysis and visualisation; (ii construction of a domain (semantic similarity network according to ontology annotations; and (iii significance analysis for estimating a contact (statistical significance network. To reduce runtime, most analyses support high-performance parallel computing. Taking as inputs a list of protein domains of interest, the package is able to easily carry out in-depth analyses in terms of functional, phenotypic and diseased relevance, and network-level understanding. More importantly, dcGOR is designed to allow users to import and analyse their own ontologies and annotations on domains (taken from SCOP, Pfam and InterPro and RNAs (from Rfam as well. The package is freely available at CRAN for easy installation, and also at GitHub for version control. The dedicated website with reproducible demos can be found at http://supfam.org/dcGOR.

  19. Viewing a World of Annotations through AnnoVIP

    OpenAIRE

    Karanasos, Konstantinos; Zoupanos, Spyros

    2010-01-01

    The proliferation of electronic content has notably lead to the apparition of large corpora of interrelated structured documents (such as HTML and XML Web pages) and semantic annotations (typically expressed in RDF), which further complement these documents. Documents and annotations may be authored independently by different users or programs. We present AnnoVIP, a peer-to-peer platform, capable of efficiently exploiting a multitude of annotated documents, based on innovative materialized vi...

  20. Search-based Automatic Image Annotation Using Geotagged Community Photos

    OpenAIRE

    Mousselly Sergieh, Hatem

    2014-01-01

    In the Web 2.0 era, platforms for sharing and collaboratively annotating images with keywords, called tags, became very popular. Tags are a powerful means for organizing and retrieving photos. However, manual tagging is time consuming. Recently, the sheer amount of user-tagged photos available on the Web encouraged researchers to explore new techniques for automatic image annotation. The idea is to annotate an unlabeled image by propagating the labels of community photos that are visually sim...

  1. DIYA: a bacterial annotation pipeline for any genomics lab

    OpenAIRE

    Stewart, Andrew C.; Osborne, Brian; Read, Timothy D

    2009-01-01

    Summary:DIYA (Do-It-Yourself Annotator) is a modular and configurable open source pipeline software, written in Perl, used for the rapid annotation of bacterial genome sequences. The software is currently used to take DNA contigs as input, either in the form of complete genomes or the result of shotgun sequencing, and produce an annotated sequence in Genbank file format as output. Availability: Distribution and source code are available at (https://sourceforge.net/projects/diyg/). Contact: tr...

  2. Barcode Annotations for Medical Image Retrieval: A Preliminary Investigation

    OpenAIRE

    Tizhoosh, Hamid R.

    2015-01-01

    This paper proposes to generate and to use barcodes to annotate medical images and/or their regions of interest such as organs, tumors and tissue types. A multitude of efficient feature-based image retrieval methods already exist that can assign a query image to a certain image class. Visual annotations may help to increase the retrieval accuracy if combined with existing feature-based classification paradigms. Whereas with annotations we usually mean textual descriptions, in this paper barco...

  3. An Extensible, Kinematically-Based Gesture Annotation Scheme

    OpenAIRE

    Martell, Craig H.

    2002-01-01

    Chapter 1 in the book: Advances in Natural Multimodal Dialogue Systems Annotated corpora have played a critical role in speech and natural language research; and, there is an increasing interest in corpora-based research in sign language and gesture as well. We present a non-semantic, geometrically-based annotation scheme, FORM, which allows an annotator to capture the kinematic information in a gesture just from videos of speakers. In addition, FORM stores this gestural in...

  4. Gene Ontology annotation quality analysis in model eukaryotes

    OpenAIRE

    Buza, Teresia J; McCarthy, Fiona M; Wang, Nan; Bridges, Susan M.; Burgess, Shane C.

    2008-01-01

    Functional analysis using the Gene Ontology (GO) is crucial for array analysis, but it is often difficult for researchers to assess the amount and quality of GO annotations associated with different sets of gene products. In many cases the source of the GO annotations and the date the GO annotations were last updated is not apparent, further complicating a researchers’ ability to assess the quality of the GO data provided. Moreover, GO biocurators need to ensure that the GO quality is maintai...

  5. Snap: An Integrated SNP Annotation Platform

    DEFF Research Database (Denmark)

    Li, S.; Ma, L.; Li, H.;

    2007-01-01

    Snap (Single Nucleotide Polymorphism Annotation Platform) is a server designed to comprehensively analyze single genes and relationships between genes basing on SNPs in the human genome. The aim of the platform is to facilitate the study of SNP finding and analysis within the framework of medical...... research. Using a user-friendly web interface, genes can be searched by name, description, position, SNP ID or clone name. Several public databases are integrated, including gene information from Ensembl, protein features from Uniprot/SWISS-PROT, Pfam and DAS-CBS. Gene relationships are fetched from BIND...

  6. Evaluating Modelling Approaches for Medical Image Annotations

    CERN Document Server

    Opitz, Jasmin; Sattler, Ulrike

    2010-01-01

    Information system designers face many challenges w.r.t. selecting appropriate semantic technologies and deciding on a modelling approach for their system. However, there is no clear methodology yet to evaluate "semantically enriched" information systems. In this paper we present a case study on different modelling approaches for annotating medical images and introduce a conceptual framework that can be used to analyse the fitness of information systems and help designers to spot the strengths and weaknesses of various modelling approaches as well as managing trade-offs between modelling effort and their potential benefits.

  7. FINDING GENERIFS VIA GENE ONTOLOGY ANNOTATIONS

    OpenAIRE

    Lu, Zhiyong; Cohen, K Bretonnel; Hunter, Lawrence

    2006-01-01

    A Gene Reference Into Function (GeneRIF) is a concise phrase describing a function of a gene in the Entrez Gene database. Applying techniques from the area of natural language processing known as automatic summarization, it is possible to link the Entrez Gene database, the Gene Ontology, and the biomedical literature. A system was implemented that automatically suggests a sentence from a PubMed/MEDLINE abstract as a candidate GeneRIF by exploiting a gene’s GO annotations along with location f...

  8. EST Express: PHP/MySQL based automated annotation of ESTs from expression libraries

    Directory of Open Access Journals (Sweden)

    Pardinas Jose R

    2008-04-01

    Full Text Available Abstract Background Several biological techniques result in the acquisition of functional sets of cDNAs that must be sequenced and analyzed. The emergence of redundant databases such as UniGene and centralized annotation engines such as Entrez Gene has allowed the development of software that can analyze a great number of sequences in a matter of seconds. Results We have developed "EST Express", a suite of analytical tools that identify and annotate ESTs originating from specific mRNA populations. The software consists of a user-friendly GUI powered by PHP and MySQL that allows for online collaboration between researchers and continuity with UniGene, Entrez Gene and RefSeq. Two key features of the software include a novel, simplified Entrez Gene parser and tools to manage cDNA library sequencing projects. We have tested the software on a large data set (2,016 samples produced by subtractive hybridization. Conclusion EST Express is an open-source, cross-platform web server application that imports sequences from cDNA libraries, such as those generated through subtractive hybridization or yeast two-hybrid screens. It then provides several layers of annotation based on Entrez Gene and RefSeq to allow the user to highlight useful genes and manage cDNA library projects.

  9. A Novel Approach to Semantic and Coreference Annotation at LLNL

    Energy Technology Data Exchange (ETDEWEB)

    Firpo, M

    2005-02-04

    A case is made for the importance of high quality semantic and coreference annotation. The challenges of providing such annotation are described. Asperger's Syndrome is introduced, and the connections are drawn between the needs of text annotation and the abilities of persons with Asperger's Syndrome to meet those needs. Finally, a pilot program is recommended wherein semantic annotation is performed by people with Asperger's Syndrome. The primary points embodied in this paper are as follows: (1) Document annotation is essential to the Natural Language Processing (NLP) projects at Lawrence Livermore National Laboratory (LLNL); (2) LLNL does not currently have a system in place to meet its need for text annotation; (3) Text annotation is challenging for a variety of reasons, many related to its very rote nature; (4) Persons with Asperger's Syndrome are particularly skilled at rote verbal tasks, and behavioral experts agree that they would excel at text annotation; and (6) A pilot study is recommend in which two to three people with Asperger's Syndrome annotate documents and then the quality and throughput of their work is evaluated relative to that of their neuro-typical peers.

  10. Review of actinide-sediment reactions with an annotated bibliography

    Energy Technology Data Exchange (ETDEWEB)

    Ames, L.L.; Rai, D.; Serne, R.J.

    1976-02-10

    The annotated bibliography is divided into sections on chemistry and geochemistry, migration and accumulation, cultural distributions, natural distributions, and bibliographies and annual reviews. (LK)

  11. The UniProt-GO Annotation database in 2011

    Science.gov (United States)

    Dimmer, Emily C.; Huntley, Rachael P.; Alam-Faruque, Yasmin; Sawford, Tony; O'Donovan, Claire; Martin, Maria J.; Bely, Benoit; Browne, Paul; Mun Chan, Wei; Eberhardt, Ruth; Gardner, Michael; Laiho, Kati; Legge, Duncan; Magrane, Michele; Pichler, Klemens; Poggioli, Diego; Sehra, Harminder; Auchincloss, Andrea; Axelsen, Kristian; Blatter, Marie-Claude; Boutet, Emmanuel; Braconi-Quintaje, Silvia; Breuza, Lionel; Bridge, Alan; Coudert, Elizabeth; Estreicher, Anne; Famiglietti, Livia; Ferro-Rojas, Serenella; Feuermann, Marc; Gos, Arnaud; Gruaz-Gumowski, Nadine; Hinz, Ursula; Hulo, Chantal; James, Janet; Jimenez, Silvia; Jungo, Florence; Keller, Guillaume; Lemercier, Phillippe; Lieberherr, Damien; Masson, Patrick; Moinat, Madelaine; Pedruzzi, Ivo; Poux, Sylvain; Rivoire, Catherine; Roechert, Bernd; Schneider, Michael; Stutz, Andre; Sundaram, Shyamala; Tognolli, Michael; Bougueleret, Lydie; Argoud-Puy, Ghislaine; Cusin, Isabelle; Duek- Roggli, Paula; Xenarios, Ioannis; Apweiler, Rolf

    2012-01-01

    The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360 000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a greater information content enabled by GO Consortium annotation format developments. Detailed, manual GO annotations obtained from the curation of peer-reviewed papers are directly contributed by all UniProt curators and supplemented with manual and electronic annotations from 36 model organism and domain-focused scientific resources. The inclusion of high-quality, automatic annotation predictions ensures the UniProt GO annotation dataset supplies functional information to a wide range of proteins, including those from poorly characterized, non-model organism species. UniProt GO annotations are freely available in a range of formats accessible by both file downloads and web-based views. In addition, the introduction of a new, normalized file format in 2010 has made for easier handling of the complete UniProt-GOA data set. PMID:22123736

  12. The UniProt-GO Annotation database in 2011.

    Science.gov (United States)

    Dimmer, Emily C; Huntley, Rachael P; Alam-Faruque, Yasmin; Sawford, Tony; O'Donovan, Claire; Martin, Maria J; Bely, Benoit; Browne, Paul; Mun Chan, Wei; Eberhardt, Ruth; Gardner, Michael; Laiho, Kati; Legge, Duncan; Magrane, Michele; Pichler, Klemens; Poggioli, Diego; Sehra, Harminder; Auchincloss, Andrea; Axelsen, Kristian; Blatter, Marie-Claude; Boutet, Emmanuel; Braconi-Quintaje, Silvia; Breuza, Lionel; Bridge, Alan; Coudert, Elizabeth; Estreicher, Anne; Famiglietti, Livia; Ferro-Rojas, Serenella; Feuermann, Marc; Gos, Arnaud; Gruaz-Gumowski, Nadine; Hinz, Ursula; Hulo, Chantal; James, Janet; Jimenez, Silvia; Jungo, Florence; Keller, Guillaume; Lemercier, Phillippe; Lieberherr, Damien; Masson, Patrick; Moinat, Madelaine; Pedruzzi, Ivo; Poux, Sylvain; Rivoire, Catherine; Roechert, Bernd; Schneider, Michael; Stutz, Andre; Sundaram, Shyamala; Tognolli, Michael; Bougueleret, Lydie; Argoud-Puy, Ghislaine; Cusin, Isabelle; Duek-Roggli, Paula; Xenarios, Ioannis; Apweiler, Rolf

    2012-01-01

    The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360,000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a greater information content enabled by GO Consortium annotation format developments. Detailed, manual GO annotations obtained from the curation of peer-reviewed papers are directly contributed by all UniProt curators and supplemented with manual and electronic annotations from 36 model organism and domain-focused scientific resources. The inclusion of high-quality, automatic annotation predictions ensures the UniProt GO annotation dataset supplies functional information to a wide range of proteins, including those from poorly characterized, non-model organism species. UniProt GO annotations are freely available in a range of formats accessible by both file downloads and web-based views. In addition, the introduction of a new, normalized file format in 2010 has made for easier handling of the complete UniProt-GOA data set. PMID:22123736

  13. Gene Ontology annotation quality analysis in model eukaryotes

    Science.gov (United States)

    Buza, Teresia J.; McCarthy, Fiona M.; Wang, Nan; Bridges, Susan M.; Burgess, Shane C.

    2008-01-01

    Functional analysis using the Gene Ontology (GO) is crucial for array analysis, but it is often difficult for researchers to assess the amount and quality of GO annotations associated with different sets of gene products. In many cases the source of the GO annotations and the date the GO annotations were last updated is not apparent, further complicating a researchers’ ability to assess the quality of the GO data provided. Moreover, GO biocurators need to ensure that the GO quality is maintained and optimal for the functional processes that are most relevant for their research community. We report the GO Annotation Quality (GAQ) score, a quantitative measure of GO quality that includes breadth of GO annotation, the level of detail of annotation and the type of evidence used to make the annotation. As a case study, we apply the GAQ scoring method to a set of diverse eukaryotes and demonstrate how the GAQ score can be used to track changes in GO annotations over time and to assess the quality of GO annotations available for specific biological processes. The GAQ score also allows researchers to quantitatively assess the functional data available for their experimental systems (arrays or databases). PMID:18187504

  14. Fish utilisation of wetland nurseries with complex hydrological connectivity.

    Directory of Open Access Journals (Sweden)

    Ben Davis

    Full Text Available The physical and faunal characteristics of coastal wetlands are driven by dynamics of hydrological connectivity to adjacent habitats. Wetlands on estuary floodplains are particularly dynamic, driven by a complex interplay of tidal marine connections and seasonal freshwater flooding, often with unknown consequences for fish using these habitats. To understand the patterns and subsequent processes driving fish assemblage structure in such wetlands, we examined the nature and diversity of temporal utilisation patterns at a species or genus level over three annual cycles in a tropical Australian estuarine wetland system. Four general patterns of utilisation were apparent based on CPUE and size-structure dynamics: (i classic nursery utlisation (use by recently settled recruits for their first year (ii interrupted peristence (iii delayed recruitment (iv facultative wetland residence. Despite the small self-recruiting 'facultative wetland resident' group, wetland occupancy seems largely driven by connectivity to the subtidal estuary channel. Variable connection regimes (i.e. frequency and timing of connections within and between different wetland units (e.g. individual pools, lagoons, swamps will therefore interact with the diversity of species recruitment schedules to generate variable wetland assemblages in time and space. In addition, the assemblage structure is heavily modified by freshwater flow, through simultaneously curtailing persistence of the 'interrupted persistence' group, establishing connectivity for freshwater spawned members of both the 'facultative wetland resident' and 'delayed recruitment group', and apparently mediating use of intermediate nursery habitats for marine-spawned members of the 'delayed recruitment' group. The diversity of utilisation pattern and the complexity of associated drivers means assemblage compositions, and therefore ecosystem functioning, is likely to vary among years depending on variations in hydrological

  15. Zirconia/Titania Catalysts for Carbon Dioxide Utilisation

    OpenAIRE

    Al-Shafei, E.N.

    2015-01-01

    Reaction and conversion of CO2 to chemicals is a challenging area of research. The objective of this work is to study and investigate the use of mixed metal oxide Zr/Ti oxide and related catalysts for the conversion and utilisation of CO2. The first reaction studied was propane dehydrogenation using CO2 to produce propene. Then, the study extended to investigate the direct reaction of CO2 as whole molecule with methane, ethane, acetylene, ethylene and propane to synthesis carboxylic acids. ...

  16. Health care utilisation in Europe: new evidence from the ECHP

    OpenAIRE

    Teresa Bago d’Uva; Jones, Andrew M.

    2006-01-01

    The ECHP is used to analyse the utilisation of health care in Europe. We estimate a new latent class hurdle model for panel data and compare it with the latent class NegBin model and the standard hurdle model. Latent class specifications outperform the standard hurdle model but the latent class hurdle model reveals income e¤ects on the probability of visiting a doctor that are masked in the NegBin model. For visits to specialist, low users are more income elastic than high users and the proba...

  17. ECOLOGICAL AND TECHNICAL REQUIREMENTS OF RADIOACTIVE WASTE UTILISATION

    Directory of Open Access Journals (Sweden)

    Gabriel Borowski

    2013-01-01

    Full Text Available The paper presents a survey of radioactive waste disposal technologies used worldwide in terms of their influence upon natural environment. Typical sources of radioactive waste from medicine and industry were presented. In addition, various types of radioactive waste, both liquid and solid, were described. Requirements and conditions of the waste’s storage were characterised. Selected liquid and solid waste processing technologies were shown. It was stipulated that contemporary methods of radioactive waste utilisation enable their successful neutralisation. The implementation of these methods ought to be mandated by ecological factors first and only then economical ones.

  18. Utilisation and Management Changes in South Kyrgyzstan's Mountain Forests

    Institute of Scientific and Technical Information of China (English)

    Matthias Schmidt

    2005-01-01

    Using political ecology as its conceptual framework, this paper focuses on the changes in forest utilisation and management of South Kyrgyzstan's walnut-fruit forests over the last century. The aim of this study on human-environment interactions is to investigate the relationship between actors on the one side, their interests and demands, and the forests and forested lands on the other. Forest resource utilisation and management - and even the recognition of different forest products as resources - are connected with political and socio-economic conditions that change with time. The walnut-fruit forests of South Kyrgyzstan are unique, characterised by high biodiversity and a multiplicity of usable products; and they have been utilised for a long time. Centralised and formal management of the forests started with the Russian occupation and was strengthened under Soviet rule, when the region became a part of the USSR. During this era, a state forest administration that was structured from Moscow all the way down to the local level drew up detailed plans and developed procedures for utilising the different forest products. Since the collapse of the Soviet Union, the socio-political and economic frame conditions have changed significantly, which has brought not only the sweeping changes in the managing institutions, but also the access rights and interests in the forest resources. At present, the region is suffering from a high unemployment rate, which has resulted in the forests' gaining considerable importance in the livelihood strategies of the local population. Political and economic liberalization, increased communication and trans-regional exchange relations have opened the door for international companies and agents interested in the valuable forest products. Today, walnut wood and burls, walnuts, wild apples and mushrooms are all exported to various countries in the world. Scientists and members of various international organisations stress the ecological

  19. Utilising shade to optimize UV exposure for vitamin D

    OpenAIRE

    Turnbull, D. J.; Parisi, A. V.

    2008-01-01

    Numerous studies have stated that humans need to utilise full sun radiation, at certain times of the day, to assist the body in synthesising the required levels of vitamin D3. The time needed to be spent in the full sun depends on a number of factors, for example, age, skin type, latitude, solar zenith angle. Current Australian guidelines suggest exposure to approximately 1/6 to 1/3 of a minimum erythemal dose (MED), depending on age, would be appropriate to provide ade...

  20. Utilisation of iron ore tailings as aggregates in concrete

    OpenAIRE

    Francis Atta Kuranchie; Sanjay Kumar Shukla; Daryoush Habibi; Alireza Mohyeddin

    2015-01-01

    Sustainable handling of iron ore tailings is of prime concern to all stakeholders who are into iron ore mining. This study seeks to add value to the tailings by utilising them as a replacement for aggregates in concrete. A concrete mix of grade 40 MPa was prepared in the laboratory with water–cement ratio of 0.5. The concrete were cured for 1, 2, 3, 7, 14 and 28 days. The properties of the concrete such as workability, durability, density, compressive strength and indirect tensile strength we...

  1. Pragmatics Annotated Coloured Petri Nets for Protocol Software Generation and Verification

    DEFF Research Database (Denmark)

    Simonsen, Kent Inge; Kristensen, Lars Michael; Kindler, Ekkart

    This paper presents the formal definition of Pragmatics Annotated Coloured Petri Nets (PA-CPNs). PA-CPNs represent a class of Coloured Petri Nets (CPNs) that are designed to support automated code genera-tion of protocol software. PA-CPNs restrict the structure of CPN models and allow Petri net...... elements to be annotated with so-called pragmatics, which are exploited for code generation. The approach and tool for gen-erating code is called PetriCode and has been discussed and evaluated in earlier work already. The contribution of this paper is to give a formal def-inition for PA-CPNs; in addition......, we show how the structural restrictions of PA-CPNs can be exploited for making the verification of the modelled protocols more efficient. This is done by automatically deriving progress measures for the sweep-line method, and by introducing so-called service testers, that can be used to control the...

  2. Transcriptome annotation using tandem SAGE tags

    Science.gov (United States)

    Rivals, Eric; Boureux, Anthony; Lejeune, Mireille; Ottones, Florence; Pecharromàn Pérez, Oscar; Tarhio, Jorma; Pierrat, Fabien; Ruffle, Florence; Commes, Thérèse; Marti, Jacques

    2007-01-01

    Analysis of several million expressed gene signatures (tags) revealed an increasing number of different sequences, largely exceeding that of annotated genes in mammalian genomes. Serial analysis of gene expression (SAGE) can reveal new Poly(A) RNAs transcribed from previously unrecognized chromosomal regions. However, conventional SAGE tags are too short to identify unambiguously unique sites in large genomes. Here, we design a novel strategy with tags anchored on two different restrictions sites of cDNAs. New transcripts are then tentatively defined by the two SAGE tags in tandem and by the spanning sequence read on the genome between these tagged sites. Having developed a new algorithm to locate these tag-delimited genomic sequences (TDGS), we first validated its capacity to recognize known genes and its ability to reveal new transcripts with two SAGE libraries built in parallel from a single RNA sample. Our algorithm proves fast enough to experiment this strategy at a large scale. We then collected and processed the complete sets of human SAGE tags to predict yet unknown transcripts. A cross-validation with tiling arrays data shows that 47% of these TDGS overlap transcriptional active regions. Our method provides a new and complementary approach for complex transcriptome annotation. PMID:17709346

  3. EFFICIENT VIDEO ANNOTATIONS BY AN IMAGE GROUPS

    Directory of Open Access Journals (Sweden)

    K . Mahi balan

    2015-10-01

    Full Text Available Searching desirable events in uncontrolled videos is a challenging task. So, researches mainly focus on obtaining concepts from numerous labelled videos. But it is time consuming and labour expensive to collect a large amount of required labelled videos for training event models under various condition. To avoid this problem, we propose to leverage abundant Web images for videos since Web images contain a rich source of information with many events roughly annotated and taken under various conditions. However, information from the Web is difficult .so,brute force knowledge transfer of images may hurt the video annotation performance. so, we propose a novel Group-based Domain Adaptation learning framework to leverage different groups of knowledge (source target queried from the Web image search engine to consumer videos (domain target. Different from old methods using multiple source domains of images, our method makes the Web images according to their intrinsic semantic relationships instead of source. Specifically, two different types of groups ( event-specific groups and concept-specific groups are exploited to respectively describe the event-level and concept-level semantic meanings of target-domain videos.

  4. Descartes' fly: the geometry of genomic annotation.

    Science.gov (United States)

    Kim, J

    2001-03-01

    The completion of the Drosophila melanogaster genome marks another significant milestone in the growth of sequence information. But it also contributes to the ever-widening gap between sequence information and biological knowledge. One important approach to reducing this gap is theoretical inference through computational technologies. Many computer programs have been designed to annotate genomic sequence information with biologically relevant information. Here, I suggest that all of these methods have a common structure in which the sequence fragments are "coordinated" by some method of description such as Hidden Markov models. The key to the algorithms lies in constructing the most efficient set of coordinates that allow extrapolation and interpolation from existing knowledge. Efficient extrapolation and interpolation are produced if the sequence fragments acquire a natural geometrical structure in the coordinated description. Finding such a coordinate frame is an inductive problem with no algorithmic solution. The greater part of the problem of genomic annotation lies in biological modeling of the data rather than in algorithmic improvements. PMID:11793243

  5. Trace compounds affecting biogas energy utilisation - A review

    Energy Technology Data Exchange (ETDEWEB)

    Rasi, S., E-mail: saija.rasi@gmail.com [University of Jyvaeskylae, Department of Biological and Environmental Science, P.O. Box 35, FI-40014 (Finland); Laentelae, J.; Rintala, J. [University of Jyvaeskylae, Department of Biological and Environmental Science, P.O. Box 35, FI-40014 (Finland)

    2011-11-15

    Highlights: {yields} In regards to trace compounds, landfill gases are the most studied biogases. {yields} More strict requirements are set for biogas purity with new biogas applications. {yields} With traditional applications, small variations in biogas quality are acceptable. {yields} New requirements set challenges on raw material control and biogas quality. {yields} In this study, variations in analysing methods and biogas quality are discussed. - Abstract: This paper investigates the trace compounds affecting energy utilisation in biogas that come from different production sites. With biogas being more widely used in different energy applications more interest has arisen for the specific composition of biogas. In traditional energy applications, methane and hydrogen sulphide contents have had the most influence when energy utilisation application has been considered. With more advanced processes also the quantity and quality of trace compounds is more important. In regards to trace compounds, it was found that the concentrations and the variations of volatile organic compounds (VOCs) can be high in different landfills, especially, with compounds originating from the biological degradation process (like aromatics and terpenes) as seasonal variations affect the biological degradation. Trace compounds produced by direct volatilisation (halogenated and silicon compounds) show a smaller seasonal variation. Halogenated compounds are rarely present in high concentrations in waste water treatment plant (WWTP) biogas, but the concentrations of organic silicon compounds and their variation is high. Organic silicon compounds are usually detected only in low concentrations in co-digestion plant biogas, when no WWTP sludge is used as a raw material.

  6. Renewable hydrogen utilisation for the production of methanol

    International Nuclear Information System (INIS)

    Electrolytic hydrogen production is an efficient way of storing renewable energy generated electricity and securing the contribution of renewables in the future electricity supply. The use of this hydrogen for the production of methanol results in a liquid fuel that can be utilised directly with minor changes in the existing infrastructure. To utilise the renewable generated hydrogen for production of renewable methanol, a sustainable carbon source is needed. This carbon can be provided by biomass or CO2 in the flue gases of fossil fuel-fired power stations, cement factories, fermentation processes and water purification plants. Methanol production pathways via biomass gasification and CO2 recovery from the flue gasses of a fossil fuel-fired power station have been reviewed in this study. The cost of methanol production from biomass was found to lie in the range of 300-400 Euro /tonne of methanol, and the production cost of CO2 based methanol was between 500 and 600 Euro /tonne. Despite the higher production costs compared with methanol produced by conventional natural gas reforming (i.e. 100-200 Euro /tonne, aided by the low current price of natural gas), these new processes incorporate environmentally beneficial aspects that have to be taken into account

  7. Renewable hydrogen utilisation for the production of methanol

    International Nuclear Information System (INIS)

    Electrolytic hydrogen production is an efficient way of storing renewable energy generated electricity and securing the contribution of renewables in the future electricity supply. The use of this hydrogen for the production of methanol results in a liquid fuel that can be utilised directly with minor changes in the existing infrastructure. To utilise the renewable generated hydrogen for production of renewable methanol, a sustainable carbon source is needed. This carbon can be provided by biomass or CO2 in the flue gases of fossil fuel-fired power stations, cement factories, fermentation processes and water purification plants. Methanol production pathways via biomass gasification and CO2 recovery from the flue gasses of a fossil fuel-fired power station have been reviewed in this study. The cost of methanol production from biomass was found to lie in the range of 300-400 EUR/tonne of methanol, and the production cost of CO2 based methanol was between 500 and 600 EUR/tonne. Despite the higher production costs compared with methanol produced by conventional natural gas reforming (i.e. 100-200 EUR/tonne, aided by the low current price of natural gas), these new processes incorporate environmentally beneficial aspects that have to be taken into account. (author)

  8. Trace compounds affecting biogas energy utilisation - A review

    International Nuclear Information System (INIS)

    Highlights: → In regards to trace compounds, landfill gases are the most studied biogases. → More strict requirements are set for biogas purity with new biogas applications. → With traditional applications, small variations in biogas quality are acceptable. → New requirements set challenges on raw material control and biogas quality. → In this study, variations in analysing methods and biogas quality are discussed. - Abstract: This paper investigates the trace compounds affecting energy utilisation in biogas that come from different production sites. With biogas being more widely used in different energy applications more interest has arisen for the specific composition of biogas. In traditional energy applications, methane and hydrogen sulphide contents have had the most influence when energy utilisation application has been considered. With more advanced processes also the quantity and quality of trace compounds is more important. In regards to trace compounds, it was found that the concentrations and the variations of volatile organic compounds (VOCs) can be high in different landfills, especially, with compounds originating from the biological degradation process (like aromatics and terpenes) as seasonal variations affect the biological degradation. Trace compounds produced by direct volatilisation (halogenated and silicon compounds) show a smaller seasonal variation. Halogenated compounds are rarely present in high concentrations in waste water treatment plant (WWTP) biogas, but the concentrations of organic silicon compounds and their variation is high. Organic silicon compounds are usually detected only in low concentrations in co-digestion plant biogas, when no WWTP sludge is used as a raw material.

  9. Thermal utilisation and disposal of sewage sludge; Thermische Klaerschlammverwertung -beseitigung

    Energy Technology Data Exchange (ETDEWEB)

    Baumgart, H.C. [Emscher Genossenschaft/Lippeverband, Essen (Germany). Technischer Vorstand

    2001-07-01

    Sewage sludge combustion - either in an incinerator or for heat or power generation - has always been important and is getting ever more so. From the cost aspect, it makes quite a difference whether sewage sludge is just incinerated or utilised. The author makes it clear that this cost aspect - and what it means to communities and citizens - tends to be neglected by those who favour sewage sludge combustion and utilisation. [German] Die Verbrennung von Klaerschlamm - sei es als Schlammveraschung oder als thermische oder energetische Verwertung - hat schon immer fuer grosse Klaeranlagen einen bedeutenden Stellenwert gehabt. Die Bedeutung der Verbrennung scheint in letzter Zeit sogar zuzunehmen. Unter Kostengesichtspunkten ist es ein grosser Unterschied, ob ein Klaerschlamm nur verascht oder energetisch verwertet wird. Vor dem Hintergrund der allgemeinen Diskussion um die leeren Kassen der Kommunen, um die sogenannte dritte Miete fuer den Buerger und damit die Zumutbarkeit fuer weitere Steigerungen der Abwassergebuehren stoert mich die Bagatellisierung der Kostengesichtspunkte vor allem auf Seiten derer, die die Verbrennung der Klaerschlaemme fordern. (orig.)

  10. Utilisation of iron ore tailings as aggregates in concrete

    Directory of Open Access Journals (Sweden)

    Francis Atta Kuranchie

    2015-12-01

    Full Text Available Sustainable handling of iron ore tailings is of prime concern to all stakeholders who are into iron ore mining. This study seeks to add value to the tailings by utilising them as a replacement for aggregates in concrete. A concrete mix of grade 40 MPa was prepared in the laboratory with water–cement ratio of 0.5. The concrete were cured for 1, 2, 3, 7, 14 and 28 days. The properties of the concrete such as workability, durability, density, compressive strength and indirect tensile strength were tested. A controlled mix of concrete was also prepared in similar way using conventional materials and the results were compared with the tailings concrete. It was found that the iron ore tailings may be utilised for complete replacement for conventional aggregates in concrete. The iron ore tailings aggregates concrete exhibited a good mechanical strength and even in the case of compressive strength, there was an improvement of 11.56% over conventional aggregates concrete. The indirect tensile strength did not improve against the control mix due high content of fines in the tailings aggregates but showed 4.8% improvement compared with the previous study where the conventional fine aggregates was partially replaced by 20% with iron ore tailings.

  11. Implementation and utilisation of community-based mortality surveillance: a case study from Chad

    Directory of Open Access Journals (Sweden)

    Bowden Sarah

    2012-11-01

    Full Text Available Abstract Background Prospective surveillance is a recognised approach for measuring death rates in humanitarian emergencies. However, there is limited evidence on how such surveillance should optimally be implemented and on how data are actually used by agencies. This case study investigates the implementation and utilisation of mortality surveillance data by Médecins Sans Frontières (MSF in eastern Chad. We aimed to describe and analyse the community-based mortality surveillance system, trends in mortality data and the utilisation of these data to guide MSF’s operational response. Methods The case study included 5 MSF sites including 2 refugee camps and 3 camps for internally displaced persons (IDPs. Data were obtained through key informant interviews and systematic review of MSF operational reports from 2004–2008. Results Mortality data were collected using community health workers (CHWs. Mortality generally decreased progressively. In Farchana and Breidjing refugee camps, crude death rates (CDR decreased from 0.9 deaths per 10,000 person-days in 2004 to 0.2 in 2008 and from 0.7 to 0.1, respectively. In Gassire, Ade and Kerfi IDP camps, CDR decreased from 0.4 to 0.04, 0.3 to 0.04 and 1.0 to 0.3. Death rates among children under 5 years (U5DR followed similar trends. CDR and U5DR crossed emergency thresholds in one site, Kerfi, where CDR rapidly rose to 2.1 and U5DR to 7.9 in July 2008 before rapidly decreasing to below emergency levels by September 2008. Discussion Mortality data were used regularly to monitor population health status and on two occasions as a tool for advocacy. Lessons learned included the need for improved population estimates and standardized reporting procedures for improved data quality and dissemination; the importance of a simple and flexible model for data collection; and greater investment in supervising CHWs. Conclusions This model of community based mortality surveillance can be adapted and used by

  12. A Factor Graph Approach to Automated GO Annotation.

    Science.gov (United States)

    Spetale, Flavio E; Tapia, Elizabeth; Krsticevic, Flavia; Roda, Fernando; Bulacio, Pilar

    2016-01-01

    As volume of genomic data grows, computational methods become essential for providing a first glimpse onto gene annotations. Automated Gene Ontology (GO) annotation methods based on hierarchical ensemble classification techniques are particularly interesting when interpretability of annotation results is a main concern. In these methods, raw GO-term predictions computed by base binary classifiers are leveraged by checking the consistency of predefined GO relationships. Both formal leveraging strategies, with main focus on annotation precision, and heuristic alternatives, with main focus on scalability issues, have been described in literature. In this contribution, a factor graph approach to the hierarchical ensemble formulation of the automated GO annotation problem is presented. In this formal framework, a core factor graph is first built based on the GO structure and then enriched to take into account the noisy nature of GO-term predictions. Hence, starting from raw GO-term predictions, an iterative message passing algorithm between nodes of the factor graph is used to compute marginal probabilities of target GO-terms. Evaluations on Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster protein sequences from the GO Molecular Function domain showed significant improvements over competing approaches, even when protein sequences were naively characterized by their physicochemical and secondary structure properties or when loose noisy annotation datasets were considered. Based on these promising results and using Arabidopsis thaliana annotation data, we extend our approach to the identification of most promising molecular function annotations for a set of proteins of unknown function in Solanum lycopersicum. PMID:26771463

  13. Product annotations - KOME | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available [ Credits ] BLAST Search Image Search Home About Archive Update History Contact us ...ile name: kome_product_annotation.zip File URL: ftp://ftp.biosciencedbc.jp/archiv...ate History of This Database Site Policy | Contact Us Product annotations - KOME | LSDB Archive ...

  14. Behavioral Contributions to "Teaching of Psychology": An Annotated Bibliography

    Science.gov (United States)

    Karsten, A. M.; Carr, J. E.

    2008-01-01

    An annotated bibliography that summarizes behavioral contributions to the journal "Teaching of Psychology" from 1974 to 2006 is provided. A total of 116 articles of potential utility to college-level instructors of behavior analysis and related areas were identified, annotated, and organized into nine categories for ease of accessibility.…

  15. Annotating abstract pronominal anaphora in the DAD project

    DEFF Research Database (Denmark)

    Navarretta, Costanza; Olsen, Sussi Anni

    2008-01-01

    extended scheme, which we call the DAD annotation scheme, allows to annotate information about abstract anaphora which is important to investigate their use, see Webber (1988), Gundel et al. (2003), Navarretta (2004) and which can influence their automatic treatment. Intercoder agreement scores obtained by...

  16. Beyond annotations : a proposal for extensible java (XJ).

    OpenAIRE

    Clark, Anthony; Sammut, Paul; Willans, James

    2008-01-01

    Annotations provide a limited way of extending Java in order to tailor the language for specific tasks. This paper describes a proposal for a Java extension which generalises annotations to allow Java to be a platform for developing domain specific languages.

  17. Online Metacognitive Strategies, Hypermedia Annotations, and Motivation on Hypertext Comprehension

    Science.gov (United States)

    Shang, Hui-Fang

    2016-01-01

    This study examined the effect of online metacognitive strategies, hypermedia annotations, and motivation on reading comprehension in a Taiwanese hypertext environment. A path analysis model was proposed based on the assumption that if English as a foreign language learners frequently use online metacognitive strategies and hypermedia annotations,…

  18. On Semantic Annotation in Clarin-PL Parallel Corpora

    Directory of Open Access Journals (Sweden)

    Violetta Koseska-Toszewa

    2015-12-01

    Full Text Available On Semantic Annotation in Clarin-PL Parallel CorporaIn the article, the authors present a proposal for semantic annotation in Clarin-PL parallel corpora: Polish-Bulgarian-Russian and Polish-Lithuanian ones. Semantic annotation of quantification is a novum in developing sentence level semantics in multilingual parallel corpora. This is why our semantic annotation is manual. The authors hope it will be interesting to IT specialists working on automatic processing of the given natural languages. Semantic annotation defined the way it is defined here will make contrastive studies of natural languages more efficient, which in turn will help verify the results of those studies, and will certainly improve human and machine translations.

  19. An Approach to Function Annotation for Proteins of Unknown Function (PUFs in the Transcriptome of Indian Mulberry.

    Directory of Open Access Journals (Sweden)

    K H Dhanyalakshmi

    Full Text Available The modern sequencing technologies are generating large volumes of information at the transcriptome and genome level. Translation of this information into a biological meaning is far behind the race due to which a significant portion of proteins discovered remain as proteins of unknown function (PUFs. Attempts to uncover the functional significance of PUFs are limited due to lack of easy and high throughput functional annotation tools. Here, we report an approach to assign putative functions to PUFs, identified in the transcriptome of mulberry, a perennial tree commonly cultivated as host of silkworm. We utilized the mulberry PUFs generated from leaf tissues exposed to drought stress at whole plant level. A sequence and structure based computational analysis predicted the probable function of the PUFs. For rapid and easy annotation of PUFs, we developed an automated pipeline by integrating diverse bioinformatics tools, designated as PUFs Annotation Server (PUFAS, which also provides a web service API (Application Programming Interface for a large-scale analysis up to a genome. The expression analysis of three selected PUFs annotated by the pipeline revealed abiotic stress responsiveness of the genes, and hence their potential role in stress acclimation pathways. The automated pipeline developed here could be extended to assign functions to PUFs from any organism in general. PUFAS web server is available at http://caps.ncbs.res.in/pufas/ and the web service is accessible at http://capservices.ncbs.res.in/help/pufas.

  20. Genotyping and annotation of Affymetrix SNP arrays

    DEFF Research Database (Denmark)

    Lamy, Philippe; Andersen, Claus Lindbjerg; Wikman, Friedrik;

    2006-01-01

    In this paper we develop a new method for genotyping Affymetrix single nucleotide polymorphism (SNP) array. The method is based on (i) using multiple arrays at the same time to determine the genotypes and (ii) a model that relates intensities of individual SNPs to each other. The latter point...... allows us to annotate SNPs that have poor performance, either because of poor experimental conditions or because for one of the alleles the probes do not behave in a dose-response manner. Generally, our method agrees well with a method developed by Affymetrix. When both methods make a call they agree in...... 99.25% (using standard settings) of the cases, using a sample of 113 Affymetrix 10k SNP arrays. In the majority of cases where the two methods disagree, our method makes a genotype call, whereas the method by Affymetrix makes a no call, i.e. the genotype of the SNP is not determined. By visualization...

  1. A visualization tool for violent scenes detection

    OpenAIRE

    Maniry, Dominique; Acar, Esra; Hopfgartner, Frank; Albayrak, Sahin

    2014-01-01

    We present a browser-based visualization tool that allows users to explore movies and online videos based on the violence level of these videos. The system offers visualizations of annotations and results of the MediaEval 2012 Affect Task and can interactively download and analyze content from video hosting sites like YouTube.

  2. Machine-Tool Technology Instructor's Sourcebook.

    Science.gov (United States)

    Tammer, Anthony M.

    This document lists and annotates commercial and noncommercial resources pertaining to machine-tool technology. Following an introduction that explains how the document came to be written, the subjects of succeeding chapters are (1) periodicals; (2) associations; (3) audiovisual resources, including a subject index; (4) publishers, including a…

  3. Software Tool for Researching Annotations of Proteins (STRAP): Open-Source Protein Annotation Software with Data Visualization

    OpenAIRE

    Bhatia, Vivek N.; Perlman, David H.; Costello, Catherine E.; McComb, Mark E.

    2009-01-01

    In order that biological meaning may be derived and testable hypotheses may be built from proteomics experiments, assignments of proteins identified by mass spectrometry or other techniques must be supplemented with additional notation, such as information on known protein functions, protein-protein interactions, or biological pathway associations. Collecting, organizing, and interpreting this data often requires the input of experts in the biological field of study, in addition to the time-c...

  4. The GOA database in 2009--an integrated Gene Ontology Annotation resource

    OpenAIRE

    Barrell, D.; Dimmer, E.; Huntley, R. P.; Binns, D.; O Donovan, C.; Apweiler, R.

    2009-01-01

    The Gene Ontology Annotation (GOA) project at the EBI (http://www.ebi.ac.uk/goa) provides high-quality electronic and manual associations (annotations) of Gene Ontology (GO) terms to UniProt Knowledgebase (UniProtKB) entries. Annotations created by the project are collated with annotations from external databases to provide an extensive, publicly available GO annotation resource. Currently covering over 160 000 taxa, with greater than 32 million annotations, GOA remains the largest and most c...

  5. DIDA: A curated and annotated digenic diseases database.

    Science.gov (United States)

    Gazzo, Andrea M; Daneels, Dorien; Cilia, Elisa; Bonduelle, Maryse; Abramowicz, Marc; Van Dooren, Sonia; Smits, Guillaume; Lenaerts, Tom

    2016-01-01

    DIDA (DIgenic diseases DAtabase) is a novel database that provides for the first time detailed information on genes and associated genetic variants involved in digenic diseases, the simplest form of oligogenic inheritance. The database is accessible via http://dida.ibsquare.be and currently includes 213 digenic combinations involved in 44 different digenic diseases. These combinations are composed of 364 distinct variants, which are distributed over 136 distinct genes. The web interface provides browsing and search functionalities, as well as documentation and help pages, general database statistics and references to the original publications from which the data have been collected. The possibility to submit novel digenic data to DIDA is also provided. Creating this new repository was essential as current databases do not allow one to retrieve detailed records regarding digenic combinations. Genes, variants, diseases and digenic combinations in DIDA are annotated with manually curated information and information mined from other online resources. Next to providing a unique resource for the development of new analysis methods, DIDA gives clinical and molecular geneticists a tool to find the most comprehensive information on the digenic nature of their diseases of interest. PMID:26481352

  6. Modeling and Annotating the Expressive Semantics of Dance Videos

    CERN Document Server

    Kannan, Rajkumar

    2010-01-01

    Dance videos are interesting and semantics-intensive. At the same time, they are the complex type of videos compared to all other types such as sports, news and movie videos. In fact, dance video is the one which is less explored by the researchers across the globe. Dance videos exhibit rich semantics such as macro features and micro features and can be classified into several types. Hence, the conceptual modeling of the expressive semantics of the dance videos is very crucial and complex. This paper presents a generic Dance Video Semantics Model (DVSM) in order to represent the semantics of the dance videos at different granularity levels, identified by the components of the accompanying song. This model incorporates both syntactic and semantic features of the videos and introduces a new entity type called, Agent, to specify the micro features of the dance videos. The instantiations of the model are expressed as graphs. The model is implemented as a tool using J2SE and JMF to annotate the macro and micro fea...

  7. Gender and the utilisation of health services in the Ashanti Region, Ghana.

    OpenAIRE

    Buor, D.

    2004-01-01

    The survey seeks to structure a model for gender-based health services utilisation for the Ashanti Region of Ghana, and in addition, recommend intervention measures to ensure gender equity in the utilisation of health services. A sample size of 650 covered over 3108 houses, and the main research instruments were the questionnaire and formal interview. A multiple regression model is used for the analysis of the relationship between the complex independent variables and utilisation by gender. R...

  8. Gene Ontology annotations at SGD: new data sources and annotation methods

    OpenAIRE

    Hong, Eurie L.; Balakrishnan, Rama; Dong, Qing; Christie, Karen R.; Park, Julie; Binkley, Gail; Costanzo, Maria C.; Dwight, Selina S.; Engel, Stacia R.; Fisk, Dianna G.; Hirschman, Jodi E.; Hitz, Benjamin C.; Krieger, Cynthia J.; Livstone, Michael S.; Miyasato, Stuart R.

    2007-01-01

    The Saccharomyces Genome Database (SGD; http://www.yeastgenome.org/) collects and organizes biological information about the chromosomal features and gene products of the budding yeast Saccharomyces cerevisiae. Although published data from traditional experimental methods are the primary sources of evidence supporting Gene Ontology (GO) annotations for a gene product, high-throughput experiments and computational predictions can also provide valuable insights in the absence of an extensive bo...

  9. Semi-automatic conversion of BioProp semantic annotation to PASBio annotation

    OpenAIRE

    Dai Hong-Jie; Tsai Richard; Huang Chi-Hsin; Hsu Wen-Lian

    2008-01-01

    Abstract Background Semantic role labeling (SRL) is an important text analysis technique. In SRL, sentences are represented by one or more predicate-argument structures (PAS). Each PAS is composed of a predicate (verb) and several arguments (noun phrases, adverbial phrases, etc.) with different semantic roles, including main arguments (agent or patient) as well as adjunct arguments (time, manner, or location). PropBank is the most widely used PAS corpus and annotation format in the newswire d...

  10. The Collation of Three Versions of Front Annotations of the Siku Quanshu: Based on 365 Pieces of Front Annotations

    Directory of Open Access Journals (Sweden)

    Wen-Chin Lan

    2015-06-01

    Full Text Available A bibliographic annotation (tiyao提要 is a brief description of the author and content of a book as well as a comment on, or a critique of, the book. The Siku Quanshu Zongmu (四庫全書總目 has long been viewed as a model of the traditional Chinese annotated bibliography and its bibliographic annotations have been praised by many scholars. It is suggested that these annotations can be used as examples for learning how to write bibliographic annotations. The compilation of the Siku Quanshu Zongmu went through three stages: (1 individual draft annotations (分纂稿 written by various scholars, (2 front annotations (書前提要 revised and modified by the officials of the Siku Quanshu Project, and (3 finalized annotations (總目提要 mainly edited and compiled by Ji Yun (紀昀. Initially, the Siku Quanshu had seven written copies and there were seven sets of front annotations. They were housed separately in the seven chambers that Qianlong Emperor (乾隆, r. 1736-1795 built to store the Siku Quanshu. Currently, only three of the seven sets are intact and extant, including Wenyuange (文淵閣, Wensuge (文溯閣, and Wenjinge ( 文津閣. This study attempts to conduct a collation project of the three versions of front annotations. We chose 365 pieces of front annotations from the aforementioned three sets, respectively. The results corroborate that there exist variations and differences among the three sets of front annotations. This paper presents three examples to illustrate how the collation task was done. Since these annotations were transcribed manually, it is quite common to notice that the three sets might use variant forms for the same character. The descriptions of author, title, or number of volumes might be different as well. In particular, the annotation for the same book might be different slightly or significantly among the three sets. This paper is a summary report of the preliminary findings of the collation task

  11. CpGAVAS, an integrated web server for the annotation, visualization, analysis, and GenBank submission of completely sequenced chloroplast genome sequences

    Directory of Open Access Journals (Sweden)

    Liu Chang

    2012-12-01

    Full Text Available Abstract Background The complete sequences of chloroplast genomes provide wealthy information regarding the evolutionary history of species. With the advance of next-generation sequencing technology, the number of completely sequenced chloroplast genomes is expected to increase exponentially, powerful computational tools annotating the genome sequences are in urgent need. Results We have developed a web server CPGAVAS. The server accepts a complete chloroplast genome sequence as input. First, it predicts protein-coding and rRNA genes based on the identification and mapping of the most similar, full-length protein, cDNA and rRNA sequences by integrating results from Blastx, Blastn, protein2genome and est2genome programs. Second, tRNA genes and inverted repeats (IR are identified using tRNAscan, ARAGORN and vmatch respectively. Third, it calculates the summary statistics for the annotated genome. Fourth, it generates a circular map ready for publication. Fifth, it can create a Sequin file for GenBank submission. Last, it allows the extractions of protein and mRNA sequences for given list of genes and species. The annotation results in GFF3 format can be edited using any compatible annotation editing tools. The edited annotations can then be uploaded to CPGAVAS for update and re-analyses repeatedly. Using known chloroplast genome sequences as test set, we show that CPGAVAS performs comparably to another application DOGMA, while having several superior functionalities. Conclusions CPGAVAS allows the semi-automatic and complete annotation of a chloroplast genome sequence, and the visualization, editing and analysis of the annotation results. It will become an indispensible tool for researchers studying chloroplast genomes. The software is freely accessible from http://www.herbalgenomics.org/cpgavas.

  12. WriteOn â A Tool for Effective Classroom Presentations

    OpenAIRE

    Eligeti, Vinod

    2005-01-01

    This thesis provides an introduction to an advance in technology-aided instruction. Most of the research in this area has focused on PowerPoint® based applications or white board-centered electronic ink applications with the capability of broadcasting slides, ink annotations and so forth, used for presentation or classroom lectures. But these tools lack the capability of annotating on any kind of applications with active content playing (a movie or a simulation, for instance) in the backgrou...

  13. Argo: enabling the development of bespoke workflows and services for disease annotation.

    Science.gov (United States)

    Batista-Navarro, Riza; Carter, Jacob; Ananiadou, Sophia

    2016-01-01

    Argo (http://argo.nactem.ac.uk) is a generic text mining workbench that can cater to a variety of use cases, including the semi-automatic annotation of literature. It enables its technical users to build their own customised text mining solutions by providing a wide array of interoperable and configurable elementary components that can be seamlessly integrated into processing workflows. With Argo's graphical annotation interface, domain experts can then make use of the workflows' automatically generated output to curate information of interest.With the continuously rising need to understand the aetiology of diseases as well as the demand for their informed diagnosis and personalised treatment, the curation of disease-relevant information from medical and clinical documents has become an indispensable scientific activity. In the Fifth BioCreative Challenge Evaluation Workshop (BioCreative V), there was substantial interest in the mining of literature for disease-relevant information. Apart from a panel discussion focussed on disease annotations, the chemical-disease relations (CDR) track was also organised to foster the sharing and advancement of disease annotation tools and resources.This article presents the application of Argo's capabilities to the literature-based annotation of diseases. As part of our participation in BioCreative V's User Interactive Track (IAT), we demonstrated and evaluated Argo's suitability to the semi-automatic curation of chronic obstructive pulmonary disease (COPD) phenotypes. Furthermore, the workbench facilitated the development of some of the CDR track's top-performing web services for normalising disease mentions against the Medical Subject Headings (MeSH) database. In this work, we highlight Argo's support for developing various types of bespoke workflows ranging from ones which enabled us to easily incorporate information from various databases, to those which train and apply machine learning-based concept recognition models

  14. Technologies for the utilisation of biogenic waste in the bioeconomy.

    Science.gov (United States)

    O'Callaghan, Kenneth

    2016-05-01

    A brief review has been done of technologies involved in the exploitation of biogenic wastes, in order to provide an introduction to the subject from the technological perspective. Biogenic waste materials and biomass have historically been utilised for thousands of years, but a new conversation is emerging on the role of these materials in modern bioeconomies. Due to the nature of the products and commodities now required, a modern bioeconomy is not simply a rerun of former ones. This new dialogue needs to help us understand how technologies for managing and processing biogenic wastes--both established and novel--should be deployed and integrated (or not) to meet the requirements of the sustainability, closed-loop and resource-security agendas that evidently sit behind the bioeconomy aspirations now being voiced in many countries and regions of the world. PMID:26769498

  15. Ethanol production by recombinant and natural xylose-utilising yeasts

    Energy Technology Data Exchange (ETDEWEB)

    Eliasson, Anna

    2000-07-01

    The xylose-fermenting capacity of recombinant Saccharomyces cerevisiae carrying XYL1 and XYL2 from Pichia stipitis, which encode xylose reductase (XR) and xylitol dehydrogenase (XDH), respectively, is poor due to high xylitol formation. Whereas, P. stipitis exhibits high ethanol yield on xylose, the tolerance towards inhibitors in the lignocellulosic hydrolysate is low. A recombinant strain possessing the advantageous characteristics of both S. cerevisiae and P. stipitis would constitute a biocatalyst capable of efficient ethanol production from lignocellulosic hydrolysate. In the work presented in this thesis, factors influencing xylose fermentation in recombinant S. cerevisiae and in the natural xylose-fermenting yeast P. stipitis have been identified and investigated. Anaerobic xylulose fermentation was compared in strains of Zygosaccharomyces and S. cerevisiae, mutants and wild-type strains to identify host strain background and genetic modifications beneficial for xylose fermentation. The greatest positive effect was found for over-expression of the gene XKS1 for the pentose phosphate pathway (PPP) enzyme xylulokinase (XK), which increased the ethanol yield by almost 85%. The Zygosaccharomyces strains tested formed large amounts of polyols, making them unsuitable as host strains. The XR/XDH/XK ratio was found to determine whether carbon accumulated in a xylitol pool or was further utilised for ethanol production in recombinant xylose-utilising S. cerevisiae. Simulations, based on a kinetic model, and anaerobic xylose cultivation experiments implied that a 1:{>=}10:{>=}4 relation was optimal in minimising xylitol formation. Ethanol formation increased with decreasing XR/XDH ratio, whereas xylitol formation decreased and XK overexpression was necessary for adequate ethanol formation. Based on the knowledge of optimal enzyme ratios, a stable, xylose-utilising strain, S. cerevisiae TMB 3001, was constructed by chromosomal integration of the XYL1 and XYL2 genes

  16. Six Key Topics for Automated Assessment Utilisation and Acceptance

    Directory of Open Access Journals (Sweden)

    Torsten REINERS

    2011-04-01

    Full Text Available Automated assessment technologies have been used in education for decades (e.g., computerised multiple choice tests. In contrast, Automated Essay Grading (AEG technologies: have existed for decades; are `good in theory' (e.g., as accurate as humans, temporally and financially efficient, and can enhance formative feedback, and yet; are ostensibly used comparatively infrequently in Australian universities. To empirically examine these experiential observations we conducted a national survey to explore the use of automated assessment in Australian universities and examine why adoption of AEG is limited. Quantitative and qualitative data were collected in an online survey from a sample of 265 staff and students from 5 Australian universities. The type of assessment used by the greatest proportion of respondents was essays/reports (82.6%, however very few respondents had used AEG (3.8%. Recommendations are made regarding methods to promote technology utilisation, including the use of innovative dissemination channels such as 3D Virtual Worlds.

  17. A safety system for a laser-beam utilising facility

    International Nuclear Information System (INIS)

    A safety system for a laser-beam utilising facility incorporates a safety enclosure and an infra-red monitoring system for detecting the development of hot spots at internal surfaces of the enclosure walls and ceiling which may occur as a result of stray laser radiation impinging on such surfaces. The development of a hot spot leads to shutting off the laser source or interruption of the beams by means of a shutter. The facility may be a welding or cutting apparatus and may be used with nuclear fuel elements. The monitoring system may be a scanning system. Two such scanning systems may be provided, scanning at different speeds, to detect respectively hot spots and the presence of a human body within the safety enclosure. (author)

  18. Thorium and plutonium utilisation in pebble-bed modular reactor

    International Nuclear Information System (INIS)

    Thorium and plutonium utilisation in a high temperature gas-cooled pebble-bed reactor is investigated with the aim to predict the economic value of vast thorium reserves in Turkey. A pebble-bed reactor of the type designed by PBMR Pty. of South Africa is taken as the investigated system. The equilibrium core of a PBMR is considered and neutronics analyses of such a core are performed through the use of the SCALE-4.4 computer code system KENOV.a module. Various cross-section libraries are used to calculate the criticality of the core. Burn-up calculations of the core are performed by coupling the KENOV.a module with the ORIGEN-S module. Calculations are carried out for various U-Th, U-Pu-Th and U-Pu combinations. The results are preliminary in nature and the work is currently proceeding as planned. (author)

  19. Solar energy utilisation and energy conservation in buildings

    International Nuclear Information System (INIS)

    Full text: The paper involves testing and improving the performance of solar water heaters under all possible local solar and weather conditions. A new design of stratified energy storage tanks have been experimentally and theoretically studied by which an improvement of about 15% in system efficiency has been observed over well-mixed tanks. Solar space heating and cooling using absorption systems has also been investigated where both performance and economical return are assessed for local lebanese conditions. Several projects are ongoing related to solar energy utilisation including the use of heat pipes, experimental studies for new means for energy conversion. The paper presents the design and testing of solar water heaters; modeling and simulation of solar-powered air-conditioning absorption system performance in Beirut and energy conservation in Lebanese residential and office buildings and the code-of-practice

  20. Current and potential utilisation of biomass energy in Fiji

    International Nuclear Information System (INIS)

    Energy from biomass accounts for an average of 43% of the primary energy used in developing countries, with some countries totally dependent on biomass for all their energy needs. The most common use for biomass for energy is the provision of heat for cooking and heating; other uses include steam and electricity generation and crop and food drying. Fiji, a developing country, uses energy from wood and coconut wastes for cooking and copra drying. Bagasse from sugar mills is used to generate process steam as well as some 15 MW of electricity, for mill consumption and for sale to the national grid. Other, relatively small scale uses for biomass include the generation of steam and electricity for industry. This paper attempts to quantify the amount of biomass, in its various forms, available in Fiji and assesses the current potential utilisation of biomass for energy in Fiji. (author)

  1. Effect of ethnic background on Danish hospital utilisation patterns

    DEFF Research Database (Denmark)

    Krasnik, Allan; Nørredam, Marie Louise; Sorensen, Tine Moller;

    2002-01-01

    The aim of the study is to examine possible ethnic differences in the utilisation patterns of hospitalised immigrants versus patients born in Denmark. Data were obtained from the Register of Prevention at Statistics Denmark. This register includes both clinical and socio-demographic data. All...... patients discharged as inpatients during 1997 at Bispebjerg Hospital (a major hospital in Copenhagen) were identified through the Register of Prevention and linked to data concerning diagnosis, place of birth, age and gender. To compare immigrants with patients born in Denmark, a study group and a...... reference group were formed. The final study group consisted of all patients characterised by 22 major diagnostic categories and born outside the five Nordic countries (altogether 858 persons accounting for 976 inpatient contacts). The reference group consisted of 2004 patients accounting for 2432 inpatient...

  2. Diffusion et utilisation des TIC en France et en Europe

    OpenAIRE

    Berret, Pierre; Chantepie, Philippe

    2015-01-01

    L’exploitation par le DEPS des enquêtes communautaires sur l’utilisation des TIC par les ménages et les particuliers, coordonnées, harmonisées et publiées par Eurostat, permet de dresser un portrait comparatif et en tendances de l’équipement en TIC, des modes d’accès à l’internet des ménages dans l’UE- 27 selon leurs caractéristiques socio-démographiques. Elle met en lumière l’intensification des usages numériques des particuliers, élucide les facteurs de développement des TIC que sont les us...

  3. Utilisation of payment instruments at a retail chain in Gauteng

    Directory of Open Access Journals (Sweden)

    Adriaan M. Bester

    2015-02-01

    Full Text Available Purpose: The purpose of this research was to determine the influence of race and income on the preferred payment instrument at pay points in a retail store in Pretoria Gauteng.Problem investigated: The method of payment, as well as the way these payment methods have been utilised, has evolved throughout history. Cash has stayed at the top of the payment instrument deck as a payment choice for the past 10 decades. With the expansion of technology payment instruments evolved to facilitate exchange between merchant and consumer. The preferred method of payment at a retail store in Gauteng, indicating whether consumers prefer cash payments or the use of cards was investigated. Further to this the difference in payment method between the different races and income groups was identified.Methodology: A quantitative survey research method was used. The statistical analysis entailed correlations using the Cramer’s V to test the dependency between two variables and the degree of dependency of variables, after which the Chi-Square test was also applied.Value of the research: The indication of consumer preference of payment method will have implications on which possibilities are available at the point of sale. Cash is no longer the only possible payment instrument; cards, debit and credit, are as easily used by consumers. Both banks and merchants will find this information important, since they need to make provision for different payment options. The results further distinguished consumer behaviour amongst different race groups and income groups.Conclusion: The research confirmed the previous findings in other countries that consumers have preconceived ideas on which payment instrument they would utilise at point of sale(POS.

  4. Biocarburants : la Commission propose d’encourager leur utilisation

    Directory of Open Access Journals (Sweden)

    Vermeersch Georges

    2002-01-01

    Full Text Available Depuis longtemps, la Commission, le Parlement et le Conseil encouragent le développement des sources d’énergie renouvelables, et plus particulièrement des biocarburants. Cela s’est traduit, entre autres, par la publication en novembre 2000 d’un livre vert intitulé « Vers une stratégie européenne de sécurité d’approvisionnement énergétique », qui fixe comme objectif, d’ici 2020, le remplacement de 20% des carburants classiques par des carburants de substitution pour le transport routier. Plus récemment, en juin 2001, au sommet de Göteborg, a été souligné le rôle important des biocarburants dans la lutte contre le changement climatique et le développement des énergies propres. Ces encouragements restaient au niveau de la déclaration d’intention faute de moyens administratifs et fiscaux pour bâtir une véritable stratégie. Depuis le 7 novembre 2001, les choses semblent évoluer : en effet, à cette date, le collège des Commissaires a adopté une communication sur les carburants de substitution pour les transports routiers et une série de mesures visant à promouvoir l’utilisation des biocarburants. De plus - et c’est ce qui est fondamental - cette communication était assortie de deux propositions de directives, l’une visant à promouvoir l’utilisation des biocarburants dans les transports, l’autre concernant la possibilité d’appliquer un taux d’accises réduit sur certaines huiles minérales qui contiennent des biocarburants et sur les biocarburants.

  5. Utilising shade to optimize UV exposure for vitamin D

    Directory of Open Access Journals (Sweden)

    D. J. Turnbull

    2008-06-01

    Full Text Available Numerous studies have stated that humans need to utilise full sun radiation, at certain times of the day, to assist the body in synthesising the required levels of vitamin D3. The time needed to be spent in the full sun depends on a number of factors, for example, age, skin type, latitude, solar zenith angle. Current Australian guidelines suggest exposure to approximately 1/6 to 1/3 of a minimum erythemal dose (MED, depending on age, would be appropriate to provide adequate vitamin D3 levels. The aim of the study was to determine the exposure times to diffuse solar UV to receive exposures of 1/6 and 1/3 MED for a changing solar zenith angle in order to assess the possible role that diffuse UV (scattered radiation may play in vitamin D3 effective UV exposures (UVD3. Diffuse and global erythemal UV measurements were conducted at five minute intervals over a twelve month period for a solar zenith angle range of 4° to 80° at a latitude of 27.6° S. For a diffuse UV exposure of 1/3 MED, solar zenith angles smaller than approximately 50° can be utilised for exposure times of less than 10 min. Spectral measurements showed that, for a solar zenith angle of 40°, the UVA (315–400 nm in the diffuse component of the solar UV is reduced by approximately 62% compared to the UVA in the global UV, whereas UVD3 wavelengths are only reduced by approximately 43%. At certain latitudes, diffuse UV under shade may play an important role in providing the human body with adequate levels of UVD3 (290–315 nm radiation without experiencing the high levels of UVA observed in full sun.

  6. Utilising shade to optimize UV exposure for vitamin D

    Science.gov (United States)

    Turnbull, D. J.; Parisi, A. V.

    2008-06-01

    Numerous studies have stated that humans need to utilise full sun radiation, at certain times of the day, to assist the body in synthesising the required levels of vitamin D3. The time needed to be spent in the full sun depends on a number of factors, for example, age, skin type, latitude, solar zenith angle. Current Australian guidelines suggest exposure to approximately 1/6 to 1/3 of a minimum erythemal dose (MED), depending on age, would be appropriate to provide adequate vitamin D3 levels. The aim of the study was to determine the exposure times to diffuse solar UV to receive exposures of 1/6 and 1/3 MED for a changing solar zenith angle in order to assess the possible role that diffuse UV (scattered radiation) may play in vitamin D3 effective UV exposures (UVD3). Diffuse and global erythemal UV measurements were conducted at five minute intervals over a twelve month period for a solar zenith angle range of 4° to 80° at a latitude of 27.6° S. For a diffuse UV exposure of 1/3 MED, solar zenith angles smaller than approximately 50° can be utilised for exposure times of less than 10 min. Spectral measurements showed that, for a solar zenith angle of 40°, the UVA (315-400 nm) in the diffuse component of the solar UV is reduced by approximately 62% compared to the UVA in the global UV, whereas UVD3 wavelengths are only reduced by approximately 43%. At certain latitudes, diffuse UV under shade may play an important role in providing the human body with adequate levels of UVD3 (290-315 nm) radiation without experiencing the high levels of UVA observed in full sun.

  7. Utilising shade to optimize UV exposure for vitamin D

    Directory of Open Access Journals (Sweden)

    D. J. Turnbull

    2008-01-01

    Full Text Available Numerous studies have stated that humans need to utilise full sun radiation, at certain times of the day, to assist the body in synthesising the required levels of vitamin D3. The time needed to be spent in the full sun depends on a number of factors, for example, age, skin type, latitude, solar zenith angle. Current Australian guidelines suggest exposure to approximately 1/6 to 1/3 of a minimum erythemal dose (MED, depending on age, would be appropriate to provide adequate vitamin D3 levels. The aim of the study was to determine the exposure times to diffuse solar UV to receive exposures of 1/6 and 1/3 MED for a changing solar zenith angle in order to assess the possible role that diffuse UV (scattered radiation may play in vitamin D3 effective UV exposures (UVD3. Diffuse and global erythemal UV measurements were conducted at five minute intervals over a twelve month period for a solar zenith angle range of 4° to 80° at a latitude of 27.6° S. For diffuse UV exposures of 1/6 and 1/3 MED, solar zenith angles smaller than 60° and 50° respectively can be utilised for exposure times of less than 10 min. Spectral measurements showed that, for a solar zenith angle of 40°, the UVA (315–400 nm in the diffuse component of the solar UV is reduced by approximately 62% compared to the UVA in the global UV, whereas UVD3 wavelengths are only reduced by approximately 43%. At certain latitudes, diffuse UV under shade may play an important role in providing the human body with adequate levels of UVD3 (290–330 nm radiation without experiencing the high levels of damaging UVA observed in full sun.

  8. Recent improvements to the SMART domain-based sequence annotation resource

    Science.gov (United States)

    Letunic, Ivica; Goodstadt, Leo; Dickens, Nicholas J.; Doerks, Tobias; Schultz, Joerg; Mott, Richard; Ciccarelli, Francesca; Copley, Richard R.; Ponting, Chris P.; Bork, Peer

    2002-01-01

    SMART (Simple Modular Architecture Research Tool, http://smart.embl-heidelberg.de) is a web-based resource used for the annotation of protein domains and the analysis of domain architectures, with particular emphasis on mobile eukaryotic domains. Extensive annotation for each domain family is available, providing information relating to function, subcellular localization, phyletic distribution and tertiary structure. The January 2002 release has added more than 200 hand-curated domain models. This brings the total to over 600 domain families that are widely represented among nuclear, signalling and extracellular proteins. Annotation now includes links to the Online Mendelian Inheritance in Man (OMIM) database in cases where a human disease is associated with one or more mutations in a particular domain. We have implemented new analysis methods and updated others. New advanced queries provide direct access to the SMART relational database using SQL. This database now contains information on intrinsic sequence features such as transmembrane regions, coiled-coils, signal peptides and internal repeats. SMART output can now be easily included in users’ documents. A SMART mirror has been created at http://smart.ox.ac.uk. PMID:11752305

  9. Recent improvements to the SMART domain-based sequence annotation resource.

    Science.gov (United States)

    Letunic, Ivica; Goodstadt, Leo; Dickens, Nicholas J; Doerks, Tobias; Schultz, Joerg; Mott, Richard; Ciccarelli, Francesca; Copley, Richard R; Ponting, Chris P; Bork, Peer

    2002-01-01

    SMART (Simple Modular Architecture Research Tool, http://smart.embl-heidelberg.de) is a web-based resource used for the annotation of protein domains and the analysis of domain architectures, with particular emphasis on mobile eukaryotic domains. Extensive annotation for each domain family is available, providing information relating to function, subcellular localization, phyletic distribution and tertiary structure. The January 2002 release has added more than 200 hand-curated domain models. This brings the total to over 600 domain families that are widely represented among nuclear, signalling and extracellular proteins. Annotation now includes links to the Online Mendelian Inheritance in Man (OMIM) database in cases where a human disease is associated with one or more mutations in a particular domain. We have implemented new analysis methods and updated others. New advanced queries provide direct access to the SMART relational database using SQL. This database now contains information on intrinsic sequence features such as transmembrane regions, coiled-coils, signal peptides and internal repeats. SMART output can now be easily included in users' documents. A SMART mirror has been created at http://smart.ox.ac.uk. PMID:11752305

  10. ERAIZDA: a model for holistic annotation of animal infectious and zoonotic diseases.

    Science.gov (United States)

    Buza, Teresia M; Jack, Sherman W; Kirunda, Halid; Khaitsa, Margaret L; Lawrence, Mark L; Pruett, Stephen; Peterson, Daniel G

    2015-01-01

    There is an urgent need for a unified resource that integrates trans-disciplinary annotations of emerging and reemerging animal infectious and zoonotic diseases. Such data integration will provide wonderful opportunity for epidemiologists, researchers and health policy makers to make data-driven decisions designed to improve animal health. Integrating emerging and reemerging animal infectious and zoonotic disease data from a large variety of sources into a unified open-access resource provides more plausible arguments to achieve better understanding of infectious and zoonotic diseases. We have developed a model for interlinking annotations of these diseases. These diseases are of particular interest because of the threats they pose to animal health, human health and global health security. We demonstrated the application of this model using brucellosis, an infectious and zoonotic disease. Preliminary annotations were deposited into VetBioBase database (http://vetbiobase.igbb.msstate.edu). This database is associated with user-friendly tools to facilitate searching, retrieving and downloading of disease-related information. Database URL: http://vetbiobase.igbb.msstate.edu. PMID:26581408

  11. Domain-based small molecule binding site annotation

    Directory of Open Access Journals (Sweden)

    Dumontier Michel

    2006-03-01

    Full Text Available Abstract Background Accurate small molecule binding site information for a protein can facilitate studies in drug docking, drug discovery and function prediction, but small molecule binding site protein sequence annotation is sparse. The Small Molecule Interaction Database (SMID, a database of protein domain-small molecule interactions, was created using structural data from the Protein Data Bank (PDB. More importantly it provides a means to predict small molecule binding sites on proteins with a known or unknown structure and unlike prior approaches, removes large numbers of false positive hits arising from transitive alignment errors, non-biologically significant small molecules and crystallographic conditions that overpredict ion binding sites. Description Using a set of co-crystallized protein-small molecule structures as a starting point, SMID interactions were generated by identifying protein domains that bind to small molecules, using NCBI's Reverse Position Specific BLAST (RPS-BLAST algorithm. SMID records are available for viewing at http://smid.blueprint.org. The SMID-BLAST tool provides accurate transitive annotation of small-molecule binding sites for proteins not found in the PDB. Given a protein sequence, SMID-BLAST identifies domains using RPS-BLAST and then lists potential small molecule ligands based on SMID records, as well as their aligned binding sites. A heuristic ligand score is calculated based on E-value, ligand residue identity and domain entropy to assign a level of confidence to hits found. SMID-BLAST predictions were validated against a set of 793 experimental small molecule interactions from the PDB, of which 472 (60% of predicted interactions identically matched the experimental small molecule and of these, 344 had greater than 80% of the binding site residues correctly identified. Further, we estimate that 45% of predictions which were not observed in the PDB validation set may be true positives. Conclusion By

  12. TOPSAN: use of a collaborative environment for annotating, analyzing and disseminating data on JCSG and PSI structures

    International Nuclear Information System (INIS)

    Specific use cases of TOPSAN, an innovative collaborative platform for creating, sharing and distributing annotations and insights about protein structures, such as those determined by high-throughput structural genomics in the Protein Structure Initiative (PSI), are described. TOPSAN is the main annotation platform for JCSG structures and serves as a conduit for initiating collaborations with the biological community, as illustrated in this special issue of Acta Crystallographica Section F. Developed at the JCSG with the goal of opening a dialogue on the novel protein structures with the broader biological community, TOPSAN is a unique tool for fostering distributed collaborations and provides an efficient pathway to peer-reviewed publications. The NIH Protein Structure Initiative centers, such as the Joint Center for Structural Genomics (JCSG), have developed highly efficient technological platforms that are capable of experimentally determining the three-dimensional structures of hundreds of proteins per year. However, the overwhelming majority of the almost 5000 protein structures determined by these centers have yet to be described in the peer-reviewed literature. In a high-throughput structural genomics environment, the process of structure determination occurs independently of any associated experimental characterization of function, which creates a challenge for the annotation and analysis of structures and the publication of these results. This challenge has been addressed by developing TOPSAN (‘The Open Protein Structure Annotation Network’), which enables the generation of knowledge via collaborations among globally distributed contributors supported by automated amalgamation of available information. TOPSAN currently provides annotations for all protein structures determined by the JCSG in addition to preliminary annotations on a large number of structures from the other PSI production centers. TOPSAN-enabled collaborations have resulted in

  13. Scoring consensus of multiple ECG annotators by optimal sequence alignment.

    Science.gov (United States)

    Haghpanahi, Masoumeh; Sameni, Reza; Borkholder, David A

    2014-01-01

    Development of ECG delineation algorithms has been an area of intense research in the field of computational cardiology for the past few decades. However, devising evaluation techniques for scoring and/or merging the results of such algorithms, both in the presence or absence of gold standards, still remains as a challenge. This is mainly due to existence of missed or erroneous determination of fiducial points in the results of different annotation algorithms. The discrepancy between different annotators increases when the reference signal includes arrhythmias or significant noise and its morphology deviates from a clean ECG signal. In this work, we propose a new approach to evaluate and compare the results of different annotators under such conditions. Specifically, we use sequence alignment techniques similar to those used in bioinformatics for the alignment of gene sequences. Our approach is based on dynamic programming where adequate mismatch penalties, depending on the type of the fiducial point and the underlying signal, are defined to optimally align the annotation sequences. We also discuss how to extend the algorithm for more than two sequences by using suitable data structures to align multiple annotation sequences with each other. Once the sequences are aligned, different heuristics are devised to evaluate the performance against a gold standard annotation, or to merge the results of multiple annotations when no gold standard exists. PMID:25570339

  14. Fuzzy Emotional Semantic Analysis and Automated Annotation of Scene Images

    Directory of Open Access Journals (Sweden)

    Jianfang Cao

    2015-01-01

    Full Text Available With the advances in electronic and imaging techniques, the production of digital images has rapidly increased, and the extraction and automated annotation of emotional semantics implied by images have become issues that must be urgently addressed. To better simulate human subjectivity and ambiguity for understanding scene images, the current study proposes an emotional semantic annotation method for scene images based on fuzzy set theory. A fuzzy membership degree was calculated to describe the emotional degree of a scene image and was implemented using the Adaboost algorithm and a back-propagation (BP neural network. The automated annotation method was trained and tested using scene images from the SUN Database. The annotation results were then compared with those based on artificial annotation. Our method showed an annotation accuracy rate of 91.2% for basic emotional values and 82.4% after extended emotional values were added, which correspond to increases of 5.5% and 8.9%, respectively, compared with the results from using a single BP neural network algorithm. Furthermore, the retrieval accuracy rate based on our method reached approximately 89%. This study attempts to lay a solid foundation for the automated emotional semantic annotation of more types of images and therefore is of practical significance.

  15. Fuzzy emotional semantic analysis and automated annotation of scene images.

    Science.gov (United States)

    Cao, Jianfang; Chen, Lichao

    2015-01-01

    With the advances in electronic and imaging techniques, the production of digital images has rapidly increased, and the extraction and automated annotation of emotional semantics implied by images have become issues that must be urgently addressed. To better simulate human subjectivity and ambiguity for understanding scene images, the current study proposes an emotional semantic annotation method for scene images based on fuzzy set theory. A fuzzy membership degree was calculated to describe the emotional degree of a scene image and was implemented using the Adaboost algorithm and a back-propagation (BP) neural network. The automated annotation method was trained and tested using scene images from the SUN Database. The annotation results were then compared with those based on artificial annotation. Our method showed an annotation accuracy rate of 91.2% for basic emotional values and 82.4% after extended emotional values were added, which correspond to increases of 5.5% and 8.9%, respectively, compared with the results from using a single BP neural network algorithm. Furthermore, the retrieval accuracy rate based on our method reached approximately 89%. This study attempts to lay a solid foundation for the automated emotional semantic annotation of more types of images and therefore is of practical significance. PMID:25838818

  16. MalaCards: an integrated compendium for diseases and their annotation.

    Science.gov (United States)

    Rappaport, Noa; Nativ, Noam; Stelzer, Gil; Twik, Michal; Guan-Golan, Yaron; Stein, Tsippi Iny; Bahir, Iris; Belinky, Frida; Morrey, C Paul; Safran, Marilyn; Lancet, Doron

    2013-01-01

    Comprehensive disease classification, integration and annotation are crucial for biomedical discovery. At present, disease compilation is incomplete, heterogeneous and often lacking systematic inquiry mechanisms. We introduce MalaCards, an integrated database of human maladies and their annotations, modeled on the architecture and strategy of the GeneCards database of human genes. MalaCards mines and merges 44 data sources to generate a computerized card for each of 16 919 human diseases. Each MalaCard contains disease-specific prioritized annotations, as well as inter-disease connections, empowered by the GeneCards relational database, its searches and GeneDecks set analyses. First, we generate a disease list from 15 ranked sources, using disease-name unification heuristics. Next, we use four schemes to populate MalaCards sections: (i) directly interrogating disease resources, to establish integrated disease names, synonyms, summaries, drugs/therapeutics, clinical features, genetic tests and anatomical context; (ii) searching GeneCards for related publications, and for associated genes with corresponding relevance scores; (iii) analyzing disease-associated gene sets in GeneDecks to yield affiliated pathways, phenotypes, compounds and GO terms, sorted by a composite relevance score and presented with GeneCards links; and (iv) searching within MalaCards itself, e.g. for additional related diseases and anatomical context. The latter forms the basis for the construction of a disease network, based on shared MalaCards annotations, embodying associations based on etiology, clinical features and clinical conditions. This broadly disposed network has a power-law degree distribution, suggesting that this might be an inherent property of such networks. Work in progress includes hierarchical malady classification, ontological mapping and disease set analyses, striving to make MalaCards an even more effective tool for biomedical research. Database URL: http

  17. A hybrid system using symbolic and numeric knowledge for the semantic annotation of sulco-gyral anatomy in brain MRI images.

    Science.gov (United States)

    Mechouche, Ammar; Morandi, Xavier; Golbreich, Christine; Gibaud, Bernard

    2009-08-01

    This paper describes an interactive system for the semantic annotation of brain magnetic resonance images. The system uses both a numerical atlas and symbolic knowledge of brain anatomical structures depicted using the Semantic Web standards. This knowledge is combined with graphical data, automatically extracted from the images by imaging tools. The annotations of parts of gyri and sulci, in a region of interest, rely on constraint satisfaction problem solving and description logics inferences. The system is run on a client-server architecture, using Web services and including a sophisticated visualization tool. An evaluation of the system was done using normal (healthy) and pathological cases. The results obtained so far demonstrate that the system produces annotations with high precision and quality. PMID:19622437

  18. Pragmatics Annotated Coloured Petri Nets for Protocol Software Generation and Verification

    DEFF Research Database (Denmark)

    Fagerland Simonsen, Kent Inge; Kristensen, Lars Michael; Kindler, Ekkart

    PetriCode is a tool that supports automated generation of protocol software from a restricted class of Coloured Petri Nets (CPNs) called Pragmatics Annotated Coloured Petri Nets (PA-CPNs). Petri-Code and PA-CPNs have been designed with five main requirements in mind, which include the same model...... being used for verification and code generation. The PetriCode approach has been discussed and evaluated in earlier papers already. In this paper, we give a formal definition of PA-CPNs and demonstrate how the specific structure of PA-CPNs can be exploited for verification purposes....

  19. The UniProt-GO Annotation database in 2011

    OpenAIRE

    Dimmer, E. C.; Huntley, R. P.; Alam-Faruque, Y.; Sawford, T.; O'Donovan, C.; Martin, M. J.; Bely, B.; Browne, P.; Mun Chan, W.; Eberhardt, R.; Gardner, M; Laiho, K; Legge, D.; Magrane, M.; Pichler, K.

    2011-01-01

    The GO annotation dataset provided by the UniProt Consortium (GOA: http://www.ebi.ac.uk/GOA) is a comprehensive set of evidenced-based associations between terms from the Gene Ontology resource and UniProtKB proteins. Currently supplying over 100 million annotations to 11 million proteins in more than 360 000 taxa, this resource has increased 2-fold over the last 2 years and has benefited from a wealth of checks to improve annotation correctness and consistency as well as now supplying a grea...

  20. Formalisation d'annotations produites par des apprenants

    OpenAIRE

    Mille, Dominique

    2005-01-01

    L'objet de cet article est la description d'une formalisation computable des annotations produites par des apprenants, représentée par une ontologie. Cette formalisation explicite la sémantique des annotations grâce à des attributs auxquels le lecteur devrait donner une valeur. Elle contient également les valeurs possibles de ces attributs. L'intérêt d'une telle formalisation est de couvrir toutes les annotations produites par des apprenants, et d'expliciter tout ce qui constitue leur sens, a...

  1. Annotation of the protein coding regions of the equine genome

    DEFF Research Database (Denmark)

    Hestand, Matthew S.; Kalbfleisch, Theodore S.; Coleman, Stephen J.; Zeng, Zheng; Liu, Jinze; Orlando, Ludovic Antoine Alexandre; MacLeod, James N.

    2015-01-01

    Current gene annotation of the horse genome is largely derived from in silico predictions and cross-species alignments. Only a small number of genes are annotated based on equine EST and mRNA sequences. To expand the number of equine genes annotated from equine experimental evidence, we sequenced m...... appear to be small errors in the equine reference genome, since they are also identified as homozygous variants by genomic DNA resequencing of the reference horse. Taken together, we provide a resource of equine mRNA structures and protein coding variants that will enhance equine and cross...

  2. DDBJ in collaboration with mass-sequencing teams on annotation

    OpenAIRE

    Tateno, Y; Saitou, N; Okubo, K; Sugawara, H.; Gojobori, T

    2004-01-01

    In the past year, we at DDBJ (DNA Data Bank of Japan; http://www.ddbj.nig.ac.jp) collected and released 1 066 084 entries or 718 072 425 bases including the whole chromosome 22 of chimpanzee, the whole-genome shotgun sequences of silkworm and various others. On the other hand, we hosted workshops for human full-length cDNA annotation and participated in jamborees of mouse full-length cDNA annotation. The annotated data are made public at DDBJ. We are also in collaboration with a RIKEN team to...

  3. Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae

    Energy Technology Data Exchange (ETDEWEB)

    Rutledge, Alexandra C.; Jones, Marcus B.; Chauhan, Sadhana; Purvine, Samuel O.; Sanford, James; Monroe, Matthew E.; Brewer, Heather M.; Payne, Samuel H.; Ansong, Charles; Frank, Bryan C.; Smith, Richard D.; Peterson, Scott; Motin, Vladimir L.; Adkins, Joshua N.

    2012-03-27

    Genome sequencing continues to be a rapidly evolving technology, yet most downstream aspects of genome annotation pipelines remain relatively stable or are even being abandoned. To date, the perceived value of manual curation for genome annotations is not offset by the real cost and time associated with the process. In order to balance the large number of sequences generated, the annotation process is now performed almost exclusively in an automated fashion for most genome sequencing projects. One possible way to reduce errors inherent to automated computational annotations is to apply data from 'omics' measurements (i.e. transcriptional and proteomic) to the un-annotated genome with a proteogenomic-based approach. This approach does require additional experimental and bioinformatics methods to include omics technologies; however, the approach is readily automatable and can benefit from rapid developments occurring in those research domains as well. The annotation process can be improved by experimental validation of transcription and translation and aid in the discovery of annotation errors. Here the concept of annotation refinement has been extended to include a comparative assessment of genomes across closely related species, as is becoming common in sequencing efforts. Transcriptomic and proteomic data derived from three highly similar pathogenic Yersiniae (Y. pestis CO92, Y. pestis pestoides F, and Y. pseudotuberculosis PB1/+) was used to demonstrate a comprehensive comparative omic-based annotation methodology. Peptide and oligo measurements experimentally validated the expression of nearly 40% of each strain's predicted proteome and revealed the identification of 28 novel and 68 previously incorrect protein-coding sequences (e.g., observed frameshifts, extended start sites, and translated pseudogenes) within the three current Yersinia genome annotations. Gene loss is presumed to play a major role in Y. pestis acquiring its niche as a virulent

  4. The VerCors tool for verification of concurrent programs

    NARCIS (Netherlands)

    Blom, Stefan; Huisman, Marieke; Jones, Cliff; Pihlajasaari, Pekka; Sun, Jun

    2014-01-01

    The VerCors tool implements thread-modular static verification of concurrent programs, annotated with functional properties and heap access permissions. The tool supports both generic multithreaded and vector-based programming models. In particular, it can verify multithreaded programs written in Ja

  5. Biofuels and climate neutrality - system analysis of production and utilisation

    International Nuclear Information System (INIS)

    The objectives of this study were to investigate to what extent biofuels can be said to be climate neutral. An assessment of greenhouse gas emissions from the production and utilisation chains of a number of solid biofuels were made based on data available in the literature. The data has been used for making radiative forcing calculations. The study also includes a comparison between imported and domestic solid biofuels. We conclude that none of the investigated biofuel chains are 'climate neutral', since all of them result in net emissions of greenhouse gases. However, all of the chains result in lower emissions than corresponding emissions from the use of fossil fuels. The emission estimates for the fuel chains varies depending on fuels and on how system boundaries have been set in the different studies. The following factors can contribute significantly to the total emissions of greenhouse gases of the production and utilisation chain of a biofuel: impact of production system on soil carbon storage, land use methods (especially use of drained peatlands), the use of fertilisers (both direct and indirect), combustion technology, refining of the fuel (i.e. pelletisation) and storage (especially of comminuted fuels). Other sources that also contribute to the emissions during a production and utilisation chain are; harvesting machines, transportation and waste handling. The climate impacts of the greenhouse gas emissions from one of the biofuels, i.e. forest residues, were compared to the impacts of fossil fuels by the concept of radiative forcing. In the radiative forcing calculations the CO2 emissions from combustion of biofuels and the CO2 emissions that would have occurred if the residues had been left in the forest to decompose were included, and their different dynamics taken into consideration. The decomposition results in CO2 emissions during a long time period and in an amount equalling those that are emitted during combustion. Only a minor part is due to

  6. Gender and the utilisation of health services in the Ashanti Region, Ghana.

    NARCIS (Netherlands)

    Buor, D.

    2004-01-01

    The survey seeks to structure a model for gender-based health services utilisation for the Ashanti Region of Ghana, and in addition, recommend intervention measures to ensure gender equity in the utilisation of health services. A sample size of 650 covered over 3108 houses, and the main research ins

  7. Drug utilisation by children and adolescents with mental retardation : a population study

    NARCIS (Netherlands)

    Tobi, H; Scheers, T; Netjes, KA; Mulder, EJ; de Bildt, A; Minderaa, RB

    2005-01-01

    Objective: Little is known about the utilisation of drugs by mentally retarded children; population studies are even more sparse. In this study the chronic drug utilisation in children aged 4-18 years with mental retardation in a large population in the Netherlands was investigated. Methods: Through

  8. Drug utilisation by children and adolescents with mental retardation: a population study

    NARCIS (Netherlands)

    Tobi, H; Scheers, T.; Netjes, K.A.; Mulder, E.J.; De Bildt, A.; Minderaa, R.B

    2005-01-01

    Objective: Little is known about the utilisation of drugs by mentally retarded children; population studies are even more sparse. In this study the chronic drug utilisation in children aged 4-18 years with mental retardation in a large population in the Netherlands was investigated. Methods: Through

  9. FunnyBase: a systems level functional annotation of Fundulus ESTs for the analysis of gene expression

    OpenAIRE

    Kolell Kevin J; Wyckoff Gerald J; Whitehead J Andrew; Roach Jennifer L; VanWye Jeffrey D; Oleksiak Marjorie F; Paschall Justin E; Crawford Douglas L

    2004-01-01

    Abstract Background While studies of non-model organisms are critical for many research areas, such as evolution, development, and environmental biology, they present particular challenges for both experimental and computational genomic level research. Resources such as mass-produced microarrays and the computational tools linking these data to functional annotation at the system and pathway level are rarely available for non-model species. This type of "systems-level" analysis is critical to...

  10. Genome Wide Re-Annotation of Caldicellulosiruptor saccharolyticus with New Insights into Genes Involved in Biomass Degradation and Hydrogen Production

    Science.gov (United States)

    Chowdhary, Nupoor; Selvaraj, Ashok; KrishnaKumaar, Lakshmi; Kumar, Gopal Ramesh

    2015-01-01

    Caldicellulosiruptor saccharolyticus has proven itself to be an excellent candidate for biological hydrogen (H2) production, but still it has major drawbacks like sensitivity to high osmotic pressure and low volumetric H2 productivity, which should be considered before it can be used industrially. A whole genome re-annotation work has been carried out as an attempt to update the incomplete genome information that causes gap in the knowledge especially in the area of metabolic engineering, to improve the H2 producing capabilities of C. saccharolyticus. Whole genome re-annotation was performed through manual means for 2,682 Coding Sequences (CDSs). Bioinformatics tools based on sequence similarity, motif search, phylogenetic analysis and fold recognition were employed for re-annotation. Our methodology could successfully add functions for 409 hypothetical proteins (HPs), 46 proteins previously annotated as putative and assigned more accurate functions for the known protein sequences. Homology based gene annotation has been used as a standard method for assigning function to novel proteins, but over the past few years many non-homology based methods such as genomic context approaches for protein function prediction have been developed. Using non-homology based functional prediction methods, we were able to assign cellular processes or physical complexes for 249 hypothetical sequences. Our re-annotation pipeline highlights the addition of 231 new CDSs generated from MicroScope Platform, to the original genome with functional prediction for 49 of them. The re-annotation of HPs and new CDSs is stored in the relational database that is available on the MicroScope web-based platform. In parallel, a comparative genome analyses were performed among the members of genus Caldicellulosiruptor to understand the function and evolutionary processes. Further, with results from integrated re-annotation studies (homology and genomic context approach), we strongly suggest that Csac

  11. Genome Wide Re-Annotation of Caldicellulosiruptor saccharolyticus with New Insights into Genes Involved in Biomass Degradation and Hydrogen Production.

    Directory of Open Access Journals (Sweden)

    Nupoor Chowdhary

    Full Text Available Caldicellulosiruptor saccharolyticus has proven itself to be an excellent candidate for biological hydrogen (H2 production, but still it has major drawbacks like sensitivity to high osmotic pressure and low volumetric H2 productivity, which should be considered before it can be used industrially. A whole genome re-annotation work has been carried out as an attempt to update the incomplete genome information that causes gap in the knowledge especially in the area of metabolic engineering, to improve the H2 producing capabilities of C. saccharolyticus. Whole genome re-annotation was performed through manual means for 2,682 Coding Sequences (CDSs. Bioinformatics tools based on sequence similarity, motif search, phylogenetic analysis and fold recognition were employed for re-annotation. Our methodology could successfully add functions for 409 hypothetical proteins (HPs, 46 proteins previously annotated as putative and assigned more accurate functions for the known protein sequences. Homology based gene annotation has been used as a standard method for assigning function to novel proteins, but over the past few years many non-homology based methods such as genomic context approaches for protein function prediction have been developed. Using non-homology based functional prediction methods, we were able to assign cellular processes or physical complexes for 249 hypothetical sequences. Our re-annotation pipeline highlights the addition of 231 new CDSs generated from MicroScope Platform, to the original genome with functional prediction for 49 of them. The re-annotation of HPs and new CDSs is stored in the relational database that is available on the MicroScope web-based platform. In parallel, a comparative genome analyses were performed among the members of genus Caldicellulosiruptor to understand the function and evolutionary processes. Further, with results from integrated re-annotation studies (homology and genomic context approach, we strongly

  12. Needs-oriented discharge planning and monitoring for high utilisers of psychiatric services (NODPAM: Design and methods

    Directory of Open Access Journals (Sweden)

    Steinert Tilman

    2008-07-01

    Full Text Available Abstract Background Attempts to reduce high utilisation of psychiatric inpatient care by targeting the critical time of hospital discharge have been rare. Methods This paper presents design and methods of the study "Effectiveness and Cost-Effectiveness of Needs-Oriented Discharge Planning and Monitoring for High Utilisers of Psychiatric Services" (NODPAM, a multicentre RCT conducted in five psychiatric hospitals in Germany. Inclusion criteria are receipt of inpatient psychiatric care, adult age, diagnosis of schizophrenia or affective disorder, defined high utilisation of psychiatric care during two years prior to the current admission, and given informed consent. Consecutive recruitment started in April 2006. Since then, during a period of 18 months, comprehensive outcome data of 490 participants is being collected at baseline and during three follow-up measurement points. The manualised intervention applies principles of needs-led care and focuses on the inpatient-outpatient transition. A trained intervention worker provides two intervention sessions: (a Discharge planning: Just before discharge with the patient and responsible clinician at the inpatient service; (b Monitoring: Three months after discharge with the patient and outpatient clinician. A written treatment plan is signed by all participants after each session. Primary endpoints are whether participants in the intervention group will show fewer hospital days and readmissions to hospital. Secondary endpoints are better compliance with aftercare, better clinical outcome and quality of life, as well as cost-effectiveness and cost-utility. Discussion If a needs-oriented discharge planning and monitoring proves to be successful in this RCT, a tool will be at hand to improve patient outcome and reduce costs via harmonising fragmented mental health service provision. Trial Registration ISRCTN59603527

  13. Annotation et rature Annotation and Deletion: Outline of a Sociology of Forms

    Directory of Open Access Journals (Sweden)

    Axel Pohn-Weidinger

    2012-05-01

    Full Text Available Ce texte interroge les traces graphiques laissées sur un corpus de formulaires de demande de logement social telles qu’annotations, ratures, biffures et commentaires griffonnés. L’étude de ces traces, laissées en marge des catégories de l’imprimé administratif lors du remplissage, montre le recours au droit comme une opération problématique. Pour les administrés, il s’agit de décrire leur situation de vie de sorte à établir l’éligibilité à un droit, mais bien souvent il est impossible de traduire celle-ci dans les catégories préétablies du formulaire. Les annotations et commentaires laissés sur le formulaire tentent alors d’ouvrir la catégorisation juridique des situations à une prise en compte de la singularité des circonstances de vie du demandeur. Elles montrent le recours au droit comme un accomplissement réflexif, un travail à la fois sur sa propre perception de sa situation et sur celle que l’institution offre à travers le formulaire, et dont la négociation et la mise en œuvre sont au cœur de la production du dossier administratif.This text examines the graphical traces left on a collection of social housing application forms: annotations, erasures, crossed-out words and scribbled-out comments. The study of these traces, left in the margins of the categories on printed administrative forms in the process of being completed, shows the exercising of a right as a problematic operation. Citizens making applications must describe their living situation in a way that will establish their eligibility for a right, but quite often it is impossible to convey this through the form’s predetermined categories. The annotations and comments left on the form attempt to open the legal classification of situations to considering the uniqueness of the applicant’s living circumstances. They show the use of a right as an introspective accomplishment, requiring applicants to work both on their own perception of

  14. Annotated Bibliography of Recent Research Related to Academic Advising

    Science.gov (United States)

    Mottarella, Karen, Comp.

    2011-01-01

    This article presents an annotated bibliography of recent research related to academic advising. It includes research papers that focus on advising and a special section of the "Journal of Career Development" that is devoted to multicultural graduate advising relationships.

  15. Geothermal wetlands: an annotated bibliography of pertinent literature

    Energy Technology Data Exchange (ETDEWEB)

    Stanley, N.E.; Thurow, T.L.; Russell, B.F.; Sullivan, J.F.

    1980-05-01

    This annotated bibliography covers the following topics: algae, wetland ecosystems; institutional aspects; macrophytes - general, production rates, and mineral absorption; trace metal absorption; wetland soils; water quality; and other aspects of marsh ecosystems. (MHR)

  16. OntoELAN: An Ontology-based Linguistic Multimedia Annotator

    CERN Document Server

    Chebotko, Artem; Lu, Shiyong; Fotouhi, Farshad; Aristar, Anthony; Brugman, Hennie; Klassmann, Alexander; Sloetjes, Han; Russel, Albert; Wittenburg, Peter

    2009-01-01

    Despite its scientific, political, and practical value, comprehensive information about human languages, in all their variety and complexity, is not readily obtainable and searchable. One reason is that many language data are collected as audio and video recordings which imposes a challenge to document indexing and retrieval. Annotation of multimedia data provides an opportunity for making the semantics explicit and facilitates the searching of multimedia documents. We have developed OntoELAN, an ontology-based linguistic multimedia annotator that features: (1) support for loading and displaying ontologies specified in OWL; (2) creation of a language profile, which allows a user to choose a subset of terms from an ontology and conveniently rename them if needed; (3) creation of ontological tiers, which can be annotated with profile terms and, therefore, corresponding ontological terms; and (4) saving annotations in the XML format as Multimedia Ontology class instances and, linked to them, class instances of o...

  17. A Machine Learning Based Analytical Framework for Semantic Annotation Requirements

    CERN Document Server

    Hassanzadeh, Hamed; 10.5121/ijwest.2011.2203

    2011-01-01

    The Semantic Web is an extension of the current web in which information is given well-defined meaning. The perspective of Semantic Web is to promote the quality and intelligence of the current web by changing its contents into machine understandable form. Therefore, semantic level information is one of the cornerstones of the Semantic Web. The process of adding semantic metadata to web resources is called Semantic Annotation. There are many obstacles against the Semantic Annotation, such as multilinguality, scalability, and issues which are related to diversity and inconsistency in content of different web pages. Due to the wide range of domains and the dynamic environments that the Semantic Annotation systems must be performed on, the problem of automating annotation process is one of the significant challenges in this domain. To overcome this problem, different machine learning approaches such as supervised learning, unsupervised learning and more recent ones like, semi-supervised learning and active learn...

  18. An Annotated Checklist of the Fishes of Samoa

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — All fishes currently known from the Samoan Islands are listed by their scientific and Samoan names. Species entries are annotated to include the initial Samoan...

  19. Annotation sémantique de pages web

    OpenAIRE

    Tenier, Sylvain; Napoli, Amedeo; Polanco, Xavier; Toussaint, Yannick

    2006-01-01

    Cet article présente un système automatique d'annotation sémantique de pages web. Les systèmes d'annotation automatique existants sont essentiellement syntaxiques, même lorsque les travaux visent à produire une annotation sémantique. La prise en compte d'informations sémantiques sur le domaine pour l'annotation d'un élément dans une page web à partir d'une ontologie suppose d'aborder conjointement deux problèmes : (1) l'identification de la structure syntaxique caractérisant cet élément dans ...

  20. Annotation Method (AM): SE28_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2013A ...

  1. Annotation Method (AM): SE4_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available compound name or compound category name can assign, predicted molecular formulas are used for the annotatio...n. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  2. Annotation Method (AM): SE15_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAOT201112 ...

  3. Annotation Method (AM): SE26_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  4. Annotation Method (AM): SE34_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  5. Annotation Method (AM): SE10_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  6. Annotation Method (AM): SE27_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  7. Annotation Method (AM): SE16_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  8. Annotation Method (AM): SE32_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  9. Annotation Method (AM): SE2_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available compound name or compound category name can assign, predicted molecular formulas are used for the annotatio...n. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2011A ...

  10. Annotation Method (AM): SE6_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available compound name or compound category name can assign, predicted molecular formulas are used for the annotatio...n. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAOT2012A ...

  11. Annotation Method (AM): SE11_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  12. Annotation Method (AM): SE12_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  13. Annotation Method (AM): SE14_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  14. Annotation Method (AM): SE13_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  15. Annotation Method (AM): SE20_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. Terms of chemical category

  16. Annotation Method (AM): SE17_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  17. Annotation Method (AM): SE5_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available compound name or compound category name can assign, predicted molecular formulas are used for the annotatio...n. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  18. Annotation Method (AM): SE30_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  19. Annotation Method (AM): SE31_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...

  20. Annotation Method (AM): SE33_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available o compound name or compound category name can assign, predicted molecular formulas are used for the annotati...on. Peaks without predicted molecular formula are assigned as unidentified peak. TogoAnalysisMethodID=TAFT2012A ...