WorldWideScience

Sample records for annotation organization interpretation

  1. Systematic interpretation of microarray data using experiment annotations

    Directory of Open Access Journals (Sweden)

    Frohme Marcus

    2006-12-01

    Full Text Available Abstract Background Up to now, microarray data are mostly assessed in context with only one or few parameters characterizing the experimental conditions under study. More explicit experiment annotations, however, are highly useful for interpreting microarray data, when available in a statistically accessible format. Results We provide means to preprocess these additional data, and to extract relevant traits corresponding to the transcription patterns under study. We found correspondence analysis particularly well-suited for mapping such extracted traits. It visualizes associations both among and between the traits, the hereby annotated experiments, and the genes, revealing how they are all interrelated. Here, we apply our methods to the systematic interpretation of radioactive (single channel and two-channel data, stemming from model organisms such as yeast and drosophila up to complex human cancer samples. Inclusion of technical parameters allows for identification of artifacts and flaws in experimental design. Conclusion Biological and clinical traits can act as landmarks in transcription space, systematically mapping the variance of large datasets from the predominant changes down toward intricate details.

  2. Annotate-it: a Swiss-knife approach to annotation, analysis and interpretation of single nucleotide variation in human disease.

    Science.gov (United States)

    Sifrim, Alejandro; Van Houdt, Jeroen Kj; Tranchevent, Leon-Charles; Nowakowska, Beata; Sakai, Ryo; Pavlopoulos, Georgios A; Devriendt, Koen; Vermeesch, Joris R; Moreau, Yves; Aerts, Jan

    2012-01-01

    The increasing size and complexity of exome/genome sequencing data requires new tools for clinical geneticists to discover disease-causing variants. Bottlenecks in identifying the causative variation include poor cross-sample querying, constantly changing functional annotation and not considering existing knowledge concerning the phenotype. We describe a methodology that facilitates exploration of patient sequencing data towards identification of causal variants under different genetic hypotheses. Annotate-it facilitates handling, analysis and interpretation of high-throughput single nucleotide variant data. We demonstrate our strategy using three case studies. Annotate-it is freely available and test data are accessible to all users at http://www.annotate-it.org.

  3. 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/.

  4. Decoding transcriptional enhancers: Evolving from annotation to functional interpretation.

    Science.gov (United States)

    Engel, Krysta L; Mackiewicz, Mark; Hardigan, Andrew A; Myers, Richard M; Savic, Daniel

    2016-09-01

    Deciphering the intricate molecular processes that orchestrate the spatial and temporal regulation of genes has become an increasingly major focus of biological research. The differential expression of genes by diverse cell types with a common genome is a hallmark of complex cellular functions, as well as the basis for multicellular life. Importantly, a more coherent understanding of gene regulation is critical for defining developmental processes, evolutionary principles and disease etiologies. Here we present our current understanding of gene regulation by focusing on the role of enhancer elements in these complex processes. Although functional genomic methods have provided considerable advances to our understanding of gene regulation, these assays, which are usually performed on a genome-wide scale, typically provide correlative observations that lack functional interpretation. Recent innovations in genome editing technologies have placed gene regulatory studies at an exciting crossroads, as systematic, functional evaluation of enhancers and other transcriptional regulatory elements can now be performed in a coordinated, high-throughput manner across the entire genome. This review provides insights on transcriptional enhancer function, their role in development and disease, and catalogues experimental tools commonly used to study these elements. Additionally, we discuss the crucial role of novel techniques in deciphering the complex gene regulatory landscape and how these studies will shape future research. PMID:27224938

  5. 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 ...

  6. Evaluating annotations of an Agilent expression chip suggests that many features cannot be interpreted

    Directory of Open Access Journals (Sweden)

    Ried Thomas

    2009-11-01

    Full Text Available Abstract Background While attempting to reanalyze published data from Agilent 4 × 44 human expression chips, we found that some of the 60-mer olignucleotide features could not be interpreted as representing single human genes. For example, some of the oligonucleotides align with the transcripts of more than one gene. We decided to check the annotations for all autosomes and the X chromosome systematically using bioinformatics methods. Results Out of 42683 reporters, we found that 25505 (60% passed all our tests and are considered "fully valid". 9964 (23% reporters did not have a meaningful identifier, mapped to the wrong chromosome, or did not pass basic alignment tests preventing us from correlating the expression values of these reporters with a unique annotated human gene. The remaining 7214 (17% reporters could be associated with either a unique gene or a unique intergenic location, but could not be mapped to a transcript in RefSeq. The 7214 reporters are further partitioned into three different levels of validity. Conclusion Expression array studies should evaluate the annotations of reporters and remove those reporters that have suspect annotations. This evaluation can be done systematically and semi-automatically, but one must recognize that data sources are frequently updated leading to slightly changing validation results over time.

  7. 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

  8. Interpreting functional effects of coding variants: challenges in proteome-scale prediction, annotation and assessment.

    Science.gov (United States)

    Shameer, Khader; Tripathi, Lokesh P; Kalari, Krishna R; Dudley, Joel T; Sowdhamini, Ramanathan

    2016-09-01

    Accurate assessment of genetic variation in human DNA sequencing studies remains a nontrivial challenge in clinical genomics and genome informatics. Ascribing functional roles and/or clinical significances to single nucleotide variants identified from a next-generation sequencing study is an important step in genome interpretation. Experimental characterization of all the observed functional variants is yet impractical; thus, the prediction of functional and/or regulatory impacts of the various mutations using in silico approaches is an important step toward the identification of functionally significant or clinically actionable variants. The relationships between genotypes and the expressed phenotypes are multilayered and biologically complex; such relationships present numerous challenges and at the same time offer various opportunities for the design of in silico variant assessment strategies. Over the past decade, many bioinformatics algorithms have been developed to predict functional consequences of single nucleotide variants in the protein coding regions. In this review, we provide an overview of the bioinformatics resources for the prediction, annotation and visualization of coding single nucleotide variants. We discuss the currently available approaches and major challenges from the perspective of protein sequence, structure, function and interactions that require consideration when interpreting the impact of putatively functional variants. We also discuss the relevance of incorporating integrated workflows for predicting the biomedical impact of the functionally important variations encoded in a genome, exome or transcriptome. Finally, we propose a framework to classify variant assessment approaches and strategies for incorporation of variant assessment within electronic health records.

  9. 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

  10. An Annotated Bibliography of Materials Designed and Organized for Adult Use in Discussion Groups.

    Science.gov (United States)

    Ellison, John W.

    This first annotated bibliography of materials designed and organized for adult use in disucssion groups includes both book and nonbook material. Areas dealt with are: art, censorship, change, child guidance, communication, crime, democracy, economics, education, evolution, food, foreign affairs, forgetting, generation gap, gold, good and evil,…

  11. Thermal effects on aquatic organisms: annotated bibliography of the 1974 literature

    International Nuclear Information System (INIS)

    The annotated bibliography covers the 1974 literature concerning thermal effects on aquatic organisms. Emphasis is placed on the effects of the release of thermal effluents on aquatic ecosystems. Indexes are provided for: author, keywords, subject category, geographic location, taxon, and title (alphabetical listing of keyword-in-context of the nontrivial words in the title). (CH)

  12. Thermal effects on aquatic organisms: an annotated bibliography of the 1977 literature

    International Nuclear Information System (INIS)

    This bibliography, containing 537 references from the 1977 literature, is the seventh in a series of annotated bibliographies on the effects of heat on aquatic organisms. The effects of thermal discharges at power plant sites are emphasized. Laboratory and field studies on temperature tolerance and the effects of temperature changes on reproduction, development, growth, distribution, physiology, and sensitivity to other stresses are included. References in the bibliography are divided into three subject categories: marine systems, freshwater systems, and estuaries. The references are arranged alphabetically by first author. Indexes are provided for author, keywords, subject category, geographic location of the study, taxon, and title

  13. Snpdat: Easy and rapid annotation of results from de novo snp discovery projects for model and non-model organisms

    Directory of Open Access Journals (Sweden)

    Doran Anthony G

    2013-02-01

    Full Text Available Abstract Background Single nucleotide polymorphisms (SNPs are the most abundant genetic variant found in vertebrates and invertebrates. SNP discovery has become a highly automated, robust and relatively inexpensive process allowing the identification of many thousands of mutations for model and non-model organisms. Annotating large numbers of SNPs can be a difficult and complex process. Many tools available are optimised for use with organisms densely sampled for SNPs, such as humans. There are currently few tools available that are species non-specific or support non-model organism data. Results Here we present SNPdat, a high throughput analysis tool that can provide a comprehensive annotation of both novel and known SNPs for any organism with a draft sequence and annotation. Using a dataset of 4,566 SNPs identified in cattle using high-throughput DNA sequencing we demonstrate the annotations performed and the statistics that can be generated by SNPdat. Conclusions SNPdat provides users with a simple tool for annotation of genomes that are either not supported by other tools or have a small number of annotated SNPs available. SNPdat can also be used to analyse datasets from organisms which are densely sampled for SNPs. As a command line tool it can easily be incorporated into existing SNP discovery pipelines and fills a niche for analyses involving non-model organisms that are not supported by many available SNP annotation tools. SNPdat will be of great interest to scientists involved in SNP discovery and analysis projects, particularly those with limited bioinformatics experience.

  14. Prediction of organ toxicity endpoints by QSAR modeling based on precise chemical-histopathology annotations.

    Science.gov (United States)

    Myshkin, Eugene; Brennan, Richard; Khasanova, Tatiana; Sitnik, Tatiana; Serebriyskaya, Tatiana; Litvinova, Elena; Guryanov, Alexey; Nikolsky, Yuri; Nikolskaya, Tatiana; Bureeva, Svetlana

    2012-09-01

    The ability to accurately predict the toxicity of drug candidates from their chemical structure is critical for guiding experimental drug discovery toward safer medicines. Under the guidance of the MetaTox consortium (Thomson Reuters, CA, USA), which comprised toxicologists from the pharmaceutical industry and government agencies, we created a comprehensive ontology of toxic pathologies for 19 organs, classifying pathology terms by pathology type and functional organ substructure. By manual annotation of full-text research articles, the ontology was populated with chemical compounds causing specific histopathologies. Annotated compound-toxicity associations defined histologically from rat and mouse experiments were used to build quantitative structure-activity relationship models predicting subcategories of liver and kidney toxicity: liver necrosis, liver relative weight gain, liver lipid accumulation, nephron injury, kidney relative weight gain, and kidney necrosis. All models were validated using two independent test sets and demonstrated overall good performance: initial validation showed 0.80-0.96 sensitivity (correctly predicted toxic compounds) and 0.85-1.00 specificity (correctly predicted non-toxic compounds). Later validation against a test set of compounds newly added to the database in the 2 years following initial model generation showed 75-87% sensitivity and 60-78% specificity. General hepatotoxicity and nephrotoxicity models were less accurate, as expected for more complex endpoints.

  15. 航拍胶片注释信息自动解译算法研究%Research on Automatic Interpretation Algorithm of Annotation Information in Aerial Photos

    Institute of Scientific and Technical Information of China (English)

    王志强; 程红; 梁勇; 吴迪

    2012-01-01

    In the annotation information of aerial photos exist the posture parameters of aircraft and working parameters of camera. Correct interpretation of the annotation information has an important role in image processing afterwards. In this paper, the process of annotation information in aerial photos is introduced,including location, threshold processing,character segmentation and interpretation,especially the processing of character threshold segmentation is researched, A threshold segmentation algorithm based on CASDA and Niblack is proposed. The automatic interpretation of annotation information in aerial photos is realized and the experiments show the algorithm is adaptable and operable.%航拍胶片注释信息记录着航拍过程中飞机的姿态参数及相机的工作参数,其正确解译对后期的图像处理尤为重要.本文介绍了航拍胶片注释信息解译的主要步骤,包括注释信息块的定位、阈值分割、标识符分割和标识符解译,重点研究了字符的阈值分割处理方法,提出了基于CASDA与Niblack相结合的阈值分割算法.实验表明,本文算法具有较好的可操作性和适应性,能够有效地对航拍胶片注释信息进行自动解译.

  16. Transformative Learning in Nonprofit Organizations: A Feminist Interpretive Inquiry

    Science.gov (United States)

    English, Leona M.; Peters, Nancy

    2012-01-01

    This article reports on interpretive research, influenced by a feminist theoretical framework, with 8 women, in their 20s to 60s, who work or volunteer in feminist nonprofit organizations. Particular emphasis is placed on their experience of transformative learning in these organizations; the linkages with the theory of transformative learning;…

  17. Organic chemical aging mechanisms: An annotated bibliography. Waste Tank Safety Program

    Energy Technology Data Exchange (ETDEWEB)

    Samuels, W.D.; Camaioni, D.M.; Nelson, D.A.

    1993-09-01

    An annotated bibliography has been compiled of the potential chemical and radiological aging mechanisms of the organic constituents (non-ferrocyanide) that would likely be found in the UST at Hanford. The majority of the work that has been conducted on the aging of organic chemicals used for extraction and processing of nuclear materials has been in conjunction with the acid or PUREX type processes. At Hanford the waste being stored in the UST has been stabilized with caustic. The aging factors that were used in this work were radiolysis, hydrolysis and nitrite/nitrate oxidation. The purpose of this work was two-fold: to determine whether or not research had been or is currently being conducted on the species associated with the Hanford UST waste, either as a mixture or as individual chemicals or chemical functionalities, and to determine what areas of chemical aging need to be addressed by further research.

  18. Thermal effects on aquatic organisms: an annotated bibliography of the 1977 literature

    Energy Technology Data Exchange (ETDEWEB)

    Talmage, S.S. (comp.)

    1978-12-01

    This bibliography, containing 537 references from the 1977 literature, is the seventh in a series of annotated bibliographies on the effects of heat on aquatic organisms. The effects of thermal discharges at power plant sites are emphasized. Laboratory and field studies on temperature tolerance and the effects of temperature changes on reproduction, development, growth, distribution, physiology, and sensitivity to other stresses are included. References in the bibliography are divided into three subject categories: marine systems, freshwater systems, and estuaries. The references are arranged alphabetically by first author. Indexes are provided for author, keywords, subject category, geographic location of the study, taxon, and title (alphabetical listing of keywords-in-context of nontrivial words in the title).

  19. Exploiting Semantic Annotations and Q-Learning for Constructing an Efficient Hierarchy/Graph Texts Organization

    Directory of Open Access Journals (Sweden)

    Asmaa M. El-Said

    2015-01-01

    Full Text Available Tremendous growth in the number of textual documents has produced daily requirements for effective development to explore, analyze, and discover knowledge from these textual documents. Conventional text mining and managing systems mainly use the presence or absence of key words to discover and analyze useful information from textual documents. However, simple word counts and frequency distributions of term appearances do not capture the meaning behind the words, which results in limiting the ability to mine the texts. This paper proposes an efficient methodology for constructing hierarchy/graph-based texts organization and representation scheme based on semantic annotation and Q-learning. This methodology is based on semantic notions to represent the text in documents, to infer unknown dependencies and relationships among concepts in a text, to measure the relatedness between text documents, and to apply mining processes using the representation and the relatedness measure. The representation scheme reflects the existing relationships among concepts and facilitates accurate relatedness measurements that result in a better mining performance. An extensive experimental evaluation is conducted on real datasets from various domains, indicating the importance of the proposed approach.

  20. Exploiting semantic annotations and Q-learning for constructing an efficient hierarchy/graph texts organization.

    Science.gov (United States)

    El-Said, Asmaa M; Eldesoky, Ali I; Arafat, Hesham A

    2015-01-01

    Tremendous growth in the number of textual documents has produced daily requirements for effective development to explore, analyze, and discover knowledge from these textual documents. Conventional text mining and managing systems mainly use the presence or absence of key words to discover and analyze useful information from textual documents. However, simple word counts and frequency distributions of term appearances do not capture the meaning behind the words, which results in limiting the ability to mine the texts. This paper proposes an efficient methodology for constructing hierarchy/graph-based texts organization and representation scheme based on semantic annotation and Q-learning. This methodology is based on semantic notions to represent the text in documents, to infer unknown dependencies and relationships among concepts in a text, to measure the relatedness between text documents, and to apply mining processes using the representation and the relatedness measure. The representation scheme reflects the existing relationships among concepts and facilitates accurate relatedness measurements that result in a better mining performance. An extensive experimental evaluation is conducted on real datasets from various domains, indicating the importance of the proposed approach.

  1. 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.

  2. ORGANIZING SCENARIO VARIABLES BY APPLYING THE INTERPRETATIVE STRUCTURAL MODELING (ISM

    Directory of Open Access Journals (Sweden)

    Daniel Estima de Carvalho

    2009-10-01

    Full Text Available The scenario building method is a thought mode - taken to effect in an optimized, strategic manner - based on trends and uncertain events, concerning a large variety of potential results that may impact the future of an organization.In this study, the objective is to contribute towards a possible improvement in Godet and Schoemaker´s scenario preparation methods, by employing the Interpretative Structural Modeling (ISM as a tool for the analysis of variables.Given this is an exploratory theme, bibliographical research with tool definition and analysis, examples extraction from literature and a comparison exercise of referred methods, were undertaken.It was verified that ISM may substitute or complement the original tools for the analysis of variables of scenarios per Godet and Schoemaker’s methods, given the fact that it enables an in-depth analysis of relations between variables in a shorter period of time, facilitating both structuring and construction of possible scenarios.Key-words: Strategy. Future studies. Interpretative Structural Modeling.

  3. 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 ...

  4. JAABA: interactive machine learning for automatic annotation of animal behavior

    OpenAIRE

    Kabra, Mayank; Robie, Alice A.; Rivera-Alba, Marta; Branson, Steven; Branson, Kristin

    2013-01-01

    We present a machine learning-based system for automatically computing interpretable, quantitative measures of animal behavior. Through our interactive system, users encode their intuition about behavior by annotating a small set of video frames. These manual labels are converted into classifiers that can automatically annotate behaviors in screen-scale data sets. Our general-purpose system can create a variety of accurate individual and social behavior classifiers for different organisms, in...

  5. Verification of the Chromosome Region 9q21 Association with Pelvic Organ Prolapse Using RegulomeDB Annotations

    Directory of Open Access Journals (Sweden)

    Maryam B. Khadzhieva

    2015-01-01

    Full Text Available Pelvic organ prolapse (POP is a common highly disabling disorder with a large hereditary component. It is characterized by a loss of pelvic floor support that leads to the herniation of the uterus in or outside the vagina. Genome-wide linkage studies have shown an evidence of POP association with the region 9q21 and six other loci in European pedigrees. The aim of our study was to test the above associations in a case-control study in Russian population. Twelve SNPs including SNPs cited in the above studies and those selected using the RegulomeDB annotations for the region 9q21 were genotyped in 210 patients with POP (stages III-IV and 292 controls with no even minimal POP. Genotyping was performed using the polymerase chain reaction with confronting two-pair primers (PCR–CTPP. Association analyses were conducted for individual SNPs, 9q21 haplotypes, and SNP-SNP interactions. SNP rs12237222 with the highest RegulomeDB score 1a appeared to be the key SNP in haplotypes associated with POP. Other RegulomeDB Category 1 SNPs, rs12551710 and rs2236479 (scores 1d and 1f, resp., exhibited epistatic effects. In this study, we verified the region 9q21 association with POP in Russians, using RegulomeDB annotations.

  6. 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

  7. 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...

  8. Thermal effects on aquatic organisms. Annotated bibliography of the 1975 literature

    International Nuclear Information System (INIS)

    Abstracts are presented of 716 papers published during 1975 concerning thermal effects on aquatic organisms. Indexes are included for author, subject category, geographic location, toxon, title, and keywords

  9. 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

  10. Thermal effects on aquatic organisms. Annotated bibliography of the 1975 literature

    Energy Technology Data Exchange (ETDEWEB)

    Coutant, C.C.; Talmage, S.S.; Carrier, R.F.; Collier, B.N.; Dailey, N.S. (comps.)

    1976-10-01

    Abstracts are presented of 716 papers published during 1975 concerning thermal effects on aquatic organisms. Indexes are included for author, subject category, geographic location, toxon, title, and keywords. (CH)

  11. 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.

  12. Human Genome Annotation

    Science.gov (United States)

    Gerstein, Mark

    A central problem for 21st century science is annotating the human genome and making this annotation useful for the interpretation of personal genomes. My talk will focus on annotating the 99% of the genome that does not code for canonical genes, concentrating on intergenic features such as structural variants (SVs), pseudogenes (protein fossils), binding sites, and novel transcribed RNAs (ncRNAs). In particular, I will describe how we identify regulatory sites and variable blocks (SVs) based on processing next-generation sequencing experiments. I will further explain how we cluster together groups of sites to create larger annotations. Next, I will discuss a comprehensive pseudogene identification pipeline, which has enabled us to identify >10K pseudogenes in the genome and analyze their distribution with respect to age, protein family, and chromosomal location. Throughout, I will try to introduce some of the computational algorithms and approaches that are required for genome annotation. Much of this work has been carried out in the framework of the ENCODE, modENCODE, and 1000 genomes projects.

  13. Raman spectroscopy: Caution when interpreting organic carbon from oxidising environments

    Science.gov (United States)

    Brolly, Connor; Parnell, John; Bowden, Stephen

    2016-02-01

    Oxidation on Mars is primarily caused by the high influx of cosmic and solar radiation which interacts with the Martian surface. The evidence of this can be seen in the ubiquitous red colouration of the Martian sediment. This radiation will destroy most signals of life in the top few metres of the Martian surface. If organic carbon (one of the building blocks of life) is present within the accessible Martian sediments, it is very likely that it will have experienced some oxidation. ESA's ExoMars mission set to fly in 2018, has on board a miniaturised Raman spectrometer. As Raman spectroscopy is sensitive to carbonaceous material and will be primarily used to characterise organics, it is essential that the effect oxidation has on the Raman carbon signal is assessed. Oxidised carbonaceous shales were analysed using Raman spectroscopy to assess this issue. Results show that haematite has a band which occurs in the same frequency as the carbon D band, which cannot be distinguished from each other. This can lead to a misidentification of the carbon D band and a misinterpretation of the carbon order. Consequently, caution must be taken when applying Raman spectroscopy for organic carbon analysis in oxidised terrestrial and extraterrestrial environments, including on Mars.

  14. 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.

  15. Genomic organization, annotation, and ligand-receptor inferences of chicken chemokines and chemokine receptor genes based on comparative genomics

    Directory of Open Access Journals (Sweden)

    Sze Sing-Hoi

    2005-03-01

    Full Text Available Abstract Background Chemokines and their receptors play important roles in host defense, organogenesis, hematopoiesis, and neuronal communication. Forty-two chemokines and 19 cognate receptors have been found in the human genome. Prior to this report, only 11 chicken chemokines and 7 receptors had been reported. The objectives of this study were to systematically identify chicken chemokines and their cognate receptor genes in the chicken genome and to annotate these genes and ligand-receptor binding by a comparative genomics approach. Results Twenty-three chemokine and 14 chemokine receptor genes were identified in the chicken genome. All of the chicken chemokines contained a conserved CC, CXC, CX3C, or XC motif, whereas all the chemokine receptors had seven conserved transmembrane helices, four extracellular domains with a conserved cysteine, and a conserved DRYLAIV sequence in the second intracellular domain. The number of coding exons in these genes and the syntenies are highly conserved between human, mouse, and chicken although the amino acid sequence homologies are generally low between mammalian and chicken chemokines. Chicken genes were named with the systematic nomenclature used in humans and mice based on phylogeny, synteny, and sequence homology. Conclusion The independent nomenclature of chicken chemokines and chemokine receptors suggests that the chicken may have ligand-receptor pairings similar to mammals. All identified chicken chemokines and their cognate receptors were identified in the chicken genome except CCR9, whose ligand was not identified in this study. The organization of these genes suggests that there were a substantial number of these genes present before divergence between aves and mammals and more gene duplications of CC, CXC, CCR, and CXCR subfamilies in mammals than in aves after the divergence.

  16. Optimization of de novo transcriptome assembly from high-throughput short read sequencing data improves functional annotation for non-model organisms

    Directory of Open Access Journals (Sweden)

    Haznedaroglu Berat Z

    2012-07-01

    Full Text Available Abstract Background The k-mer hash length is a key factor affecting the output of de novo transcriptome assembly packages using de Bruijn graph algorithms. Assemblies constructed with varying single k-mer choices might result in the loss of unique contiguous sequences (contigs and relevant biological information. A common solution to this problem is the clustering of single k-mer assemblies. Even though annotation is one of the primary goals of a transcriptome assembly, the success of assembly strategies does not consider the impact of k-mer selection on the annotation output. This study provides an in-depth k-mer selection analysis that is focused on the degree of functional annotation achieved for a non-model organism where no reference genome information is available. Individual k-mers and clustered assemblies (CA were considered using three representative software packages. Pair-wise comparison analyses (between individual k-mers and CAs were produced to reveal missing Kyoto Encyclopedia of Genes and Genomes (KEGG ortholog identifiers (KOIs, and to determine a strategy that maximizes the recovery of biological information in a de novo transcriptome assembly. Results Analyses of single k-mer assemblies resulted in the generation of various quantities of contigs and functional annotations within the selection window of k-mers (k-19 to k-63. For each k-mer in this window, generated assemblies contained certain unique contigs and KOIs that were not present in the other k-mer assemblies. Producing a non-redundant CA of k-mers 19 to 63 resulted in a more complete functional annotation than any single k-mer assembly. However, a fraction of unique annotations remained (~0.19 to 0.27% of total KOIs in the assemblies of individual k-mers (k-19 to k-63 that were not present in the non-redundant CA. A workflow to recover these unique annotations is presented. Conclusions This study demonstrated that different k-mer choices result in various quantities

  17. 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 ...

  18. KONEVİ’S ANNOTATION OF HAFIZ DIVAN AND HIS SUFIC INTERPRETATION KONEVÎ’NİN HÂFIZ DİVANI ŞERHİ VE TASAVVUFÎ YORUMU ÜZERİNE BAZI DÜŞÜNCELER

    Directory of Open Access Journals (Sweden)

    İbrahim KAYA

    2011-01-01

    Full Text Available Hâfız whose nickname is lisanu’l-gayb has been beloved, approved and memorized by a large mass of people in a wide geographic area. Annotations were written in Persian for Persians and they were also written in Turkish for Turks who don’t know Persian. The writers who wrote the annotations of whole Hâfız Divan in Turkish are limited. The annotations are written by Sururî, Şem’î, Sûdî and Konevî. These authors except Konevî lived nearly in the same period. Şem’î and Sûdî met each other. Konevî lived two centuries later than above authors. The annotations of Sürûrî, Şem’î and Konevî drew attention especially in terms sufic interpretation. In this article some introductory information about Konevî’s annotation which was criticised because of its extreme sufic interpretation will be given. Then the meanings of the text that Konevî gave will be classified from different point of view and these meanings will be compared with the meanings that Sûdî and Gölpınarlı gave. Lisanü’l-gayb lakabıyla anılan Hâfız’ın şiirleri olduça geniş bir coğrafyada geniş bir kitle tarafından sevilmiş, beğenilmiş ve ezberlenmişir. Farsça bilenlerin bu şiirleri daha iyi anlamaları için şerhler yazıldığı gibi Farsça bilmeyenler için de Türkçe şerhler yazılmıştır. Hâfız Divanı’nın tamamına Türkçe şerh yazan kişiler sınırlıdır. Bunlar Sürûrî, Şem’î, Sûdî ve Konevî’dir. Konevî’nin dışındakiler birbirine oldukça yakın bir zaman diliminde yaşamışlardır. Şem’î ile Sûdî birbirleriyle görüşmüşlerdir. Konevî bunlardan iki yüzyıl sonra yaşamıştır. Sürûrî, Şem’î ve Konevî şerhleri tasavvufî yorumların ön plana çıktığı şerhlerdir. Makalede bu şerhlerin içinde tasavvufî yorumlarındaki aşırılık ile eleştiri konusu olan Konevî şerhi hakkında bazı tanıtıcı bilgiler verdikten sonra onun metne verdiği anlamlar değişik a

  19. 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

  20. Bioinformatics for plant genome annotation

    NARCIS (Netherlands)

    Fiers, M.W.E.J.

    2006-01-01

    Large amounts of genome sequence data are available and much more will become available in the near future. A DNA sequence alone has, however, limited use. Genome annotation is required to assign biological interpretation to the DNA sequence. This thesis describ

  1. 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

  2. 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/.

  3. Menzerath-Altmann Law: Statistical Mechanical Interpretation as Applied to a Linguistic Organization

    Science.gov (United States)

    Eroglu, Sertac

    2014-10-01

    The distribution behavior described by the empirical Menzerath-Altmann law is frequently encountered during the self-organization of linguistic and non-linguistic natural organizations at various structural levels. This study presents a statistical mechanical derivation of the law based on the analogy between the classical particles of a statistical mechanical organization and the distinct words of a textual organization. The derived model, a transformed (generalized) form of the Menzerath-Altmann model, was termed as the statistical mechanical Menzerath-Altmann model. The derived model allows interpreting the model parameters in terms of physical concepts. We also propose that many organizations presenting the Menzerath-Altmann law behavior, whether linguistic or not, can be methodically examined by the transformed distribution model through the properly defined structure-dependent parameter and the energy associated states.

  4. Towards a Library of Standard Operating Procedures (SOPs) for (meta)genomic annotation

    Energy Technology Data Exchange (ETDEWEB)

    Kyrpides, Nikos; Angiuoli, Samuel V.; Cochrane, Guy; Field, Dawn; Garrity, George; Gussman, Aaron; Kodira, Chinnappa D.; Klimke, William; Kyrpides, Nikos; Madupu, Ramana; Markowitz, Victor; Tatusova, Tatiana; Thomson, Nick; White, Owen

    2008-04-01

    Genome annotations describe the features of genomes and accompany sequences in genome databases. The methodologies used to generate genome annotation are diverse and typically vary amongst groups. Descriptions of the annotation procedure are helpful in interpreting genome annotation data. Standard Operating Procedures (SOPs) for genome annotation describe the processes that generate genome annotations. Some groups are currently documenting procedures but standards are lacking for structure and content of annotation SOPs. In addition, there is no central repository to store and disseminate procedures and protocols for genome annotation. We highlight the importance of SOPs for genome annotation and endorse a central online repository of SOPs.

  5. Amino acid sequences of predicted proteins and their annotation for 95 organism species. - Gclust Server | LSDB Archive [Life Science Database Archive metadata

    Lifescience Database Archive (English)

    Full Text Available ID ID of a sequence Cluster ID ID of cluster. gclust_cluster is referenced. Annotation in original... database Annotation at the original website Species Species name Length Amino acid sequen

  6. Parameters of the Menzerath-Altmann law: Statistical mechanical interpretation as applied to a linguistic organization

    CERN Document Server

    Eroglu, Sertac

    2013-01-01

    The distribution behavior dictated by the Menzerath-Altmann (MA) law is frequently encountered in linguistic and natural organizations at various structural levels. The mathematical form of this empirical law comprises three fitting parameters whose values tend to be elusive, especially in inter-organizational studies. To allow interpretation of these parameters and better understand such distribution behavior, we present a statistical mechanical approach based on an analogy between the classical particles of a statistical mechanical organization and the number of distinct words in a textual organization. With this derivation, we achieve a transformed (generalized) form of the MA model, termed the statistical mechanical Menzerath-Altmann (SMMA) model. This novel transformed model consists of four parameters, one of which is a structure-dependent input parameter, and three of which are free-fitting parameters. Using distinct word data sets from two text corpora, we verified that the SMMA model describes the sa...

  7. The case for not interpreting unconscious mental life in consulting to organizations.

    Science.gov (United States)

    Zaleznik, A

    1995-11-01

    DESPITE differing theoretical orientations in psychoanalysis, there is general agreement that its distinctive feature among all therapies is its attempt to bring to consciousness mental conflict that is unconscious. Does this distinctive feature of psychoanalysis apply in organizational consultation? I argue that unlike clinical psychoanalysis, more harm than good occurs when consultants attempt to interpret unconscious material to clients in organizations. The main use of psychoanalytic psychology in consulting work is for observation and understanding on the part of the consultant, who as an advisor presents recommendations aimed at enhancing rationality. PMID:8746493

  8. 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.

  9. Interpretation of organic components from positive matrix factorization of aerosol mass spectrometric data

    Directory of Open Access Journals (Sweden)

    I. M. Ulbrich

    2008-04-01

    Full Text Available The organic aerosol (OA dataset from an Aerodyne Aerosol Mass Spectrometer (Q-AMS collected at the Pittsburgh Air Quality Study in September 2002 was analyzed for components with Positive Matrix Factorization (PMF. Three components – hydrocarbon-like organic aerosol OA (HOA, a highly-oxygenated OA (OOA-I that correlates well with sulfate, and a less-oxygenated, semi-volatile OA (OOA-II that correlates well with nitrate and chloride – are identified and interpreted as primary combustion emissions, aged SOA, and semivolatile, less aged SOA, respectively. The complexity of interpreting the PMF solutions of unit mass resolution (UMR AMS data is illustrated by a detailed analysis of the solutions as a function of number of components and rotational state. A public database of AMS spectra has been created to aid this type of analysis. A sensitivity analysis with realistic synthetic data is also used to characterize the behavior of PMF for choosing the best number of factors, rotations of non-unique solutions, and the retrievability of more (or less correlated factors. The ambient and synthetic data indicate that the variation of the PMF quality of fit parameter (Q, a normalized chi-squared metric vs. number of factors in the solution is useful to identify the minimum number of factors, but more detailed analysis and interpretation is needed to choose the best number of factors. The maximum value of the rotational matrix is not useful for determining the best number of factors. In synthetic datasets, factors are "split" into two or more components when solving for more factors than were used in the input. Elements of the "splitting" behavior are observed in solutions of real datasets with several factors. Significant structure remains in the residual of the real dataset after physically-meaningful factors have been assigned and an unrealistic number of factors would be required to explain the remaining variance. This residual structure appears to

  10. Corpus annotation for mining biomedical events from literature

    Directory of Open Access Journals (Sweden)

    Tsujii Jun'ichi

    2008-01-01

    Full Text Available Abstract Background Advanced Text Mining (TM such as semantic enrichment of papers, event or relation extraction, and intelligent Question Answering have increasingly attracted attention in the bio-medical domain. For such attempts to succeed, text annotation from the biological point of view is indispensable. However, due to the complexity of the task, semantic annotation has never been tried on a large scale, apart from relatively simple term annotation. Results We have completed a new type of semantic annotation, event annotation, which is an addition to the existing annotations in the GENIA corpus. The corpus has already been annotated with POS (Parts of Speech, syntactic trees, terms, etc. The new annotation was made on half of the GENIA corpus, consisting of 1,000 Medline abstracts. It contains 9,372 sentences in which 36,114 events are identified. The major challenges during event annotation were (1 to design a scheme of annotation which meets specific requirements of text annotation, (2 to achieve biology-oriented annotation which reflect biologists' interpretation of text, and (3 to ensure the homogeneity of annotation quality across annotators. To meet these challenges, we introduced new concepts such as Single-facet Annotation and Semantic Typing, which have collectively contributed to successful completion of a large scale annotation. Conclusion The resulting event-annotated corpus is the largest and one of the best in quality among similar annotation efforts. We expect it to become a valuable resource for NLP (Natural Language Processing-based TM in the bio-medical domain.

  11. Cost-effectiveness analysis of computerized ECG interpretation system in an ambulatory health care organization.

    Science.gov (United States)

    Carel, R S

    1982-04-01

    The cost-effectiveness of a computerized ECG interpretation system in an ambulatory health care organization has been evaluated in comparison with a conventional (manual) system. The automated system was shown to be more cost-effective at a minimum load of 2,500 patients/month. At larger monthly loads an even greater cost-effectiveness was found, the average cost/ECG being about $2. In the manual system the cost/unit is practically independent of patient load. This is primarily due to the fact that 87% of the cost/ECG is attributable to wages and fees of highly trained personnel. In the automated system, on the other hand, the cost/ECG is heavily dependent on examinee load. This is due to the relatively large impact of equipment depreciation on fixed (and total) cost. Utilization of a computer-assisted system leads to marked reduction in cardiologists' interpretation time, substantially shorter turnaround time (of unconfirmed reports), and potential provision of simultaneous service at several remotely located "heart stations."

  12. Challenges for biological interpretation of environmental proteomics data in non-model organisms.

    Science.gov (United States)

    Dowd, W Wesley

    2012-11-01

    Environmental physiology, toxicology, and ecology and evolution stand to benefit substantially from the relatively recent surge of "omics" technologies into these fields. These approaches, and proteomics in particular, promise to elucidate novel and integrative functional responses of organisms to diverse environmental challenges, over a variety of time scales and at different levels of organization. However, application of proteomics to environmental questions suffers from several challenges--some unique to high-throughput technologies and some relevant to many related fields--that may confound downstream biological interpretation of the data. I explore three of these challenges in environmental proteomics, emphasizing the dependence of biological conclusions on (1) the specific experimental context, (2) the choice of statistical analytical methods, and (3) the degree of proteome coverage and protein identification rates, both of which tend to be much less than 100% (i.e., analytical incompleteness). I use both a review of recent publications and data generated from my previous and ongoing proteomics studies of coastal marine animals to examine the causes and consequences of these challenges, in one case analyzing the same multivariate proteomics data set using 29 different combinations of statistical techniques common in the literature. Although some of the identified issues await further critical assessment and debate, when possible I offer suggestions for meeting these three challenges.

  13. 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 ...

  14. 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.

  15. 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

  16. 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/

  17. 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.

  18. Collaborative annotation of 3D crystallographic models.

    Science.gov (United States)

    Hunter, J; Henderson, M; Khan, I

    2007-01-01

    This paper describes the AnnoCryst system-a tool that was designed to enable authenticated collaborators to share online discussions about 3D crystallographic structures through the asynchronous attachment, storage, and retrieval of annotations. Annotations are personal comments, interpretations, questions, assessments, or references that can be attached to files, data, digital objects, or Web pages. The AnnoCryst system enables annotations to be attached to 3D crystallographic models retrieved from either private local repositories (e.g., Fedora) or public online databases (e.g., Protein Data Bank or Inorganic Crystal Structure Database) via a Web browser. The system uses the Jmol plugin for viewing and manipulating the 3D crystal structures but extends Jmol by providing an additional interface through which annotations can be created, attached, stored, searched, browsed, and retrieved. The annotations are stored on a standardized Web annotation server (Annotea), which has been extended to support 3D macromolecular structures. Finally, the system is embedded within a security framework that is capable of authenticating users and restricting access only to trusted colleagues.

  19. Annotation for information extraction from mammography reports.

    Science.gov (United States)

    Bozkurt, Selen; Gulkesen, Kemal Hakan; Rubin, Daniel

    2013-01-01

    Inter and intra-observer variability in mammographic interpretation is a challenging problem, and decision support systems (DSS) may be helpful to reduce variation in practice. Since radiology reports are created as unstructured text reports, Natural language processing (NLP) techniques are needed to extract structured information from reports in order to provide the inputs to DSS. Before creating NLP systems, producing high quality annotated data set is essential. The goal of this project is to develop an annotation schema to guide the information extraction tasks needed from free-text mammography reports. PMID:23823416

  20. 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.

  1. 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 ...

  2. 78 FR 30245 - Electric Reliability Organization Interpretation of Specific Requirements of the Disturbance...

    Science.gov (United States)

    2013-05-22

    ... 7, 2012, the NERC BOT adopted the proposed interpretation of BAL-002-1. \\16\\ Id. 12. In its Petition... Environmental Policy Act, Order No. 486, 52 FR 47897 (Dec. 17, 1987), FERC Stats. & Regs. Regulations Preambles... to make a paper filing. 30. Commenters that are not able to file comments electronically must send...

  3. 75 FR 80391 - Electric Reliability Organization Interpretations of Interconnection Reliability Operations and...

    Science.gov (United States)

    2010-12-22

    ... interpretation fails to specify that a Special Protection System that has lost a communication channel be... such that electric system faults will be cleared, even if a component of the Protection System fails... Protection System. Should a communication channel fail at the time the Special Protection System is...

  4. An Introduction to Genome Annotation.

    Science.gov (United States)

    Campbell, Michael S; Yandell, Mark

    2015-12-17

    Genome projects have evolved from large international undertakings to tractable endeavors for a single lab. Accurate genome annotation is critical for successful genomic, genetic, and molecular biology experiments. These annotations can be generated using a number of approaches and available software tools. This unit describes methods for genome annotation and a number of software tools commonly used in gene annotation.

  5. Linking DICOM pixel data with radiology reports using automatic semantic annotation

    Science.gov (United States)

    Pathak, Sayan D.; Kim, Woojin; Munasinghe, Indeera; Criminisi, Antonio; White, Steve; Siddiqui, Khan

    2012-02-01

    Improved access to DICOM studies to both physicians and patients is changing the ways medical imaging studies are visualized and interpreted beyond the confines of radiologists' PACS workstations. While radiologists are trained for viewing and image interpretation, a non-radiologist physician relies on the radiologists' reports. Consequently, patients historically have been typically informed about their imaging findings via oral communication with their physicians, even though clinical studies have shown that patients respond to physician's advice significantly better when the individual patients are shown their own actual data. Our previous work on automated semantic annotation of DICOM Computed Tomography (CT) images allows us to further link radiology report with the corresponding images, enabling us to bridge the gap between image data with the human interpreted textual description of the corresponding imaging studies. The mapping of radiology text is facilitated by natural language processing (NLP) based search application. When combined with our automated semantic annotation of images, it enables navigation in large DICOM studies by clicking hyperlinked text in the radiology reports. An added advantage of using semantic annotation is the ability to render the organs to their default window level setting thus eliminating another barrier to image sharing and distribution. We believe such approaches would potentially enable the consumer to have access to their imaging data and navigate them in an informed manner.

  6. Genome Annotation Transfer Utility (GATU: rapid annotation of viral genomes using a closely related reference genome

    Directory of Open Access Journals (Sweden)

    Upton Chris

    2006-06-01

    Full Text Available Abstract Background Since DNA sequencing has become easier and cheaper, an increasing number of closely related viral genomes have been sequenced. However, many of these have been deposited in GenBank without annotations, severely limiting their value to researchers. While maintaining comprehensive genomic databases for a set of virus families at the Viral Bioinformatics Resource Center http://www.biovirus.org and Viral Bioinformatics – Canada http://www.virology.ca, we found that researchers were unnecessarily spending time annotating viral genomes that were close relatives of already annotated viruses. We have therefore designed and implemented a novel tool, Genome Annotation Transfer Utility (GATU, to transfer annotations from a previously annotated reference genome to a new target genome, thereby greatly reducing this laborious task. Results GATU transfers annotations from a reference genome to a closely related target genome, while still giving the user final control over which annotations should be included. GATU also detects open reading frames present in the target but not the reference genome and provides the user with a variety of bioinformatics tools to quickly determine if these ORFs should also be included in the annotation. After this process is complete, GATU saves the newly annotated genome as a GenBank, EMBL or XML-format file. The software is coded in Java and runs on a variety of computer platforms. Its user-friendly Graphical User Interface is specifically designed for users trained in the biological sciences. Conclusion GATU greatly simplifies the initial stages of genome annotation by using a closely related genome as a reference. It is not intended to be a gene prediction tool or a "complete" annotation system, but we have found that it significantly reduces the time required for annotation of genes and mature peptides as well as helping to standardize gene names between related organisms by transferring reference genome

  7. 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...

  8. 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.

  9. 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.

  10. Deliberative Engagement within the World Trade Organization: A Functional Substitute for Authoritative Interpretations

    DEFF Research Database (Denmark)

    Creamer, Cosette; Godzimirska, Zuzanna

    The transition from the General Agreement on Tariffs and Trade dispute settlement proceedings to the Dispute Settlement Mechanism (DSM) of the World Trade Organization represented a notable instance of judicialization within international economic governance, in that it significantly increased th...

  11. The Future of Organization Design: An Interpretative Synthesis in Three Themes

    Directory of Open Access Journals (Sweden)

    Richard M. Burton

    2013-04-01

    Full Text Available In the inaugural issue of the Journal of Organization Design (Vol. 1, #1, 2012, noted scholars and experienced practitioners presented their views on the future of organization design. The seven wise and provocative statements were subsequently discussed by members of the Organizational Design Community at a conference held at Harvard University on August 3, 2012. I was asked by JOD to monitor the discussion and identify the broad organization design themes that emerged. Although the discussion was wide ranging, three themes were noticeable. The first theme is that there are fundamentals of organization design, and all agreed that design involves creating a cohesive socio-technical system from a number of constituent elements. The second theme is that the boundaries of many newer organizational forms extend beyond that of the single firm, so the scope of organization design needs to expand to include ecosystems, collaborative communities, industries, and other supra-firm architectures. The third theme involves time and change, requiring a shift in focus from how organizations become stable and predictable to how they can become more agile.

  12. 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.…

  13. Deliberative Engagement within the World Trade Organization: A Functional Substitute for Authoritative Interpretations

    DEFF Research Database (Denmark)

    Creamer, Cosette; Godzimirska, Zuzanna

    2016-01-01

    The transition from the General Agreement on Tariffs and Trade (GATT) dispute settlement proceedings to the Dispute Settlement Mechanism (DSM) of the World Trade Organization (WTO) represented a notable instance of judicialization within international economic governance. Since it began ruling on...

  14. Understanding Information Security Culture in an Organization: An Interpretive Case Study

    Science.gov (United States)

    Bess, Donald Arlo

    2012-01-01

    Information systems are considered to be a critical and strategic part of most organizations today. Because of this it has become increasingly important to ensure that there is an effective information security program in place protecting those information systems. It has been well established by researchers that the success of an information…

  15. 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,…

  16. 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

  17. 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.

  18. 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...

  19. Intellectuals in China: Annotations.

    Science.gov (United States)

    Parker, Franklin

    This annotated bibliography of 72 books, journal articles, government reports, and newspaper feature stories focuses on the changing role of intellectuals in China, primarily since the 1949 Chinese Revolution. Particular attention is given to the Hundred Flowers Movement of 1957 and the Cultural Revolution. Most of the cited works are in English,…

  20. 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.…

  1. Annotation of Ehux ESTs

    Energy Technology Data Exchange (ETDEWEB)

    Kuo, Alan; Grigoriev, Igor

    2009-06-12

    22 percent ESTs do no align with scaffolds. EST Pipeleine assembles 17126 consensi from the noaligned ESTs. Annotation Pipeline predicts 8564 ORFS on the consensi. Domain analysis of ORFs reveals missing genes. Cluster analysis reveals missing genes. Expression analysis reveals potential strain specific genes.

  2. Molecular Paleohydrology: Interpreting the Hydrogen- Isotopic Composition of Lipid Biomarkers from Photosynthesizing Organisms

    OpenAIRE

    D. Sachse; Billault, I.; G. J. Bowen; CHIKARAISHI, Y.; Dawson, T E; Feakins, S.J.; Freeman, Katherine; Magill, C.R.; McInerney, F.A.; Meer, M.T.J. van der; Polissar, P.; Robins, R.J.; Sachs, J.P.; Schmidt, H.L.; Sessions, A.L.

    2012-01-01

    Hydrogen-isotopic abundances of lipid biomarkers are emerging as important proxies in the study of ancient environments and ecosystems. A decade ago, pioneering studies made use of new analytical methods and demonstrated that the hydrogen-isotopic composition of individual lipids from aquatic and terrestrial organisms can be related to the composition of their growth (i.e., environmental) water. Subsequently, compound-specific deuterium/hydrogen (D/H) ratios of sedimentary biomarkers have bee...

  3. 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

  4. 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

  5. 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).

  6. Effective function annotation through catalytic residue conservation.

    Science.gov (United States)

    George, Richard A; Spriggs, Ruth V; Bartlett, Gail J; Gutteridge, Alex; MacArthur, Malcolm W; Porter, Craig T; Al-Lazikani, Bissan; Thornton, Janet M; Swindells, Mark B

    2005-08-30

    Because of the extreme impact of genome sequencing projects, protein sequences without accompanying experimental data now dominate public databases. Homology searches, by providing an opportunity to transfer functional information between related proteins, have become the de facto way to address this. Although a single, well annotated, close relationship will often facilitate sufficient annotation, this situation is not always the case, particularly if mutations are present in important functional residues. When only distant relationships are available, the transfer of function information is more tenuous, and the likelihood of encountering several well annotated proteins with different functions is increased. The consequence for a researcher is a range of candidate functions with little way of knowing which, if any, are correct. Here, we address the problem directly by introducing a computational approach to accurately identify and segregate related proteins into those with a functional similarity and those where function differs. This approach should find a wide range of applications, including the interpretation of genomics/proteomics data and the prioritization of targets for high-throughput structure determination. The method is generic, but here we concentrate on enzymes and apply high-quality catalytic site data. In addition to providing a series of comprehensive benchmarks to show the overall performance of our approach, we illustrate its utility with specific examples that include the correct identification of haptoglobin as a nonenzymatic relative of trypsin, discrimination of acid-d-amino acid ligases from a much larger ligase pool, and the successful annotation of BioH, a structural genomics target.

  7. Detecting and interpreting distortions in hierarchical organization of complex time series

    CERN Document Server

    Drożdż, Stanisław

    2015-01-01

    Hierarchical organization is a cornerstone of complexity and multifractality constitutes its central quantifying concept. For model uniform cascades the corresponding singularity spectra are symmetric while those extracted from empirical data are often asymmetric. Using the selected time series representing such diverse phenomena like price changes and inter-transaction times in the financial markets, sentence length variability in the narrative texts, Missouri River discharge and Sunspot Number variability as examples, we show that the resulting singularity spectra appear strongly asymmetric, more often left-sided but in some cases also right-sided. We present a unified view on the origin of such effects and indicate that they may be crucially informative for identifying composition of the time series. One particularly intriguing case of this later kind of asymmetry is detected in the daily reported Sunspot Number variability. This signals that either the commonly used famous Wolf formula distorts the real d...

  8. The arbitration-extension hypothesis: a hierarchical interpretation of the functional organization of the basal ganglia

    Directory of Open Access Journals (Sweden)

    Iman eKamali Sarvestani

    2011-03-01

    Full Text Available Based on known anatomy and physiology, we present a hypothesis where the basal gangliamotor loop is hierarchically organized in two main subsystems: the arbitration system andthe extension system. The arbitration system, comprised of the subthalamic nucleus, globuspallidus, and pedunculopontine nucleus, serves the role of selecting one out of several candidateactions as they are ascending from various brain stem motor regions and aggregated in thecentromedian thalamus or descending from the extension system or from the cerebral cortex.This system is an action-input/action-output system whose winner-take-all mechanism findsthe strongest response among several candidates to execute. This decision is communicatedback to the brain stem by facilitating the desired action via cholinergic/glutamatergic projectionsand suppressing conflicting alternatives via GABAergic connections. The extension system,comprised of the striatum and, again, globus pallidus, can extend the repertoire of responsesby learning to associate novel complex states to certain actions. This system is a state-input/action-output system, whose organization enables it to encode arbitrarily complex Booleanlogic rules using striatal neurons that only fire given specific constellations of inputs (BooleanAND and pallidal neurons that are silenced by any striatal input (Boolean OR. We demonstratethe capabilities of this hierarchical system by a computational model where a simulatedgeneric animal interacts with an environment by selecting direction of movement basedon combinations of sensory stimuli, some being appetitive, others aversive or neutral. Whilethe arbitration system can autonomously handle conflicting actions proposed by brain stemmotor nuclei, the extension system is required to execute learned actions not suggested byexternal motor centers. Being precise in the functional role of each component of the system,this hypothesis generates several readily testable predictions.

  9. 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...

  10. 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 ...

  11. 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/.

  12. 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

  13. Transcriptator: An Automated Computational Pipeline to Annotate Assembled Reads and Identify Non Coding RNA.

    Directory of Open Access Journals (Sweden)

    Kumar Parijat Tripathi

    Full Text Available RNA-seq is a new tool to measure RNA transcript counts, using high-throughput sequencing at an extraordinary accuracy. It provides quantitative means to explore the transcriptome of an organism of interest. However, interpreting this extremely large data into biological knowledge is a problem, and biologist-friendly tools are lacking. In our lab, we developed Transcriptator, a web application based on a computational Python pipeline with a user-friendly Java interface. This pipeline uses the web services available for BLAST (Basis Local Search Alignment Tool, QuickGO and DAVID (Database for Annotation, Visualization and Integrated Discovery tools. It offers a report on statistical analysis of functional and Gene Ontology (GO annotation's enrichment. It helps users to identify enriched biological themes, particularly GO terms, pathways, domains, gene/proteins features and protein-protein interactions related informations. It clusters the transcripts based on functional annotations and generates a tabular report for functional and gene ontology annotations for each submitted transcript to the web server. The implementation of QuickGo web-services in our pipeline enable the users to carry out GO-Slim analysis, whereas the integration of PORTRAIT (Prediction of transcriptomic non coding RNA (ncRNA by ab initio methods helps to identify the non coding RNAs and their regulatory role in transcriptome. In summary, Transcriptator is a useful software for both NGS and array data. It helps the users to characterize the de-novo assembled reads, obtained from NGS experiments for non-referenced organisms, while it also performs the functional enrichment analysis of differentially expressed transcripts/genes for both RNA-seq and micro-array experiments. It generates easy to read tables and interactive charts for better understanding of the data. The pipeline is modular in nature, and provides an opportunity to add new plugins in the future. Web application is

  14. Laboratory Experiments and Modeling for Interpreting Field Studies of Secondary Organic Aerosol Formation Using an Oxidation Flow Reactor

    Energy Technology Data Exchange (ETDEWEB)

    Jimenez, Jose-Luis [Univ. of Colorado, Boulder, CO (United States)

    2016-02-01

    This grant was originally funded for deployment of a suite of aerosol instrumentation by our group in collaboration with other research groups and DOE/ARM to the Ganges Valley in India (GVAX) to study aerosols sources and processing. Much of the first year of this grant was focused on preparations for GVAX. That campaign was cancelled due to political reasons and with the consultation with our program manager, the research of this grant was refocused to study the applications of oxidation flow reactors (OFRs) for investigating secondary organic aerosol (SOA) formation and organic aerosol (OA) processing in the field and laboratory through a series of laboratory and modeling studies. We developed a gas-phase photochemical model of an OFR which was used to 1) explore the sensitivities of key output variables (e.g., OH exposure, O3, HO2/OH) to controlling factors (e.g., water vapor, external reactivity, UV irradiation), 2) develop simplified OH exposure estimation equations, 3) investigate under what conditions non-OH chemistry may be important, and 4) help guide design of future experiments to avoid conditions with undesired chemistry for a wide range of conditions applicable to the ambient, laboratory, and source studies. Uncertainties in the model were quantified and modeled OH exposure was compared to tracer decay measurements of OH exposure in the lab and field. Laboratory studies using OFRs were conducted to explore aerosol yields and composition from anthropogenic and biogenic VOC as well as crude oil evaporates. Various aspects of the modeling and laboratory results and tools were applied to interpretation of ambient and source measurements using OFR. Additionally, novel measurement methods were used to study gas/particle partitioning. The research conducted was highly successful and details of the key results are summarized in this report through narrative text, figures, and a complete list of publications acknowledging this grant.

  15. The Performance Career of Charles Dickens: An Annotated Bibliography.

    Science.gov (United States)

    Gentile, John Samuel

    Offered in response to the broad appeal of Charles Dickens's performance career to various disciplines, this annotated bibliography lists 40 resources concerned with Dickens's success as a performer interpreting his literary works. The resources are categorized under books, theses and dissertations, articles in scholarly journals, nineteenth…

  16. Fluorescence quantum yields of natural organic matter and organic compounds: Implications for the fluorescence-based interpretation of organic matter composition

    DEFF Research Database (Denmark)

    Wünsch, Urban; Murphy, Kathleen R.; Stedmon, Colin

    2015-01-01

    to more than 200 modeled spectra (PARAFAC components) in the OpenFluor database. Apparent matches, based on spectral similarity, were subsequently evaluated using molar fluorescence and absorbance. Five organic compounds were potential matches with PARAFAC components from 16 studies; however, the ability...

  17. MetaStorm: A Public Resource for Customizable Metagenomics Annotation.

    Science.gov (United States)

    Arango-Argoty, Gustavo; Singh, Gargi; Heath, Lenwood S; Pruden, Amy; Xiao, Weidong; Zhang, Liqing

    2016-01-01

    Metagenomics is a trending research area, calling for the need to analyze large quantities of data generated from next generation DNA sequencing technologies. The need to store, retrieve, analyze, share, and visualize such data challenges current online computational systems. Interpretation and annotation of specific information is especially a challenge for metagenomic data sets derived from environmental samples, because current annotation systems only offer broad classification of microbial diversity and function. Moreover, existing resources are not configured to readily address common questions relevant to environmental systems. Here we developed a new online user-friendly metagenomic analysis server called MetaStorm (http://bench.cs.vt.edu/MetaStorm/), which facilitates customization of computational analysis for metagenomic data sets. Users can upload their own reference databases to tailor the metagenomics annotation to focus on various taxonomic and functional gene markers of interest. MetaStorm offers two major analysis pipelines: an assembly-based annotation pipeline and the standard read annotation pipeline used by existing web servers. These pipelines can be selected individually or together. Overall, MetaStorm provides enhanced interactive visualization to allow researchers to explore and manipulate taxonomy and functional annotation at various levels of resolution. PMID:27632579

  18. MetaStorm: A Public Resource for Customizable Metagenomics Annotation

    Science.gov (United States)

    Arango-Argoty, Gustavo; Singh, Gargi; Heath, Lenwood S.; Pruden, Amy; Xiao, Weidong; Zhang, Liqing

    2016-01-01

    Metagenomics is a trending research area, calling for the need to analyze large quantities of data generated from next generation DNA sequencing technologies. The need to store, retrieve, analyze, share, and visualize such data challenges current online computational systems. Interpretation and annotation of specific information is especially a challenge for metagenomic data sets derived from environmental samples, because current annotation systems only offer broad classification of microbial diversity and function. Moreover, existing resources are not configured to readily address common questions relevant to environmental systems. Here we developed a new online user-friendly metagenomic analysis server called MetaStorm (http://bench.cs.vt.edu/MetaStorm/), which facilitates customization of computational analysis for metagenomic data sets. Users can upload their own reference databases to tailor the metagenomics annotation to focus on various taxonomic and functional gene markers of interest. MetaStorm offers two major analysis pipelines: an assembly-based annotation pipeline and the standard read annotation pipeline used by existing web servers. These pipelines can be selected individually or together. Overall, MetaStorm provides enhanced interactive visualization to allow researchers to explore and manipulate taxonomy and functional annotation at various levels of resolution. PMID:27632579

  19. Semantic Based Image Annotation Using Descriptive Features and Retagging approach

    Directory of Open Access Journals (Sweden)

    P.Nagarani

    2012-02-01

    Full Text Available The Semantic based annotation of an image is very important and a difficult task in content-based image retrieval (CBIR. The low-level features of the images are described using color and the texture features and the proposed model is used for semantic annotation of images. Also the textual annotations or the tags with multimedia content are the most effective approaches to organize and to support search over digital images and multimedia databases. The quality of the tags was refined using Image retagging method. The process is given as a multi-path graph based problem, which in parallel identifies the visual content of the images, semantic correlation of the tags as well as the primary information provided by users. The image annotation preferred because as the countless images exist in our lives it is not possible to annotate them all by hand. And so annotation by computer is a potential and promising solution to this problem precisely. The ability to annotate images semantically based on the objects that they contain is essential in image retrieval as it provides the mechanism to take advantage of existing text retrieval system

  20. Semantic Based Image Annotation Using Descriptive Features and Retagging approach

    Directory of Open Access Journals (Sweden)

    P.Nagarani

    2012-03-01

    Full Text Available The Semantic based annotation of an image is very important and a difficult task in content-based image retrieval (CBIR. The low-level features of the images are described using color and the texture features and the proposed model is used for semantic annotation of images. Also the textual annotations or the tags with multimedia content are the most effective approaches to organize and to support search over digital images and multimedia databases. The quality of the tags was refined using Image retagging method. Theprocess is given as a multi-path graph based problem, which in parallel identifies the visual content of the images, semantic correlation of the tags as well as the primary information provided by users. The image annotation preferred because as the countless images exist in our lives it is not possible to annotate them all by hand. And so annotation by computer is a potential and promising solution to thisproblem precisely. The ability to annotate images semantically based on the objects that they contain is essential in image retrieval as it provides the mechanism to take advantage of existing text retrieval systems.

  1. Enriching a biomedical event corpus with meta-knowledge annotation

    Directory of Open Access Journals (Sweden)

    Thompson Paul

    2011-10-01

    Full Text Available Abstract Background Biomedical papers contain rich information about entities, facts and events of biological relevance. To discover these automatically, we use text mining techniques, which rely on annotated corpora for training. In order to extract protein-protein interactions, genotype-phenotype/gene-disease associations, etc., we rely on event corpora that are annotated with classified, structured representations of important facts and findings contained within text. These provide an important resource for the training of domain-specific information extraction (IE systems, to facilitate semantic-based searching of documents. Correct interpretation of these events is not possible without additional information, e.g., does an event describe a fact, a hypothesis, an experimental result or an analysis of results? How confident is the author about the validity of her analyses? These and other types of information, which we collectively term meta-knowledge, can be derived from the context of the event. Results We have designed an annotation scheme for meta-knowledge enrichment of biomedical event corpora. The scheme is multi-dimensional, in that each event is annotated for 5 different aspects of meta-knowledge that can be derived from the textual context of the event. Textual clues used to determine the values are also annotated. The scheme is intended to be general enough to allow integration with different types of bio-event annotation, whilst being detailed enough to capture important subtleties in the nature of the meta-knowledge expressed in the text. We report here on both the main features of the annotation scheme, as well as its application to the GENIA event corpus (1000 abstracts with 36,858 events. High levels of inter-annotator agreement have been achieved, falling in the range of 0.84-0.93 Kappa. Conclusion By augmenting event annotations with meta-knowledge, more sophisticated IE systems can be trained, which allow interpretative

  2. 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

    suggest that Csac_0437 and Csac_0424 encode for glycoside hydrolases (GH and are proposed to be involved in the decomposition of recalcitrant plant polysaccharides. Similarly, HPs: Csac_0732, Csac_1862, Csac_1294 and Csac_0668 are suggested to play a significant role in biohydrogen production. Function prediction of these HPs by using our integrated approach will considerably enhance the interpretation of large-scale experiments targeting this industrially important organism.

  3. Nutrition Intensity in Ternary Diagrams Interpretation for Some Ornamental Species Cultivated on Organic Substrate with Increased Biological Activity

    Directory of Open Access Journals (Sweden)

    Roxana Maria MADJAR

    2014-12-01

    Full Text Available Nowadays, many biodegradable organic wastes no longer need to represent an environmental hazard and as a consequence, they could be recycled to obtain horticultural substrates. An experiment was conducted on two deciduous (Tamarix tetrandra, Ligustrum ovalifolium ‘Aureum’ and two coniferous species (Chamaecyparis pisifera ‘Boulevard’, Chamaecyparis lawsoniana ‘Stardust’ grown on a soil mixture of forestry compost, leaves compost, peat and grape marc compost. The aim of the research was to investigate the response to fertilization and to obtain valuable information regarding absorption rate of nutritive elements during vegetation. Nitrogen data show a lowering of its nutritive equilibrium point towards autumn in the leaves of deciduous shrubs species. Resorption of nutrients before leaves fall occurs due to conservation process in woody plants with deciduous leaves. In the case of coniferous species the lowering of nitrogen content is less intense. The monthly fertilization with Coïc solution indicates no influence on nitrogen metabolism of this species. The exception was on Ligustrum with differences between nitrogen content in fertilized and unfertilized plants. The phosphorus nutritive equilibrium point reveals a decrease during the summer months (July - August, the species presenting the lowest values in this period and the cause of this behaviour was the plants adaptation to high temperature and low humidity. Potassium nutritive equilibrium data indicates small differences in the unfertilized plants in comparison with those fertilized in all species. The novelty of the research is represented by the ternary diagrams N-P-K that were constructed, interpreted and reported for dendrologic species.

  4. 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

  5. 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

  6. Just Do It: Resources for Interpretive Planning

    Science.gov (United States)

    Koepler, Jes

    2008-01-01

    Now that you have finished reading this journal issue and understand what interpretive planning is and when to apply it, how can you get started and just "do" it? This article provides an annotated list of practical handbooks and internet resources that provide guidelines for museum practitioners to engage in interpretive planning at institutions…

  7. Sentiment Analysis of Document Based on Annotation

    CERN Document Server

    Shukla, Archana

    2011-01-01

    I present a tool which tells the quality of document or its usefulness based on annotations. Annotation may include comments, notes, observation, highlights, underline, explanation, question or help etc. comments are used for evaluative purpose while others are used for summarization or for expansion also. Further these comments may be on another annotation. Such annotations are referred as meta-annotation. All annotation may not get equal weightage. My tool considered highlights, underline as well as comments to infer 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 the annotation present on the documents as well as it also computes sentiment scores of all annotation which includes comments to obtain the collective sentiments about the document or to judge the quality of document. I demonstrate the use of tool on research paper.

  8. Representing NCBO Annotator results in standard RDF with the Annotation Ontology

    OpenAIRE

    Melzi, Soumia; Jonquet, Clement

    2014-01-01

    International audience; Semantic annotation is part of the Semantic Web vision. The Annotation Ontology is a model that have been proposed to represent any annotations in standard RDF. The NCBO Annotator Web service is a broadly used service for annotations in the biomedical domain, offered within the BioPortal platform and giving access to more than 350+ ontologies. This paper presents a new output format to represent the NCBO Annotator results in RDF with the Annotation Ontology. We briefly...

  9. A Data-Oriented Approach to Semantic Interpretation

    CERN Document Server

    Bod, R; Scha, R; Bod, Rens; Bonnema, Remko; Scha, Remko

    1996-01-01

    In Data-Oriented Parsing (DOP), an annotated language corpus is used as a stochastic grammar. The most probable analysis of a new input sentence is constructed by combining sub-analyses from the corpus in the most probable way. This approach has been succesfully used for syntactic analysis, using corpora with syntactic annotations such as the Penn Treebank. If a corpus with semantically annotated sentences is used, the same approach can also generate the most probable semantic interpretation of an input sentence. The present paper explains this semantic interpretation method, and summarizes the results of a preliminary experiment. Semantic annotations were added to the syntactic annotations of most of the sentences of the ATIS corpus. A data-oriented semantic interpretation algorithm was succesfully tested on this semantically enriched corpus.

  10. 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.

  11. Re-annotation and re-analysis of the Campylobacter jejuni NCTC11168 genome sequence

    Directory of Open Access Journals (Sweden)

    Dorrell Nick

    2007-06-01

    Full Text Available Abstract Background Campylobacter jejuni is the leading bacterial cause of human gastroenteritis in the developed world. To improve our understanding of this important human pathogen, the C. jejuni NCTC11168 genome was sequenced and published in 2000. The original annotation was a milestone in Campylobacter research, but is outdated. We now describe the complete re-annotation and re-analysis of the C. jejuni NCTC11168 genome using current database information, novel tools and annotation techniques not used during the original annotation. Results Re-annotation was carried out using sequence database searches such as FASTA, along with programs such as TMHMM for additional support. The re-annotation also utilises sequence data from additional Campylobacter strains and species not available during the original annotation. Re-annotation was accompanied by a full literature search that was incorporated into the updated EMBL file [EMBL: AL111168]. The C. jejuni NCTC11168 re-annotation reduced the total number of coding sequences from 1654 to 1643, of which 90.0% have additional information regarding the identification of new motifs and/or relevant literature. Re-annotation has led to 18.2% of coding sequence product functions being revised. Conclusions Major updates were made to genes involved in the biosynthesis of important surface structures such as lipooligosaccharide, capsule and both O- and N-linked glycosylation. This re-annotation will be a key resource for Campylobacter research and will also provide a prototype for the re-annotation and re-interpretation of other bacterial genomes.

  12. 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

  13. [From the qi annotation in Xiaozhenjie to qi view in the ancient time].

    Science.gov (United States)

    Jiang, Shan; Zhao, Jingsheng

    2016-04-01

    Xiaozhenjie (Miraculous Pivot Chapter 3: Annotation of Fine Needle) is the earliest annotation of Jiuzhen Shieryuan (Miraculous Pivot Chapter 1: Nine Needles and Twelve Yuan-Primary Acupoints). There are particularly 24 annotations of qi in the chapter. Based on the original literature, the styles of qi annotationsl were divided into three categories. By comparing with the original text, semantic features of qi annotations were reasoned. In reference to the understandings and notes of qi annotations given by the scholars of different dynasties, the origin of qi connotation in the ancient time was clarified so as to provide the historical evidence to the for-mation of this unique "qi language" and "qi worldview". It presents the instructive significance to understand and interpret "qi" for the scholars in the modern time. PMID:27352510

  14. LNG annotated bibliography

    Energy Technology Data Exchange (ETDEWEB)

    Bomelburg, H.J.; Counts, C.A.; Cowan, C.E.; Davis, W.E.; DeSteese, J.G.; Pelto, P.J.

    1982-09-01

    This document updates the bibliography published in Liquefied Gaseous Fuels Safety and Environmental Control Assessment Program: third status report (PNL-4172) and is a complete listing of literature reviewed and reported under the LNG Technical Surveillance Task. The bibliography is organized alphabetically by author.

  15. Nutrition and Mental Retardation. An Annotated Bibliography, 1964-1970.

    Science.gov (United States)

    Springer, Ninfa Saturnino

    This annotated bibliography is primarily organized for nutritionists. It presents selected articles published from 1964 to the present. All aspects of nutrition in mental retardation are covered excepting inborn errors of metabolism. Sections are included on: (1) nutrition, birthweight, and mental retardation; (2) nutrition, growth, and mental…

  16. Resources for Teaching about Human Rights: An Annotated List.

    Science.gov (United States)

    Totten, Samuel

    1985-01-01

    The following resources are cited in this annotated bibliography dealing with human rights: general references (background readings for teachers and students); classroom materials; fiction; audiovisuals; periodicals; and organizations and associations dedicated to the investigation of human rights infractions or education and communication on…

  17. Annotated Bibliography on Ethology in Education. Ecological Theory of Teaching.

    Science.gov (United States)

    Miller, Kevin; Frey, Susan

    This annotated bibliography focuses on the ethological study of child development and the educational process. Topics covered include: (1) evolution; (2) dominance hierarchies and social organization; (3) agonistic, affiliative, and epistemic behaviors; (4) nonverbal communication; (5) play; (6) biological constraints on learning; and (7) relevant…

  18. Education and Training. Annotated Bibliography. Author and Subject Index.

    Science.gov (United States)

    United Nations Food and Agriculture Organization, Rome (Italy).

    Food and Agriculture Organization (FAO) publications and documents issued by the Human Resources and Institutions division and by other technical divisions in the technical, economic, and social fields are selected, annotated and indexed in this bibliography. Documents issued prior to 1967 are not included but can be found in the Rural…

  19. History of American Communication Education: A Selected, Annotated Basic Bibliography.

    Science.gov (United States)

    Friedrich, Gustav W.

    Noting that only a fraction of the articles in speech journals have been concerned with the history of speech education in the United States, this annotated bibliography provides a broad guide to the materials necessary for understanding that history. The 45 citations are organized in six sections concerned with: (1) historical background; (2)…

  20. 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…

  1. Annotated Bibliography on Humanistic Education

    Science.gov (United States)

    Ganung, Cynthia

    1975-01-01

    Part I of this annotated bibliography deals with books and articles on such topics as achievement motivation, process education, transactional analysis, discipline without punishment, role-playing, interpersonal skills, self-acceptance, moral education, self-awareness, values clarification, and non-verbal communication. Part II focuses on…

  2. Multicultural Education. An Annotated Bibliography.

    Science.gov (United States)

    Narang, H. L.

    This annotated bibliography contains references to books, journal articles, ERIC documents, doctoral dissertations, and audio-visual materials on the subject of multicultural education. Topics include integrating multiculturalism in school subjects, prejudice and discrimination, intercultural communication, ethnic identity and ethnic bias.…

  3. Nikos Kazantzakis: An Annotated Bibliography.

    Science.gov (United States)

    Qiu, Kui

    This research paper consists of an annotated bibliography about Nikos Kazantzakis, one of the major modern Greek writers and author of "The Last Temptation of Christ,""Zorba the Greek," and many other works. Because of Kazantzakis' position in world literature there are many critical works about him; however, bibliographical control of these works…

  4. Toward a new countermovement: a framework for interpreting the contradictory interventions of migrant civil society organizations in urban labor markets

    OpenAIRE

    Nina Martin

    2011-01-01

    Low-wage migrant workers in the United States confront a perilous labor market, where wages are low, the risk of injury on the job is high, and the fear of apprehension by immigration authorities is widespread. There is increasing empirical evidence that civil society organizations are becoming involved in mediating labor-market problems, but work remains to be done in developing a robust theoretical conception of why such organizations are involved in this arena and how we might evaluate the...

  5. Interpretability formalized

    NARCIS (Netherlands)

    Joosten, Joost Johannes

    2004-01-01

    The dissertation is in the first place a treatment of mathematical interpretations. Interpretations themselves will be studied, but also shall they be used to study formal theories. Interpretations, when used in comparing theories, tell us, in a natural way, something about proof-strength of form

  6. 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)

  7. Semantic annotation for live and posterity logging of video documents

    Science.gov (United States)

    Bertini, Marco; Del Bimbo, Alberto; Nunziati, W.

    2003-06-01

    Broadcasters usually envision two basic applications for video databases: Live Logging and Posterity Logging. The former aims at providing effective annotation of video in quasi-real time and supports extraction of meaningful clips from the live stream; it is usually performed by assistant producers working at the same location of the event. The latter provides annotation for later reuse of video material and is the prerequisite for retrieval by content from video digital libraries; it is performed by trained librarians. Both require that annotation is performed, at a great extent, automatically. Video information structure must encompass both low-intermediate level video organization and event relationships that define specific highlights and situations. Analysis of the visual data of the video stream permits to extract hints, identify events and detect highlights. All of this must be supported by a-priori knowledge of the video domain and effective reasoning engines capable to capture the inherent semantics of the visual events.

  8. 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

  9. Are clickthrough data reliable as image annotations?

    NARCIS (Netherlands)

    Tsikrika, T.; Diou, C.; Vries, A.P. de; Delopoulos, A.

    2009-01-01

    We examine the reliability of clickthrough data as concept-based image annotations, by comparing them against manual annotations, for different concept categories. Our analysis shows that, for many concepts, the image annotations generated by using clickthrough data are reliable, with up to 90% of t

  10. 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.

  11. 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.

  12. MEGAnnotator: a user-friendly pipeline for microbial genomes assembly and annotation.

    Science.gov (United States)

    Lugli, Gabriele Andrea; Milani, Christian; Mancabelli, Leonardo; van Sinderen, Douwe; Ventura, Marco

    2016-04-01

    Genome annotation is one of the key actions that must be undertaken in order to decipher the genetic blueprint of organisms. Thus, a correct and reliable annotation is essential in rendering genomic data valuable. Here, we describe a bioinformatics pipeline based on freely available software programs coordinated by a multithreaded script named MEGAnnotator (Multithreaded Enhanced prokaryotic Genome Annotator). This pipeline allows the generation of multiple annotated formats fulfilling the NCBI guidelines for assembled microbial genome submission, based on DNA shotgun sequencing reads, and minimizes manual intervention, while also reducing waiting times between software program executions and improving final quality of both assembly and annotation outputs. MEGAnnotator provides an efficient way to pre-arrange the assembly and annotation work required to process NGS genome sequence data. The script improves the final quality of microbial genome annotation by reducing ambiguous annotations. Moreover, the MEGAnnotator platform allows the user to perform a partial annotation of pre-assembled genomes and includes an option to accomplish metagenomic data set assemblies. MEGAnnotator platform will be useful for microbiologists interested in genome analyses of bacteria as well as those investigating the complexity of microbial communities that do not possess the necessary skills to prepare their own bioinformatics pipeline.

  13. Systematic Functional Annotation and Visualization of Biological Networks.

    Science.gov (United States)

    Baryshnikova, Anastasia

    2016-06-22

    Large-scale biological networks represent relationships between genes, but our understanding of how networks are functionally organized is limited. Here, I describe spatial analysis of functional enrichment (SAFE), a systematic method for annotating biological networks and examining their functional organization. SAFE visualizes the network in 2D space and measures the continuous distribution of functional enrichment across local neighborhoods, producing a list of the associated functions and a map of their relative positioning. I applied SAFE to annotate the Saccharomyces cerevisiae genetic interaction similarity network and protein-protein interaction network with gene ontology terms. SAFE annotations of the genetic network matched manually derived annotations, while taking less than 1% of the time, and proved robust to noise and sensitive to biological signal. Integration of genetic interaction and chemical genomics data using SAFE revealed a link between vesicle-mediate transport and resistance to the anti-cancer drug bortezomib. These results demonstrate the utility of SAFE for examining biological networks and understanding their functional organization. PMID:27237738

  14. Believe It or Not: Adding Belief Annotations to Databases

    CERN Document Server

    Gatterbauer, Wolfgang; Khoussainova, Nodira; Suciu, Dan

    2009-01-01

    We propose a database model that allows users to annotate data with belief statements. Our motivation comes from scientific database applications where a community of users is working together to assemble, revise, and curate a shared data repository. As the community accumulates knowledge and the database content evolves over time, it may contain conflicting information and members can disagree on the information it should store. For example, Alice may believe that a tuple should be in the database, whereas Bob disagrees. He may also insert the reason why he thinks Alice believes the tuple should be in the database, and explain what he thinks the correct tuple should be instead. We propose a formal model for Belief Databases that interprets users' annotations as belief statements. These annotations can refer both to the base data and to other annotations. We give a formal semantics based on a fragment of multi-agent epistemic logic and define a query language over belief databases. We then prove a key technic...

  15. Interpretation of complexometric titration data: An intercomparison of methods for estimating models of trace metal complexation by natural organic ligands

    NARCIS (Netherlands)

    Pižeta, I.; Sander, S.G.; Hudson, R.J.M.; Omanovic, D.; Baars, O.; Barbeau, K.A.; Buck, K.N.; Bundy, R.M.; Carrasco, G.; Croot, P.L.; Garnier, C.; Gerringa, L.J.A.; Gledhill, M.; Hirose, K.; Kondo, Y.; Laglera, L.M.; Nuester, J.; Rijkenberg, M.J.A.; Takeda, S.; Twining, B.S.; Wells, M.

    2015-01-01

    With the common goal of more accurately and consistently quantifying ambient concentrations of free metal ions and natural organic ligands in aquatic ecosystems, researchers from 15 laboratories that routinely analyze trace metal speciation participated in an intercomparison of statistical methods u

  16. MAKER2: an annotation pipeline and genome-database management tool for second-generation genome projects

    Directory of Open Access Journals (Sweden)

    Holt Carson

    2011-12-01

    Full Text Available Abstract Background Second-generation sequencing technologies are precipitating major shifts with regards to what kinds of genomes are being sequenced and how they are annotated. While the first generation of genome projects focused on well-studied model organisms, many of today's projects involve exotic organisms whose genomes are largely terra incognita. This complicates their annotation, because unlike first-generation projects, there are no pre-existing 'gold-standard' gene-models with which to train gene-finders. Improvements in genome assembly and the wide availability of mRNA-seq data are also creating opportunities to update and re-annotate previously published genome annotations. Today's genome projects are thus in need of new genome annotation tools that can meet the challenges and opportunities presented by second-generation sequencing technologies. Results We present MAKER2, a genome annotation and data management tool designed for second-generation genome projects. MAKER2 is a multi-threaded, parallelized application that can process second-generation datasets of virtually any size. We show that MAKER2 can produce accurate annotations for novel genomes where training-data are limited, of low quality or even non-existent. MAKER2 also provides an easy means to use mRNA-seq data to improve annotation quality; and it can use these data to update legacy annotations, significantly improving their quality. We also show that MAKER2 can evaluate the quality of genome annotations, and identify and prioritize problematic annotations for manual review. Conclusions MAKER2 is the first annotation engine specifically designed for second-generation genome projects. MAKER2 scales to datasets of any size, requires little in the way of training data, and can use mRNA-seq data to improve annotation quality. It can also update and manage legacy genome annotation datasets.

  17. 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...

  18. Aldo-keto reductase (AKR) superfamily: genomics and annotation.

    Science.gov (United States)

    Mindnich, Rebekka D; Penning, Trevor M

    2009-07-01

    Aldo-keto reductases (AKRs) are phase I metabolising enzymes that catalyse the reduced nicotinamide adenine dinucleotide (phosphate) (NAD(P)H)-dependent reduction of carbonyl groups to yield primary and secondary alcohols on a wide range of substrates, including aliphatic and aromatic aldehydes and ketones, ketoprostaglandins, ketosteroids and xenobiotics. In so doing they functionalise the carbonyl group for conjugation (phase II enzyme reactions). Although functionally diverse, AKRs form a protein superfamily based on their high sequence identity and common protein fold, the (alpha/beta) 8 -barrel structure. Well over 150 AKR enzymes, from diverse organisms, have been annotated so far and given systematic names according to a nomenclature that is based on multiple protein sequence alignment and degree of identity. Annotation of non-vertebrate AKRs at the National Center for Biotechnology Information or Vertebrate Genome Annotation (vega) database does not often include the systematic nomenclature name, so the most comprehensive overview of all annotated AKRs is found on the AKR website (http://www.med.upenn.edu/akr/). This site also hosts links to more detailed and specialised information (eg on crystal structures, gene expression and single nucleotide polymorphisms [SNPs]). The protein-based AKR nomenclature allows unambiguous identification of a given enzyme but does not reflect the wealth of genomic and transcriptomic variation that exists in the various databases. In this context, identification of putative new AKRs and their distinction from pseudogenes are challenging. This review provides a short summary of the characteristic features of AKR biochemistry and structure that have been reviewed in great detail elsewhere, and focuses mainly on nomenclature and database entries of human AKRs that so far have not been subject to systematic annotation. Recent developments in the annotation of SNP and transcript variance in AKRs are also summarised. PMID:19706366

  19. Aldo-keto reductase (AKR superfamily: Genomics and annotation

    Directory of Open Access Journals (Sweden)

    Mindnich Rebekka D

    2009-07-01

    Full Text Available Abstract Aldo-keto reductases (AKRs are phase I metabolising enzymes that catalyse the reduced nicotinamide adenine dinucleotide (phosphate (NAD(PH-dependent reduction of carbonyl groups to yield primary and secondary alcohols on a wide range of substrates, including aliphatic and aromatic aldehydes and ketones, ketoprostaglan-dins, ketosteroids and xenobiotics. In so doing they functionalise the carbonyl group for conjugation (phase II enzyme reactions. Although functionally diverse, AKRs form a protein superfamily based on their high sequence identity and common protein fold, the (α/(β8-barrel structure. Well over 150 AKR enzymes, from diverse organisms, have been annotated so far and given systematic names according to a nomenclature that is based on multiple protein sequence alignment and degree of identity. Annotation of non-vertebrate AKRs at the National Center for Biotechnology Information or Vertebrate Genome Annotation (vega database does not often include the systematic nomenclature name, so the most comprehensive overview of all annotated AKRs is found on the AKR website (http://www.med.upenn.edu/akr/. This site also hosts links to more detailed and specialised information (eg on crystal structures, gene expression and single nucleotide polymorphisms [SNPs]. The protein-based AKR nomenclature allows unambiguous identification of a given enzyme but does not reflect the wealth of genomic and transcriptomic variation that exists in the various databases. In this context, identification of putative new AKRs and their distinction from pseudogenes are challenging. This review provides a short summary of the characteristic features of AKR biochemistry and structure that have been reviewed in great detail elsewhere, and focuses mainly on nomenclature and database entries of human AKRs that so far have not been subject to systematic annotation. Recent developments in the annotation of SNP and transcript variance in AKRs are also summarised.

  20. Automation and Validation of Annotation for Hindi Anaphora Resolution

    Directory of Open Access Journals (Sweden)

    Pardeep Singh

    2015-10-01

    Full Text Available The process of labelling any language genre by which one can extract useful information is called annotation. This provides syntactic information about a word or a word phrase. In this paper, an effort has been made to provide the algorithm for semiautomatic annotation for Hindi text to cater anaphora resolution only. The study was conducted on twelve files of Ranchi Express available in EMILLE corpus. The corpus is originally tagged for demonstrative pronouns. The detection of the pronouns is supported by the incorporation of seven tags. However the semantic interpretation of the demonstrative pronoun is not supported in the original corpus. In this paper an effort has been made to automate the process of tagging as well as the handling of semantic information through addition tags. It was conducted on 1485 demonstrative pronouns. The average accuracy of precision, recall and F measure is 74, 71 and 72 respectively.

  1. Revealing complex function, process and pathway interactions with high-throughput expression and biological annotation data.

    Science.gov (United States)

    Singh, Nitesh Kumar; Ernst, Mathias; Liebscher, Volkmar; Fuellen, Georg; Taher, Leila

    2016-10-20

    The biological relationships both between and within the functions, processes and pathways that operate within complex biological systems are only poorly characterized, making the interpretation of large scale gene expression datasets extremely challenging. Here, we present an approach that integrates gene expression and biological annotation data to identify and describe the interactions between biological functions, processes and pathways that govern a phenotype of interest. The product is a global, interconnected network, not of genes but of functions, processes and pathways, that represents the biological relationships within the system. We validated our approach on two high-throughput expression datasets describing organismal and organ development. Our findings are well supported by the available literature, confirming that developmental processes and apoptosis play key roles in cell differentiation. Furthermore, our results suggest that processes related to pluripotency and lineage commitment, which are known to be critical for development, interact mainly indirectly, through genes implicated in more general biological processes. Moreover, we provide evidence that supports the relevance of cell spatial organization in the developing liver for proper liver function. Our strategy can be viewed as an abstraction that is useful to interpret high-throughput data and devise further experiments.

  2. Linear and nonlinear relationships between biodegradation potential and molecular descriptors/fragments for organic pollutants and a theoretical interpretation

    Energy Technology Data Exchange (ETDEWEB)

    He, Jia; Qin, Weichao; Zhang, Xujia; Wen, Yang; Su, Limin; Zhao, Yuanhui, E-mail: zhaoyh@nenu.edu.cn

    2013-02-01

    Prediction of the biodegradability of organic pollutants is an ecologically desirable and economically feasible tool for estimating the environmental fate of chemicals. In this paper, linear and nonlinear relationships between biological oxygen demand (BOD) and molecular descriptors/fragments have been investigated for 1130 organic chemicals. Significant relationships have been observed between the simple molecular descriptors and %BOD for some homologous compounds, but not for the whole set of compounds. Electronic parameters, such as E{sub HOMO} and E{sub LUMO}, are the dominant factors affecting the biodegradability for some homologous chemicals. However, other descriptors, such as molecular weight, acid dissociation constant and polarity still have a significant impact on the biodegradation. The best global model for %BOD prediction is that developed from a chain-based fragmentation scheme. At the same time, the theoretical relationship between %BOD and molecular descriptors/fragments has been investigated, based on a first-order kinetic process. The %BOD is nonlinearly, rather than linearly, related to the descriptors. The coefficients of determination can be significantly improved by using nonlinear models for the homologous compounds and the whole data set. After analysing 1130 ready and not ready biodegradable compounds using 23 simple descriptors and various fragmentation schemes, it was revealed that biodegradation could be well predicted from a chain-based fragmentation scheme, a decision tree and a %BOD model. The models were capable of separating NRB and RB with an overall accuracy of 87.2%, 83.0% and 82.5%, respectively. The best classification model developed was a chain-based model but it used 155 fragments. The simplest model was a decision tree which only used 10 structural fragments. The effect of structures on the biodegradation has been analysed and the biodegradation pathway and mechanisms have been discussed based on activating and

  3. EST-PAC a web package for EST annotation and protein sequence prediction

    Directory of Open Access Journals (Sweden)

    Strahm Yvan

    2006-10-01

    Full Text Available Abstract With the decreasing cost of DNA sequencing technology and the vast diversity of biological resources, researchers increasingly face the basic challenge of annotating a larger number of expressed sequences tags (EST from a variety of species. This typically consists of a series of repetitive tasks, which should be automated and easy to use. The results of these annotation tasks need to be stored and organized in a consistent way. All these operations should be self-installing, platform independent, easy to customize and amenable to using distributed bioinformatics resources available on the Internet. In order to address these issues, we present EST-PAC a web oriented multi-platform software package for expressed sequences tag (EST annotation. EST-PAC provides a solution for the administration of EST and protein sequence annotations accessible through a web interface. Three aspects of EST annotation are automated: 1 searching local or remote biological databases for sequence similarities using Blast services, 2 predicting protein coding sequence from EST data and, 3 annotating predicted protein sequences with functional domain predictions. In practice, EST-PAC integrates the BLASTALL suite, EST-Scan2 and HMMER in a relational database system accessible through a simple web interface. EST-PAC also takes advantage of the relational database to allow consistent storage, powerful queries of results and, management of the annotation process. The system allows users to customize annotation strategies and provides an open-source data-management environment for research and education in bioinformatics.

  4. A collection of bioconductor methods to visualize gene-list annotations

    Directory of Open Access Journals (Sweden)

    Kibbe Warren A

    2010-01-01

    Full Text Available Abstract Background Gene-list annotations are critical for researchers to explore the complex relationships between genes and functionalities. Currently, the annotations of a gene list are usually summarized by a table or a barplot. As such, potentially biologically important complexities such as one gene belonging to multiple annotation categories are difficult to extract. We have devised explicit and efficient visualization methods that provide intuitive methods for interrogating the intrinsic connections between biological categories and genes. Findings We have constructed a data model and now present two novel methods in a Bioconductor package, "GeneAnswers", to simultaneously visualize genes, concepts (a.k.a. annotation categories, and concept-gene connections (a.k.a. annotations: the "Concept-and-Gene Network" and the "Concept-and-Gene Cross Tabulation". These methods have been tested and validated with microarray-derived gene lists. Conclusions These new visualization methods can effectively present annotations using Gene Ontology, Disease Ontology, or any other user-defined gene annotations that have been pre-associated with an organism's genome by human curation, automated pipelines, or a combination of the two. The gene-annotation data model and associated methods are available in the Bioconductor package called "GeneAnswers " described in this publication.

  5. Objective interpretation as conforming interpretation

    Directory of Open Access Journals (Sweden)

    Lidka Rodak

    2011-12-01

    Full Text Available The practical discourse willingly uses the formula of “objective interpretation”, with no regards to its controversial nature that has been discussed in literature.The main aim of the article is to investigate what “objective interpretation” could mean and how it could be understood in the practical discourse, focusing on the understanding offered by judicature.The thesis of the article is that objective interpretation, as identified with textualists’ position, is not possible to uphold, and should be rather linked with conforming interpretation. And what this actually implies is that it is not the virtue of certainty and predictability – which are usually associated with objectivity- but coherence that makes the foundation of applicability of objectivity in law.What could be observed from the analyses, is that both the phenomenon of conforming interpretation and objective interpretation play the role of arguments in the interpretive discourse, arguments that provide justification that interpretation is not arbitrary or subjective. With regards to the important part of the ideology of legal application which is the conviction that decisions should be taken on the basis of law in order to exclude arbitrariness, objective interpretation could be read as a question “what kind of authority “supports” certain interpretation”? that is almost never free of judicial creativity and judicial activism.One can say that, objective and conforming interpretation are just another arguments used in legal discourse.

  6. Semantic Annotation Framework For Intelligent Information Retrieval Using KIM Architecture

    Directory of Open Access Journals (Sweden)

    Sanjay Kumar Malik

    2010-11-01

    Full Text Available Due to the explosion of information/knowledge on the web and wide use of search engines for desiredinformation,the role of knowledge management(KM is becoming more significant in an organization.Knowledge Management in an Organization is used to create ,capture, store, share, retrieve and manageinformation efficiently. The semantic web, an intelligent and meaningful web, tend to provide a promisingplatform for knowledge management systems and vice versa, since they have the potential to give eachother the real substance for machine-understandable web resources which in turn will lead to anintelligent, meaningful and efficient information retrieval on web. Today,the challenge for web communityis to integrate the distributed heterogeneous resources on web with an objective of an intelligent webenvironment focusing on data semantics and user requirements. Semantic Annotation(SA is being widelyused which is about assigning to the entities in the text and links to their semantic descriptions. Varioustools like KIM, Amaya etc may be used for semantic Annotation.In this paper, we introduce semantic annotation as one of the key technology in an intelligent webenvironment , then revisit and review, discuss and explore about Knowledge Management and SemanticAnnotation. A Knowledge Management Framework and a Framework for Semantic Annotation andSemantic Search with Knowledge Base(GATE and Ontology have been presented. Then KIM Annotationplatform architecture including KIM Ontology(KIMO, KIM Knowledge Base and KIM front ends havebeen highlighted. Finally, intelligent pattern search and concerned GATE framework with a KIMAnnotation Example have been illiustrated towards an intelligent information retrieval

  7. Gene coexpression network analysis as a source of functional annotation for rice genes.

    Directory of Open Access Journals (Sweden)

    Kevin L Childs

    Full Text Available With the existence of large publicly available plant gene expression data sets, many groups have undertaken data analyses to construct gene coexpression networks and functionally annotate genes. Often, a large compendium of unrelated or condition-independent expression data is used to construct gene networks. Condition-dependent expression experiments consisting of well-defined conditions/treatments have also been used to create coexpression networks to help examine particular biological processes. Gene networks derived from either condition-dependent or condition-independent data can be difficult to interpret if a large number of genes and connections are present. However, algorithms exist to identify modules of highly connected and biologically relevant genes within coexpression networks. In this study, we have used publicly available rice (Oryza sativa gene expression data to create gene coexpression networks using both condition-dependent and condition-independent data and have identified gene modules within these networks using the Weighted Gene Coexpression Network Analysis method. We compared the number of genes assigned to modules and the biological interpretability of gene coexpression modules to assess the utility of condition-dependent and condition-independent gene coexpression networks. For the purpose of providing functional annotation to rice genes, we found that gene modules identified by coexpression analysis of condition-dependent gene expression experiments to be more useful than gene modules identified by analysis of a condition-independent data set. We have incorporated our results into the MSU Rice Genome Annotation Project database as additional expression-based annotation for 13,537 genes, 2,980 of which lack a functional annotation description. These results provide two new types of functional annotation for our database. Genes in modules are now associated with groups of genes that constitute a collective functional

  8. Interpretability Logic

    OpenAIRE

    de Visser, A.

    2008-01-01

    Interpretations are much used in metamathematics. The first application that comes to mind is their use in reductive Hilbert-style programs. Think of the kind of program proposed by Simpson, Feferman or Nelson (see Simpson[1988], Feferman[1988], Nelson[1986]). Here they serve to compare the strength of theories, or better to prove conservation results within a properly weak theory. An advantage of using interpretations is that even if their use should -perhaps- be classified as a prooftheoret...

  9. 关于组织出卖人体器官罪的解读及完善%A study on interpreting and improving the Crime of Organizing to Sell Human Organs

    Institute of Scientific and Technical Information of China (English)

    黄金

    2013-01-01

    近年来,随着人体器官强制摘取、非法买卖器官等危害行为日益猖獗,《中华人民共和国刑法修正案(八)》第37条的出台标志着组织出卖人体器官罪正式入刑,对人体器官买卖行为起到了极大的遏制作用。面对组织出卖人体器官罪在理论和实践中的争议,应从此罪的构成要件以及适用中的司法难题两方面入手,正确理解组织出卖人体器官罪的内涵;并应结合国际、国内关于器官移植犯罪方面的规定,完善相应立法。%In recent years, the crimes of organizing to s ell human organs have become more and more serious, thus China's Criminal Law Amendment (h)"added the crime of organizing to sell human organs to punish this crime. In this paper, we give interpretation to the crime of organizing to sell human organs with its dispute in theory and practice, and make suggestions for improving crime of organizing to sell human organs combining with international and domestic provisions about the organ transplant crime.

  10. 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 ...

  11. Intra-species sequence comparisons for annotating genomes

    Energy Technology Data Exchange (ETDEWEB)

    Boffelli, Dario; Weer, Claire V.; Weng, Li; Lewis, Keith D.; Shoukry, Malak I.; Pachter, Lior; Keys, David N.; Rubin, Edward M.

    2004-07-15

    Analysis of sequence variation among members of a single species offers a potential approach to identify functional DNA elements responsible for biological features unique to that species. Due to its high rate of allelic polymorphism and ease of genetic manipulability, we chose the sea squirt, Ciona intestinalis, to explore intra-species sequence comparisons for genome annotation. A large number of C. intestinalis specimens were collected from four continents and a set of genomic intervals amplified, resequenced and analyzed to determine the mutation rates at each nucleotide in the sequence. We found that regions with low mutation rates efficiently demarcated functionally constrained sequences: these include a set of noncoding elements, which we showed in C intestinalis transgenic assays to act as tissue-specific enhancers, as well as the location of coding sequences. This illustrates that comparisons of multiple members of a species can be used for genome annotation, suggesting a path for the annotation of the sequenced genomes of organisms occupying uncharacterized phylogenetic branches of the animal kingdom and raises the possibility that the resequencing of a large number of Homo sapiens individuals might be used to annotate the human genome and identify sequences defining traits unique to our species. The sequence data from this study has been submitted to GenBank under accession nos. AY667278-AY667407.

  12. 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

  13. ANNOTATION SUPPORTED OCCLUDED OBJECT TRACKING

    Directory of Open Access Journals (Sweden)

    Devinder Kumar

    2012-08-01

    Full Text Available Tracking occluded objects at different depths has become as extremely important component of study for any video sequence having wide applications in object tracking, scene recognition, coding, editing the videos and mosaicking. The paper studies the ability of annotation to track the occluded object based on pyramids with variation in depth further establishing a threshold at which the ability of the system to track the occluded object fails. Image annotation is applied on 3 similar video sequences varying in depth. In the experiment, one bike occludes the other at a depth of 60cm, 80cm and 100cm respectively. Another experiment is performed on tracking humans with similar depth to authenticate the results. The paper also computes the frame by frame error incurred by the system, supported by detailed simulations. This system can be effectively used to analyze the error in motion tracking and further correcting the error leading to flawless tracking. This can be of great interest to computer scientists while designing surveillance systems etc.

  14. In depth annotation of the Anopheles gambiae mosquito midgut transcriptome

    OpenAIRE

    Padrón, Alejandro; Molina-Cruz, Alvaro; Quinones, Mariam; Ribeiro, José MC; Ramphul, Urvashi; Rodrigues, Janneth; Shen, Kui; Haile, Ashley; Ramirez, José Luis; Barillas-Mury, Carolina

    2014-01-01

    Background Genome sequencing of Anopheles gambiae was completed more than ten years ago and has accelerated research on malaria transmission. However, annotation needs to be refined and verified experimentally, as most predicted transcripts have been identified by comparative analysis with genomes from other species. The mosquito midgut—the first organ to interact with Plasmodium parasites—mounts effective antiplasmodial responses that limit parasite survival and disease transmission. High-th...

  15. Interpreting Physics

    CERN Document Server

    MacKinnon, Edward

    2012-01-01

    This book is the first to offer a systematic account of the role of language in the development and interpretation of physics. An historical-conceptual analysis of the co-evolution of mathematical and physical concepts leads to the classical/quatum interface. Bohrian orthodoxy stresses the indispensability of classical concepts and the functional role of mathematics. This book analyses ways of extending, and then going beyond this orthodoxy orthodoxy. Finally, the book analyzes how a revised interpretation of physics impacts on basic philosophical issues: conceptual revolutions, realism, and r

  16. The 2008 update of the Aspergillus nidulans genome annotation: A community effort

    DEFF Research Database (Denmark)

    Wortman, Jennifer Russo; Gilsenan, Jane Mabey; Joardar, Vinita;

    2009-01-01

    The identification and annotation of protein-coding genes is one of the primary goals of whole-genome sequencing projects, and the accuracy of predicting the primary protein products of gene expression is vital to the interpretation of the available data and the design of downstream functional ap...

  17. The 2008 update of the Aspergillus nidulans genome annotation : a community effort

    NARCIS (Netherlands)

    Wortman, Jennifer Russo; Gilsenan, Jane Mabey; Joardar, Vinita; Deegan, Jennifer; Clutterbuck, John; Andersen, Mikael R; Archer, David; Bencina, Mojca; Braus, Gerhard; Coutinho, Pedro; von Döhren, Hans; Doonan, John; Driessen, Arnold J M; Durek, Pawel; Espeso, Eduardo; Fekete, Erzsébet; Flipphi, Michel; Estrada, Carlos Garcia; Geysens, Steven; Goldman, Gustavo; de Groot, Piet W J; Hansen, Kim; Harris, Steven D; Heinekamp, Thorsten; Helmstaedt, Kerstin; Henrissat, Bernard; Hofmann, Gerald; Homan, Tim; Horio, Tetsuya; Horiuchi, Hiroyuki; James, Steve; Jones, Meriel; Karaffa, Levente; Karányi, Zsolt; Kato, Masashi; Keller, Nancy; Kelly, Diane E; Kiel, Jan A K W; Kim, Jung-Mi; van der Klei, Ida J; Klis, Frans M; Kovalchuk, Andriy; Krasevec, Nada; Kubicek, Christian P; Liu, Bo; Maccabe, Andrew; Meyer, Vera; Mirabito, Pete; Miskei, Márton; Mos, Magdalena; Mullins, Jonathan; Nelson, David R; Nielsen, Jens; Oakley, Berl R; Osmani, Stephen A; Pakula, Tiina; Paszewski, Andrzej; Paulsen, Ian; Pilsyk, Sebastian; Pócsi, István; Punt, Peter J; Ram, Arthur F J; Ren, Qinghu; Robellet, Xavier; Robson, Geoff; Seiboth, Bernhard; van Solingen, Piet; Specht, Thomas; Sun, Jibin; Taheri-Talesh, Naimeh; Takeshita, Norio; Ussery, Dave; vanKuyk, Patricia A; Visser, Hans; van de Vondervoort, Peter J I; de Vries, Ronald P; Walton, Jonathan; Xiang, Xin; Xiong, Yi; Zeng, An Ping; Brandt, Bernd W; Cornell, Michael J; van den Hondel, Cees A M J J; Visser, Jacob; Oliver, Stephen G; Turner, Geoffrey

    2009-01-01

    The identification and annotation of protein-coding genes is one of the primary goals of whole-genome sequencing projects, and the accuracy of predicting the primary protein products of gene expression is vital to the interpretation of the available data and the design of downstream functional appli

  18. The 2008 update of the Aspergillus nidulans genome annotation: A community effort

    NARCIS (Netherlands)

    J.R. Wortman; J.M. Gilsenan; V. Joardar; J. Deegan; J. Clutterbuck; M.R. Andersen; D. Archer; M. Bencina; G. Braus; P. Coutinho; H. von Döhren; J. Doonan; A.J.M. Driessen; P. Durek; E. Espeso; E. Fekete; M. Flipphi; C.G. Estrada; S. Geysens; G. Goldman; P.W.J. de Groot; K. Hansen; S.D. Harris; T. Heinekamp; K. Helmstaedt; B. Henrissat; G. Hofmann; T. Homan; T. Horio; H. Horiuchi; S. James; M. Jones; L. Karaffa; Z. Karányi; M. Kato; N. Keller; D.E. Kelly; J.A.K.W. Kiel; J.M. Kim; I.J. van der Klei; F.M. Klis; A. Kovalchuk; N. Kraševec; C.P. Kubicek; B. Liu; A. MacCabe; V. Meyer; P. Mirabito; M. Miskei; M. Mos; J. Mullins; D.R. Nelson; J. Nielsen; B.R. Oakley; S.A. Osmani; T. Pakula; A. Paszewski; I. Paulsen; S. Pilsyk; I. Pócsi; P.J. Punt; A.F.J. Ram; Q. Ren; X. Robellet; G. Robson; B. Seiboth; P. van Solingen; T. Specht; J. Sun; N. Taheri-Talesh; N. Takeshita; D. Ussery; P.A. vanKuyk; H. Visser; P.J.I. van de Vondervoort; R.P. de Vries; J. Walton; X. Xiang; Y. Xiong; A.P. Zeng; B.W. Brandt; M.J. Cornell; C.A.M.J.J. van den Hondel; J. Visser; S.G. Oliver; G. Turner

    2009-01-01

    The identification and annotation of protein-coding genes is one of the primary goals of whole-genome sequencing projects, and the accuracy of predicting the primary protein products of gene expression is vital to the interpretation of the available data and the design of downstream functional appli

  19. The 2008 update of the Aspergillus nidulans genome annotation : A community effort

    NARCIS (Netherlands)

    Wortman, Jennifer Russo; Gilsenan, Jane Mabey; Joardar, Vinita; Deegan, Jennifer; Clutterbuck, John; Andersen, Mikael R.; Archer, David; Bencina, Mojca; Braus, Gerhard; Coutinho, Pedro; von Doehren, Hans; Doonan, John; Driessen, Arnold J. M.; Durek, Pawel; Espeso, Eduardo; Fekete, Erzsebet; Flipphi, Michel; Garcia Estrada, Carlos; Geysens, Steven; Goldman, Gustavo; de Groot, Piet W. J.; Hansen, Kim; Harris, Steven D.; Heinekamp, Thorsten; Helmstaedt, Kerstin; Henrissat, Bernard; Hofmann, Gerald; Homan, Tim; Horio, Tetsuya; Horiuchi, Hiroyuki; James, Steve; Jones, Meriel; Karaffa, Levente; Karanyi, Zsolt; Kato, Masashi; Keller, Nancy; Kelly, Diane E.; Kiel, Jan A. K. W.; Kim, Jung-Mi; van der Klei, Ida J.; Klis, Frans M.; Kovalchuk, Andriy; Krasevec, Nada; Kubicek, Christian P.; Liu, Bo; MacCabe, Andrew; Meyer, Vera; Mirabito, Pete; Miskei, Marton; Mos, Magdalena; Mullins, Jonathan; Nelson, David R.; Nielsen, Jens; Oakley, Berl R.; Osmani, Stephen A.; Pakula, Tiina; Paszewski, Andrzej; Paulsen, Ian; Pilsyk, Sebastian; Pocsi, Istvan; Punt, Peter J.; Ram, Arthur F. J.; Ren, Qinghu; Robellet, Xavier; Robson, Geoff; Seiboth, Bernhard; van Solingen, Piet; Specht, Thomas; Sun, Jibin; Taheri-Talesh, Naimeh; Takeshita, Norio; Ussery, Dave; Vankuyk, Patricia A.; Visser, Hans; de Vondervoort, Peter J. I. van; Walton, Jonathan; Xiang, Xin; Xiong, Yi; Zeng, An Ping; Brandt, Bernd W.; Cornell, Michael J.; van den Hondel, Cees A. M. J. J.; Visser, Jacob; Oliver, Stephen G.; Turner, Geoffrey; Kraševec, Nada; Kuyk, Patricia A. van; Döhren, D.H.; van Seilboth, B; de Vries, R.

    2009-01-01

    The identification and annotation of protein-coding genes is one of the primary goals of whole-genome sequencing projects, and the accuracy of predicting the primary protein products of gene expression is vital to the interpretation of the available data and the design of downstream functional appli

  20. What Determines Inter-Coder Agreement in Manual Annotations? A Meta-Analytic Investigation

    NARCIS (Netherlands)

    P.S. Bayerl (Petra Saskia); K.I. Paul

    2011-01-01

    textabstractRecent discussions of annotator agreement have mostly centered around its calculation and interpretation, and the correct choice of indices. Although these discussions are important, they only consider the "back-end" of the story, namely, what to do once the data are collected. Just as i

  1. FUNC: a package for detecting significant associations between gene sets and ontological annotations

    Directory of Open Access Journals (Sweden)

    Rahm Erhard

    2007-02-01

    Full Text Available Abstract Background Genome-wide expression, sequence and association studies typically yield large sets of gene candidates, which must then be further analysed and interpreted. Information about these genes is increasingly being captured and organized in ontologies, such as the Gene Ontology. Relationships between the gene sets identified by experimental methods and biological knowledge can be made explicit and used in the interpretation of results. However, it is often difficult to assess the statistical significance of such analyses since many inter-dependent categories are tested simultaneously. Results We developed the program package FUNC that includes and expands on currently available methods to identify significant associations between gene sets and ontological annotations. Implemented are several tests in particular well suited for genome wide sequence comparisons, estimates of the family-wise error rate, the false discovery rate, a sensitive estimator of the global significance of the results and an algorithm to reduce the complexity of the results. Conclusion FUNC is a versatile and useful tool for the analysis of genome-wide data. It is freely available under the GPL license and also accessible via a web service.

  2. 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

  3. 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...

  4. Ground Truth Annotation in T Analyst

    DEFF Research Database (Denmark)

    2015-01-01

    This video shows how to annotate the ground truth tracks in the thermal videos. The ground truth tracks are produced to be able to compare them to tracks obtained from a Computer Vision tracking approach. The program used for annotation is T-Analyst, which is developed by Aliaksei Laureshyn, Ph...

  5. Creating Gaze Annotations in Head Mounted Displays

    DEFF Research Database (Denmark)

    Mardanbeigi, Diako; Qvarfordt, Pernilla

    2015-01-01

    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, ...

  6. 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...

  7. Using Rhetorical Annotations for Generating Video Documentaries

    NARCIS (Netherlands)

    Bocconi, S.; Nack, F.-M.; Hardman, L.

    2005-01-01

    We use rhetorical annotations to specify a generation process that can assemble meaningful video sequences with a communicative goal and an argumentative progression. Our annotation schema encodes the verbal information contained in the audio channel, identifying the claims the interviewees make and

  8. Using rhetorical annotations for generating video documentaries

    NARCIS (Netherlands)

    Bocconi, S.; Nack, F.-M.; Hardman, L.

    2005-01-01

    We use rhetorical annotations to specify a generation process that can assemble meaningful video sequences with a communicative goal and an argumentative progression. Our annotation schema encodes the verbal information contained in the audio channel, identifying the claims the interviewees make and

  9. 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

    Use of Semantic Web technologies for data management in the Earth sciences (and beyond) has great potential but is still in its early stages, since the challenges of translating data into a more explicit or semantic form for immediate use within applications has not been fully addressed. In this abstract we help address this challenge by introducing the SemantEco Annotator, which enables anyone, regardless of expertise, to semantically annotate tabular Earth Science data and translate it into linked data format, while applying the logic inherent in community-standard vocabularies to guide the process. The Annotator was conceived under a desire to unify dataset content from a variety of sources under common vocabularies, for use in semantically-enabled web applications. Our current use case employs linked data generated by the Annotator for use in the SemantEco environment, which utilizes semantics to help users explore, search, and visualize water or air quality measurement and species occurrence data through a map-based interface. The generated data can also be used immediately to facilitate discovery and search capabilities within 'big data' environments. The Annotator provides a method for taking information about a dataset, that may only be known to its maintainers, and making it explicit, in a uniform and machine-readable fashion, such that a person or information system can more easily interpret the underlying structure and meaning. Its primary mechanism is to enable a user to formally describe how columns of a tabular dataset relate and/or describe entities. For example, if a user identifies columns for latitude and longitude coordinates, we can infer the data refers to a point that can be plotted on a map. Further, it can be made explicit that measurements of 'nitrate' and 'NO3-' are of the same entity through vocabulary assignments, thus more easily utilizing data sets that use different nomenclatures. The Annotator provides an extensive and searchable

  10. Interpreting Metonymy.

    Science.gov (United States)

    Pankhurst, Anne

    1994-01-01

    This paper examines some of the problems associated with interpreting metonymy, a figure of speech in which an attribute or commonly associated feature is used to name or designate something. After defining metonymy and outlining the principles of metonymy, the paper explains the differences between metonymy, synecdoche, and metaphor. It is…

  11. RiceDB: A Web-Based Integrated Database for Annotating Rice Microarray

    Institute of Scientific and Technical Information of China (English)

    HE Fei; SHI Qing-yun; CHEN Ming; WU Ping

    2007-01-01

    RiceDB, a web-based integrated database to annotate rice microarray in various biological contexts was developed. It is composed of eight modules. RiceMap module archives the process of Affymetrix probe sets mapping to different databases about rice, and aims to the genes represented by a microarray set by retrieving annotation information via the identifier or accession number of every database; RiceGO module indicates the association between a microarray set and gene ontology (GO) categories; RiceKO module is used to annotate a microarray set based on the KEGG biochemical pathways; RiceDO module indicates the information of domain associated with a microarray set; RiceUP module is used to obtain promoter sequences for all genes represented by a microarray set; RiceMR module lists potential microRNA which regulated the genes represented by a microarray set; RiceCD and RiceGF are used to annotate the genes represented by a microarray set in the context of chromosome distribution and rice paralogous family distribution. The results of automatic annotation are mostly consistent with manual annotation. Biological interpretation of the microarray data is quickened by the help of RiceDB.

  12. 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.

  13. 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...

  14. 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

  15. 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

  16. 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

    . An increase in the number and size of GO groups without any noticeable decrease of the link density within the groups indicated that this expansion significantly broadens the public GO annotation without diluting its quality. We revealed that functional GO annotation correlates mostly with clustering in a physical interaction protein network, while its overlap with indirect regulatory network communities is two to three times smaller. Conclusion Protein functional annotations extracted by the NLP technology expand and enrich the existing GO annotation system. The GO functional modularity correlates mostly with the clustering in the physical interaction network, suggesting that the essential role of structural organization maintained by these interactions. Reciprocally, clustering of proteins in physical interaction networks can serve as an evidence for their functional similarity.

  17. Prediction of blood:air and fat:air partition coefficients of volatile organic compounds for the interpretation of data in breath gas analysis.

    Science.gov (United States)

    Kramer, Christian; Mochalski, Paweł; Unterkofler, Karl; Agapiou, Agapios; Ruzsanyi, Veronika; Liedl, Klaus R

    2016-03-01

    In this article, a database of blood:air and fat:air partition coefficients (λ b:a and λ f:a) is reported for estimating 1678 volatile organic compounds recently reported to appear in the volatilome of the healthy human. For this purpose, a quantitative structure-property relationship (QSPR) approach was applied and a novel method for Henry's law constants prediction developed. A random forest model based on Molecular Operating Environment 2D (MOE2D) descriptors based on 2619 literature-reported Henry's constant values was built. The calculated Henry's law constants correlate very well (R(2) test  =  0.967) with the available experimental data. Blood:air and fat:air partition coefficients were calculated according to the method proposed by Poulin and Krishnan using the estimated Henry's constant values. The obtained values correlate reasonably well with the experimentally determined ones for a test set of 90 VOCs (R(2)  =  0.95). The provided data aim to fill in the literature data gap and further assist the interpretation of results in studies of the human volatilome. PMID:26815030

  18. 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.

  19. Recognising and Interpreting Named Temporal Expressions

    DEFF Research Database (Denmark)

    Brucato, Matteo; Derczynski, Leon; Llorens, Hectjor;

    2013-01-01

    expressions is mature in many languages. However, there is a class of expressions that are less typical, very varied, and difficult to automatically interpret. These indicate dates and times, but are harder to detect because they often do not contain time words and are not used frequently enough to appear...... in conventional temporally-annotated corpora – for example Michaelmas or Vasant Panchami. UsingWikipedia and linked data, we automatically construct a resource of English named temporal expressions, and use it to extract training examples from a large corpus. These examples are then used to train and evaluate...... a named temporal expression recogniser. We also introduce and evaluate rules for automatically interpreting these expressions, and we observe that use of the rules improves temporal annotation performance over existing corpora....

  20. 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.

  1. 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......) language drift on Twitter is significant, and while off-the-shelf systems have been reported to perform well on in-sample data, they often perform poorly on new samples of tweets, (b) state-of-the-art performance across various datasets can beobtained from crowdsourced annotations, making it more feasible...

  2. Learning Joint Query Interpretation and Response Ranking

    OpenAIRE

    Sawant, Uma; Chakrabarti, Soumen

    2012-01-01

    Thanks to information extraction and semantic Web efforts, search on unstructured text is increasingly refined using semantic annotations and structured knowledge bases. However, most users cannot become familiar with the schema of knowledge bases and ask structured queries. Interpreting free-format queries into a more structured representation is of much current interest. The dominant paradigm is to segment or partition query tokens by purpose (references to types, entities, attribute names,...

  3. Annotation and Curation of Uncharacterized proteins- Challenges

    Directory of Open Access Journals (Sweden)

    Johny eIjaq

    2015-03-01

    Full Text Available Hypothetical Proteins are the proteins that are predicted to be expressed from an open reading frame (ORF, constituting a substantial fraction of proteomes in both prokaryotes and eukaryotes. Genome projects have led to the identification of many therapeutic targets, the putative function of the protein and their interactions. In this review we have enlisted various methods. Annotation linked to structural and functional prediction of hypothetical proteins assist in the discovery of new structures and functions serving as markers and pharmacological targets for drug designing, discovery and screening. Mass spectrometry is an analytical technique for validating protein characterisation. Matrix-assisted laser desorption ionization–mass spectrometry (MALDI-MS is an efficient analytical method. Microarrays and Protein expression profiles help understanding the biological systems through a systems-wide study of proteins and their interactions with other proteins and non-proteinaceous molecules to control complex processes in cells and tissues and even whole organism. Next generation sequencing technology accelerates multiple areas of genomics research.

  4. 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 ...

  5. Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project : open letter

    NARCIS (Netherlands)

    Archibald, A.L.; Bottema, C.D.; Brauning, R.; Burgess, S.C.; Burt, D.W.; Casas, E.; Cheng, H.H.; Clarke, L.; Couldrey, C.; Dalrymple, B.P.; Elsik, C.G.; Foissac, S.; Giuffra, E.; Groenen, M.A.M.; Hayes, B.J.; Huang, L.S.; Khatib, H.; Kijas, J.W.; Kim, H.; Lunney, J.K.; McCarthy, F.M.; McEwan, J.; Moore, S.; Nanduri, B.; Notredame, C.; Palti, Y.; Plastow, G.S.; Reecy, J.M.; Rohrer, G.; Sarropoulou, E.; Schmidt, C.J.; Silverstein, J.; Tellam, R.L.; Tixier-Boichard, M.; Tosser-klopp, G.; Tuggle, C.K.; Vilkki, J.; White, S.N.; Zhao, S.; Zhou, H.

    2015-01-01

    We describe the organization of a nascent international effort, the Functional Annotation of Animal Genomes (FAANG) project, whose aim is to produce comprehensive maps of functional elements in the genomes of domesticated animal species.

  6. 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...

  7. Annotation of Scientific Summaries for Information Retrieval

    CERN Document Server

    Ibekwe-Sanjuan, Fidelia; Eric, Sanjuan; Eric, Charton

    2011-01-01

    We present a methodology combining surface NLP and Machine Learning techniques for ranking asbtracts and generating summaries based on annotated corpora. The corpora were annotated with meta-semantic tags indicating the category of information a sentence is bearing (objective, findings, newthing, hypothesis, conclusion, future work, related work). The annotated corpus is fed into an automatic summarizer for query-oriented abstract ranking and multi- abstract summarization. To adapt the summarizer to these two tasks, two novel weighting functions were devised in order to take into account the distribution of the tags in the corpus. Results, although still preliminary, are encouraging us to pursue this line of work and find better ways of building IR systems that can take into account semantic annotations in a corpus.

  8. 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.

  9. Using a Problem Solving-Cooperative Learning Approach to Improve Students' Skills for Interpreting [Superscript 1]H NMR Spectra of Unknown Compounds in an Organic Spectroscopy Course

    Science.gov (United States)

    Angawi, Rihab F.

    2014-01-01

    To address third- and fourth-year chemistry students' difficulties with the challenge of interpreting [superscript 1]H NMR spectra, a problem solving-cooperative learning technique was incorporated in a Spectra of Organic Compounds course. Using this approach helped students deepen their understanding of the basics of [superscript 1]H NMR…

  10. 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...

  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...... to 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. 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...

  13. 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.

  14. Mammographic interpretation

    International Nuclear Information System (INIS)

    For mammography to be an effective diagnostic method, it must be performed to a very high standard of quality. Otherwise many lesions, in particular cancer in its early stages, will simply not be detectable on the films, regardless of the skill of the mammographer. Mammographic interpretation consists of two basic steps: perception and analysis. The process of mammographic interpretation begins with perception of the lesion on the mammogram. Perception is influenced by several factors. One of the most important is the parenchymal pattern of the breast tissue, detection of pathologic lesions being easier with fatty involution. The mammographer should use a method for the systematic viewing of the mammograms that will ensure that all parts of each mammogram are carefully searched for the presence of lesions. The method of analysis proceeds according to the type of lesion. The contour analysis of primary importance in the evaluation of circumscribed tumors. After having analyzed the contour and density of a lesion and considered its size, the mammographer should be fairly certain whether the circumscribed tumor is benign or malignant. Fine-needle puncture and/or US may assist the mammographer in making this decision. Painstaking analysis is required because many circumscribed tumors do not need to be biopsied. The perception of circumscribed tumors seldom causes problems, but their analysis needs careful attention. On the other hand, the major challenge with star-shaped lesions is perception. They may be difficult to discover when small. Although the final diagnosis of a stellate lesion can be made only with the help of histologic examination, the preoperative mammorgraphic differential diagnosis can be highly accurate. The differential diagnostic problem is between malignant tumors (scirrhous carcinoma), on the one hand, and traumatic fat necrosis as well as radial scars on the other hand

  15. Conceptual approach through an annotation process for the representation and the information contents enhancement in economic intelligence (EI)

    CERN Document Server

    Sidhom, Sahbi

    2008-01-01

    In the era of the information society, the impact of the information systems on the economy of material and immaterial is certainly perceptible. With regards to the information resources of an organization, the annotation involved to enrich informational content, to track the intellectual activities on a document and to set the added value on information for the benefit of solving a decision-making problem in the context of economic intelligence. Our contribution is distinguished by the representation of an annotation process and its inherent concepts to lead the decisionmaker to an anticipated decision: the provision of relevant and annotated information. Such information in the system is made easy by taking into account the diversity of resources and those that are well annotated so formally and informally by the EI actors. A capital research framework consist of integrating in the decision-making process the annotator activity, the software agent (or the reasoning mechanisms) and the information resources ...

  16. 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...

  17. Recherche basée sur l’annotation automatique des images à l'aide de photos collaboratives géolocalisées

    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...

  18. Towards the VWO Annotation Service: a Success Story of the IMAGE RPI Expert Rating System

    Science.gov (United States)

    Reinisch, B. W.; Galkin, I. A.; Fung, S. F.; Benson, R. F.; Kozlov, A. V.; Khmyrov, G. M.; Garcia, L. N.

    2010-12-01

    Interpretation of Heliophysics wave data requires specialized knowledge of wave phenomena. Users of the virtual wave observatory (VWO) will greatly benefit from a data annotation service that will allow querying of data by phenomenon type, thus helping accomplish the VWO goal to make Heliophysics wave data searchable, understandable, and usable by the scientific community. Individual annotations can be sorted by phenomenon type and reduced into event lists (catalogs). However, in contrast to the event lists, annotation records allow a greater flexibility of collaborative management by more easily admitting operations of addition, revision, or deletion. They can therefore become the building blocks for an interactive Annotation Service with a suitable graphic user interface to the VWO middleware. The VWO Annotation Service vision is an interactive, collaborative sharing of domain expert knowledge with fellow scientists and students alike. An effective prototype of the VWO Annotation Service has been in operation at the University of Massachusetts Lowell since 2001. An expert rating system (ERS) was developed for annotating the IMAGE radio plasma imager (RPI) active sounding data containing 1.2 million plasmagrams. The RPI data analysts can use ERS to submit expert ratings of plasmagram features, such as presence of echo traces resulted from reflected RPI signals from distant plasma structures. Since its inception in 2001, the RPI ERS has accumulated 7351 expert plasmagram ratings in 16 phenomenon categories, together with free-text descriptions and other metadata. In addition to human expert ratings, the system holds 225,125 ratings submitted by the CORPRAL data prospecting software that employs a model of the human pre-attentive vision to select images potentially containing interesting features. The annotation records proved to be instrumental in a number of investigations where manual data exploration would have been prohibitively tedious and expensive

  19. 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.

  20. Mercator: a fast and simple web server for genome scale functional annotation of plant sequence data.

    Science.gov (United States)

    Lohse, Marc; Nagel, Axel; Herter, Thomas; May, Patrick; Schroda, Michael; Zrenner, Rita; Tohge, Takayuki; Fernie, Alisdair R; Stitt, Mark; Usadel, Björn

    2014-05-01

    Next-generation technologies generate an overwhelming amount of gene sequence data. Efficient annotation tools are required to make these data amenable to functional genomics analyses. The Mercator pipeline automatically assigns functional terms to protein or nucleotide sequences. It uses the MapMan 'BIN' ontology, which is tailored for functional annotation of plant 'omics' data. The classification procedure performs parallel sequence searches against reference databases, compiles the results and computes the most likely MapMan BINs for each query. In the current version, the pipeline relies on manually curated reference classifications originating from the three reference organisms (Arabidopsis, Chlamydomonas, rice), various other plant species that have a reviewed SwissProt annotation, and more than 2000 protein domain and family profiles at InterPro, CDD and KOG. Functional annotations predicted by Mercator achieve accuracies above 90% when benchmarked against manual annotation. In addition to mapping files for direct use in the visualization software MapMan, Mercator provides graphical overview charts, detailed annotation information in a convenient web browser interface and a MapMan-to-GO translation table to export results as GO terms. Mercator is available free of charge via http://mapman.gabipd.org/web/guest/app/Mercator.

  1. GO annotation in InterPro: why stability does not indicate accuracy in a sea of changing annotations.

    Science.gov (United States)

    Sangrador-Vegas, Amaia; Mitchell, Alex L; Chang, Hsin-Yu; Yong, Siew-Yit; Finn, Robert D

    2016-01-01

    The removal of annotation from biological databases is often perceived as an indicator of erroneous annotation. As a corollary, annotation stability is considered to be a measure of reliability. However, diverse data-driven events can affect the stability of annotations in both primary protein sequence databases and the protein family databases that are built upon the sequence databases and used to help annotate them. Here, we describe some of these events and their consequences for the InterPro database, and demonstrate that annotation removal or reassignment is not always linked to incorrect annotation by the curator. Database URL: http://www.ebi.ac.uk/interpro.

  2. MixtureTree annotator: a program for automatic colorization and visual annotation of MixtureTree.

    Directory of Open Access Journals (Sweden)

    Shu-Chuan Chen

    Full Text Available The MixtureTree Annotator, written in JAVA, allows the user to automatically color any phylogenetic tree in Newick format generated from any phylogeny reconstruction program and output the Nexus file. By providing the ability to automatically color the tree by sequence name, the MixtureTree Annotator provides a unique advantage over any other programs which perform a similar function. In addition, the MixtureTree Annotator is the only package that can efficiently annotate the output produced by MixtureTree with mutation information and coalescent time information. In order to visualize the resulting output file, a modified version of FigTree is used. Certain popular methods, which lack good built-in visualization tools, for example, MEGA, Mesquite, PHY-FI, TreeView, treeGraph and Geneious, may give results with human errors due to either manually adding colors to each node or with other limitations, for example only using color based on a number, such as branch length, or by taxonomy. In addition to allowing the user to automatically color any given Newick tree by sequence name, the MixtureTree Annotator is the only method that allows the user to automatically annotate the resulting tree created by the MixtureTree program. The MixtureTree Annotator is fast and easy-to-use, while still allowing the user full control over the coloring and annotating process.

  3. MixtureTree annotator: a program for automatic colorization and visual annotation of MixtureTree.

    Science.gov (United States)

    Chen, Shu-Chuan; Ogata, Aaron

    2015-01-01

    The MixtureTree Annotator, written in JAVA, allows the user to automatically color any phylogenetic tree in Newick format generated from any phylogeny reconstruction program and output the Nexus file. By providing the ability to automatically color the tree by sequence name, the MixtureTree Annotator provides a unique advantage over any other programs which perform a similar function. In addition, the MixtureTree Annotator is the only package that can efficiently annotate the output produced by MixtureTree with mutation information and coalescent time information. In order to visualize the resulting output file, a modified version of FigTree is used. Certain popular methods, which lack good built-in visualization tools, for example, MEGA, Mesquite, PHY-FI, TreeView, treeGraph and Geneious, may give results with human errors due to either manually adding colors to each node or with other limitations, for example only using color based on a number, such as branch length, or by taxonomy. In addition to allowing the user to automatically color any given Newick tree by sequence name, the MixtureTree Annotator is the only method that allows the user to automatically annotate the resulting tree created by the MixtureTree program. The MixtureTree Annotator is fast and easy-to-use, while still allowing the user full control over the coloring and annotating process.

  4. Interpreting the Ultraviolet Aerosol Index Observed with the OMI Satellite Instrument to Understand Absorption by Organic Carbon Aerosols and Implications for Atmospheric Oxidation

    Science.gov (United States)

    Hammer, M. S.; Martin, R.; van Donkelaar, A.; Buchard, V.; Torres, O.; Ridley, D. A.; Spurr, R. J. D.

    2015-12-01

    Absorption of solar radiation by aerosols plays a major role in radiative forcing and atmospheric photochemistry. Many atmospheric chemistry models tend to overestimate tropospheric OH concentrations compared to observations. Accurately representing aerosol absorption in the UV could help rectify the discrepancies between simulated and observed OH concentrations. We develop a simulation of the Ultraviolet Aerosol Index (UVAI), using the 3-D chemical transport model GEOS-Chem coupled with the Vector Linearized Discrete Ordinate Radiative Transfer model (VLIDORT). The simulation is applied to interpret UVAI observations from the Ozone Monitoring Instrument (OMI). Simulated and observed values are highly consistent in regions where mineral dust dominates the UVAI, but a large negative bias (-0.4 to -1.0) exists between simulated and observed values in biomass burning regions. We implement optical properties for absorbing organic aerosol, known as brown carbon (BrC), into GEOS-Chem and evaluate the simulation with observed UVAI values over biomass burning regions. The spectral dependence of absorption after adding BrC to the model is broadly consistent with reported observations for biomass burning aerosol, with Absorbing Angstrom Exponent (AAE) values ranging from 2.7 in the UV to 1.3 across the UV-Near IR spectrum. The addition of absorbing BrC decreases the mean bias between simulated and OMI UVAI values from -0.60 to -0.08 over North Africa in January, from -0.40 to -0.003 over South Asia in April, from -1.0 to -0.24 over southern Africa in July, and from -0.50 to +0.34 over South America in September. We assess the effect of the additional UV absorption by BrC on atmospheric photochemistry by examining ozone photolysis frequencies (J(O(1D))) and tropospheric OH concentrations in GEOS-Chem. The inclusion of BrC decreases J(O(1D)) and OH by up to 35% over biomass burning regions, and reduces the global bias in OH.

  5. Interpretation training influences memory for prior interpretations

    NARCIS (Netherlands)

    E. Salemink; P. Hertel; B. Mackintosh

    2010-01-01

    Anxiety is associated with memory biases when the initial interpretation of the event is taken into account. This experiment examined whether modification of interpretive bias retroactively affects memory for prior events and their initial interpretation. Before training, participants imagined thems

  6. The Interpretation of Texts, People and Other Artifacts

    OpenAIRE

    DENNETT, Daniel C.

    1990-01-01

    I want to explore four different exercises of interpretation: (1) the interpretation of texts (or hermeneutics), (2) the interpretation of people (otherwise known as "attribution" psychology, or cognitive or intentional psychology), (3) the interpretation of other artifacts (which I shall call artifact hermeneutics), (4) the interpretation of organism design in evolutionary biology--the controversial interpretive activity known as adaptationism.

  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. Interpreting the Ultraviolet Aerosol Index Observed with the OMI Satellite Instrument to Understand Absorption by Organic Aerosols: Implications for Atmospheric Oxidation and Direct Radiative Effects

    Science.gov (United States)

    Hammer, Melanie S.; Martin, Randall V.; Donkelaar, Aaron van; Buchard, Virginie; Torres, Omar; Ridley, David A.; Spurr, Robert J. D.

    2016-01-01

    Satellite observations of the ultraviolet aerosol index (UVAI) are sensitive to absorption of solar radiation by aerosols; this absorption affects photolysis frequencies and radiative forcing. We develop a global simulation of the UVAI using the 3-D chemical transport model GEOSChem coupled with the Vector Linearized Discrete Ordinate Radiative Transfer model (VLIDORT). The simulation is applied to interpret UVAI observations from the Ozone Monitoring Instrument (OMI) for the year 2007. Simulated and observed values are highly consistent in regions where mineral dust dominates the UVAI, but a large negative bias (-0.32 to -0.97) exists between simulated and observed values in biomass burning regions. We determine effective optical properties for absorbing organic aerosol, known as brown carbon (BrC), and implement them into GEOS-Chem to better represent observed UVAI values over biomass burning regions. The inclusion of absorbing BrC decreases the mean bias between simulated and OMI UVAI values from -0.57 to -0.09 over West Africa in January, from -0.32 to +0.0002 over South Asia in April, from -0.97 to -0.22 over southern Africa in July, and from -0.50 to +0.33 over South America in September. The spectral dependence of absorption after including BrC in the model is broadly consistent with reported observations for biomass burning aerosol, with absorbing Angstrom exponent (AAE) values ranging from 2.9 in the ultraviolet (UV) to 1.3 across the UV-Near IR spectrum. We assess the effect of the additional UV absorption by BrC on atmospheric photochemistry by examining tropospheric hydroxyl radical (OH) concentrations in GEOS-Chem. The inclusion of BrC decreases OH by up to 30% over South America in September, up to 20% over southern Africa in July, and up to 15% over other biomass burning regions. Global annual mean OH concentrations in GEOS-Chem decrease due to the presence of absorbing BrC, increasing the methyl chloroform lifetime from 5.62 to 5.68 years, thus

  9. Interpreting the Ultraviolet Aerosol Index observed with the OMI satellite instrument to understand absorption by organic aerosols: implications for atmospheric oxidation and direct radiative effects

    Directory of Open Access Journals (Sweden)

    M. S. Hammer

    2015-10-01

    Full Text Available Satellite observations of the Ultraviolet Aerosol Index (UVAI are sensitive to absorption of solar radiation by aerosols; this absorption affects photolysis frequencies and radiative forcing. We develop a global simulation of the UVAI using the 3-D chemical transport model GEOS-Chem coupled with the Vector Linearized Discrete Ordinate Radiative Transfer model (VLIDORT. The simulation is applied to interpret UVAI observations from the Ozone Monitoring Instrument (OMI for the year 2007. Simulated and observed values are highly consistent in regions where mineral dust dominates the UVAI, but a large negative bias (−0.32 to −0.97 exists between simulated and observed values in biomass burning regions. We determine effective optical properties for absorbing organic aerosol, known as brown carbon (BrC, and implement them into GEOS-Chem to better represent observed UVAI values over biomass burning regions. The addition of absorbing BrC decreases the mean bias between simulated and OMI UVAI values from −0.57 to −0.09 over West Africa in January, from −0.32 to +0.0002 over South Asia in April, from −0.97 to −0.22 over southern Africa in July, and from −0.50 to +0.33 over South America in September. The spectral dependence of absorption after adding BrC to the model is broadly consistent with reported observations for biomass burning aerosol, with Absorbing Angstrom Exponent (AAE values ranging from 2.9 in the ultraviolet (UV to 1.3 across the UV-Near IR spectrum. We assess the effect of the additional UV absorption by BrC on atmospheric photochemistry by examining tropospheric hydroxyl radical (OH concentrations in GEOS-Chem. The inclusion of BrC decreases OH by up to 35 % over South America in September, up to 25 % over southern Africa in July, and up to 20 % over other biomass burning regions. Global annual mean OH concentrations in GEOS-Chem decrease due to the presence of absorbing BrC, increasing the methyl chloroform lifetime from 5

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

    CERN Document Server

    Amdouni, Soumaya; Bouabid, Sondes

    2011-01-01

    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. 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.

  12. Annotation of selection strengths in viral genomes

    DEFF Research Database (Denmark)

    McCauley, Stephen; de Groot, Saskia; Mailund, Thomas;

    2007-01-01

    - and intergenomic regions. The presence of multiple coding regions complicates the concept of Ka/Ks ratio, and thus begs for an alternative approach when investigating selection strengths. Building on the paper by McCauley & Hein (2006), we develop a method for annotating a viral genome coding in overlapping...... may thus achieve an annotation both of coding regions as well as selection strengths, allowing us to investigate different selection patterns and hypotheses. Results: We illustrate our method by applying it to a multiple alignment of four HIV2 sequences, as well as four Hepatitis B sequences. We...... obtain an annotation of the coding regions, as well as a posterior probability for each site of the strength of selection acting on it. From this we may deduce the average posterior selection acting on the different genes. Whilst we are encouraged to see in HIV2, that the known to be conserved genes gag...

  13. 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 ...

  14. I2Cnet medical image annotation service.

    Science.gov (United States)

    Chronaki, C E; Zabulis, X; Orphanoudakis, S C

    1997-01-01

    I2Cnet (Image Indexing by Content network) aims to provide services related to the content-based management of images in healthcare over the World-Wide Web. Each I2Cnet server maintains an autonomous repository of medical images and related information. The annotation service of I2Cnet allows specialists to interact with the contents of the repository, adding comments or illustrations to medical images of interest. I2Cnet annotations may be communicated to other users via e-mail or posted to I2Cnet for inclusion in its local repositories. This paper discusses the annotation service of I2Cnet and argues that such services pave the way towards the evolution of active digital medical image libraries.

  15. Interpreting social enterprises

    Directory of Open Access Journals (Sweden)

    Carlo Borzaga

    2012-09-01

    Full Text Available Institutional and organizational variety is increasingly characterizing advanced economic systems. While traditional economic theories have focused almost exclusively on profit-maximizing (i.e., for-profit enterprises and on publicly-owned organizations, the increasing relevance of non-profit organizations, and especially of social enterprises, requires scientists to reflect on a new comprehensive economic approach for explaining this organizational variety. This paper examines the main limitations of the orthodox and institutional theories and asserts the need for creating and testing a new theoretical framework, which considers the way in which diverse enterprises pursue their goals, the diverse motivations driving actors and organizations, and the different learning patterns and routines within organizations. The new analytical framework proposed in the paper draws upon recent developments in the theories of the firm, mainly of an evolutionary and behavioral kind. The firm is interpreted as a coordination mechanism of economic activity, and one whose objectives need not coincide with profit maximization. On the other hand, economic agents driven by motivational complexity and intrinsic, non-monetary motivation play a crucial role in forming firm activity over and above purely monetary and financial objectives. The new framework is thought to be particularly suitable to correctly interpret the emergence and role of nontraditional organizational and ownership forms that are not driven by the profit motive (non-profit organizations, mainly recognized in the legal forms of cooperative firms, non-profit organizations and social enterprises. A continuum of organizational forms ranging from profit making activities to public benefit activities, and encompassing mutual benefit organizations as its core constituent, is envisaged and discussed.

  16. 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....

  17. 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.

  18. 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 ...

  19. Solar Tutorial and Annotation Resource (STAR)

    Science.gov (United States)

    Showalter, C.; Rex, R.; Hurlburt, N. E.; Zita, E. J.

    2009-12-01

    We have written a software suite designed to facilitate solar data analysis by scientists, students, and the public, anticipating enormous datasets from future instruments. Our “STAR" suite includes an interactive learning section explaining 15 classes of solar events. Users learn software tools that exploit humans’ superior ability (over computers) to identify many events. Annotation tools include time slice generation to quantify loop oscillations, the interpolation of event shapes using natural cubic splines (for loops, sigmoids, and filaments) and closed cubic splines (for coronal holes). Learning these tools in an environment where examples are provided prepares new users to comfortably utilize annotation software with new data. Upon completion of our tutorial, users are presented with media of various solar events and asked to identify and annotate the images, to test their mastery of the system. Goals of the project include public input into the data analysis of very large datasets from future solar satellites, and increased public interest and knowledge about the Sun. In 2010, the Solar Dynamics Observatory (SDO) will be launched into orbit. SDO’s advancements in solar telescope technology will generate a terabyte per day of high-quality data, requiring innovation in data management. While major projects develop automated feature recognition software, so that computers can complete much of the initial event tagging and analysis, still, that software cannot annotate features such as sigmoids, coronal magnetic loops, coronal dimming, etc., due to large amounts of data concentrated in relatively small areas. Previously, solar physicists manually annotated these features, but with the imminent influx of data it is unrealistic to expect specialized researchers to examine every image that computers cannot fully process. A new approach is needed to efficiently process these data. Providing analysis tools and data access to students and the public have proven

  20. 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 ...

  1. Ranking Biomedical Annotations with Annotator’s Semantic Relevancy

    Directory of Open Access Journals (Sweden)

    Aihua Wu

    2014-01-01

    Full Text Available Biomedical annotation is a common and affective artifact for researchers to discuss, show opinion, and share discoveries. It becomes increasing popular in many online research communities, and implies much useful information. Ranking biomedical annotations is a critical problem for data user to efficiently get information. As the annotator’s knowledge about the annotated entity normally determines quality of the annotations, we evaluate the knowledge, that is, semantic relationship between them, in two ways. The first is extracting relational information from credible websites by mining association rules between an annotator and a biomedical entity. The second way is frequent pattern mining from historical annotations, which reveals common features of biomedical entities that an annotator can annotate with high quality. We propose a weighted and concept-extended RDF model to represent an annotator, a biomedical entity, and their background attributes and merge information from the two ways as the context of an annotator. Based on that, we present a method to rank the annotations by evaluating their correctness according to user’s vote and the semantic relevancy between the annotator and the annotated entity. The experimental results show that the approach is applicable and efficient even when data set is large.

  2. Enhanced oil recovery using improved aqueous fluid-injection methods: an annotated bibliography. [328 citations

    Energy Technology Data Exchange (ETDEWEB)

    Meister, M.J.; Kettenbrink, G.K.; Collins, A.G.

    1976-10-01

    This annotated bibliography contains abstracts, prepared by the authors, of articles published between 1968 and early 1976 on tests of improved aqueous fluid injection methods (i.e., polymer and surfactant floods). The abstracts have been written and organized to facilitate studies of the oil recovery potential of polymer and surfactant floods under known reservoir conditions. 328 citations.

  3. White-Collar Crime and the Law: An Annotated Bibliography. Teaching Resource Bulletin No. 1.

    Science.gov (United States)

    Tillman, Robert

    This annotated bibliography of materials concerning white collar crime is directed at undergraduate students and instructors. Materials are organized into eight subject headings: (1) theoretical statements; (2) data sources; (3) financial institutions fraud; (4) environmental crimes; (5) workplace safety; (6) computer crimes; (7) miscellaneous…

  4. ASGARD: an open-access database of annotated transcriptomes for emerging model arthropod species.

    Science.gov (United States)

    Zeng, Victor; Extavour, Cassandra G

    2012-01-01

    The increased throughput and decreased cost of next-generation sequencing (NGS) have shifted the bottleneck genomic research from sequencing to annotation, analysis and accessibility. This is particularly challenging for research communities working on organisms that lack the basic infrastructure of a sequenced genome, or an efficient way to utilize whatever sequence data may be available. Here we present a new database, the Assembled Searchable Giant Arthropod Read Database (ASGARD). This database is a repository and search engine for transcriptomic data from arthropods that are of high interest to multiple research communities but currently lack sequenced genomes. We demonstrate the functionality and utility of ASGARD using de novo assembled transcriptomes from the milkweed bug Oncopeltus fasciatus, the cricket Gryllus bimaculatus and the amphipod crustacean Parhyale hawaiensis. We have annotated these transcriptomes to assign putative orthology, coding region determination, protein domain identification and Gene Ontology (GO) term annotation to all possible assembly products. ASGARD allows users to search all assemblies by orthology annotation, GO term annotation or Basic Local Alignment Search Tool. User-friendly features of ASGARD include search term auto-completion suggestions based on database content, the ability to download assembly product sequences in FASTA format, direct links to NCBI data for predicted orthologs and graphical representation of the location of protein domains and matches to similar sequences from the NCBI non-redundant database. ASGARD will be a useful repository for transcriptome data from future NGS studies on these and other emerging model arthropods, regardless of sequencing platform, assembly or annotation status. This database thus provides easy, one-stop access to multi-species annotated transcriptome information. We anticipate that this database will be useful for members of multiple research communities, including developmental

  5. An annotated bibliography of completed and in-progress behavioral research for the Office of Buildings and Community Systems. [About 1000 items, usually with abstracts

    Energy Technology Data Exchange (ETDEWEB)

    Weijo, R.O.; Roberson, B.F.; Eckert, R.; Anderson, M.R.

    1988-05-01

    This report provides an annotated bibliography of completed and in-progress consumer decision research useful for technology transfer and commercialization planning by the US Department of Energy's (DOE) Office of Buildings and Community Systems (OBCS). This report attempts to integrate the consumer research studies conducted across several public and private organizations over the last four to five years. Some of the sources of studies included in this annotated bibliography are DOE National Laboratories, public and private utilities, trade associations, states, and nonprofit organizations. This study divides the articles identified in this annotated bibliography into sections that are consistent with or similar to the system of organization used by OBCS.

  6. 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

  7. Bibliografia de Aztlan: An Annotated Chicano Bibliography.

    Science.gov (United States)

    Barrios, Ernie, Ed.

    More than 300 books and articles published from 1920 to 1971 are reviewed in this annotated bibliography of literature on the Chicano. The citations and reviews are categorized by subject area and deal with contemporary Chicano history, education, health, history of Mexico, literature, native Americans, philosophy, political science, pre-Columbian…

  8. Annotated bibliography of psychomotor testing. Technical report

    Energy Technology Data Exchange (ETDEWEB)

    Ervin, C.

    1987-03-01

    An annotated bibliography of 67 publications in the field of psychomotor testing has been prepared. The collection includes technical reports, journal articles, presented at scientific meetings, books and conference proceedings. The publications were assembled as preliminary work in the development of a dexterity test battery designed to measure the effects of chemical-defense-treatment drugs.

  9. 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

  10. 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.

  11. 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.

  12. Genotyping and annotation of Affymetrix SNP arrays

    DEFF Research Database (Denmark)

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

    2006-01-01

    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...

  13. 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.

  14. 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...

  15. 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.

  16. Nutrition & Adolescent Pregnancy: A Selected Annotated Bibliography.

    Science.gov (United States)

    National Agricultural Library (USDA), Washington, DC.

    This annotated bibliography on nutrition and adolescent pregnancy is intended to be a source of technical assistance for nurses, nutritionists, physicians, educators, social workers, and other personnel concerned with improving the health of teenage mothers and their babies. It is divided into two major sections. The first section lists selected…

  17. La Mujer Chicana: An Annotated Bibliography, 1976.

    Science.gov (United States)

    Chapa, Evey, Ed.; And Others

    Intended to provide interested persons, researchers, and educators with information about "la mujer Chicana", this annotated bibliography cites 320 materials published between 1916 and 1975, with the majority being between 1960 and 1975. The 12 sections cover the following subject areas: Chicana publications; Chicana feminism and "el movimiento";…

  18. 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.

  19. 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…

  20. 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.

  1. Postsecondary Peer Cooperative Learning Programs: Annotated Bibliography

    Science.gov (United States)

    Arendale, David R., Comp.

    2005-01-01

    Purpose: This annotated bibliography is focused intentionally on postsecondary peer cooperative learning programs that increasing student achievement. Peer learning has been popular in education for decades. As both a pedagogy and learning strategy, it has been frequently adapted for a wide range of academic content areas at the elementary,…

  2. Small Group Communication: An Annotated Bibliography.

    Science.gov (United States)

    Gouran, Dennis S.; Guadagnino, Christopher S.

    This annotated bibliography includes sources of information that are primarily concerned with problem solving, decision making, and processes of social influence in small groups, and secondarily deal with other aspects of communication and interaction in groups, such as conflict management and negotiation. The 57 entries, all dating from 1980…

  3. Ludwig von Mises: An Annotated Bibliography.

    Science.gov (United States)

    Gordon, David

    A 117-item annotated bibliography of books, articles, essays, lectures, and reviews by economist Ludwig von Mises is presented. The bibliography is arranged chronologicaly, and is followed by an alphabetical listing of the citations, excluding books. An index and information on the Ludwig von Mises Institute at Auburn University (Alabama) are…

  4. 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…

  5. DNAVis: interactive visualization of comparative genome annotations

    NARCIS (Netherlands)

    Fiers, M.W.E.J.; Wetering, van de H.; Peeters, T.H.J.M.; Wijk, van J.J.; Nap, J.P.H.

    2006-01-01

    The software package DNAVis offers a fast, interactive and real-time visualization of DNA sequences and their comparative genome annotations. DNAVis implements advanced methods of information visualization such as linked views, perspective walls and semantic zooming, in addition to the display of he

  6. 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...

  7. 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,…

  8. 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

  9. Computer systems for annotation of single molecule fragments

    Energy Technology Data Exchange (ETDEWEB)

    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.

  10. 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. ...

  11. Construction of coffee transcriptome networks based on gene annotation semantics.

    Science.gov (United States)

    Castillo, Luis F; Galeano, Narmer; Isaza, Gustavo A; Gaitán, Alvaro

    2012-07-24

    Gene annotation is a process that encompasses multiple approaches on the analysis of nucleic acids or protein sequences in order to assign structural and functional characteristics to gene models. When thousands of gene models are being described in an organism genome, construction and visualization of gene networks impose novel challenges in the understanding of complex expression patterns and the generation of new knowledge in genomics research. In order to take advantage of accumulated text data after conventional gene sequence analysis, this work applied semantics in combination with visualization tools to build transcriptome networks from a set of coffee gene annotations. A set of selected coffee transcriptome sequences, chosen by the quality of the sequence comparison reported by Basic Local Alignment Search Tool (BLAST) and Interproscan, were filtered out by coverage, identity, length of the query, and e-values. Meanwhile, term descriptors for molecular biology and biochemistry were obtained along the Wordnet dictionary in order to construct a Resource Description Framework (RDF) using Ruby scripts and Methontology to find associations between concepts. Relationships between sequence annotations and semantic concepts were graphically represented through a total of 6845 oriented vectors, which were reduced to 745 non-redundant associations. A large gene network connecting transcripts by way of relational concepts was created where detailed connections remain to be validated for biological significance based on current biochemical and genetics frameworks. Besides reusing text information in the generation of gene connections and for data mining purposes, this tool development opens the possibility to visualize complex and abundant transcriptome data, and triggers the formulation of new hypotheses in metabolic pathways analysis.

  12. 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...

  13. 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...

  14. 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...

  15. 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...

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

    Science.gov (United States)

    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; Wu, Chunlei

    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-based model for organizing and querying biological annotation information. MyGene.info and MyVariant.info are provided as high-performance web services, accessible at http://mygene.info and http://myvariant.info . Both are offered free of charge to the research community. PMID:27154141

  17. Deep annotation of Populus trichocarpa microRNAs from diverse tissue sets.

    Directory of Open Access Journals (Sweden)

    Joshua R Puzey

    Full Text Available Populus trichocarpa is an important woody model organism whose entire genome has been sequenced. This resource has facilitated the annotation of microRNAs (miRNAs, which are short non-coding RNAs with critical regulatory functions. However, despite their developmental importance, P. trichocarpa miRNAs have yet to be annotated from numerous important tissues. Here we significantly expand the breadth of tissue sampling and sequencing depth for miRNA annotation in P. trichocarpa using high-throughput smallRNA (sRNA sequencing. miRNA annotation was performed using three individual next-generation sRNA sequencing runs from separate leaves, xylem, and mechanically treated xylem, as well as a fourth run using a pooled sample containing vegetative apices, male flowers, female flowers, female apical buds, and male apical and lateral buds. A total of 276 miRNAs were identified from these datasets, including 155 previously unannotated miRNAs, most of which are P. trichocarpa specific. Importantly, we identified several xylem-enriched miRNAs predicted to target genes known to be important in secondary growth, including the critical reaction wood enzyme xyloglucan endo-transglycosylase/hydrolase and vascular-related transcription factors. This study provides a thorough genome-wide annotation of miRNAs in P. trichocarpa through deep sRNA sequencing from diverse tissue sets. Our data significantly expands the P. trichocarpa miRNA repertoire, which will facilitate a broad range of research in this major model system.

  18. Annotation of the protein coding regions of the equine genome

    DEFF Research Database (Denmark)

    Hestand, Matthew S.; Kalbfleisch, Theodore S.; Coleman, Stephen J.;

    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...

  19. 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...

  20. 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

  1. Real-Time Biological Annotation of Synthetic Compounds.

    Science.gov (United States)

    Gerry, Christopher J; Hua, Bruce K; Wawer, Mathias J; Knowles, Jonathan P; Nelson, Shawn D; Verho, Oscar; Dandapani, Sivaraman; Wagner, Bridget K; Clemons, Paul A; Booker-Milburn, Kevin I; Boskovic, Zarko V; Schreiber, Stuart L

    2016-07-20

    Organic chemists are able to synthesize molecules in greater number and chemical complexity than ever before. Yet, a majority of these compounds go untested in biological systems, and those that do are often tested long after the chemist can incorporate the results into synthetic planning. We propose the use of high-dimensional "multiplex" assays, which are capable of measuring thousands of cellular features in one experiment, to annotate rapidly and inexpensively the biological activities of newly synthesized compounds. This readily accessible and inexpensive "real-time" profiling method can be used in a prospective manner to facilitate, for example, the efficient construction of performance-diverse small-molecule libraries that are enriched in bioactives. Here, we demonstrate this concept by synthesizing ten triads of constitutionally isomeric compounds via complexity-generating photochemical and thermal rearrangements and measuring compound-induced changes in cellular morphology via an imaging-based "cell painting" assay. Our results indicate that real-time biological annotation can inform optimization efforts and library syntheses by illuminating trends relating to biological activity that would be difficult to predict if only chemical structure were considered. We anticipate that probe and drug discovery will benefit from the use of optimization efforts and libraries that implement this approach. PMID:27398798

  2. Interpreters, Interpreting, and the Study of Bilingualism.

    Science.gov (United States)

    Valdes, Guadalupe; Angelelli, Claudia

    2003-01-01

    Discusses research on interpreting focused specifically on issues raised by this literature about the nature of bilingualism. Suggests research carried out on interpreting--while primarily produced with a professional audience in mind and concerned with improving the practice of interpreting--provides valuable insights about complex aspects of…

  3. Normalizing XRF-scanner data: A cautionary note on the interpretation of high-resolution records from organic-rich lakes

    Science.gov (United States)

    Löwemark, L.; Chen, H.-F.; Yang, T.-N.; Kylander, M.; Yu, E.-F.; Hsu, Y.-W.; Lee, T.-Q.; Song, S.-R.; Jarvis, S.

    2011-04-01

    X-ray fluorescence (XRF) scanning of unlithified, untreated sediment cores is becoming an increasingly common method used to obtain paleoproxy data from lake records. XRF-scanning is fast and delivers high-resolution records of relative variations in the elemental composition of the sediment. However, lake sediments display extreme variations in their organic matter content, which can vary from just a few percent to well over 50%. As XRF scanners are largely insensitive to organic material in the sediment, increasing levels of organic material effectively dilute those components that can be measured, such as the lithogenic material (the closed-sum effect). Consequently, in sediments with large variations in organic material, the measured variations in an element will to a large extent mirror the changes in organic material. It is therefore necessary to normalize the elements in the lithogenic component of the sediment against a conservative element to allow changes in the input of the elements to be addressed. In this study we show that Al, which is the lightest element that can be measured using the Itrax XRF-scanner, can be used to effectively normalize the elements of the lithogenic fraction of the sediment against variations in organic content. We also show that care must be taken when choosing resolution and exposure time to ensure optimal output from the measurements.

  4. How well are protein structures annotated in secondary databases?

    Science.gov (United States)

    Rother, Kristian; Michalsky, Elke; Leser, Ulf

    2005-09-01

    We investigated to what extent Protein Data Bank (PDB) entries are annotated with second-party information based on existing cross-references between PDB and 15 other databases. We report 2 interesting findings. First, there is a clear "annotation gap" for structures less than 7 years old for secondary databases that are manually curated. Second, the examined databases overlap with each other quite well, dividing the PDB into 2 well-annotated thirds and one poorly annotated third. Both observations should be taken into account in any study depending on the selection of protein structures by their annotation.

  5. On Teaching of Interpreting from Interpretive Theory

    Institute of Scientific and Technical Information of China (English)

    栗蔷薇; 赵保成

    2013-01-01

      This paper aims to explore teaching of interpreting nowadays by starting from the interpretive theory and its characteristics. The author believes that the theory is mainly based on the study of interpretation practice, whose core content, namely,“deverbalization”has made great strides and breakthroughs in the theory of translation;when we examine translation, or rather interpretation once again from the bi-perspective of language and culture, we will have come across new thoughts in terms of translation as well as teaching of interpreting.

  6. Image Semantic Automatic Annotation by Relevance Feedback

    Institute of Scientific and Technical Information of China (English)

    ZHANG Tong-zhen; SHEN Rui-min

    2007-01-01

    A large semantic gap exists between content based index retrieval (CBIR) and high-level semantic, additional semantic information should be attached to the images, it refers in three respects including semantic representation model, semantic information building and semantic retrieval techniques. In this paper, we introduce an associated semantic network and an automatic semantic annotation system. In the system, a semantic network model is employed as the semantic representation model, it uses semantic keywords, linguistic ontology and low-level features in semantic similarity calculating. Through several times of users' relevance feedback, semantic network is enriched automatically. To speed up the growth of semantic network and get a balance annotation, semantic seeds and semantic loners are employed especially.

  7. 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...

  8. 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.

  9. REQUIREMENTS FOR A GENERAL INTERPRETATION THEORY

    Directory of Open Access Journals (Sweden)

    Anda Laura Lungu Petruescu

    2013-06-01

    Full Text Available Time has proved that Economic Analysis is not enough as to ensure all the needs of the economic field. The present study wishes to propose a new approach method of the economic phenomena and processes based on the researches made outside the economic space- a new general interpretation theory- which is centered on the human being as the basic actor of economy. A general interpretation theory must assure the interpretation of the causalities among the economic phenomena and processes- causal interpretation; the interpretation of the correlations and dependencies among indicators- normative interpretation; the interpretation of social and communicational processes in economic organizations- social and communicational interpretation; the interpretation of the community status of companies- transsocial interpretation; the interpretation of the purposes of human activities and their coherency – teleological interpretation; the interpretation of equilibrium/ disequilibrium from inside the economic systems- optimality interpretation. In order to respond to such demands, rigor, pragmatism, praxiology and contextual connectors are required. In order to progress, the economic science must improve its language, both its syntax and its semantics. The clarity of exposure requires a language clarity and the scientific theory progress asks for the need of hypotheses in the building of the theories. The switch from the common language to the symbolic one means the switch from ambiguity to rigor and rationality, that is order in thinking. But order implies structure, which implies formalization. Our paper should be a plea for these requirements, requirements which should be fulfilled by a modern interpretation theory.

  10. 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.

  11. 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...

  12. 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

  13. 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...

  14. Deburring: an annotated bibliography. Volume VI

    Energy Technology Data Exchange (ETDEWEB)

    Gillespie, L.K.

    1980-07-01

    An annotated summary of 138 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 proces economics, burr properties, and how to design to minimize burr problems. Research studies are identified as are the materials deburred.

  15. Frenchglen Interpretive Plan

    Data.gov (United States)

    US Fish and Wildlife Service, Department of the Interior — The purpose of this interpretive plan is to provide guidance for the development of the interpretive exhibits for the Frenchglen Interpretive Center, as well as the...

  16. Annotation-free probabilistic atlas learning for robust anatomy detection in CT images

    Science.gov (United States)

    Franz, Astrid; Schadewaldt, Nicole; Schulz, Heinrich; Vik, Torbjørn; Kausch, Lisa; Modersitzki, Jan; Wiemker, Rafael; Bystrov, Daniel

    2015-03-01

    A fully automatic method generating a whole body atlas from CT images is presented. The atlas serves as a reference space for annotations. It is based on a large collection of partially overlapping medical images and a registration scheme. The atlas itself consists of probabilistic tissue type maps and can represent anatomical variations. The registration scheme is based on an entropy-like measure of these maps and is robust with respect to field-of-view variations. In contrast to other atlas generation methods, which typically rely on a sufficiently large set of annotations on training cases, the presented method requires only the images. An iterative refinement strategy is used to automatically stitch the images to build the atlas. Affine registration of unseen CT images to the probabilistic atlas can be used to transfer reference annotations, e.g. organ models for segmentation initialization or reference bounding boxes for field-of-view selection. The robustness and generality of the method is shown using a three-fold cross-validation of the registration on a set of 316 CT images of unknown content and large anatomical variability. As an example, 17 organs are annotated in the atlas reference space and their localization in the test images is evaluated. The method yields a recall (sensitivity), specificity and precision of at least 96% and thus performs excellent in comparison to competitors.

  17. Seq2Ref: a web server to facilitate functional interpretation

    Directory of Open Access Journals (Sweden)

    Li Wenlin

    2013-01-01

    Full Text Available Abstract Background The size of the protein sequence database has been exponentially increasing due to advances in genome sequencing. However, experimentally characterized proteins only constitute a small portion of the database, such that the majority of sequences have been annotated by computational approaches. Current automatic annotation pipelines inevitably introduce errors, making the annotations unreliable. Instead of such error-prone automatic annotations, functional interpretation should rely on annotations of ‘reference proteins’ that have been experimentally characterized or manually curated. Results The Seq2Ref server uses BLAST to detect proteins homologous to a query sequence and identifies the reference proteins among them. Seq2Ref then reports publications with experimental characterizations of the identified reference proteins that might be relevant to the query. Furthermore, a plurality-based rating system is developed to evaluate the homologous relationships and rank the reference proteins by their relevance to the query. Conclusions The reference proteins detected by our server will lend insight into proteins of unknown function and provide extensive information to develop in-depth understanding of uncharacterized proteins. Seq2Ref is available at: http://prodata.swmed.edu/seq2ref.

  18. Production of trichothecenes and other secondary metabolites by Fusarium culmorum and Fusarium equiseti on common laboratory media and a soil organic matter agar: An ecological interpretation

    DEFF Research Database (Denmark)

    Hestbjerg, H.; Nielsen, Kristian Fog; Thrane, Ulf;

    2002-01-01

    trichothecene production was detected for 94 of 102 F culmorum isolates, only 8 of 57 F equiseti isolates were positive. Profiles of secondary metabolites were compared by following growth on yeast extract sucrose agar (YES), potato sucrose agar (PSA), and an agar medium, prepared from soil organic matter (SOM...

  19. 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.

  20. 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

  1. Algae from the arid southwestern United States: an annotated bibliography

    Energy Technology Data Exchange (ETDEWEB)

    Thomas, W.H.; Gaines, S.R.

    1983-06-01

    Desert algae are attractive biomass producers for capturing solar energy through photosynthesis of organic matter. They are probably capable of higher yields and efficiencies of light utilization than higher plants, and are already adapted to extremes of sunlight intensity, salinity and temperature such as are found in the desert. This report consists of an annotated bibliography of the literature on algae from the arid southwestern United States. It was prepared in anticipation of efforts to isolate desert algae and study their yields in the laboratory. These steps are necessary prior to setting up outdoor algal culture ponds. Desert areas are attractive for such applications because land, sunlight, and, to some extent, water resources are abundant there. References are sorted by state.

  2. DATA ANNOTATION AND RELATIONS MODELING FOR INTEGRATED OMICS IN CLINICAL RESEARCH

    Directory of Open Access Journals (Sweden)

    Arno Lukas

    2010-07-01

    Full Text Available Omics has massively permeated translational clinical research with numerous diseases being covered by Omics studies from the genome to the metabolome level. Integrating these disease specific Omics tracks appears a logical next step for building the fundament of Systems Biology and Systems Medicine. Here, coherence of individual Omics tracks regarding clinical hypothesis, samples and clinical descriptors, and finally data handling and integration become pivotal. We present a data integration, annotation and relations modeling concept for heterogeneous Omics data and workflows. With molecular features at the center of all Omics we link the result profiles from different Omics tracks characterizing a specific disease phenotype to a common human molecular reference network for allowing a seamless integration and subsequent support in interpretation of Omics screening results. Our concept rests on data structures for representing objects specified by metadata and content. For handling diverse Omics tracks a flexible structure for content is proposed allowing data representation at different levels of granularity as demanded by the type of Omics and specific type of data. Content on the molecular level includes deep annotation of molecular features on gene and protein level. Based on this annotation pair-wise relations between molecular objects are built, traversing the molecular annotation into a network of relations (molecular feature graph. Such a relation network is also built on the Omics data level, combining explicit relations derived from study setup and implicit relations generated by mining metadata and content (Omics data graph. Finally both graphs are merged utilizing the molecular feature level as common denominator, enabling a persistent integration and subsequently interpretation of Omics profiling results in the realm of a given clinical hypothesis. We present a case study on integrating transcriptomics and proteomics data on chronic

  3. BIOFILTER AS A FUNCTIONAL ANNOTATION PIPELINE FOR COMMON AND RARE COPY NUMBER BURDEN.

    Science.gov (United States)

    Kim, Dokyoon; Lucas, Anastasia; Glessner, Joseph; Verma, Shefali S; Bradford, Yuki; Li, Ruowang; Frase, Alex T; Hakonarson, Hakon; Peissig, Peggy; Brilliant, Murray; Ritchie, Marylyn D

    2016-01-01

    Recent studies on copy number variation (CNV) have suggested that an increasing burden of CNVs is associated with susceptibility or resistance to disease. A large number of genes or genomic loci contribute to complex diseases such as autism. Thus, total genomic copy number burden, as an accumulation of copy number change, is a meaningful measure of genomic instability to identify the association between global genetic effects and phenotypes of interest. However, no systematic annotation pipeline has been developed to interpret biological meaning based on the accumulation of copy number change across the genome associated with a phenotype of interest. In this study, we develop a comprehensive and systematic pipeline for annotating copy number variants into genes/genomic regions and subsequently pathways and other gene groups using Biofilter - a bioinformatics tool that aggregates over a dozen publicly available databases of prior biological knowledge. Next we conduct enrichment tests of biologically defined groupings of CNVs including genes, pathways, Gene Ontology, or protein families. We applied the proposed pipeline to a CNV dataset from the Marshfield Clinic Personalized Medicine Research Project (PMRP) in a quantitative trait phenotype derived from the electronic health record - total cholesterol. We identified several significant pathways such as toll-like receptor signaling pathway and hepatitis C pathway, gene ontologies (GOs) of nucleoside triphosphatase activity (NTPase) and response to virus, and protein families such as cell morphogenesis that are associated with the total cholesterol phenotype based on CNV profiles (permutation p-value pipeline could improve the interpretability of copy number burden analysis where hundreds of loci or genes contribute toward disease susceptibility via biological knowledge groups such as pathways. This CNV annotation pipeline with Biofilter can be used for CNV data from any genotyping or sequencing platform and to

  4. Analyzing and Interpreting Historical Sources

    DEFF Research Database (Denmark)

    Kipping, Matthias; Wadhwani, Dan; Bucheli, Marcelo

    2014-01-01

    This chapter outlines a methodology for the interpretation of historical sources, helping to realize their full potential for the study of organization, while overcoming their challenges in terms of distortions created by time, changes in context, and selective production or preservation. Drawing...

  5. High-throughput proteogenomics of Ruegeria pomeroyi: seeding a better genomic annotation for the whole marine Roseobacter clade

    Directory of Open Access Journals (Sweden)

    Christie-Oleza Joseph A

    2012-02-01

    Full Text Available Abstract Background The structural and functional annotation of genomes is now heavily based on data obtained using automated pipeline systems. The key for an accurate structural annotation consists of blending similarities between closely related genomes with biochemical evidence of the genome interpretation. In this work we applied high-throughput proteogenomics to Ruegeria pomeroyi, a member of the Roseobacter clade, an abundant group of marine bacteria, as a seed for the annotation of the whole clade. Results A large dataset of peptides from R. pomeroyi was obtained after searching over 1.1 million MS/MS spectra against a six-frame translated genome database. We identified 2006 polypeptides, of which thirty-four were encoded by open reading frames (ORFs that had not previously been annotated. From the pool of 'one-hit-wonders', i.e. those ORFs specified by only one peptide detected by tandem mass spectrometry, we could confirm the probable existence of five additional new genes after proving that the corresponding RNAs were transcribed. We also identified the most-N-terminal peptide of 486 polypeptides, of which sixty-four had originally been wrongly annotated. Conclusions By extending these re-annotations to the other thirty-six Roseobacter isolates sequenced to date (twenty different genera, we propose the correction of the assigned start codons of 1082 homologous genes in the clade. In addition, we also report the presence of novel genes within operons encoding determinants of the important tricarboxylic acid cycle, a feature that seems to be characteristic of some Roseobacter genomes. The detection of their corresponding products in large amounts raises the question of their function. Their discoveries point to a possible theory for protein evolution that will rely on high expression of orphans in bacteria: their putative poor efficiency could be counterbalanced by a higher level of expression. Our proteogenomic analysis will increase

  6. Proteomic detection of non-annotated protein-coding genes in Pseudomonas fluorescens Pf0-1.

    Science.gov (United States)

    Kim, Wook; Silby, Mark W; Purvine, Sam O; Nicoll, Julie S; Hixson, Kim K; Monroe, Matt; Nicora, Carrie D; Lipton, Mary S; Levy, Stuart B

    2009-12-24

    Genome sequences are annotated by computational prediction of coding sequences, followed by similarity searches such as BLAST, which provide a layer of possible functional information. While the existence of processes such as alternative splicing complicates matters for eukaryote genomes, the view of bacterial genomes as a linear series of closely spaced genes leads to the assumption that computational annotations that predict such arrangements completely describe the coding capacity of bacterial genomes. We undertook a proteomic study to identify proteins expressed by Pseudomonas fluorescens Pf0-1 from genes that were not predicted during the genome annotation. Mapping peptides to the Pf0-1 genome sequence identified sixteen non-annotated protein-coding regions, of which nine were antisense to predicted genes, six were intergenic, and one read in the same direction as an annotated gene but in a different frame. The expression of all but one of the newly discovered genes was verified by RT-PCR. Few clues as to the function of the new genes were gleaned from informatic analyses, but potential orthologs in other Pseudomonas genomes were identified for eight of the new genes. The 16 newly identified genes improve the quality of the Pf0-1 genome annotation, and the detection of antisense protein-coding genes indicates the under-appreciated complexity of bacterial genome organization.

  7. Proteomic detection of non-annotated protein-coding genes in Pseudomonas fluorescens Pf0-1.

    Directory of Open Access Journals (Sweden)

    Wook Kim

    Full Text Available Genome sequences are annotated by computational prediction of coding sequences, followed by similarity searches such as BLAST, which provide a layer of possible functional information. While the existence of processes such as alternative splicing complicates matters for eukaryote genomes, the view of bacterial genomes as a linear series of closely spaced genes leads to the assumption that computational annotations that predict such arrangements completely describe the coding capacity of bacterial genomes. We undertook a proteomic study to identify proteins expressed by Pseudomonas fluorescens Pf0-1 from genes that were not predicted during the genome annotation. Mapping peptides to the Pf0-1 genome sequence identified sixteen non-annotated protein-coding regions, of which nine were antisense to predicted genes, six were intergenic, and one read in the same direction as an annotated gene but in a different frame. The expression of all but one of the newly discovered genes was verified by RT-PCR. Few clues as to the function of the new genes were gleaned from informatic analyses, but potential orthologs in other Pseudomonas genomes were identified for eight of the new genes. The 16 newly identified genes improve the quality of the Pf0-1 genome annotation, and the detection of antisense protein-coding genes indicates the under-appreciated complexity of bacterial genome organization.

  8. Proteomic Detection of Non-Annotated Protein-Coding Genes in Pseudomonas fluorescens Pf0-1

    Energy Technology Data Exchange (ETDEWEB)

    Kim, Wook; Silby, Mark W.; Purvine, Samuel O.; Nicoll, Julie S.; Hixson, Kim K.; Monroe, Matthew E.; Nicora, Carrie D.; Lipton, Mary S.; Levy, Stuart B.

    2009-12-24

    Genome sequences are annotated by computational prediction of coding sequences, followed by similarity searches such as BLAST, which provide a layer of (possible) functional information. While the existence of processes such as alternative splicing complicates matters for eukaryote genomes, the view of bacterial genomes as a linear series of closely spaced genes leads to the assumption that computational annotations which predict such arrangements completely describe the coding capacity of bacterial genomes. We undertook a proteomic study to identify proteins expressed by Pseudomonas fluorescens Pf0-1 from genes which were not predicted during the genome annotation. Mapping peptides to the Pf0-1 genome sequence identified sixteen non-annotated protein-coding regions, of which nine were antisense to predicted genes, six were intergenic, and one read in the same direction as an annotated gene but in a different frame. The expression of all but one of the newly discovered genes was verified by RT-PCR. Few clues as to the function of the new genes were gleaned from informatic analyses, but potential orthologues in other Pseudomonas genomes were identified for eight of the new genes. The 16 newly identified genes improve the quality of the Pf0-1 genome annotation, and the detection of antisense protein-coding genes indicates the under-appreciated complexity of bacterial genome organization.

  9. 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

  10. On court interpreters' visibility

    DEFF Research Database (Denmark)

    Dubslaff, Friedel; Martinsen, Bodil

    on the interpreter's interpersonal role and, in particular, on signs of the interpreter's visibility, i.e. active co-participation. At first sight, the interpreting assignment in question seems to be a short and simple routine task which would not require the interpreter to deviate from the traditional picture...... of the service rendered/received. The paper presents a small-scale case study based on an interpreted witness interrogation. Recent research on the interpreter's role has shown that interpreters across all settings perceive themselves as "visible" (Angelelli 2003, 2004). This has led us to focus...

  11. 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...

  12. Annotated research bibliography for geothermal reservoir engineering

    Energy Technology Data Exchange (ETDEWEB)

    Sudol, G.A.; Harrison, R.F.; Ramey, H.J. Jr.

    1979-08-01

    This bibliography is divided into the following subject areas: formation evaluation, modeling, exploitation strategies, and interpretation of production trends. A subject/author index is included. (MHR)

  13. Eval: A software package for analysis of genome annotations

    OpenAIRE

    Brent Michael R; Keibler Evan

    2003-01-01

    Abstract Summary Eval is a flexible tool for analyzing the performance of gene annotation systems. It provides summaries and graphical distributions for many descriptive statistics about any set of annotations, regardless of their source. It also compares sets of predictions to standard annotations and to one another. Input is in the standard Gene Transfer Format (GTF). Eval can be run interactively or via the command line, in which case output options include easily parsable tab-delimited fi...

  14. 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...

  15. 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

  16. Correction of the Caulobacter crescentus NA1000 genome annotation.

    Science.gov (United States)

    Ely, Bert; Scott, LaTia Etheredge

    2014-01-01

    Bacterial genome annotations are accumulating rapidly in the GenBank database and the use of automated annotation technologies to create these annotations has become the norm. However, these automated methods commonly result in a small, but significant percentage of genome annotation errors. To improve accuracy and reliability, we analyzed the Caulobacter crescentus NA1000 genome utilizing computer programs Artemis and MICheck to manually examine the third codon position GC content, alignment to a third codon position GC frame plot peak, and matches in the GenBank database. We identified 11 new genes, modified the start site of 113 genes, and changed the reading frame of 38 genes that had been incorrectly annotated. Furthermore, our manual method of identifying protein-coding genes allowed us to remove 112 non-coding regions that had been designated as coding regions. The improved NA1000 genome annotation resulted in a reduction in the use of rare codons since noncoding regions with atypical codon usage were removed from the annotation and 49 new coding regions were added to the annotation. Thus, a more accurate codon usage table was generated as well. These results demonstrate that a comparison of the location of peaks third codon position GC content to the location of protein coding regions could be used to verify the annotation of any genome that has a GC content that is greater than 60%.

  17. Correction of the Caulobacter crescentus NA1000 genome annotation.

    Directory of Open Access Journals (Sweden)

    Bert Ely

    Full Text Available Bacterial genome annotations are accumulating rapidly in the GenBank database and the use of automated annotation technologies to create these annotations has become the norm. However, these automated methods commonly result in a small, but significant percentage of genome annotation errors. To improve accuracy and reliability, we analyzed the Caulobacter crescentus NA1000 genome utilizing computer programs Artemis and MICheck to manually examine the third codon position GC content, alignment to a third codon position GC frame plot peak, and matches in the GenBank database. We identified 11 new genes, modified the start site of 113 genes, and changed the reading frame of 38 genes that had been incorrectly annotated. Furthermore, our manual method of identifying protein-coding genes allowed us to remove 112 non-coding regions that had been designated as coding regions. The improved NA1000 genome annotation resulted in a reduction in the use of rare codons since noncoding regions with atypical codon usage were removed from the annotation and 49 new coding regions were added to the annotation. Thus, a more accurate codon usage table was generated as well. These results demonstrate that a comparison of the location of peaks third codon position GC content to the location of protein coding regions could be used to verify the annotation of any genome that has a GC content that is greater than 60%.

  18. 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)

  19. 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.

  20. Semantator: semantic annotator for converting biomedical text to linked data.

    Science.gov (United States)

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

    2013-10-01

    More than 80% of biomedical data is embedded in plain text. The unstructured nature of these text-based documents makes it challenging to easily browse and query the data of interest in them. One approach to facilitate browsing and querying biomedical text is to convert the plain text to a linked web of data, i.e., converting data originally in free text to structured formats with defined meta-level semantics. In this paper, we introduce Semantator (Semantic Annotator), a semantic-web-based environment for annotating data of interest in biomedical documents, browsing and querying the annotated data, and interactively refining annotation results if needed. Through Semantator, information of interest can be either annotated manually or semi-automatically using plug-in information extraction tools. The annotated results will be stored in RDF and can be queried using the SPARQL query language. In addition, semantic reasoners can be directly applied to the annotated data for consistency checking and knowledge inference. Semantator has been released online and was used by the biomedical ontology community who provided positive feedbacks. Our evaluation results indicated that (1) Semantator can perform the annotation functionalities as designed; (2) Semantator can be adopted in real applications in clinical and transactional research; and (3) the annotated results using Semantator can be easily used in Semantic-web-based reasoning tools for further inference.

  1. 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.

  2. Low-level radioactive waste technology: a selected, annotated bibliography

    Energy Technology Data Exchange (ETDEWEB)

    Fore, C.S.; Vaughan, N.D.; Hyder, L.K.

    1980-10-01

    This annotated bibliography of 447 references contains scientific, technical, economic, and regulatory information relevant to low-level radioactive waste technology. The bibliography focuses on environmental transport, disposal site, and waste treatment studies. The publication covers both domestic and foreign literature for the period 1952 to 1979. Major chapters selected are Chemical and Physical Aspects; Container Design and Performance; Disposal Site; Environmental Transport; General Studies and Reviews; Geology, Hydrology and Site Resources; Regulatory and Economic Aspects; Transportation Technology; Waste Production; and Waste Treatment. Specialized data fields have been incorporated into the data file to improve the ease and accuracy of locating pertinent references. Specific radionuclides for which data are presented are listed in the Measured Radionuclides field, and specific parameters which affect the migration of these radionuclides are presented in the Measured Parameters field. In addition, each document referenced in this bibliography has been assigned a relevance number to facilitate sorting the documents according to their pertinence to low-level radioactive waste technology. The documents are rated 1, 2, 3, or 4, with 1 indicating direct applicability to low-level radioactive waste technology and 4 indicating that a considerable amount of interpretation is required for the information presented to be applied. The references within each chapter are arranged alphabetically by leading author, corporate affiliation, or title of the document. Indexes are provide for (1) author(s), (2) keywords, (3) subject category, (4) title, (5) geographic location, (6) measured parameters, (7) measured radionuclides, and (8) publication description.

  3. Low-level radioactive waste technology: a selected, annotated bibliography

    International Nuclear Information System (INIS)

    This annotated bibliography of 447 references contains scientific, technical, economic, and regulatory information relevant to low-level radioactive waste technology. The bibliography focuses on environmental transport, disposal site, and waste treatment studies. The publication covers both domestic and foreign literature for the period 1952 to 1979. Major chapters selected are Chemical and Physical Aspects; Container Design and Performance; Disposal Site; Environmental Transport; General Studies and Reviews; Geology, Hydrology and Site Resources; Regulatory and Economic Aspects; Transportation Technology; Waste Production; and Waste Treatment. Specialized data fields have been incorporated into the data file to improve the ease and accuracy of locating pertinent references. Specific radionuclides for which data are presented are listed in the Measured Radionuclides field, and specific parameters which affect the migration of these radionuclides are presented in the Measured Parameters field. In addition, each document referenced in this bibliography has been assigned a relevance number to facilitate sorting the documents according to their pertinence to low-level radioactive waste technology. The documents are rated 1, 2, 3, or 4, with 1 indicating direct applicability to low-level radioactive waste technology and 4 indicating that a considerable amount of interpretation is required for the information presented to be applied. The references within each chapter are arranged alphabetically by leading author, corporate affiliation, or title of the document. Indexes are provide for (1) author(s), (2) keywords, (3) subject category, (4) title, (5) geographic location, (6) measured parameters, (7) measured radionuclides, and (8) publication description

  4. 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.

  5. 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.

  6. On Prerequisites of Interpreters

    Institute of Scientific and Technical Information of China (English)

    范文

    2006-01-01

    Interpreters are invariably playing a crucial role in international affairs. Those who regularly read pictorials or watch TV news programs know best why interpreters are always placed between two leaders. That is because interpreters are indispensable if any two VIPs aim to achieve further understanding, to eliminate bilateral distrust or even establish alliance with each other, a fact may partly account for why so many students are swarming into translation schools. Are they able to become interpreters? What are the prerequisites for an interpreter? This article will, taking into operative factors as complete as possible, provide a basic framework under which prerequisites of interpreters are structured.

  7. InterPreting effects of TOCinert organic content on source rock Potential using S2 vs. TOC graPh in Maamba Coalfield,southern Zambia

    Institute of Scientific and Technical Information of China (English)

    Cryton Phiri; WANG Pujun; G Roland Nguimbi; Abdallah-Yousif Ibrahim Hassan

    2014-01-01

    The authors Present the effects of the total organic carbon( TOCinert )during Pyrolysis and how it overall affects the estimates of the hydrocarbon index( HI)using the cross Plot S2 vs. TOC graPh. A total of 21 drillcore samPles consisting of the non-carbonaceous mudstones,carbonaceous mudstones,coaly mudstones and coals with S2 >0. 35 are selected and used. The average TOC for the samPled PoPulation is 10. 36 wt%. TOCinert measured from the S2 vs. TOC graPh is 2. 97 wt% and the average Pyrolysable TOClive is 7. 39 wt%. The HI is 102 mg HC/g TOC and the Pyrolysable HI is 175 mg HC/g TOC,indicating that the TOCinert or mi-neral matrix adsorbs some of the hydrocarbons liberated during Pyrolysis resulting into the low HI values which affects the correct determination of the source rock Potential. Other aPPlications of the S2 vs. TOC cross Plot have been used to determine the dePositional system tracts. The high stand system tract is also determined through this method.

  8. Australian sea-floor survey data, with images and expert annotations

    OpenAIRE

    Bewley, Michael; Friedman, Ariell; Ferrari, Renata; Hill, Nicole; Hovey, Renae; Barrett, Neville; Pizarro, Oscar; Figueira, Will; Meyer, Lisa; Babcock, Russ; Bellchambers, Lynda; Byrne, Maria; Williams, Stefan B.

    2015-01-01

    This Australian benthic data set (BENTHOZ-2015) consists of an expert-annotated set of georeferenced benthic images and associated sensor data, captured by an autonomous underwater vehicle (AUV) around Australia. This type of data is of interest to marine scientists studying benthic habitats and organisms. AUVs collect georeferenced images over an area with consistent illumination and altitude, and make it possible to generate broad scale, photo-realistic 3D maps. Marine scientists then typic...

  9. Transcript Mapping and Genome Annotation of Ascidian mtDNA Using EST Data

    OpenAIRE

    Gissi, Carmela; Pesole, Graziano

    2003-01-01

    Mitochondrial transcripts of two ascidian species were reconstructed through sequence assembly of publicly available ESTs resembling mitochondrial DNA sequences (mt-ESTs). This strategy allowed us to analyze processing and mapping of the mitochondrial transcripts and to investigate the gene organization of a previously uncharacterized mitochondrial genome (mtDNA). This new strategy would greatly facilitate the sequencing and annotation of mtDNAs. In Ciona intestinalis, the assembled mt-...

  10. Organizations

    DEFF Research Database (Denmark)

    Hatch, Mary Jo

    Most of us recognize that organizations are everywhere. You meet them on every street corner in the form of families and shops, study in them, work for them, buy from them, pay taxes to them. But have you given much thought to where they came from, what they are today, and what they might become...... and considers many more. Mary Jo Hatch introduces the concept of organizations by presenting definitions and ideas drawn from the a variety of subject areas including the physical sciences, economics, sociology, psychology, anthropology, literature, and the visual and performing arts. Drawing on examples from...... prehistory and everyday life, from the animal kingdom as well as from business, government, and other formal organizations, Hatch provides a lively and thought provoking introduction to the process of organization....

  11. Emissions and ambient distributions of Biogenic Volatile Organic Compounds (BVOC in a ponderosa pine ecosystem: interpretation of PTR-MS mass spectra

    Directory of Open Access Journals (Sweden)

    S. Kim

    2010-02-01

    Full Text Available Two proton-transfer-reaction mass spectrometry systems were deployed at the Bio-hydro-atmosphere interactions of Energy, Aerosols, Carbon, H2O, Organics and Nitrogen-Southern Rocky Mountain 2008 field campaign (BEACHON-SRM08; July to September, 2008 at the Manitou Forest Observatory in a ponderosa pine woodland near Woodland Park, Colorado USA. The two PTR-MS systems simultaneously measured BVOC emissions and ambient distributions of their oxidation products. Here, we present mass spectral analysis in a wide range of masses (m/z 40+ to 210+ to assess our understanding of BVOC emissions and their photochemical processing inside of the forest canopy. The biogenic terpenoids, 2-methyl-3-butene-2-ol (MBO, 50.2% and several monoterpenes (MT, 33.5% were identified as the dominant BVOC emissions from a transmission corrected mass spectrum (PTR-MS, averaged over the daytime (11 a.m. to 3 p.m., local time of three days. To assess contributions of oxidation products of local BVOC, we calculate an oxidation product spectrum with the OH- and ozone-initiated oxidation product distribution mass spectra of two major BVOC emissions at the ecosystem (MBO and β-pinene that were observed from laboratory oxidation experiments. The majority (~76% of the total signal in the transmission corrected PTR-MS spectra could be explained by identified compounds. The remainder are attributed to oxidation products of BVOC emitted from nearby ecosystems and transported to the site, and oxidation products of unidentified BVOC emitted from the ponderosa pine ecosystem.

  12. Transcriptomal Changes and Functional Annotation of the Developing Nonhuman Primate Choroid Plexus

    Directory of Open Access Journals (Sweden)

    Joakim eEk

    2015-03-01

    Full Text Available The choroid plexuses are small organs that protrude into each brain ventricle producing cerebrospinal fluid that constantly bathes the brain. These organs differentiate early in development just after neural closure at a stage when the brain is little vascularized. In recent years the plexus has been shown to have a much more active role in brain development than previously appreciated thereby it can influence both neurogenesis and neural migration by secreting factors into the CSF. However, much of choroid plexus developmental function is still unclear. Most previous studies on this organ have been undertaken in rodents but translation into humans is not straightforward since they have a different timing of brain maturation processes. We have collected choroid plexus from three fetal gestational ages of a nonhuman primate, the baboon, which has much closer brain development to humans. The transcriptome of the plexuses was determined by next generation sequencing and Ingenuity Pathway Analysis software was used to annotate functions and enrichment of pathways of changes in the transcriptome. The number of unique transcripts decreased with development and the majority of differentially expressed transcripts were down-regulated through development suggesting a more complex and active plexus earlier in fetal development. The functional annotation indicated changes across widespread biological functions in plexus development. In particular we find age-dependent regulation of genes associated with annotation categories: Gene Expression, Development of Cardiovascular System, Nervous System Development and Molecular Transport. Our observations support the idea that the choroid plexus has roles in shaping brain development.

  13. Transcriptomal changes and functional annotation of the developing non-human primate choroid plexus.

    Science.gov (United States)

    Ek, C Joakim; Nathanielsz, Peter; Li, Cun; Mallard, Carina

    2015-01-01

    The choroid plexuses are small organs that protrude into each brain ventricle producing cerebrospinal fluid that constantly bathes the brain. These organs differentiate early in development just after neural closure at a stage when the brain is little vascularized. In recent years the plexus has been shown to have a much more active role in brain development than previously appreciated thereby it can influence both neurogenesis and neural migration by secreting factors into the CSF. However, much of choroid plexus developmental function is still unclear. Most previous studies on this organ have been undertaken in rodents but translation into humans is not straightforward since they have a different timing of brain maturation processes. We have collected choroid plexus from three fetal gestational ages of a non-human primate, the baboon, which has much closer brain development to humans. The transcriptome of the plexuses was determined by next generation sequencing and Ingenuity Pathway Analysis software was used to annotate functions and enrichment of pathways of changes in the transcriptome. The number of unique transcripts decreased with development and the majority of differentially expressed transcripts were down-regulated through development suggesting a more complex and active plexus earlier in fetal development. The functional annotation indicated changes across widespread biological functions in plexus development. In particular we find age-dependent regulation of genes associated with annotation categories: Gene Expression, Development of Cardiovascular System, Nervous System Development and Molecular Transport. Our observations support the idea that the choroid plexus has roles in shaping brain development. PMID:25814924

  14. Genre and Interpretation

    DEFF Research Database (Denmark)

    Auken, Sune

    2015-01-01

    Despite the immensity of genre studies as well as studies in interpretation, our understanding of the relationship between genre and interpretation is sketchy at best. The article attempts to unravel some of intricacies of that relationship through an analysis of the generic interpretation carrie...

  15. Interpreting. PEPNet Tipsheet

    Science.gov (United States)

    Darroch, Kathleen

    2010-01-01

    An interpreter's role is to facilitate communication and convey all auditory and signed information so that both hearing and deaf individuals may fully interact. The common types of services provided by interpreters are: (1) American Sign Language (ASL) Interpretation--a visual-gestural language with its own linguistic features; (2) Sign Language…

  16. Engineering Definitional Interpreters

    DEFF Research Database (Denmark)

    Midtgaard, Jan; Ramsay, Norman; Larsen, Bradford

    2013-01-01

    A definitional interpreter should be clear and easy to write, but it may run 4--10 times slower than a well-crafted bytecode interpreter. In a case study focused on implementation choices, we explore ways of making definitional interpreters faster without expending much programming effort. We imp...

  17. About quantum mechanics interpretation

    OpenAIRE

    Kyriakos, Alexander G.

    2002-01-01

    There is a certainty that the modern (Copenhagen's) interpretation of quantum mechanics is correct. However, the some physicist had the opinion that the modern quantum mechanics is a phenomenological theory. The suggested theory is the new quantum mechanics interpretation that is entirely according to the modern interpretation and gives a number of results, which naturally explain the postulates of the modern quantum mechanics.

  18. Annotation Method (AM): SE40_AM1 [Metabolonote[Archive

    Lifescience Database Archive (English)

    Full Text Available used for annotation and identification of the compounds. Retension time of 56 authentic chemicals (13-OxoOD...lcone, Nicotinamide, Nicotinate, Pantothenate, Phloretin, Prunin, Rutin, S-Adenosyl-L-methionine, Tomatine, UMP, Uridine) are used for annotation and identification of the compounds. ...

  19. 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 ...

  20. From the Margins to the Center: The Future of Annotation.

    Science.gov (United States)

    Wolfe, Joanna L.; Neuwirth, Christine M.

    2001-01-01

    Describes the importance of annotation to reading and writing practices and reviews new technologies that complicate the ways annotation can be used to support and enhance traditional reading, writing, and collaboration processes. Emphasizes issues and methods that will be productive for enhancing theories of workplace and classroom communication…

  1. Annotation-Based Whole Genomic Prediction and Selection

    DEFF Research Database (Denmark)

    Kadarmideen, Haja; Do, Duy Ngoc; Janss, Luc;

    in their contribution to estimated genomic variances and in prediction of genomic breeding values by applying SNP annotation approaches to feed efficiency. Ensembl Variant Predictor (EVP) and Pig QTL database were used as the source of genomic annotation for 60K chip. Genomic prediction was performed using the Bayes...... prove useful for less heritable traits such as diseases and fertility...

  2. MUTAGEN: Multi-user tool for annotating GENomes

    DEFF Research Database (Denmark)

    Brugger, K.; Redder, P.; Skovgaard, Marie

    2003-01-01

    MUTAGEN is a free prokaryotic annotation system. It offers the advantages of genome comparison, graphical sequence browsers, search facilities and open-source for user-specific adjustments. The web-interface allows several users to access the system from standard desktop computers. The Sulfolobus...... acidocaldarius genome, and several plasmids and viruses have so far been analysed and annotated using MUTAGEN....

  3. 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.

  4. JAFA: a protein function annotation meta-server

    DEFF Research Database (Denmark)

    Friedberg, Iddo; Harder, Tim; Godzik, Adam

    2006-01-01

    With the high number of sequences and structures streaming in from genomic projects, there is a need for more powerful and sophisticated annotation tools. Most problematic of the annotation efforts is predicting gene and protein function. Over the past few years there has been considerable progress...

  5. 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.

  6. 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

  7. 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,…

  8. 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...

  9. Titles for Technology: An Annotated Bibliography. Compiled at the 1967 Summer Institute of Technology for Children (Marlton, N.J.)

    Science.gov (United States)

    New Jersey State Dept. of Education, Trenton. Div. of Vocational Education.

    This annotated bibliography includes about 400 books which are suitable for use in elementary industrial arts. These books, available in the state library system of New Jersey, are organized under 50 topics such as: (1) Automation, (2) Graphic Arts, (3) Machines, (4) Space Travel, and (5) Tools and Measuring. Most of the citations are children's…

  10. 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.

  11. 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.

  12. 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...

  13. The Disease and Gene Annotations (DGA): an annotation resource for human disease.

    Science.gov (United States)

    Peng, Kai; Xu, Wei; Zheng, Jianyong; Huang, Kegui; Wang, Huisong; Tong, Jiansong; Lin, Zhifeng; Liu, Jun; Cheng, Wenqing; Fu, Dong; Du, Pan; Kibbe, Warren A; Lin, Simon M; Xia, Tian

    2013-01-01

    Disease and Gene Annotations database (DGA, http://dga.nubic.northwestern.edu) is a collaborative effort aiming to provide a comprehensive and integrative annotation of the human genes in disease network context by integrating computable controlled vocabulary of the Disease Ontology (DO version 3 revision 2510, which has 8043 inherited, developmental and acquired human diseases), NCBI Gene Reference Into Function (GeneRIF) and molecular interaction network (MIN). DGA integrates these resources together using semantic mappings to build an integrative set of disease-to-gene and gene-to-gene relationships with excellent coverage based on current knowledge. DGA is kept current by periodically reparsing DO, GeneRIF, and MINs. DGA provides a user-friendly and interactive web interface system enabling users to efficiently query, download and visualize the DO tree structure and annotations as a tree, a network graph or a tabular list. To facilitate integrative analysis, DGA provides a web service Application Programming Interface for integration with external analytic tools.

  14. Mathematical Language / Scientific Interpretation / Theological Interpretation

    Directory of Open Access Journals (Sweden)

    Bodea Marcel Smilihon

    2015-05-01

    Full Text Available The specific languages referred to in this presentation are: scientific language, mathematical language, theological language and philosophical language. Cosmological, scientific or theological models understood as distinct interpretations of a common symbolic language do not ensure, by such a common basis, a possible or legitimate correspondence of certain units of meaning. Mathematics understood as a symbolic language used in scientific and theological interpretation does not bridge between science and theology. Instead, it only allows the assertion of a rational-mathematical unity in expression. In this perspective, theology is nothing less rational than science. The activity of interpretation has an interdisciplinary character, it is a necessary condition of dialogue. We cannot speak about dialogue without communication between various fields, without passing from one specialized language to another specialized language. The present paper proposes to suggest this aspect.

  15. 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

  16. Interpretation biases in paranoia.

    Science.gov (United States)

    Savulich, George; Freeman, Daniel; Shergill, Sukhi; Yiend, Jenny

    2015-01-01

    Information in the environment is frequently ambiguous in meaning. Emotional ambiguity, such as the stare of a stranger, or the scream of a child, encompasses possible good or bad emotional consequences. Those with elevated vulnerability to affective disorders tend to interpret such material more negatively than those without, a phenomenon known as "negative interpretation bias." In this study we examined the relationship between vulnerability to psychosis, measured by trait paranoia, and interpretation bias. One set of material permitted broadly positive/negative (valenced) interpretations, while another allowed more or less paranoid interpretations, allowing us to also investigate the content specificity of interpretation biases associated with paranoia. Regression analyses (n=70) revealed that trait paranoia, trait anxiety, and cognitive inflexibility predicted paranoid interpretation bias, whereas trait anxiety and cognitive inflexibility predicted negative interpretation bias. In a group comparison those with high levels of trait paranoia were negatively biased in their interpretations of ambiguous information relative to those with low trait paranoia, and this effect was most pronounced for material directly related to paranoid concerns. Together these data suggest that a negative interpretation bias occurs in those with elevated vulnerability to paranoia, and that this bias may be strongest for material matching paranoid beliefs. We conclude that content-specific biases may be important in the cause and maintenance of paranoid symptoms.

  17. The High Throughput Sequence Annotation Service (HT-SAS – the shortcut from sequence to true Medline words

    Directory of Open Access Journals (Sweden)

    Siedlecki Pawel

    2009-05-01

    Full Text Available Abstract Background Advances in high-throughput technologies available to modern biology have created an increasing flood of experimentally determined facts. Ordering, managing and describing these raw results is the first step which allows facts to become knowledge. Currently there are limited ways to automatically annotate such data, especially utilizing information deposited in published literature. Results To aid researchers in describing results from high-throughput experiments we developed HT-SAS, a web service for automatic annotation of proteins using general English words. For each protein a poll of Medline abstracts connected to homologous proteins is gathered using the UniProt-Medline link. Overrepresented words are detected using binomial statistics approximation. We tested our automatic approach with a protein test set from SGD to determine the accuracy and usefulness of our approach. We also applied the automatic annotation service to improve annotations of proteins from Plasmodium bergei expressed exclusively during the blood stage. Conclusion Using HT-SAS we created new, or enriched already established annotations for over 20% of proteins from Plasmodium bergei expressed in the blood stage, deposited in PlasmoDB. Our tests show this approach to information extraction provides highly specific keywords, often also when the number of abstracts is limited. Our service should be useful for manual curators, as a complement to manually curated information sources and for researchers working with protein datasets, especially from poorly characterized organisms.

  18. UP-TORR: online tool for accurate and Up-to-Date annotation of RNAi Reagents.

    Science.gov (United States)

    Hu, Yanhui; Roesel, Charles; Flockhart, Ian; Perkins, Lizabeth; Perrimon, Norbert; Mohr, Stephanie E

    2013-09-01

    RNA interference (RNAi) is a widely adopted tool for loss-of-function studies but RNAi results only have biological relevance if the reagents are appropriately mapped to genes. Several groups have designed and generated RNAi reagent libraries for studies in cells or in vivo for Drosophila and other species. At first glance, matching RNAi reagents to genes appears to be a simple problem, as each reagent is typically designed to target a single gene. In practice, however, the reagent-gene relationship is complex. Although the sequences of oligonucleotides used to generate most types of RNAi reagents are static, the reference genome and gene annotations are regularly updated. Thus, at the time a researcher chooses an RNAi reagent or analyzes RNAi data, the most current interpretation of the RNAi reagent-gene relationship, as well as related information regarding specificity (e.g., predicted off-target effects), can be different from the original interpretation. Here, we describe a set of strategies and an accompanying online tool, UP-TORR (for Updated Targets of RNAi Reagents; www.flyrnai.org/up-torr), useful for accurate and up-to-date annotation of cell-based and in vivo RNAi reagents. Importantly, UP-TORR automatically synchronizes with gene annotations daily, retrieving the most current information available, and for Drosophila, also synchronizes with the major reagent collections. Thus, UP-TORR allows users to choose the most appropriate RNAi reagents at the onset of a study, as well as to perform the most appropriate analyses of results of RNAi-based studies.

  19. 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.

  20. Citrus sinensis annotation project (CAP): a comprehensive database for sweet orange genome.

    Science.gov (United States)

    Wang, Jia; Chen, Dijun; Lei, Yang; Chang, Ji-Wei; Hao, Bao-Hai; Xing, Feng; Li, Sen; Xu, Qiang; Deng, Xiu-Xin; Chen, Ling-Ling

    2014-01-01

    Citrus is one of the most important and widely grown fruit crop with global production ranking firstly among all the fruit crops in the world. Sweet orange accounts for more than half of the Citrus production both in fresh fruit and processed juice. We have sequenced the draft genome of a double-haploid sweet orange (C. sinensis cv. Valencia), and constructed the Citrus sinensis annotation project (CAP) to store and visualize the sequenced genomic and transcriptome data. CAP provides GBrowse-based organization of sweet orange genomic data, which integrates ab initio gene prediction, EST, RNA-seq and RNA-paired end tag (RNA-PET) evidence-based gene annotation. Furthermore, we provide a user-friendly web interface to show the predicted protein-protein interactions (PPIs) and metabolic pathways in sweet orange. CAP provides comprehensive information beneficial to the researchers of sweet orange and other woody plants, which is freely available at http://citrus.hzau.edu.cn/.

  1. FunnyBase: a systems level functional annotation of Fundulus ESTs for the analysis of gene expression

    Directory of Open Access Journals (Sweden)

    Kolell Kevin J

    2004-12-01

    Full Text Available 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 the understanding of patterns of gene expression that underlie biological processes. Results We describe a bioinformatics pipeline known as FunnyBase that has been used to store, annotate, and analyze 40,363 expressed sequence tags (ESTs from the heart and liver of the fish, Fundulus heteroclitus. Primary annotations based on sequence similarity are linked to networks of systematic annotation in Gene Ontology (GO and the Kyoto Encyclopedia of Genes and Genomes (KEGG and can be queried and computationally utilized in downstream analyses. Steps are taken to ensure that the annotation is self-consistent and that the structure of GO is used to identify higher level functions that may not be annotated directly. An integrated framework for cDNA library production, sequencing, quality control, expression data generation, and systems-level analysis is presented and utilized. In a case study, a set of genes, that had statistically significant regression between gene expression levels and environmental temperature along the Atlantic Coast, shows a statistically significant (P Conclusion The methods described have application for functional genomics studies, particularly among non-model organisms. The web interface for FunnyBase can be accessed at http://genomics.rsmas.miami.edu/funnybase/super_craw4/. Data and source code are available by request at jpaschall@bioinfobase.umkc.edu.

  2. 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.

  3. Open semantic annotation of scientific publications using DOMEO

    Directory of Open Access Journals (Sweden)

    Ciccarese Paolo

    2012-04-01

    Full Text Available Abstract Background Our group has developed a useful shared software framework for performing, versioning, sharing and viewing Web annotations of a number of kinds, using an open representation model. Methods The Domeo Annotation Tool was developed in tandem with this open model, the Annotation Ontology (AO. Development of both the Annotation Framework and the open model was driven by requirements of several different types of alpha users, including bench scientists and biomedical curators from university research labs, online scientific communities, publishing and pharmaceutical companies. Several use cases were incrementally implemented by the toolkit. These use cases in biomedical communications include personal note-taking, group document annotation, semantic tagging, claim-evidence-context extraction, reagent tagging, and curation of textmining results from entity extraction algorithms. Results We report on the Domeo user interface here. Domeo has been deployed in beta release as part of the NIH Neuroscience Information Framework (NIF, http://www.neuinfo.org and is scheduled for production deployment in the NIF’s next full release. Future papers will describe other aspects of this work in detail, including Annotation Framework Services and components for integrating with external textmining services, such as the NCBO Annotator web service, and with other textmining applications using the Apache UIMA framework.

  4. 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

  5. Interpreting land records

    CERN Document Server

    Wilson, Donald A

    2014-01-01

    Base retracement on solid research and historically accurate interpretation Interpreting Land Records is the industry's most complete guide to researching and understanding the historical records germane to land surveying. Coverage includes boundary retracement and the primary considerations during new boundary establishment, as well as an introduction to historical records and guidance on effective research and interpretation. This new edition includes a new chapter titled "Researching Land Records," and advice on overcoming common research problems and insight into alternative resources wh

  6. Systems Analysis for Interpretation of Phosphoproteomics Data

    DEFF Research Database (Denmark)

    Munk, Stephanie; Refsgaard, Jan C; Olsen, Jesper V

    2016-01-01

    Global phosphoproteomics investigations yield overwhelming datasets with up to tens of thousands of quantified phosphosites. The main challenge after acquiring such large-scale data is to extract the biological meaning and relate this to the experimental question at hand. Systems level analysis...... provides the best means for extracting functional insights from such types of datasets, and this has primed a rapid development of bioinformatics tools and resources over the last decade. Many of these tools are specialized databases that can be mined for annotation and pathway enrichment, whereas others...... provide a platform to generate functional protein networks and explore the relations between proteins of interest. The use of these tools requires careful consideration with regard to the input data, and the interpretation demands a critical approach. This chapter provides a summary of the most...

  7. 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

  8. Eval: A software package for analysis of genome annotations

    Directory of Open Access Journals (Sweden)

    Brent Michael R

    2003-10-01

    Full Text Available Abstract Summary Eval is a flexible tool for analyzing the performance of gene annotation systems. It provides summaries and graphical distributions for many descriptive statistics about any set of annotations, regardless of their source. It also compares sets of predictions to standard annotations and to one another. Input is in the standard Gene Transfer Format (GTF. Eval can be run interactively or via the command line, in which case output options include easily parsable tab-delimited files. Availability To obtain the module package with documentation, go to http://genes.cse.wustl.edu/ and follow links for Resources, then Software. Please contact brent@cse.wustl.edu

  9. An annotation system for 3D fluid flow visualization

    Science.gov (United States)

    Loughlin, Maria M.; Hughes, John F.

    1995-01-01

    Annotation is a key activity of data analysis. However, current systems for data analysis focus almost exclusively on visualization. We propose a system which integrates annotations into a visualization system. Annotations are embedded in 3D data space, using the Post-it metaphor. This embedding allows contextual-based information storage and retrieval, and facilitates information sharing in collaborative environments. We provide a traditional database filter and a Magic Lens filter to create specialized views of the data. The system has been customized for fluid flow applications, with features which allow users to store parameters of visualization tools and sketch 3D volumes.

  10. 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...

  11. An interpretation of the CONSERT and SESAME-PP results based on new permittivity measurements of porous water ice and ice-basaltic/organic dust mixtures suggests an increase of porosity with depth in 67P.

    Science.gov (United States)

    Brouet, Yann; Levasseur-Regourd, Anny-Chantal; Sabouroux, Pierre; Neves, Luisa; Encrenaz, Pierre; Poch, Olivier; Pommerol, Antoine; Thomas, Nicolas; Kofman, Wlodek; Le Gall, Alice; Ciarletti, Valérie; Hérique, Alain; Lethuillier, Anthony

    2016-10-01

    The CONSERT bistatic radar on Rosetta and Philae sounded the interior of the small lobe of 67P/C-G at 90 MHz and determined the average of the real part of the complex permittivity (hereafter ɛ') to be equal to 1.27±0.05 [1,2]. The permittivity probe (PP) of the SESAME package sounded the near-surface in the 400–800 Hz range and derived a lower limit of ɛ' equal to 2.45±0.20 [3,4]. At the time of the measurements, the temperature was found to be below 150 K at Philae's location and expected to be close or below 100 K inside the nucleus [4-6].The complex permittivity depends of the frequency, the composition, the porosity and the temperature of the material [7,8,9]. These parameters have to be taken into account to interpret the permittivity values. The non-dispersive behavior of ɛ' below 150 K [9], allows us to compare the CONSERT and SESAME-PP results and to interpret their difference in terms of porosity and/or composition. For this purpose we use a semi-empirical formula obtained from reproducible permittivity measurements performed in the laboratory at 243 K on water ice particles and ice-basaltic dust mixtures [10], with a controlled porosity in the 26–91% range and dust-to-ice volumetric ratios in the 0.1–2.8 range. The influence of the presence of organic materials on ɛ' is also discussed based on new measurements of analogues of complex extraterrestrial organic matter [11]. Our results suggest an increase of the porosity of the small lobe of 67P with depth [11], in agreement Lethuillier et al. [4]'s conclusion using a different method.[1]Kofman et al., 1998. Adv. Space Res., 21, 1589.[2]Ciarletti et al., 2015. A&A, 583, A40.[3]Seidensticker et al., 2007. Space Sci. Rev., 128, 301.[4]Lethuillier et al., 2016. A&A, 591, A32.[5]Spohn et al., 2015. Science, 349, aab0464.[6]Festou et al. (Eds.), Comets II. Univ. of Arizona Press.[7]Campbell and Ulrichs, 1969. J. Geophys. Res., 74, 5867.[8]Brouet et al., 2015. A&A, 583, A39.[9]Mattei et al., 2014

  12. Semantic annotation for biological information retrieval system.

    Science.gov (United States)

    Oshaiba, Mohamed Marouf Z; El Houby, Enas M F; Salah, Akram

    2015-01-01

    Online literatures are increasing in a tremendous rate. Biological domain is one of the fast growing domains. Biological researchers face a problem finding what they are searching for effectively and efficiently. The aim of this research is to find documents that contain any combination of biological process and/or molecular function and/or cellular component. This research proposes a framework that helps researchers to retrieve meaningful documents related to their asserted terms based on gene ontology (GO). The system utilizes GO by semantically decomposing it into three subontologies (cellular component, biological process, and molecular function). Researcher has the flexibility to choose searching terms from any combination of the three subontologies. Document annotation is taking a place in this research to create an index of biological terms in documents to speed the searching process. Query expansion is used to infer semantically related terms to asserted terms. It increases the search meaningful results using the term synonyms and term relationships. The system uses a ranking method to order the retrieved documents based on the ranking weights. The proposed system achieves researchers' needs to find documents that fit the asserted terms semantically.

  13. Prosody and Interpretation

    Science.gov (United States)

    Erekson, James A.

    2010-01-01

    Prosody is a means for "reading with expression" and is one aspect of oral reading competence. This theoretical inquiry asserts that prosody is central to interpreting text, and draws distinctions between "syntactic" prosody (for phrasing) and "emphatic" prosody (for interpretation). While reading with expression appears as a criterion in major…

  14. The Ruby Interpreter

    OpenAIRE

    Hutton, Graham

    1993-01-01

    Ruby is a relational calculus for designing digital circuits. This document is a guide to the Ruby interpreter, which allows a special class of $quot;implementable$quot; Ruby programs to be executed. The Ruby interpreter is written in the functional programming language Lazy ML, and is used under the interactive Lazy ML system.

  15. Linguistics in Text Interpretation

    DEFF Research Database (Denmark)

    Togeby, Ole

    2011-01-01

    A model for how text interpretation proceeds from what is pronounced, through what is said to what is comunicated, and definition of the concepts 'presupposition' and 'implicature'.......A model for how text interpretation proceeds from what is pronounced, through what is said to what is comunicated, and definition of the concepts 'presupposition' and 'implicature'....

  16. The Conference Interpreter Results

    OpenAIRE

    Calvo-Ferrer, José Ramón

    2013-01-01

    Conjunto de datos relativo a la investigación realizada sobre el aprendizaje de terminología especializada en segundas lenguas con el videojuego The Conference Interpreter / Dataset from the study on L2 specialised vocabulary acquisition via The Conference Interpreter educational game.

  17. Genome-wide functional annotation and structural verification of metabolic ORFeome of Chlamydomonas reinhardtii

    Directory of Open Access Journals (Sweden)

    Fan Changyu

    2011-06-01

    annotated approximately 1,400 JGI predicted metabolic ORFs that can facilitate the reconstruction and refinement of a genome-scale metabolic network. The unveiling of the metabolic potential of this organism, along with structural verification of the relevant ORFs, facilitates the selection of metabolic engineering targets with applications in bioenergy and biopharmaceuticals. The ORF clones are a resource for downstream studies.

  18. 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

  19. MitoBamAnnotator: A web-based tool for detecting and annotating heteroplasmy in human mitochondrial DNA sequences.

    Science.gov (United States)

    Zhidkov, Ilia; Nagar, Tal; Mishmar, Dan; Rubin, Eitan

    2011-11-01

    The use of Next-Generation Sequencing of mitochondrial DNA is becoming widespread in biological and clinical research. This, in turn, creates a need for a convenient tool that detects and analyzes heteroplasmy. Here we present MitoBamAnnotator, a user friendly web-based tool that allows maximum flexibility and control in heteroplasmy research. MitoBamAnnotator provides the user with a comprehensively annotated overview of mitochondrial genetic variation, allowing for an in-depth analysis with no prior knowledge in programming.

  20. Creating New Medical Ontologies for Image Annotation A Case Study

    CERN Document Server

    Stanescu, Liana; Brezovan, Marius; Mihai, Cristian Gabriel

    2012-01-01

    Creating New Medical Ontologies for Image Annotation focuses on the problem of the medical images automatic annotation process, which is solved in an original manner by the authors. All the steps of this process are described in detail with algorithms, experiments and results. The original algorithms proposed by authors are compared with other efficient similar algorithms. In addition, the authors treat the problem of creating ontologies in an automatic way, starting from Medical Subject Headings (MESH). They have presented some efficient and relevant annotation models and also the basics of the annotation model used by the proposed system: Cross Media Relevance Models. Based on a text query the system will retrieve the images that contain objects described by the keywords.

  1. 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)

  2. Descriptive Cataloging: A Selected, Annotated Bibliography, 1984-1985.

    Science.gov (United States)

    Cook, C. Donald; Jones, Ellen

    1986-01-01

    This annotated bibliography of materials published during 1984-1985 on descriptive cataloging covers bibliographic control, Anglo American Cataloging Rules, 2nd edition (AACR2), specific types of materials, authority control, retrospective conversion, management issues, expert systems, and manuals. (EM)

  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): SE29_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 ...

  6. Annotation Method (AM): SE36_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): 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 ...

  8. 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 ...

  9. Annotation Method (AM): SE8_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 ...

  10. 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 ...

  11. 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 ...

  12. Annotation Method (AM): SE7_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 ...

  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): 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 ...

  16. 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 ...

  17. Annotation Method (AM): SE9_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): SE1_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 ...

  19. 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 ...

  20. Annotation Method (AM): SE3_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 ...

  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): 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 ...

  3. 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

  4. 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 ...

  5. Annotation Method (AM): SE25_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): 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 ...

  7. 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 ...

  8. 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 ...

  9. Annotation Method (AM): SE35_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 ...

  10. 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 ...

  11. 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 ...

  12. 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 ...

  13. Effects of dehydration on performance in man: Annotated bibliography

    Science.gov (United States)

    Greenleaf, J. E.

    1973-01-01

    A compilation of studies on the effect of dehydration on human performance and related physiological mechanisms. The annotations are listed in alphabetical order by first author and cover material through June 1973.

  14. 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...

  15. 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...

  16. 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.

  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. 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

  19. 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

  20. Re-annotation of the genome sequence of Helicobacter pylori 26695.

    Science.gov (United States)

    Resende, Tiago; Correia, Daniela M; Rocha, Miguel; Rocha, Isabel

    2013-11-15

    Helicobacter pylori is a pathogenic bacterium that colonizes the human epithelia, causing duodenal and gastric ulcers, and gastric cancer. The genome of H. pylori 26695 has been previously sequenced and annotated. In addition, two genome-scale metabolic models have been developed. In order to maintain accurate and relevant information on coding sequences (CDS) and to retrieve new information, the assignment of new functions to Helicobacter pylori 26695s genes was performed in this work. The use of software tools, on-line databases and an annotation pipeline for inspecting each gene allowed the attribution of validated EC numbers and TC numbers to metabolic genes encoding enzymes and transport proteins, respectively. 1212 genes encoding proteins were identified in this annotation, being 712 metabolic genes and 500 non-metabolic, while 191 new functions were assignment to the CDS of this bacterium. This information provides relevant biological information for the scientific community dealing with this organism and can be used as the basis for a new metabolic model reconstruction.

  1. AmiGO: online access to ontology and annotation data

    Energy Technology Data Exchange (ETDEWEB)

    Carbon, Seth; Ireland, Amelia; Mungall, Christopher J.; Shu, ShengQiang; Marshall, Brad; Lewis, Suzanna

    2009-01-15

    AmiGO is a web application that allows users to query, browse, and visualize ontologies and related gene product annotation (association) data. AmiGO can be used online at the Gene Ontology (GO) website to access the data provided by the GO Consortium; it can also be downloaded and installed to browse local ontologies and annotations. AmiGO is free open source software developed and maintained by the GO Consortium.

  2. CATMAID: collaborative annotation toolkit for massive amounts of image data

    OpenAIRE

    Saalfeld, Stephan; Cardona, Albert; Hartenstein, Volker; Tomančák, Pavel

    2009-01-01

    Summary: High-resolution, three-dimensional (3D) imaging of large biological specimens generates massive image datasets that are difficult to navigate, annotate and share effectively. Inspired by online mapping applications like GoogleMaps™, we developed a decentralized web interface that allows seamless navigation of arbitrarily large image stacks. Our interface provides means for online, collaborative annotation of the biological image data and seamless sharing of regions of interest by boo...

  3. Developing a lexical resource annotated with semantic roles for Portuguese

    OpenAIRE

    Leonardo Zilio; Carlos Ramisch; Maria José Bocorny Finatto

    2014-01-01

    The objectives of this study are as follows: to present a methodology for the development of a lexical resource with semantic information; to compare semantic roles in specialized and non-specialized language; and to observe the semantic role labeling (SRL) made by a group of annotators. Two experiments revolving around SRL in Portuguese were developed: a comparison between data in specialized and non-specialized language corpora; and an annotation evaluation for verifying the agreement among...

  4. Experimental Polish-Lithuanian Corpus with the Semantic Annotation Elements

    Directory of Open Access Journals (Sweden)

    Danuta Roszko

    2015-06-01

    Full Text Available Experimental Polish-Lithuanian Corpus with the Semantic Annotation Elements In the article the authors present the experimental Polish-Lithuanian corpus (ECorpPL-LT formed for the idea of Polish-Lithuanian theoretical contrastive studies, a Polish-Lithuanian electronic dictionary, and as help for a sworn translator. The semantic annotation being brought into ECorpPL-LT is extremely useful in Polish-Lithuanian contrastive studies, and also proves helpful in translation work.

  5. Enriching a biomedical event corpus with meta-knowledge annotation

    OpenAIRE

    Thompson Paul; Nawaz Raheel; McNaught John; Ananiadou Sophia

    2011-01-01

    Abstract Background Biomedical papers contain rich information about entities, facts and events of biological relevance. To discover these automatically, we use text mining techniques, which rely on annotated corpora for training. In order to extract protein-protein interactions, genotype-phenotype/gene-disease associations, etc., we rely on event corpora that are annotated with classified, structured representations of important facts and findings contained within text. These provide an impo...

  6. Challenges in Whole-Genome Annotation of Pyrosequenced Eukaryotic Genomes

    Energy Technology Data Exchange (ETDEWEB)

    Kuo, Alan; Grigoriev, Igor

    2009-04-17

    Pyrosequencing technologies such as 454/Roche and Solexa/Illumina vastly lower the cost of nucleotide sequencing compared to the traditional Sanger method, and thus promise to greatly expand the number of sequenced eukaryotic genomes. However, the new technologies also bring new challenges such as shorter reads and new kinds and higher rates of sequencing errors, which complicate genome assembly and gene prediction. At JGI we are deploying 454 technology for the sequencing and assembly of ever-larger eukaryotic genomes. Here we describe our first whole-genome annotation of a purely 454-sequenced fungal genome that is larger than a yeast (>30 Mbp). The pezizomycotine (filamentous ascomycote) Aspergillus carbonarius belongs to the Aspergillus section Nigri species complex, members of which are significant as platforms for bioenergy and bioindustrial technology, as members of soil microbial communities and players in the global carbon cycle, and as agricultural toxigens. Application of a modified version of the standard JGI Annotation Pipeline has so far predicted ~;;10k genes. ~;;12percent of these preliminary annotations suffer a potential frameshift error, which is somewhat higher than the ~;;9percent rate in the Sanger-sequenced and conventionally assembled and annotated genome of fellow Aspergillus section Nigri member A. niger. Also,>90percent of A. niger genes have potential homologs in the A. carbonarius preliminary annotation. Weconclude, and with further annotation and comparative analysis expect to confirm, that 454 sequencing strategies provide a promising substrate for annotation of modestly sized eukaryotic genomes. We will also present results of annotation of a number of other pyrosequenced fungal genomes of bioenergy interest.

  7. Computational evaluation of TIS annotation for prokaryotic genomes

    OpenAIRE

    Zhu Huaiqiu; Ju Li-Ning; Zheng Xiaobin; Hu Gang-Qing; She Zhen-Su

    2008-01-01

    Abstract Background Accurate annotation of translation initiation sites (TISs) is essential for understanding the translation initiation mechanism. However, the reliability of TIS annotation in widely used databases such as RefSeq is uncertain due to the lack of experimental benchmarks. Results Based on a homogeneity assumption that gene translation-related signals are uniformly distributed across a genome, we have established a computational method for a large-scale quantitative assessment o...

  8. Comparative omics-driven genome annotation refinement: application across Yersiniae.

    Directory of Open Access Journals (Sweden)

    Alexandra C Schrimpe-Rutledge

    Full Text Available 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. The annotation process is now performed almost exclusively in an automated fashion to balance the large number of sequences generated. One possible way of reducing 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. Here, the concept of annotation refinement has been extended to include a comparative assessment of genomes across closely related species. Transcriptomic and proteomic data derived from 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 incorrect (i.e., observed frameshifts, extended start sites, and translated pseudogenes protein-coding sequences within the three current genome annotations. Gene loss is presumed to play a major role in Y. pestis acquiring its niche as a virulent pathogen, thus the discovery of many translated pseudogenes, including the insertion-ablated argD, underscores a need for functional analyses to investigate hypotheses related to divergence. Refinements included the discovery of a seemingly essential ribosomal protein, several virulence-associated factors, a transcriptional regulator, and many hypothetical proteins that were missed during annotation.

  9. Experimental Polish-Lithuanian Corpus with the Semantic Annotation Elements

    OpenAIRE

    Danuta Roszko; Roman Roszko

    2015-01-01

    Experimental Polish-Lithuanian Corpus with the Semantic Annotation ElementsIn the article the authors present the experimental Polish-Lithuanian corpus (ECorpPL-LT) formed for the idea of Polish-Lithuanian theoretical contrastive studies, a Polish-Lithuanian electronic dictionary, and as help for a sworn translator. The semantic annotation being brought into ECorpPL-LT is extremely useful in Polish-Lithuanian contrastive studies, and also proves helpful in translation work.

  10. A Modular Framework for Transforming Structured Data into HTML with Machine-Readable Annotations

    Science.gov (United States)

    Patton, E. W.; West, P.; Rozell, E.; Zheng, J.

    2010-12-01

    There is a plethora of web-based Content Management Systems (CMS) available for maintaining projects and data, i.a. However, each system varies in its capabilities and often content is stored separately and accessed via non-uniform web interfaces. Moving from one CMS to another (e.g., MediaWiki to Drupal) can be cumbersome, especially if a large quantity of data must be adapted to the new system. To standardize the creation, display, management, and sharing of project information, we have assembled a framework that uses existing web technologies to transform data provided by any service that supports the SPARQL Protocol and RDF Query Language (SPARQL) queries into HTML fragments, allowing it to be embedded in any existing website. The framework utilizes a two-tier XML Stylesheet Transformation (XSLT) that uses existing ontologies (e.g., Friend-of-a-Friend, Dublin Core) to interpret query results and render them as HTML documents. These ontologies can be used in conjunction with custom ontologies suited to individual needs (e.g., domain-specific ontologies for describing data records). Furthermore, this transformation process encodes machine-readable annotations, namely, the Resource Description Framework in attributes (RDFa), into the resulting HTML, so that capable parsers and search engines can extract the relationships between entities (e.g, people, organizations, datasets). To facilitate editing of content, the framework provides a web-based form system, mapping each query to a dynamically generated form that can be used to modify and create entities, while keeping the native data store up-to-date. This open framework makes it easy to duplicate data across many different sites, allowing researchers to distribute their data in many different online forums. In this presentation we will outline the structure of queries and the stylesheets used to transform them, followed by a brief walkthrough that follows the data from storage to human- and machine-accessible web

  11. MITOS: improved de novo metazoan mitochondrial genome annotation.

    Science.gov (United States)

    Bernt, Matthias; Donath, Alexander; Jühling, Frank; Externbrink, Fabian; Florentz, Catherine; Fritzsch, Guido; Pütz, Joern; Middendorf, Martin; Stadler, Peter F

    2013-11-01

    About 2000 completely sequenced mitochondrial genomes are available from the NCBI RefSeq data base together with manually curated annotations of their protein-coding genes, rRNAs, and tRNAs. This annotation information, which has accumulated over two decades, has been obtained with a diverse set of computational tools and annotation strategies. Despite all efforts of manual curation it is still plagued by misassignments of reading directions, erroneous gene names, and missing as well as false positive annotations in particular for the RNA genes. Taken together, this causes substantial problems for fully automatic pipelines that aim to use these data comprehensively for studies of animal phylogenetics and the molecular evolution of mitogenomes. The MITOS pipeline is designed to compute a consistent de novo annotation of the mitogenomic sequences. We show that the results of MITOS match RefSeq and MitoZoa in terms of annotation coverage and quality. At the same time we avoid biases, inconsistencies of nomenclature, and typos originating from manual curation strategies. The MITOS pipeline is accessible online at http://mitos.bioinf.uni-leipzig.de.

  12. A semi-automatic annotation tool for cooking video

    Science.gov (United States)

    Bianco, Simone; Ciocca, Gianluigi; Napoletano, Paolo; Schettini, Raimondo; Margherita, Roberto; Marini, Gianluca; Gianforme, Giorgio; Pantaleo, Giuseppe

    2013-03-01

    In order to create a cooking assistant application to guide the users in the preparation of the dishes relevant to their profile diets and food preferences, it is necessary to accurately annotate the video recipes, identifying and tracking the foods of the cook. These videos present particular annotation challenges such as frequent occlusions, food appearance changes, etc. Manually annotate the videos is a time-consuming, tedious and error-prone task. Fully automatic tools that integrate computer vision algorithms to extract and identify the elements of interest are not error free, and false positive and false negative detections need to be corrected in a post-processing stage. We present an interactive, semi-automatic tool for the annotation of cooking videos that integrates computer vision techniques under the supervision of the user. The annotation accuracy is increased with respect to completely automatic tools and the human effort is reduced with respect to completely manual ones. The performance and usability of the proposed tool are evaluated on the basis of the time and effort required to annotate the same video sequences.

  13. Metagenomic gene annotation by a homology-independent approach

    Energy Technology Data Exchange (ETDEWEB)

    Froula, Jeff; Zhang, Tao; Salmeen, Annette; Hess, Matthias; Kerfeld, Cheryl A.; Wang, Zhong; Du, Changbin

    2011-06-02

    Fully understanding the genetic potential of a microbial community requires functional annotation of all the genes it encodes. The recently developed deep metagenome sequencing approach has enabled rapid identification of millions of genes from a complex microbial community without cultivation. Current homology-based gene annotation fails to detect distantly-related or structural homologs. Furthermore, homology searches with millions of genes are very computational intensive. To overcome these limitations, we developed rhModeller, a homology-independent software pipeline to efficiently annotate genes from metagenomic sequencing projects. Using cellulases and carbonic anhydrases as two independent test cases, we demonstrated that rhModeller is much faster than HMMER but with comparable accuracy, at 94.5percent and 99.9percent accuracy, respectively. More importantly, rhModeller has the ability to detect novel proteins that do not share significant homology to any known protein families. As {approx}50percent of the 2 million genes derived from the cow rumen metagenome failed to be annotated based on sequence homology, we tested whether rhModeller could be used to annotate these genes. Preliminary results suggest that rhModeller is robust in the presence of missense and frameshift mutations, two common errors in metagenomic genes. Applying the pipeline to the cow rumen genes identified 4,990 novel cellulases candidates and 8,196 novel carbonic anhydrase candidates.In summary, we expect rhModeller to dramatically increase the speed and quality of metagnomic gene annotation.

  14. A Machine Learning Based Analytical Framework for Semantic Annotation Requirements

    Directory of Open Access Journals (Sweden)

    Hamed Hassanzadeh

    2011-04-01

    Full Text Available 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 changingits contents into machine understandable form. Therefore, semantic level information is one of thecornerstones of the Semantic Web. The process of adding semantic metadata to web resources is calledSemantic 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 systemsmust be performed on, the problem of automating annotation process is one of the significant challenges inthis domain. To overcome this problem, different machine learning approaches such as supervisedlearning, unsupervised learning and more recent ones like, semi-supervised learning and active learninghave been utilized. In this paper we present an inclusive layered classification of Semantic Annotationchallenges and discuss the most important issues in this field. Also, we review and analyze machinelearning applications for solving semantic annotation problems. For this goal, the article tries to closelystudy and categorize related researches for better understanding and to reach a framework that can mapmachine learning techniques into the Semantic Annotation challenges and requirements.

  15. DAVID Knowledgebase: a gene-centered database integrating heterogeneous gene annotation resources to facilitate high-throughput gene functional analysis

    Directory of Open Access Journals (Sweden)

    Baseler Michael W

    2007-11-01

    Full Text Available Abstract Background Due to the complex and distributed nature of biological research, our current biological knowledge is spread over many redundant annotation databases maintained by many independent groups. Analysts usually need to visit many of these bioinformatics databases in order to integrate comprehensive annotation information for their genes, which becomes one of the bottlenecks, particularly for the analytic task associated with a large gene list. Thus, a highly centralized and ready-to-use gene-annotation knowledgebase is in demand for high throughput gene functional analysis. Description The DAVID Knowledgebase is built around the DAVID Gene Concept, a single-linkage method to agglomerate tens of millions of gene/protein identifiers from a variety of public genomic resources into DAVID gene clusters. The grouping of such identifiers improves the cross-reference capability, particularly across NCBI and UniProt systems, enabling more than 40 publicly available functional annotation sources to be comprehensively integrated and centralized by the DAVID gene clusters. The simple, pair-wise, text format files which make up the DAVID Knowledgebase are freely downloadable for various data analysis uses. In addition, a well organized web interface allows users to query different types of heterogeneous annotations in a high-throughput manner. Conclusion The DAVID Knowledgebase is designed to facilitate high throughput gene functional analysis. For a given gene list, it not only provides the quick accessibility to a wide range of heterogeneous annotation data in a centralized location, but also enriches the level of biological information for an individual gene. Moreover, the entire DAVID Knowledgebase is freely downloadable or searchable at http://david.abcc.ncifcrf.gov/knowledgebase/.

  16. Line drawing interpretation

    CERN Document Server

    Cooper, Martin

    2010-01-01

    The computer interpretation of line drawings is a classic problem in AI and has inspired the development of some fundamental AI tools. This novel approach to drawing interpretation combines new constraints with recent advances in soft constraint programming, Based on the author's considerable research experience, this book contains state-of-the-art reviews of work in drawing interpretation and discrete optimisation and is not just restricted to drawings of polyhedral objects, but also covers complex curved objects. The book will become a standard reference in the field with its coverage of man

  17. Experiments with crowdsourced re-annotation of a POS tagging data set

    DEFF Research Database (Denmark)

    Hovy, Dirk; Plank, Barbara; Søgaard, Anders

    2014-01-01

    Crowdsourcing lets us collect multiple annotations for an item from several annotators. Typically, these are annotations for non-sequential classification tasks. While there has been some work on crowdsourcing named entity annotations, researchers have assumed that syntactic tasks such as part......-of-speech (POS) tagging cannot be crowdsourced. This paper shows that workers can actually annotate sequential data almost as well as experts. Further, we show that the models learned from crowdsourced annotations fare as well as the models learned from expert annotations in downstream tasks....

  18. Cytological artifacts masquerading interpretation

    Directory of Open Access Journals (Sweden)

    Khushboo Sahay

    2013-01-01

    Conclusions: In order to justify a cytosmear interpretation, a cytologist must be well acquainted with delayed fixation-induced cellular changes and microscopic appearances of common contaminants so as to implicate better prognosis and therapy.

  19. Interpretation of Biosphere Reserves.

    Science.gov (United States)

    Merriman, Tim

    1994-01-01

    Introduces the Man and the Biosphere Programme (MAB) to monitor the 193 biogeographical provinces of the Earth and the creation of biosphere reserves. Highlights the need for interpreters to become familiar or involved with MAB program activities. (LZ)

  20. A New Redshift Interpretation

    CERN Document Server

    Gentry, R V

    1997-01-01

    A nonhomogeneous universe with vacuum energy, but without spacetime expansion, is utilized together with gravitational and Doppler redshifts as the basis for proposing a new interpretation of the Hubble relation and the 2.7K Cosmic Blackbody Radiation.

  1. Normative interpretations of diversity

    DEFF Research Database (Denmark)

    Lægaard, Sune

    2009-01-01

    Normative interpretations of particular cases consist of normative principles or values coupled with social theoretical accounts of the empirical facts of the case. The article reviews the most prominent normative interpretations of the Muhammad cartoons controversy over the publication of drawings...... of the Prophet Muhammad in the Danish newspaper Jyllands-Posten. The controversy was seen as a case of freedom of expression, toleration, racism, (in)civility and (dis)respect, and the article notes different understandings of these principles and how the application of them to the controversy implied different...... social theoretical accounts of the case. In disagreements between different normative interpretations, appeals are often made to the ‘context', so it is also considered what roles ‘context' might play in debates over normative interpretations...

  2. MADIBA: A web server toolkit for biological interpretation of Plasmodium and plant gene clusters

    Directory of Open Access Journals (Sweden)

    Louw Abraham I

    2008-02-01

    Full Text Available Abstract Background Microarray technology makes it possible to identify changes in gene expression of an organism, under various conditions. Data mining is thus essential for deducing significant biological information such as the identification of new biological mechanisms or putative drug targets. While many algorithms and software have been developed for analysing gene expression, the extraction of relevant information from experimental data is still a substantial challenge, requiring significant time and skill. Description MADIBA (MicroArray Data Interface for Biological Annotation facilitates the assignment of biological meaning to gene expression clusters by automating the post-processing stage. A relational database has been designed to store the data from gene to pathway for Plasmodium, rice and Arabidopsis. Tools within the web interface allow rapid analyses for the identification of the Gene Ontology terms relevant to each cluster; visualising the metabolic pathways where the genes are implicated, their genomic localisations, putative common transcriptional regulatory elements in the upstream sequences, and an analysis specific to the organism being studied. Conclusion MADIBA is an integrated, online tool that will assist researchers in interpreting their results and understand the meaning of the co-expression of a cluster of genes. Functionality of MADIBA was validated by analysing a number of gene clusters from several published experiments – expression profiling of the Plasmodium life cycle, and salt stress treatments of Arabidopsis and rice. In most of the cases, the same conclusions found by the authors were quickly and easily obtained after analysing the gene clusters with MADIBA.

  3. Modal Functional (`Dialectica') Interpretation

    OpenAIRE

    Hernest, Dan; Trifonov, Trifon

    2012-01-01

    We adapt our light Dialectica interpretation to usual and light modal formulas (with universal quantification on boolean and natural variables) and prove it sound for a non-standard modal arithmetic based on Goedel's T and classical S_4. The range of this light modal Dialectica is the usual (non-modal) classical Arithmetic in all finite types (with booleans); the propositional kernel of its domain is Boolean and not S_4. The `heavy' modal Dialectica interpretation is a new technique; it canno...

  4. Sign Language Interpreters' Training

    OpenAIRE

    Andriakopoulou, Eirini; Bouras, Christos; Giannaka, Eri

    2007-01-01

    Nowadays, the evolution of technology and the increasing use of computers gave the opportunity for developing new methods of education of deaf individuals and sign language interpreters. The e-learning environments that have been developed for the education of sign language provide web-based courses, designed to effectively teach to anyone the Sign Language. Recognizing the difficulties and barriers of sign language training as well as the importance of sign language interpreters for the comm...

  5. Interpreting Territory and Power

    OpenAIRE

    Bevir, Mark

    2010-01-01

    This paper offers an interpretive alternative to the idea of the state as sovereign over a territory and possessing a monopoly of power. It interprets both Territory and Power (the book by Bulpitt) and territory and power (the objects studied in that book). Bulpitt’s ideas were part of a broader movement to rethink the state to (i) accommodate new behavioral topics, and (ii) to defend modernist empiricism and institutionalism from the positivism and general theories of behavioralism. Now w...

  6. Genome, functional gene annotation, and nuclear transformation of the heterokont oleaginous alga Nannochloropsis oceanica CCMP1779.

    Directory of Open Access Journals (Sweden)

    Astrid Vieler

    Full Text Available Unicellular marine algae have promise for providing sustainable and scalable biofuel feedstocks, although no single species has emerged as a preferred organism. Moreover, adequate molecular and genetic resources prerequisite for the rational engineering of marine algal feedstocks are lacking for most candidate species. Heterokonts of the genus Nannochloropsis naturally have high cellular oil content and are already in use for industrial production of high-value lipid products. First success in applying reverse genetics by targeted gene replacement makes Nannochloropsis oceanica an attractive model to investigate the cell and molecular biology and biochemistry of this fascinating organism group. Here we present the assembly of the 28.7 Mb genome of N. oceanica CCMP1779. RNA sequencing data from nitrogen-replete and nitrogen-depleted growth conditions support a total of 11,973 genes, of which in addition to automatic annotation some were manually inspected to predict the biochemical repertoire for this organism. Among others, more than 100 genes putatively related to lipid metabolism, 114 predicted transcription factors, and 109 transcriptional regulators were annotated. Comparison of the N. oceanica CCMP1779 gene repertoire with the recently published N. gaditana genome identified 2,649 genes likely specific to N. oceanica CCMP1779. Many of these N. oceanica-specific genes have putative orthologs in other species or are supported by transcriptional evidence. However, because similarity-based annotations are limited, functions of most of these species-specific genes remain unknown. Aside from the genome sequence and its analysis, protocols for the transformation of N. oceanica CCMP1779 are provided. The availability of genomic and transcriptomic data for Nannochloropsis oceanica CCMP1779, along with efficient transformation protocols, provides a blueprint for future detailed gene functional analysis and genetic engineering of Nannochloropsis

  7. 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

  8. 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

  9. Gene fusions and gene duplications: relevance to genomic annotation and functional analysis

    Directory of Open Access Journals (Sweden)

    Riley Monica

    2005-03-01

    Full Text Available Abstract Background Escherichia coli a model organism provides information for annotation of other genomes. Our analysis of its genome has shown that proteins encoded by fused genes need special attention. Such composite (multimodular proteins consist of two or more components (modules encoding distinct functions. Multimodular proteins have been found to complicate both annotation and generation of sequence similar groups. Previous work overstated the number of multimodular proteins in E. coli. This work corrects the identification of modules by including sequence information from proteins in 50 sequenced microbial genomes. Results Multimodular E. coli K-12 proteins were identified from sequence similarities between their component modules and non-fused proteins in 50 genomes and from the literature. We found 109 multimodular proteins in E. coli containing either two or three modules. Most modules had standalone sequence relatives in other genomes. The separated modules together with all the single (un-fused proteins constitute the sum of all unimodular proteins of E. coli. Pairwise sequence relationships among all E. coli unimodular proteins generated 490 sequence similar, paralogous groups. Groups ranged in size from 92 to 2 members and had varying degrees of relatedness among their members. Some E. coli enzyme groups were compared to homologs in other bacterial genomes. Conclusion The deleterious effects of multimodular proteins on annotation and on the formation of groups of paralogs are emphasized. To improve annotation results, all multimodular proteins in an organism should be detected and when known each function should be connected with its location in the sequence of the protein. When transferring functions by sequence similarity, alignment locations must be noted, particularly when alignments cover only part of the sequences, in order to enable transfer of the correct function. Separating multimodular proteins into module units makes

  10. DOE Hydropower Program biennial report 1990--1991 (with updated annotated bibliography)

    Energy Technology Data Exchange (ETDEWEB)

    Chappell, J.R.; Rinehart, B.N.; Sommers, G.L. (Idaho National Engineering Lab., Idaho Falls, ID (United States)); Sale, M.J. (Oak Ridge National Lab., TN (United States))

    1991-07-01

    This report summarizes the activities of the US Department of Energy's (DOE) Hydropower Program for fiscal years 1990 and 1991, and provides an annotated bibliography of research, engineering, operations, regulations, and costs of projects pertinent to hydropower development. The Hydropower Program is organized as follows: background (including Technology Development and Engineering Research and Development); Resource Assessment; National Energy Strategy; Technology Transfer; Environmental Research; and, the bibliography discusses reports written by both private and non-Federal Government sectors. Most reports are available from the National Technical Information Service. 5 figs., 2 tabs.

  11. Sequencing, analysis, and annotation of expressed sequence tags for Camelus dromedarius.

    Directory of Open Access Journals (Sweden)

    Abdulaziz M Al-Swailem

    Full Text Available Despite its economical, cultural, and biological importance, there has not been a large scale sequencing project to date for Camelus dromedarius. With the goal of sequencing complete DNA of the organism, we first established and sequenced camel EST libraries, generating 70,272 reads. Following trimming, chimera check, repeat masking, cluster and assembly, we obtained 23,602 putative gene sequences, out of which over 4,500 potentially novel or fast evolving gene sequences do not carry any homology to other available genomes. Functional annotation of sequences with similarities in nucleotide and protein databases has been obtained using Gene Ontology classification. Comparison to available full length cDNA sequences and Open Reading Frame (ORF analysis of camel sequences that exhibit homology to known genes show more than 80% of the contigs with an ORF>300 bp and approximately 40% hits extending to the start codons of full length cDNAs suggesting successful characterization of camel genes. Similarity analyses are done separately for different organisms including human, mouse, bovine, and rat. Accompanying web portal, CAGBASE (http://camel.kacst.edu.sa/, hosts a relational database containing annotated EST sequences and analysis tools with possibility to add sequences from public domain. We anticipate our results to provide a home base for genomic studies of camel and other comparative studies enabling a starting point for whole genome sequencing of the organism.

  12. Evaluation of clustering algorithms for gene expression data using gene ontology annotations

    Institute of Scientific and Technical Information of China (English)

    MA Ning; ZHANG Zheng-guo

    2012-01-01

    Background Clustering is a useful exploratory technique for interpreting gene expression data to reveal groups of genes sharing common functional attributes.Biologists frequently face the problem of choosing an appropriate algorithm.We aimed to provide a standalone,easily accessible and biologically oriented criterion for expression data clustering evaluation.Methods An external criterion utilizing annotation based similarities between genes is proposed in this work.Gene ontology information is employed as the annotation source.Comparisons among six widely used clustering algorithms over various types of gene expression data sets were carried out based on the criterion proposed.Results The rank of these algorithms given by the criterion coincides with our common knowledge.Single-linkage has significantly poorer performance,even worse than the random algorithm.Ward's method archives the best performance in most cases.Conclusions The criterion proposed has a strong ability to distinguish among different clustering algorithms with different distance measurements.It is also demonstrated that analyzing main contributors of the criterion may offer some guidelines in finding local compact clusters.As an addition,we suggest using Ward's algorithm for gene expression data analysis.

  13. Stakeholder Confidence and Radioactive Waste management - An annotated glossary of key terms

    International Nuclear Information System (INIS)

    The OECD Nuclear Energy Agency (NEA) Forum on Stakeholder Confidence (FSC) Annotated Glossary is a review of concepts central to societal decision making about radioactive waste management. It records the evolution in understanding that has taken place in the group as the FSC has worked with these concepts over time. This should be a useful resource not only for new FSC participants but also for others: this annotated glossary forms a good reference handbook for future texts regarding societal aspects of radioactive waste management and its governance. Each glossary entry is structured, to the extent possible, as follows: - The term and its variants, if any, in FSC literature are identified. - The common FSC understanding of the concept and any guidance are captured, based upon a review of all FSC documents to date. - Any evolution of the concept observed over the decade of FSC work is analysed. - The FSC interpretation of the symbolic dimension is explored. - The current status of outlook in the FSC, and intended activities according to the current Programme of Work (2010 and beyond) are assessed. Overall, although different persons and groups may assign different meanings to words, and although terminology will continue to evolve, this glossary is the FSC's 'state-of-the-art' guide to key terms in use. As such, it should prove to be a handy reference for all those interested in the governance of radioactive waste management

  14. A bottom-up approach to data annotation in neurophysiology

    Directory of Open Access Journals (Sweden)

    Jan Grewe

    2011-08-01

    Full Text Available Metadata providing information about the stimulus, data acquisition, and experimentalconditions are indispensable for the analysis and management of experimental data withina lab. However, only rarely are metadata available in a structured, comprehensive, andmachine-readable form. This poses a severe problem for finding and retrieving data, bothin the laboratory and on the various emerging public data bases. Here, we propose a simpleformat, the Open metaData Markup Language (od ML, for collecting and exchangingmetadata in an automated, computer-based fashion. In od ML arbitrary metadata informa-tion is stored as extended key-value pairs in a hierarchical structure. Central to od ML isa clear separation of format and content, i.e. neither keys nor values are defined by theformat. This makes od ML flexible enough for storing all available metadata instantly with-out the necessity to submit new keys to an ontology or controlled terminology. Commonstandard keys can be defined in od ML terminologies for guaranteeing interoperability. Westarted to define such terminologies for neurophysiological data, but aim at a communitydriven extension and refinement of the proposed definitions. By customized terminologiesthat map to these standard terminologies, metadata can be named and organized as requiredor preferred without softening the standard. Together with the respective libraries providedfor common programming languages, the od ML format can be integrated into the labora-tory workflow, facilitating automated collection of metadata information where it becomesavailable. The flexibility of od ML also encourages a community driven collection anddefinition of terms used for annotating data in the neurosciences.

  15. Knowledge Requirements Formula for Interpreters and Interpreting Training

    Institute of Scientific and Technical Information of China (English)

    高宇婷

    2009-01-01

    Based on Zhong Weihe's knowledge requirements formula for interpreters:KI=KL+EK+S(P+AP),this paper explains in detail how the different knowledge is used in the course of interpreting and provides some useful strategies in interpreting practice.

  16. Effective and Efficient Multi-Facet Web Image Annotation

    Institute of Scientific and Technical Information of China (English)

    Jia Chen; Yi-He Zhu; Hao-Fen Wang; Wei Jin; Yong Yu

    2012-01-01

    The vast amount of images available on the Web request for an effective and efficient search service to help users find relevant images.The prevalent way is to provide a keyword interface for users to submit queries.However,the amount of images without any tags or annotations are beyond the reach of manual efforts.To overcome this,automatic image annotation techniques emerge,which are generally a process of selecting a suitable set of tags for a given image without user intervention.However,there are three main challenges with respect to Web-scale image annotation:scalability,noiseresistance and diversity.Scalability has a twofold meaning:first an automatic image annotation system should be scalable with respect to billions of images on the Web; second it should be able to automatically identify several relevant tags among a huge tag set for a given image within seconds or even faster.Noise-resistance means that the system should be robust enough against typos and ambiguous terms used in tags.Diversity represents that image content may include both scenes and objects,which are further described by multiple different image features constituting different facets in annotation.In this paper,we propose a unified framework to tackle the above three challenges for automatic Web image annotation.It mainly involves two components:tag candidate retrieval and multi-facet annotation.In the former content-based indexing and concept-based codebook are leveraged to solve scalability and noise-resistance issues.In the latter the joint feature map has been designed to describe different facets of tags in annotations and the relations between these facets.Tag graph is adopted to represent tags in the entire annotation and the structured learning technique is employed to construct a learning model on top of the tag graph based on the generated joint feature map.Millions of images from Flickr are used in our evaluation.Experimental results show that we have achieved 33% performance

  17. Manual Whisker Annotator (MWA: A Modular Open-Source Tool

    Directory of Open Access Journals (Sweden)

    Brett M. Hewitt

    2016-04-01

    Full Text Available Rodents are key to generating translational data for healthcare research. Behavioural analyses, in particular, are integral to the non-invasive monitoring of rodent health and welfare. Finding quantitative behavioural measures mitigates stress, allowing for the animal behave freely while also enabling the same animal to be studied over the time-course of its life. Locomotion and whisking are both such quantitative behavioural measures, and have been found to be significantly impacted in rodent models of neurodegenerative disease. While automatic trackers of whiskers and locomotion exist, a manual tracker is required to validate these approaches, and also to annotate complex videos where these automatic versions fail. Manually annotating whiskers for research purposes is a long and tedious task and current software does little to provide an intuitive and simple interface to carry out this task. This led to the creation of the Manual Whisker Annotator (MWA. MWA is an open source, portable whisker annotation tool developed for the Windows platform. Not only does MWA make the process much quicker, it also provides added statistical tools to analyse the data. MWA was developed in C# and WPF using the .NET framework, and could be used in any situation where annotating or tracking multiple targets is desired.

  18. Fast Arc-Annotated Subsequence Matching in Linear Space

    DEFF Research Database (Denmark)

    Bille, Philip; Gørtz, Inge Li

    2010-01-01

    An arc-annotated string is a string of characters, called bases, augmented with a set; of pairs, called arcs, each connecting two bases. Given arc-annotated strings P and Q the arc-preserving subsequence problem is to determine if P can be obtained from Q by deleting bases from Q. Whenever a base...... is deleted any arc with an endpoint in that base is also deleted. Arc-annotated strings where the arcs are "nested" are a natural model of RNA molecules that captures both the primary and secondary structure of these. The arc-preserving subsequence problem for nested arc-annotated strings is basic primitive...... the previous time bound while significantly reducing the space from a quadratic term to linear. This is essential to process large RNA molecules where the space is a likely to be a bottleneck. To obtain our result we introduce several novel ideas which may be of independent interest for related problems on arc-annotated...

  19. Incorporating Feature-Based Annotations into Automatically Generated Knowledge Representations

    Science.gov (United States)

    Lumb, L. I.; Lederman, J. I.; Aldridge, K. D.

    2006-12-01

    Earth Science Markup Language (ESML) is efficient and effective in representing scientific data in an XML- based formalism. However, features of the data being represented are not accounted for in ESML. Such features might derive from events (e.g., a gap in data collection due to instrument servicing), identifications (e.g., a scientifically interesting area/volume in an image), or some other source. In order to account for features in an ESML context, we consider them from the perspective of annotation, i.e., the addition of information to existing documents without changing the originals. Although it is possible to extend ESML to incorporate feature-based annotations internally (e.g., by extending the XML schema for ESML), there are a number of complicating factors that we identify. Rather than pursuing the ESML-extension approach, we focus on an external representation for feature-based annotations via XML Pointer Language (XPointer). In previous work (Lumb &Aldridge, HPCS 2006, IEEE, doi:10.1109/HPCS.2006.26), we have shown that it is possible to extract relationships from ESML-based representations, and capture the results in the Resource Description Format (RDF). Thus we explore and report on this same requirement for XPointer-based annotations of ESML representations. As in our past efforts, the Global Geodynamics Project (GGP) allows us to illustrate with a real-world example this approach for introducing annotations into automatically generated knowledge representations.

  20. Annotations of Mexican bullfighting videos for semantic index

    Science.gov (United States)

    Montoya Obeso, Abraham; Oropesa Morales, Lester Arturo; Fernando Vázquez, Luis; Cocolán Almeda, Sara Ivonne; Stoian, Andrei; García Vázquez, Mireya Saraí; Zamudio Fuentes, Luis Miguel; Montiel Perez, Jesús Yalja; de la O Torres, Saul; Ramírez Acosta, Alejandro Alvaro

    2015-09-01

    The video annotation is important for web indexing and browsing systems. Indeed, in order to evaluate the performance of video query and mining techniques, databases with concept annotations are required. Therefore, it is necessary generate a database with a semantic indexing that represents the digital content of the Mexican bullfighting atmosphere. This paper proposes a scheme to make complex annotations in a video in the frame of multimedia search engine project. Each video is partitioned using our segmentation algorithm that creates shots of different length and different number of frames. In order to make complex annotations about the video, we use ELAN software. The annotations are done in two steps: First, we take note about the whole content in each shot. Second, we describe the actions as parameters of the camera like direction, position and deepness. As a consequence, we obtain a more complete descriptor of every action. In both cases we use the concepts of the TRECVid 2014 dataset. We also propose new concepts. This methodology allows to generate a database with the necessary information to create descriptors and algorithms capable to detect actions to automatically index and classify new bullfighting multimedia content.

  1. ESLO: from transcription to speakers' personal information annotation

    CERN Document Server

    Eshkol, Iris; Friburger, Nathalie

    2011-01-01

    This paper presents the preliminary works to put online a French oral corpus and its transcription. This corpus is the Socio-Linguistic Survey in Orleans, realized in 1968. First, we numerized the corpus, then we handwritten transcribed it with the Transcriber software adding different tags about speakers, time, noise, etc. Each document (audio file and XML file of the transcription) was described by a set of metadata stored in an XML format to allow an easy consultation. Second, we added different levels of annotations, recognition of named entities and annotation of personal information about speakers. This two annotation tasks used the CasSys system of transducer cascades. We used and modified a first cascade to recognize named entities. Then we built a second cascade to annote the designating entities, i.e. information about the speaker. These second cascade parsed the named entity annotated corpus. The objective is to locate information about the speaker and, also, what kind of information can designate ...

  2. 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.

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

    Science.gov (United States)

    Dhanyalakshmi, K H; Naika, Mahantesha B N; Sajeevan, R S; Mathew, Oommen K; Shafi, K Mohamed; Sowdhamini, Ramanathan; N Nataraja, Karaba

    2016-01-01

    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. PMID:26982336

  4. Translation, Interpreting and Lexicography

    DEFF Research Database (Denmark)

    Tarp, Sven; Dam, Helle Vrønning

    2017-01-01

    Translation, interpreting and lexicography represent three separate areas of human activity, each of them with its own theories, models and methods and, hence, with its own disciplinary underpinnings. At the same time, all three disciplines are characterized by a marked interdisciplinary dimension...... in the sense that their practice fields are typically ‘about something else’. Translators may, for example, be called upon to translate medical texts, and interpreters may be assigned to work on medical speeches. Similarly, practical lexicography may produce medical dictionaries. In this perspective, the three...... disciplines frequently come into touch with each other. This chapter discusses and explores some of the basic aspects of this interrelationship, focusing on the (potential) contribution of lexicography to translation and interpreting and on explaining the basic concepts and methods of the former discipline...

  5. Conference Interpreting Explained

    Institute of Scientific and Technical Information of China (English)

    盖孟姣

    2015-01-01

    This book written by Roderick Jones is easy to read for me.It gives me a bit confidence through reading a book and this time I know a bit about how to read a book quickly.After this,I will read more books about interpreting and translating for my further study.From my perspective,every part of this book consists of three parts,that is,the theory part,the examples part and the concluding part.Through reading this book,I know something about interpreting such as simultaneous interpreting techniques and some actual examples.Anyhow,I still need a lot of practice to improve my English capability.What I have written below is the main content of the fourth part in this book,and the feelings of my reading the book.

  6. Conjunctive interpretations of disjunctions

    Directory of Open Access Journals (Sweden)

    Robert van Rooij

    2010-09-01

    Full Text Available In this extended commentary I discuss the problem of how to account for "conjunctive" readings of some sentences with embedded disjunctions for globalist analyses of conversational implicatures. Following Franke (2010, 2009, I suggest that earlier proposals failed, because they did not take into account the interactive reasoning of what else the speaker could have said, and how else the hearer could have interpreted the (alternative sentence(s. I show how Franke's idea relates to more traditional pragmatic interpretation strategies. doi:10.3765/sp.3.11 BibTeX info

  7. Concurrent engineering teams. Volume 2: Annotated bibliography

    Science.gov (United States)

    Richter, Karen J.; Dierolf, David A.

    1990-11-01

    Specific concurrent engineering practices vary among organizations. There are, however, various management practices that appear to work well for most organizations. This paper presents the reader with specific, useful examples from several defense contractors illustrating how multifunctional concurrent engineering teams are being organized and managed and how concurrent engineering team meetings are conducted and supported. The types of computer support that could be used to enhance the efficiency and effectiveness of concurrent engineering team meetings are identified. The general findings are that there exists a direct relationship between total quality management (TQM) and concurrent engineering, and that many applications of computer-aided group problem solving are possible and practical today for the concurrent engineering team meetings. Areas identified for additional research are the documentation of the decision process and rationale during the product and process definition, the capturing of lessons learned during the implementation of concurrent engineering, and the performance evaluation and training of team members.

  8. [Analysis of the meridian-collateral theoretical framework and the conceptual annotation of YANG Shangshan].

    Science.gov (United States)

    Zhang, Jianbin

    2016-02-01

    When classifying and compiling Huangdi Neijing (The Yellow Emperor's Inner Classic), YANG Shangshan had constructed the systematic framework of the meridian-collateral theory. It has been found in the investigation of Huangdi Neijing Taisu (Grand Simplicity of The Yellow Emperor's Inner Classic) that YANG Shangshan constructed the meridian-collateral systematic framework on the foundation of meridian theory. This framework includes two parts. One is the twelve meridians and the other one is the eight extra meridians, in which, the divergent meridians are derived from the regular meridians, and the collaterals, the cutaneous regions of meridians, genjie and biaoben are attributive to the regular meridians. The theory of the jingjin of meridians should be different from meridian-collateral system. YANG Shangshan constructed and annotated the meridian-collateral system, interpreting his unique thinking and analytic foundation. Being one of the forms of meridian-collateral theory at the early stage, YANG Shangshan's discovery deserves to be considered.

  9. Arc-preserving subsequences of arc-annotated sequences

    CERN Document Server

    Popov, Vladimir Yu

    2011-01-01

    Arc-annotated sequences are useful in representing the structural information of RNA and protein sequences. The longest arc-preserving common subsequence problem has been introduced as a framework for studying the similarity of arc-annotated sequences. In this paper, we consider arc-annotated sequences with various arc structures. We consider the longest arc preserving common subsequence problem. In particular, we show that the decision version of the 1-{\\sc fragment LAPCS(crossing,chain)} and the decision version of the 0-{\\sc diagonal LAPCS(crossing,chain)} are {\\bf NP}-complete for some fixed alphabet $\\Sigma$ such that $|\\Sigma| = 2$. Also we show that if $|\\Sigma| = 1$, then the decision version of the 1-{\\sc fragment LAPCS(unlimited, plain)} and the decision version of the 0-{\\sc diagonal LAPCS(unlimited, plain)} are {\\bf NP}-complete.

  10. 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

  11. Use of Annotations for Component and Framework Interoperability

    Science.gov (United States)

    David, O.; Lloyd, W.; Carlson, J.; Leavesley, G. H.; Geter, F.

    2009-12-01

    The popular programming languages Java and C# provide annotations, a form of meta-data construct. Software frameworks for web integration, web services, database access, and unit testing now take advantage of annotations to reduce the complexity of APIs and the quantity of integration code between the application and framework infrastructure. Adopting annotation features in frameworks has been observed to lead to cleaner and leaner application code. The USDA Object Modeling System (OMS) version 3.0 fully embraces the annotation approach and additionally defines a meta-data standard for components and models. In version 3.0 framework/model integration previously accomplished using API calls is now achieved using descriptive annotations. This enables the framework to provide additional functionality non-invasively such as implicit multithreading, and auto-documenting capabilities while achieving a significant reduction in the size of the model source code. Using a non-invasive methodology leads to models and modeling components with only minimal dependencies on the modeling framework. Since models and modeling components are not directly bound to framework by the use of specific APIs and/or data types they can more easily be reused both within the framework as well as outside of it. To study the effectiveness of an annotation based framework approach with other modeling frameworks, a framework-invasiveness study was conducted to evaluate the effects of framework design on model code quality. A monthly water balance model was implemented across several modeling frameworks and several software metrics were collected. The metrics selected were measures of non-invasive design methods for modeling frameworks from a software engineering perspective. It appears that the use of annotations positively impacts several software quality measures. In a next step, the PRMS model was implemented in OMS 3.0 and is currently being implemented for water supply forecasting in the

  12. SNP annotation-based whole genomic prediction and selection

    DEFF Research Database (Denmark)

    Do, Duy Ngoc; Janss, Luc; Jensen, Just;

    2015-01-01

    into a training (968 pigs) and a validation dataset (304 pigs) by assigning records as before and after January 1, 2012, respectively. SNP were annotated by 14 different classes using Ensembl variant effect prediction. Predictive accuracy and prediction bias were calculated using Bayesian Power LASSO...... SNP to total genomic variance was similar among annotated classes across different traits. Predictive performance of SNP classes did not significantly differ from randomized SNP groups. Genomic prediction has accuracy comparable to observed phenotype, and use of genomic prediction can be cost...... effective by replacing feed intake measurement. Genomic annotation had less impact on predictive accuracy traits considered here but may be different for other traits. It is the first study to provide useful insights into biological classes of SNP driving the whole genomic prediction for complex traits in...

  13. Code Generation for Protocols from CPN models Annotated with Pragmatics

    DEFF Research Database (Denmark)

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

    of the same model and sufficiently detailed to serve as a basis for automated code generation when annotated with code generation pragmatics. Pragmatics are syntactical annotations designed to make the CPN models descriptive and to address the problem that models with enough details for generating code from...... them tend to be verbose and cluttered. Our code generation approach consists of three main steps, starting from a CPN model that the modeller has annotated with a set of pragmatics that make the protocol structure and the control-flow explicit. The first step is to compute for the CPN model, a set...... of derived pragmatics that identify control-flow structures and operations, e. g., for sending and receiving packets, and for manipulating the state. In the second step, an abstract template tree (ATT) is constructed providing an association between pragmatics and code generation templates. The ATT...

  14. Image Annotation by Latent Community Detection and Multikernel Learning.

    Science.gov (United States)

    Gu, Yun; Qian, Xueming; Li, Qing; Wang, Meng; Hong, Richang; Tian, Qi

    2015-11-01

    Automatic image annotation is an attractive service for users and administrators of online photo sharing websites. In this paper, we propose an image annotation approach that exploits latent semantic community of labels and multikernel learning (LCMKL). First, a concept graph is constructed for labels indicating the relationship between the concepts. Based on the concept graph, semantic communities are explored using an automatic community detection method. For an image to be annotated, a multikernel support vector machine is used to determine the image's latent community from its visual features. Then, a candidate label ranking based approach is determined by intracommunity and intercommunity ranking. Experiments on the NUS-WIDE database and IAPR TC-12 data set demonstrate that LCMKL outperforms some state-of-the-art approaches. PMID:26068319

  15. Translated and annotated version of the 2015-2020 National Mental Health Work Plan of the People's Republic of China.

    Science.gov (United States)

    Xiong, Wei; Phillips, Michael R

    2016-02-25

    The following document is a translation of the 2015-2020 National Mental Health Work Plan of the People's Republic of China which was issued by the General Office of China's State Council on June 4, 2015. The original Chinese version of the document is available at the official government website: http://www.gov.cn/gongbao/content/2015/content_2883226.htm The translators have added annotations at the end of the document that provide background information to help contextualize content that may be unclear to readers unfamiliar with China and explain their decisions when translating terms that can have multiple interpretations.

  16. 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.

  17. Toys and Handicapped Children: An Annotated Bibliography.

    Science.gov (United States)

    Jeffery, Gary H.

    The bibliography lists approximately 100 citations of documents discussing the ways in which toys are used with handicapped children. It is explained that the materials listed cover uses ranging from simple play and recreation to more remediation and therapy oriented approaches. Citations are organized alphabetically by author according to their…

  18. Interpreting & Biomechanics. PEPNet Tipsheet

    Science.gov (United States)

    PEPNet-Northeast, 2001

    2001-01-01

    Cumulative trauma disorder (CTD) refers to a collection of disorders associated with nerves, muscles, tendons, bones, and the neurovascular (nerves and related blood vessels) system. CTD symptoms may involve the neck, back, shoulders, arms, wrists, or hands. Interpreters with CTD may experience a variety of symptoms including: pain, joint…

  19. Explaining the Interpretive Mind.

    Science.gov (United States)

    Brockmeier, Jens

    1996-01-01

    Examines two prominent positions in the epistemological foundations of psychology--Piaget's causal explanatory claims and Vygotsky's interpretive understanding; contends that they need to be placed in their wider philosophical contexts. Argues that the danger of causally explaining cultural practices through which human beings construct and…

  20. Listening and Message Interpretation

    Science.gov (United States)

    Edwards, Renee

    2011-01-01

    Message interpretation, the notion that individuals assign meaning to stimuli, is related to listening presage, listening process, and listening product. As a central notion of communication, meaning includes (a) denotation and connotation, and (b) content and relational meanings, which can vary in ambiguity and vagueness. Past research on message…

  1. Interpretations of Greek Mythology

    NARCIS (Netherlands)

    Bremmer, Jan

    1987-01-01

    This collection of original studies offers new interpretations of some of the best known characters and themes of Greek mythology, reflecting the complexity and fascination of the Greek imagination. Following analyses of the concept of myth and the influence of the Orient on Greek mythology, the suc

  2. Interpreting the Constitution.

    Science.gov (United States)

    Brennan, William J., Jr.

    1987-01-01

    Discusses constitutional interpretations relating to capital punishment and protection of human dignity. Points out the document's effectiveness in creating a new society by adapting its principles to current problems and needs. Considers two views of the Constitution that lead to controversy over the legitimacy of judicial decisions. (PS)

  3. Diplomatic Worldview: Interpretative Pluralism

    Directory of Open Access Journals (Sweden)

    Bayzhol I. Karipbaev

    2013-01-01

    Full Text Available This article is devoted to topical issues of interpretative pluralism, which formed the basis of the modern worldview. The attitude "world as text" enables to reveal new methodological, ontological and axiological perspectives of man’s self-determination in this world, his possibilities to participate in social reality construction. Such approach, offered within postmodernism, enables to expand our epistemological horizons.

  4. Monadic abstract interpreters

    DEFF Research Database (Denmark)

    Sergey, Ilya; Devriese, Dominique; Might, Matthew;

    2013-01-01

    Recent developments in the systematic construction of abstract interpreters hinted at the possibility of a broad unification of concepts in static analysis. We deliver that unification by showing context-sensitivity, polyvariance, flow-sensitivity, reachabilitypruning, heap-cloning and cardinalit...

  5. Hypertext Annotation: Effects of Presentation Formats and Learner Proficiency on Reading Comprehension and Vocabulary Learning in Foreign Languages

    Science.gov (United States)

    Chen, I-Jung; Yen, Jung-Chuan

    2013-01-01

    This study extends current knowledge by exploring the effect of different annotation formats, namely in-text annotation, glossary annotation, and pop-up annotation, on hypertext reading comprehension in a foreign language and vocabulary acquisition across student proficiencies. User attitudes toward the annotation presentation were also…

  6. Web Image Retrieval Search Engine based on Semantically Shared Annotation

    Directory of Open Access Journals (Sweden)

    Alaa Riad

    2012-03-01

    Full Text Available This paper presents a new majority voting technique that combines the two basic modalities of Web images textual and visual features of image in a re-annotation and search based framework. The proposed framework considers each web page as a voter to vote the relatedness of keyword to the web image, the proposed approach is not only pure combination between image low level feature and textual feature but it take into consideration the semantic meaning of each keyword that expected to enhance the retrieval accuracy. The proposed approach is not used only to enhance the retrieval accuracy of web images; but also able to annotated the unlabeled images.

  7. 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

  8. Annotation-Based Whole Genomic Prediction and Selection

    DEFF Research Database (Denmark)

    Kadarmideen, Haja; Do, Duy Ngoc; Janss, Luc;

    using the BayesCπ method and applied to 1,272 Duroc pigs with both genotypic and phenotypic records including residual (RFI) and daily feed intake (DFI), average daily gain (ADG) and back fat (BF)). Records were split into a training (968 pigs) and a validation dataset (304 pigs). SNPs were annotated by...... 14 different classes. Predictive accuracy was 0.531, 0.532, 0.302, and 0.344 for DFI, RFI, ADG and BF, respectively. The contribution per SNP to total genomic variance was similar among annotated classes across different traits. Predictive performance of SNP classes did not significantly differ from...

  9. Context, Dependency and Annotation Analysis in Java EE

    OpenAIRE

    Božidar, Darko

    2012-01-01

    The goal of this bachelor’s thesis is to analyze two of Java EE’s features, CDI and annotations, and to use the acquired knowledge to build a simple web application based on CDI and developed annotations. For this purpose it was necessary to clarify what CDI does and what it offers. Previously mentioned features were therefore firstly thoroughly examined to find out what improvements to the Java EE platform, if any, they provide. The main purpose of this thesis is to explore and analyse how t...

  10. Biocuration of functional annotation at the European nucleotide archive.

    Science.gov (United States)

    Gibson, Richard; Alako, Blaise; Amid, Clara; Cerdeño-Tárraga, Ana; Cleland, Iain; Goodgame, Neil; Ten Hoopen, Petra; Jayathilaka, Suran; Kay, Simon; Leinonen, Rasko; Liu, Xin; Pallreddy, Swapna; Pakseresht, Nima; Rajan, Jeena; Rosselló, Marc; Silvester, Nicole; Smirnov, Dmitriy; Toribio, Ana Luisa; Vaughan, Daniel; Zalunin, Vadim; Cochrane, Guy

    2016-01-01

    The European Nucleotide Archive (ENA; http://www.ebi.ac.uk/ena) is a repository for the submission, maintenance and presentation of nucleotide sequence data and related sample and experimental information. In this article we report on ENA in 2015 regarding general activity, notable published data sets and major achievements. This is followed by a focus on sustainable biocuration of functional annotation, an area which has particularly felt the pressure of sequencing growth. The importance of functional annotation, how it can be submitted and the shifting role of the biocurator in the context of increasing volumes of data are all discussed. PMID:26615190

  11. Mitochondrial Disease Sequence Data Resource (MSeqDR): A global grass-roots consortium to facilitate deposition, curation, annotation, and integrated analysis of genomic data for the mitochondrial disease clinical and research communities

    NARCIS (Netherlands)

    M.J. Falk (Marni J.); L. Shen (Lishuang); M. Gonzalez (Michael); J. Leipzig (Jeremy); M.T. Lott (Marie T.); A.P.M. Stassen (Alphons P.M.); M.A. Diroma (Maria Angela); D. Navarro-Gomez (Daniel); P. Yeske (Philip); R. Bai (Renkui); R.G. Boles (Richard G.); V. Brilhante (Virginia); D. Ralph (David); J.T. DaRe (Jeana T.); R. Shelton (Robert); S.F. Terry (Sharon); Z. Zhang (Zhe); W.C. Copeland (William C.); M. van Oven (Mannis); H. Prokisch (Holger); D.C. Wallace; M. Attimonelli (Marcella); D. Krotoski (Danuta); S. Zuchner (Stephan); X. Gai (Xiaowu); S. Bale (Sherri); J. Bedoyan (Jirair); D.M. Behar (Doron); P. Bonnen (Penelope); L. Brooks (Lisa); C. Calabrese (Claudia); S. Calvo (Sarah); P.F. Chinnery (Patrick); J. Christodoulou (John); D. Church (Deanna); R. Clima (Rosanna); B.H. Cohen (Bruce H.); R.G.H. Cotton (Richard); I.F.M. de Coo (René); O. Derbenevoa (Olga); J.T. den Dunnen (Johan); D. Dimmock (David); G. Enns (Gregory); G. Gasparre (Giuseppe); A. Goldstein (Amy); I. Gonzalez (Iris); K. Gwinn (Katrina); S. Hahn (Sihoun); R.H. Haas (Richard H.); H. Hakonarson (Hakon); M. Hirano (Michio); D. Kerr (Douglas); D. Li (Dong); M. Lvova (Maria); F. Macrae (Finley); D. Maglott (Donna); E. McCormick (Elizabeth); G. Mitchell (Grant); V.K. Mootha (Vamsi K.); Y. Okazaki (Yasushi); A. Pujol (Aurora); M. Parisi (Melissa); J.C. Perin (Juan Carlos); E.A. Pierce (Eric A.); V. Procaccio (Vincent); S. Rahman (Shamima); H. Reddi (Honey); H. Rehm (Heidi); E. Riggs (Erin); R.J.T. Rodenburg (Richard); Y. Rubinstein (Yaffa); R. Saneto (Russell); M. Santorsola (Mariangela); C. Scharfe (Curt); C. Sheldon (Claire); E.A. Shoubridge (Eric); D. Simone (Domenico); B. Smeets (Bert); J.A.M. Smeitink (Jan); C. Stanley (Christine); A. Suomalainen (Anu); M.A. Tarnopolsky (Mark); I. Thiffault (Isabelle); D.R. Thorburn (David R.); J.V. Hove (Johan Van); L. Wolfe (Lynne); L.-J. Wong (Lee-Jun)

    2015-01-01

    textabstractSuccess rates for genomic analyses of highly heterogeneous disorders can be greatly improved if a large cohort of patient data is assembled to enhance collective capabilities for accurate sequence variant annotation, analysis, and interpretation. Indeed, molecular diagnostics requires th

  12. Gastrointestinal hormone research - with a Scandinavian annotation

    DEFF Research Database (Denmark)

    Rehfeld, Jens F

    2015-01-01

    as a blood-borne hormone, a neurotransmitter, a local growth factor or a fertility factor. The targets of gastrointestinal hormones are specific G-protein-coupled receptors that are expressed in the cell membranes also outside the digestive tract. Thus, gut hormones not only regulate digestive functions......Gastrointestinal hormones are peptides released from neuroendocrine cells in the digestive tract. More than 30 hormone genes are currently known to be expressed in the gut, which makes it the largest hormone-producing organ in the body. Modern biology makes it feasible to conceive the hormones...... under five headings: The structural homology groups a majority of the hormones into nine families, each of which is assumed to originate from one ancestral gene. The individual hormone gene often has multiple phenotypes due to alternative splicing, tandem organization or differentiated posttranslational...

  13. Generation, annotation, analysis and database integration of 16,500 white spruce EST clusters

    Directory of Open Access Journals (Sweden)

    Siddiqui Asim

    2005-10-01

    Full Text Available Abstract Background The sequencing and analysis of ESTs is for now the only practical approach for large-scale gene discovery and annotation in conifers because their very large genomes are unlikely to be sequenced in the near future. Our objective was to produce extensive collections of ESTs and cDNA clones to support manufacture of cDNA microarrays and gene discovery in white spruce (Picea glauca [Moench] Voss. Results We produced 16 cDNA libraries from different tissues and a variety of treatments, and partially sequenced 50,000 cDNA clones. High quality 3' and 5' reads were assembled into 16,578 consensus sequences, 45% of which represented full length inserts. Consensus sequences derived from 5' and 3' reads of the same cDNA clone were linked to define 14,471 transcripts. A large proportion (84% of the spruce sequences matched a pine sequence, but only 68% of the spruce transcripts had homologs in Arabidopsis or rice. Nearly all the sequences that matched the Populus trichocarpa genome (the only sequenced tree genome also matched rice or Arabidopsis genomes. We used several sequence similarity search approaches for assignment of putative functions, including blast searches against general and specialized databases (transcription factors, cell wall related proteins, Gene Ontology term assignation and Hidden Markov Model searches against PFAM protein families and domains. In total, 70% of the spruce transcripts displayed matches to proteins of known or unknown function in the Uniref100 database (blastx e-value Arabidopsis or rice genomes. Detailed analysis of translationally controlled tumour proteins and S-adenosylmethionine synthetase families confirmed a twofold size difference. Sequences and annotations were organized in a dedicated database, SpruceDB. Several search tools were developed to mine the data either based on their occurrence in the cDNA libraries or on functional annotations. Conclusion This report illustrates specific

  14. Assessment of organic matter resistance to biodegradation in volcanic ash soils assisted by automated interpretation of infrared spectra from humic acid and whole soil samples by using partial least squares

    Science.gov (United States)

    Hernández, Zulimar; Pérez Trujillo, Juan Pedro; Hernández-Hernández, Sergio Alexander; Almendros, Gonzalo; Sanz, Jesús

    2014-05-01

    -model for TMC was of little significance. On the other hand, the best successful prediction models using HA spectra were for SOM, TMC, allophane content and soil fungal pigments. In these particular volcanic ash soils, with large concentration of short-range minerals, the use of WS spectra, compared to the use of HA spectra, led to predict higher number of dependent variables. This is interpreted as the fact that the information of mineral constituents may help to explain soil emergent properties (e.g., SOM resilience or hydrophysical properties). The above results coincide with previous research [2] based on classification of soil properties by multidimensional scaling, where it was demonstrated that formation of stable organomineral complexes between HA and allophane coincide with large amounts of SOM and low TMC values. [1] Viscarra Rossel, R.A., Walvoort, D.J.J., McBratney, A.B., Janik, L.J. & Skjemstad, J.O. 2006. Geoderma 131, 59-75. [2] Hernández, Z., Almendros, G. 2012. Soil Biology & Biochemistry 44, 130-142. [3] Hernández, Z. 2009. Functional study of soil organic matter in vineyards from Tenerife Island (Spain). PhD. University of Alcalá, Alcalá de Henares, Madrid. [4] Viscarra-Rossel, R.A. 2008. Chemometrics & Intelligent Laboratory Systems 90, 72-83.

  15. 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

  16. Physical Interpretion of Antigravity

    CERN Document Server

    Bars, Itzhak

    2015-01-01

    Geodesic incompleteness is a problem in both general relativity and string theory. The Weyl invariant Standard Model coupled to General Relativity (SM+GR), and a similar treatment of string theory, are improved theories that are geodesically complete. A notable prediction of this approach is that there must be antigravity regions of spacetime connected to gravity regions through gravitational singularities such as those that occur in black holes and cosmological bang/crunch. Antigravity regions introduce apparent problems of ghosts that raise several questions of physical interpretation. It was shown that unitarity is not violated but there may be an instability associated with negative kinetic energies in the antigravity regions. In this paper we show that the apparent problems can be resolved with the interpretation of the theory from the perspective of observers strictly in the gravity region. Such observers cannot experience the negative kinetic energy in antigravity directly, but can only detect in and o...

  17. Interpreting coagulation assays.

    Science.gov (United States)

    Green, David

    2010-09-01

    The interpretation of coagulation assays requires knowledge of the principal clotting pathways. The activated partial thromboplastin time is sensitive to all hemostatic factors except FVII, whereas the prothrombin time reflects levels of prothrombin and FV, FVII, and FX. Using the two tests in concert is helpful in identifying hemophilia, the coagulopathy of liver disease, and disseminated intravascular coagulation. In addition, the activated partial thromboplastin time and prothrombin time are used for monitoring anticoagulant therapy with heparin and warfarin, respectively. Measurement of D-dimer is informative in patients suspected of having thrombotic disorders and determining the risk of thrombosis recurrence. Mixing tests distinguish clotting factor deficiencies from circulating anticoagulants such as heparin, the lupus anticoagulant, and antibodies directed against specific clotting factors. The modified Bethesda assay detects and provides an indication of the strength of FVIII inhibitors. However, interpreting the results of coagulation assays is not always straightforward, and expert consultation is occasionally required to resolve difficult clinical situations. PMID:20855988

  18. Annotation of two large contiguous regions from the Haemonchus contortus genome using RNA-seq and comparative analysis with Caenorhabditis elegans.

    Directory of Open Access Journals (Sweden)

    Roz Laing

    Full Text Available The genomes of numerous parasitic nematodes are currently being sequenced, but their complexity and size, together with high levels of intra-specific sequence variation and a lack of reference genomes, makes their assembly and annotation a challenging task. Haemonchus contortus is an economically significant parasite of livestock that is widely used for basic research as well as for vaccine development and drug discovery. It is one of many medically and economically important parasites within the strongylid nematode group. This group of parasites has the closest phylogenetic relationship with the model organism Caenorhabditis elegans, making comparative analysis a potentially powerful tool for genome annotation and functional studies. To investigate this hypothesis, we sequenced two contiguous fragments from the H. contortus genome and undertook detailed annotation and comparative analysis with C. elegans. The adult H. contortus transcriptome was sequenced using an Illumina platform and RNA-seq was used to annotate a 409 kb overlapping BAC tiling path relating to the X chromosome and a 181 kb BAC insert relating to chromosome I. In total, 40 genes and 12 putative transposable elements were identified. 97.5% of the annotated genes had detectable homologues in C. elegans of which 60% had putative orthologues, significantly higher than previous analyses based on EST analysis. Gene density appears to be less in H. contortus than in C. elegans, with annotated H. contortus genes being an average of two-to-three times larger than their putative C. elegans orthologues due to a greater intron number and size. Synteny appears high but gene order is generally poorly conserved, although areas of conserved microsynteny are apparent. C. elegans operons appear to be partially conserved in H. contortus. Our findings suggest that a combination of RNA-seq and comparative analysis with C. elegans is a powerful approach for the annotation and analysis of strongylid

  19. Reflections and Interpretations

    DEFF Research Database (Denmark)

    Reflections and Interpretations is an anthology on The Freedom Writers’ methodology. It is an anthology for all those with a professional need for texts explaining, not only how The Freedom Writers’ tools are being used, but also why they work so convincingly well. It is not an anthology of guide...... of guidelines; it is an anthology of explanations based on theory. And it is an anthology written by Freedom Writer Teachers – who else could do it?...

  20. Video interpretations in Danish hospitals

    DEFF Research Database (Denmark)

    Søbjerg, Lene Mosegaard; Noesgaard, Susanne; Henriksen, Jan Erik;

    2013-01-01

    This article presents a study of an RCT comparing video interpretation with in-person interpretation at the Endocrinology Ward at Odense University Hospital.......This article presents a study of an RCT comparing video interpretation with in-person interpretation at the Endocrinology Ward at Odense University Hospital....

  1. Child Drama: A Selected and Annotated Bibliography, 1974-1979.

    Science.gov (United States)

    Kennedy, Carol Jean

    The more than 200 entries in this annotated bibliography deal with drama, creative dramatics, and children's theatre. The entries for articles, papers, and books are arranged according to the following categories: (1) bibliographies and references in child drama; (2) theory, research, and methods in preschool dramatic play; (3) theory and research…

  2. Functional annotation of the human retinal pigment epithelium transcriptome

    NARCIS (Netherlands)

    J.C. Booij (Judith); S. van Soest (Simone); S.M.A. Swagemakers (Sigrid); A.H.W. Essing (Anke); J.H.M. Verkerk (Annemieke); P.J. van der Spek (Peter); T.G.M.F. Gorgels (Theo); A.A.B. Bergen (Arthur)

    2009-01-01

    textabstractBackground: 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

  3. The Dartmouth/Rassias Method: An Annotated Bibliography.

    Science.gov (United States)

    Horner, Jeanne; Stansfield, Charles

    The Dartmouth/Rassias method of foreign language instruction, which is used in many American colleges and universities, has inspired much comment in the media. This annotated bibliography describes 17 books, articles, and monographs, as well as a film, which focus on the method. (JB)

  4. Asian American Literature of Hawaii: An Annotated Bibliography.

    Science.gov (United States)

    Hiura, Arnold T.; Sumida, Stephen H.

    This annotated bibllography focuses on the drama, prose fiction, and poetry of people of Chinese, Japanese, Korean, and Filipino descent in Hawaii. All works cited were written in English, between the 1920s and 1970, with the exception of poems translated into English by their authors. The bibliography begins with an overview of the cultural and…

  5. The DNA sequence, annotation and analysis of human chromosome 3

    DEFF Research Database (Denmark)

    Muzny, Donna M; Scherer, Steven E; Kaul, Rajinder;

    2006-01-01

    After the completion of a draft human genome sequence, the International Human Genome Sequencing Consortium has proceeded to finish and annotate each of the 24 chromosomes comprising the human genome. Here we describe the sequencing and analysis of human chromosome 3, one of the largest human chr...

  6. An Annotated Bibliography of Gay and Lesbian Communication Studies.

    Science.gov (United States)

    Park, Jan Carl

    1979-01-01

    The 22 entries in this annotated bibliography represent articles that have lesbian women or gay men as subjects and that deal with a specific verbal or nonverbal communication factor. Topics covered in the entries include patterns of self-disclosure in homosexual and heterosexual college students, interpersonal conflict in homosexual relations,…

  7. 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.

  8. Genome 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 ....zip File URL: ftp://ftp.biosciencedbc.jp/archive/kome/LATEST/kome_genome_annotat...e Update History of This Database Site Policy | Contact Us Genome annotations - KOME | LSDB Archive ...

  9. Effects of Teaching Strategies in Annotated Bibliography Writing

    Science.gov (United States)

    Tan-de Ramos, Jennifer

    2015-01-01

    The study examines the effect of teaching strategies to improved writing of students in the tertiary level. Specifically, three teaching approaches--the use of modelling, grammar-based, and information element-focused--were tested on their effect on the writing of annotated bibliography in three research classes at a university in Manila.…

  10. Annotated Bibliography on Return Migration to Puerto Rico.

    Science.gov (United States)

    Carrasquillo, Angela; Carrasquillo, Ceferino

    This paper is an annotated bibliography on return migration from the mainland United States to Puerto Rico. An introduction defines the term "return migration" in the specific context of the Puerto Rican community. The introduction is followed by the bibliography, which lists and summarizes research studies and works dealing with demographic data…

  11. Generating Protocol Software from CPN Models Annotated with Pragmatics

    DEFF Research Database (Denmark)

    Simonsen, Kent Inge; Kristensen, Lars M.; Kindler, Ekkart

    2013-01-01

    and verify protocol software, but limited work exists on using CPN models of protocols as a basis for automated code generation. The contribution of this paper is a method for generating protocol software from a class of CPN models annotated with code generation pragmatics. Our code generation method...

  12. Recall Oriented Search on the Web using Semantic Annotations

    NARCIS (Netherlands)

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

    2013-01-01

    Web search engines are optimized for early precision, which makes it difficult to perform recall oriented tasks with them. In this article, we propose several ways to leverage semantic annotations and, thereby, increase the efficiency of recall oriented search tasks, with a focus on forensic investi

  13. Social Sciences in the People's Republic of China: Annotated Bibliography.

    Science.gov (United States)

    Parker, Franklin

    This annotated bibliography includes 18 journal articles, books, newspaper stories, and confernce papers focusing on official Chinese policy toward the role of the social sciences. The impact of the Chinese Cultural Revolution and the establishment of the Chinese Academy of Social Sciences in 1977 are the subjects of most of the listed sources.…

  14. Annotation: Neurofeedback--Train Your Brain to Train Behaviour

    Science.gov (United States)

    Heinrich, Hartmut; Gevensleben, Holger; Strehl, Ute

    2007-01-01

    Background: Neurofeedback (NF) is a form of behavioural training aimed at developing skills for self-regulation of brain activity. Within the past decade, several NF studies have been published that tend to overcome the methodological shortcomings of earlier studies. This annotation describes the methodical basis of NF and reviews the evidence…

  15. Optimizing high performance computing workflow for protein functional annotation.

    Science.gov (United States)

    Stanberry, Larissa; Rekepalli, Bhanu; Liu, Yuan; Giblock, Paul; Higdon, Roger; Montague, Elizabeth; Broomall, William; Kolker, Natali; Kolker, Eugene

    2014-09-10

    Functional annotation of newly sequenced genomes is one of the major challenges in modern biology. With modern sequencing technologies, the protein sequence universe is rapidly expanding. Newly sequenced bacterial genomes alone contain over 7.5 million proteins. The rate of data generation has far surpassed that of protein annotation. The volume of protein data makes manual curation infeasible, whereas a high compute cost limits the utility of existing automated approaches. In this work, we present an improved and optmized automated workflow to enable large-scale protein annotation. The workflow uses high performance computing architectures and a low complexity classification algorithm to assign proteins into existing clusters of orthologous groups of proteins. On the basis of the Position-Specific Iterative Basic Local Alignment Search Tool the algorithm ensures at least 80% specificity and sensitivity of the resulting classifications. The workflow utilizes highly scalable parallel applications for classification and sequence alignment. Using Extreme Science and Engineering Discovery Environment supercomputers, the workflow processed 1,200,000 newly sequenced bacterial proteins. With the rapid expansion of the protein sequence universe, the proposed workflow will enable scientists to annotate big genome data.

  16. 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…

  17. An annotated bibliography of parasitic Isopoda (Crustacea of Chondrichthyes

    Directory of Open Access Journals (Sweden)

    Plínio Soares Moreira

    1978-01-01

    Full Text Available This annotated bibliography is an attempt to bring together all available published records on the parasitic isopods of Chondrichthian fishes as a basic reference source. An effort was made to synonymise old names according to the presently accepted scientific names.

  18. An Annotated Bibliography on the Severely and Profoundly Mentally Retarded.

    Science.gov (United States)

    Cass, Michael, Comp.; Schilit, Jeffrey, Comp.

    Presented is an annotated bibliography with approximately 250 entries relating to the severely and profoundly retarded. Citations are listed alphabetically by author under the following categories: assessments, measurements, evaluations; associations; attending behavior; behavior modification; books; classical conditioning; cognitive development;…

  19. Annotating Evidence Based Clinical Guidelines: A Lightweight Ontology

    NARCIS (Netherlands)

    R. Hoekstra; A. de Waard; R. Vdovjak

    2012-01-01

    This paper describes a lightweight ontology for representing annotations of declarative evidence based clinical guidelines. We present the motivation and requirements for this representation, based on an analysis of several guidelines. The ontology provides the means to connect clinical questions an

  20. Reliability and effectiveness of clickthrough data for automatic image annotation

    NARCIS (Netherlands)

    Tsikrika, T.; Diou, C.; Vries, A.P. de; Delopoulos, A.

    2010-01-01

    Automatic image annotation using supervised learning is performed by concept classifiers trained on labelled example images. This work proposes the use of clickthrough data collected from search logs as a source for the automatic generation of concept training data, thus avoiding the expensive manua