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Sample records for dasmi exchanging annotating

  1. DASMI: exchanging, annotating and assessing molecular interaction data

    PubMed Central

    Blankenburg, Hagen; Finn, Robert D.; Prlić, Andreas; Jenkinson, Andrew M.; Ramírez, Fidel; Emig, Dorothea; Schelhorn, Sven-Eric; Büch, Joachim; Lengauer, Thomas; Albrecht, Mario

    2009-01-01

    Motivation: Ever increasing amounts of biological interaction data are being accumulated worldwide, but they are currently not readily accessible to the biologist at a single site. New techniques are required for retrieving, sharing and presenting data spread over the Internet. Results: We introduce the DASMI system for the dynamic exchange, annotation and assessment of molecular interaction data. DASMI is based on the widely used Distributed Annotation System (DAS) and consists of a data exchange specification, web servers for providing the interaction data and clients for data integration and visualization. The decentralized architecture of DASMI affords the online retrieval of the most recent data from distributed sources and databases. DASMI can also be extended easily by adding new data sources and clients. We describe all DASMI components and demonstrate their use for protein and domain interactions. Availability: The DASMI tools are available at http://www.dasmi.de/ and http://ipfam.sanger.ac.uk/graph. The DAS registry and the DAS 1.53E specification is found at http://www.dasregistry.org/. Contact: mario.albrecht@mpi-inf.mpg.de Supplementary information: Supplementary data and all figures in color are available at Bioinformatics online. PMID:19420069

  2. Systemic Planning: An Annotated Bibliography and Literature Guide. Exchange Bibliography No. 91.

    ERIC Educational Resources Information Center

    Catanese, Anthony James

    Systemic planning is an operational approach to using scientific rigor and qualitative judgment in a complementary manner. It integrates rigorous techniques and methods from systems analysis, cybernetics, decision theory, and work programing. The annotated reference sources in this bibliography include those works that have been most influential…

  3. An Annotated and Classified List of 16mm Films on Urban Studies: New Towns, Urban Problems, City and Regional Planning. Exchange Bibliography 838.

    ERIC Educational Resources Information Center

    Allen, Irving Lewis, Comp.

    Over 100 available 16mm films are listed in this annotated bibliography on urban studies. The listings are classified under new towns and new cities; film series on general urban problems; cinematic and artistic impressions of cities; ghetto problems, slums, and skid rows; and general urban planning, urban renewal, housing and neighborhood…

  4. Ranking Biomedical Annotations with Annotator's Semantic Relevancy

    PubMed Central

    2014-01-01

    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. PMID:24899918

  5. Ranking biomedical annotations with annotator's semantic relevancy.

    PubMed

    Wu, Aihua

    2014-01-01

    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. PMID:24899918

  6. EXCHANGE

    SciTech Connect

    Boltz, J.C.

    1992-09-01

    EXCHANGE is published monthly by the Idaho National Engineering Laboratory (INEL), a multidisciplinary facility operated for the US Department of Energy (DOE). The purpose of EXCHANGE is to inform computer users about about recent changes and innovations in both the mainframe and personal computer environments and how these changes can affect work being performed at DOE facilities.

  7. The Otter Annotation System

    PubMed Central

    Searle, Stephen M.J.; Gilbert, James; Iyer, Vivek; Clamp, Michele

    2004-01-01

    With the completion of the human genome sequence and genome sequence available for other vertebrate genomes, the task of manual annotation at the large genome scale has become a priority. Possibly even more important, is the requirement to curate and improve this annotation in the light of future data. For this to be possible, there is a need for tools to access and manage the annotation. Ensembl provides an excellent means for storing gene structures, genome features, and sequence, but it does not support the extra textual data necessary for manual annotation. We have extended Ensembl to create the Otter manual annotation system. This comprises a relational database schema for storing the manual annotation data, an application-programming interface (API) to access it, an extensible markup language (XML) format to allow transfer of the data, and a server to allow multiuser/multimachine access to the data. We have also written a data-adaptor plugin for the Apollo Browser/Editor to enable it to utilize an Otter server. The otter database is currently used by the Vertebrate Genome Annotation (VEGA) site (http://vega.sanger.ac.uk), which provides access to manually curated human chromosomes. Support is also being developed for using the AceDB annotation editor, FMap, via a perl wrapper called Lace. The Human and Vertebrate Annotation (HAVANA) group annotators at the Sanger center are using this to annotate human chromosomes 1 and 20. PMID:15123593

  8. Computing human image annotation.

    PubMed

    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

  9. SEED Software Annotations.

    ERIC Educational Resources Information Center

    Bethke, Dee; And Others

    This document provides a composite index of the first five sets of software annotations produced by Project SEED. The software has been indexed by title, subject area, and grade level, and it covers sets of annotations distributed in September 1986, April 1987, September 1987, November 1987, and February 1988. The date column in the index…

  10. Annotation extension through protein family annotation coherence metrics

    PubMed Central

    Bastos, Hugo P.; Clarke, Luka A.; Couto, Francisco M.

    2013-01-01

    Protein functional annotation consists in associating proteins with textual descriptors elucidating their biological roles. The bulk of annotation is done via automated procedures that ultimately rely on annotation transfer. Despite a large number of existing protein annotation procedures the ever growing protein space is never completely annotated. One of the facets of annotation incompleteness derives from annotation uncertainty. Often when protein function cannot be predicted with enough specificity it is instead conservatively annotated with more generic terms. In a scenario of protein families or functionally related (or even dissimilar) sets this leads to a more difficult task of using annotations to compare the extent of functional relatedness among all family or set members. However, we postulate that identifying sub-sets of functionally coherent proteins annotated at a very specific level, can help the annotation extension of other incompletely annotated proteins within the same family or functionally related set. As an example we analyse the status of annotation of a set of CAZy families belonging to the Polysaccharide Lyase class. We show that through the use of visualization methods and semantic similarity based metrics it is possible to identify families and respective annotation terms within them that are suitable for possible annotation extension. Based on our analysis we then propose a semi-automatic methodology leading to the extension of single annotation terms within these partially annotated protein sets or families. PMID:24130572

  11. An annotated energy bibliography

    NASA Technical Reports Server (NTRS)

    Blow, S. J.

    1979-01-01

    Comprehensive annotated compilation of books, journals, periodicals, and reports on energy and energy related topics, contains approximately 10,0000 tehcnical and nontechnical references from bibliographic and other sources dated January 1975 through May 1977.

  12. Semantic Annotation of Mutable Data

    PubMed Central

    Morris, Robert A.; Dou, Lei; Hanken, James; Kelly, Maureen; Lowery, David B.; Ludäscher, Bertram; Macklin, James A.; Morris, Paul J.

    2013-01-01

    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. PMID:24223697

  13. Algal functional annotation tool

    Energy Science and Technology Software Center (ESTSC)

    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 tomore » 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 on

  14. Algal functional annotation tool

    SciTech Connect

    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 on KEGG

  15. Human Genome Annotation

    NASA Astrophysics Data System (ADS)

    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.

  16. Algal functional annotation tool

    SciTech Connect

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

    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.

  17. Community gene annotation in practice

    PubMed Central

    Loveland, Jane E.; Gilbert, James G.R.; Griffiths, Ed; Harrow, Jennifer L.

    2012-01-01

    Manual annotation of genomic data is extremely valuable to produce an accurate reference gene set but is expensive compared with automatic methods and so has been limited to model organisms. Annotation tools that have been developed at the Wellcome Trust Sanger Institute (WTSI, http://www.sanger.ac.uk/.) are being used to fill that gap, as they can be used remotely and so open up viable community annotation collaborations. We introduce the ‘Blessed’ annotator and ‘Gatekeeper’ approach to Community Annotation using the Otterlace/ZMap genome annotation tool. We also describe the strategies adopted for annotation consistency, quality control and viewing of the annotation. Database URL: http://vega.sanger.ac.uk/index.html PMID:22434843

  18. Annotation: The Savant Syndrome

    ERIC Educational Resources Information Center

    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.…

  19. Collaborative Movie Annotation

    NASA Astrophysics Data System (ADS)

    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.

  20. Annotated Bibliography. First Edition.

    ERIC Educational Resources Information Center

    Haring, Norris G.

    An annotated bibliography which presents approximately 300 references from 1951 to 1973 on the education of severely/profoundly handicapped persons. Citations are grouped alphabetically by author's name within the following categories: characteristics and treatment, gross motor development, sensory and motor development, physical therapy for the…

  1. Ghostwriting: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Simmons, Donald B.

    Drawn from communication journals, historical and news magazines, business and industrial magazines, political science and world affairs journals, general interest periodicals, and literary and political review magazines, the approximately 90 entries in this annotated bibliography discuss ghostwriting as practiced through the ages and reveal the…

  2. Apollo: a sequence annotation editor

    PubMed Central

    Lewis, SE; Searle, SMJ; Harris, N; Gibson, M; Iyer, V; Richter, J; Wiel, C; Bayraktaroglu, L; Birney, E; Crosby, MA; Kaminker, JS; Matthews, BB; Prochnik, SE; Smith, CD; Tupy, JL; Rubin, GM; Misra, S; Mungall, CJ; Clamp, ME

    2002-01-01

    The well-established inaccuracy of purely computational methods for annotating genome sequences necessitates an interactive tool to allow biological experts to refine these approximations by viewing and independently evaluating the data supporting each annotation. Apollo was developed to meet this need, enabling curators to inspect genome annotations closely and edit them. FlyBase biologists successfully used Apollo to annotate the Drosophila melanogaster genome and it is increasingly being used as a starting point for the development of customized annotation editing tools for other genome projects. PMID:12537571

  3. Supporting Speech for Annotation and Asynchronous Discussion of Multimedia Presentations

    ERIC Educational Resources Information Center

    Lauer, Tobias; Busl, Sandra

    2007-01-01

    Collaborative learning with recorded lectures and presentations can be supported by allowing users to anchor notes in the documents and exchange them with other learners. While the traditional modality for annotation and discussion is text, there are a number of reasons in favour of supporting other media and modalities as well. We describe the…

  4. Annotations in Refseq (GSC8 Meeting)

    ScienceCinema

    Tatusova, Tatiana

    2011-04-28

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Tatiana Tatusova of NCBI discusses "Annotations in Refseq" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 10, 2009.

  5. Annotations in Refseq (GSC8 Meeting)

    SciTech Connect

    Tatusova, Tatiana

    2009-09-10

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. Tatiana Tatusova of NCBI discusses "Annotations in Refseq" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 10, 2009.

  6. The Ensembl gene annotation system.

    PubMed

    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

  7. The Ensembl gene annotation system

    PubMed Central

    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

    2016-01-01

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

  8. Widowed Persons Service: Selected Annotated Bibliography.

    ERIC Educational Resources Information Center

    Bressler, Dawn, Comp.; And Others

    This document presents an annotated bibliography of books and articles on topics relevant to widowhood. These annotations are included: (1) 21 annotations on the grief process; (2) 11 annotations on personal observations about widowhood; (3) 16 annotations on practical problems surrounding widowhood, including legal and financial problems and job…

  9. Communication and Gender: Annotated Bibliography

    ERIC Educational Resources Information Center

    Todd-Mancillas, William R.; Krug, Linda

    Focusing on the similarities and differences in men's and women's verbal and nonverbal communication behavior, this 33-item annotated bibliography presents a sample of articles appearing in speech communication publications on the subject. Categories of the annotated bibliography are books, sexism and sexual harassment in academia, theoretic…

  10. Drug Education: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Mathieson, Moira B.

    This bibliography consists of a total of 215 entries dealing with drug education, including curriculum guides, and drawn from documents in the ERIC system. There are two sections, the first containing 130 annotated citations of documents and journal articles, and the second containing 85 citations of journal articles without annotations, but with…

  11. Women in Communication: Annotated Bibliography.

    ERIC Educational Resources Information Center

    Mills, Carol A.

    This annotated bibliography is designed to survey the field of women in communication. The bibliography is centered on a specific context: who are and who were the women who worked in the communication field, and specifically, what were their writings like? The 56 annotations date from 1949 through 1990 and deal mostly with books (especially…

  12. Towards a Consensus Annotation System (GSC8 Meeting)

    SciTech Connect

    White, Owen

    2009-09-10

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. "Comparing Annotations: Towards Consensus Annotation" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 10, 2009

  13. Towards a Consensus Annotation System (GSC8 Meeting)

    ScienceCinema

    White, Owen [University of Maryland

    2011-04-28

    The Genomic Standards Consortium was formed in September 2005. It is an international, open-membership working body which promotes standardization in the description of genomes and the exchange and integration of genomic data. The 2009 meeting was an activity of a five-year funding "Research Coordination Network" from the National Science Foundation and was organized held at the DOE Joint Genome Institute with organizational support provided by the JGI and by the University of California - San Diego. "Comparing Annotations: Towards Consensus Annotation" at the Genomic Standards Consortium's 8th meeting at the DOE JGI in Walnut Creek, Calif. on Sept. 10, 2009

  14. Gene Ontology annotations and resources.

    PubMed

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

    2013-01-01

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

  15. Patient Education: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Simmons, Jeannette

    Topics included in this annotated bibliography on patient education are (1) background on development of patient education programs, (2) patient education interventions, (3) references for health professionals, and (4) research and evaluation in patient education. (TA)

  16. Gene Ontology Annotations and Resources

    PubMed Central

    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

  17. NCBI prokaryotic genome annotation pipeline.

    PubMed

    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

  18. Collective dynamics of social annotation

    PubMed Central

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

    2009-01-01

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

  19. Collective dynamics of social annotation.

    PubMed

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

    2009-06-30

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

  20. Whiplash: a selective annotated bibliography

    PubMed Central

    Smith, Brad MT; Adams, Alan

    1997-01-01

    Objective: To review the literature on whiplash injury including an overview, collision mechanics, pathophysiology, neurobehavioral, imaging, treatment/management, prognosis, outcomes, and litigation. Design: An annotated bibliography. Methods: A literature search of MEDLINE from 1987 to 1995 and CHIROLARS from 1900 to 1996, with emphasis on the last ten years, was performed. Conference proceedings and the personal files of the authors were searched for relevant citations. Key words utilized in the search were whiplash injury, acceleration/deceleration injury, neck pain, head pain, cognitive impairment, treatment, imaging, prognosis and litigation. Results: This annotated bibliography identifies key studies and potential models for future research. Conclusions: There is currently a lack of clinical consensus both in practice and in the literature regarding the evaluation and management of an episode of whiplash injury. This annotated bibliography has been developed in an attempt to provide an overview of the literature regarding various issues surrounding an episode of whiplash injury.

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

    PubMed

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

    2016-01-01

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

  2. Alignment-Annotator web server: rendering and annotating sequence alignments

    PubMed Central

    Gille, Christoph; Fähling, Michael; Weyand, Birgit; Wieland, Thomas; Gille, Andreas

    2014-01-01

    Alignment-Annotator is a novel web service designed to generate interactive views of annotated nucleotide and amino acid sequence alignments (i) de novo and (ii) embedded in other software. All computations are performed at server side. Interactivity is implemented in HTML5, a language native to web browsers. The alignment is initially displayed using default settings and can be modified with the graphical user interfaces. For example, individual sequences can be reordered or deleted using drag and drop, amino acid color code schemes can be applied and annotations can be added. Annotations can be made manually or imported (BioDAS servers, the UniProt, the Catalytic Site Atlas and the PDB). Some edits take immediate effect while others require server interaction and may take a few seconds to execute. The final alignment document can be downloaded as a zip-archive containing the HTML files. Because of the use of HTML the resulting interactive alignment can be viewed on any platform including Windows, Mac OS X, Linux, Android and iOS in any standard web browser. Importantly, no plugins nor Java are required and therefore Alignment-Anotator represents the first interactive browser-based alignment visualization. Availability: http://www.bioinformatics.org/strap/aa/ and http://strap.charite.de/aa/. PMID:24813445

  3. Systems Theory and Communication. Annotated Bibliography.

    ERIC Educational Resources Information Center

    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)

  4. Music Analysis: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Fink, Michael

    One hundred and forty citations comprise this annotated bibliography of books, articles, and selected dissertations that encompass trends in music theory and k-16 music education since the late 19th century. Special emphasis is upon writings since the 1950's. During earlier development, music analysts concentrated upon the elements of music (i.e.,…

  5. Teacher Aides; An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Marin County Public Schools, Corte Madera, CA.

    This annotated bibliography lists 40 items, published between 1966 and 1971, that have to do with teacher aides. The listing is arranged alphabetically by author. In addition to the abstract and standard bibliographic information, addresses where the material can be purchased are often included. The items cited include handbooks, research studies,…

  6. Staff Differentiation. An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Marin County Superintendent of Schools, Corte Madera, CA.

    This annotated bibliography reviews selected literature focusing on the concept of staff differentiation. Included are 62 items (dated 1966-1970), along with a list of mailing addresses where copies of individual items can be obtained. Also a list of 31 staff differentiation projects receiving financial assistance from the U.S. Office of Education…

  7. Infant Feeding: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Crowhurst, Christine Marie, Comp.; Kumer, Bonnie Lee, Comp.

    Intended for parents, health professionals and allied health workers, and others involved in caring for infants and young children, this annotated bibliography brings together in one selective listing a review of over 700 current publications related to infant feeding. Reflecting current knowledge in infant feeding, the bibliography has as its…

  8. English Language Learners: Annotated Bibliography

    ERIC Educational Resources Information Center

    Hector-Mason, Anestine; Bardack, Sarah

    2010-01-01

    This annotated bibliography represents a first step toward compiling a comprehensive overview of current research on issues related to English language learners (ELLs). It is intended to be a resource for researchers, policymakers, administrators, and educators who are engaged in efforts to bridge the divide between research, policy, and practice…

  9. Vietnamese Amerasians: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Johnson, Mark C.; And Others

    This annotated bibliography on Vietnamese Amerasians includes primary and secondary sources as well as reviews of three documentary films. Sources were selected in order to provide an overview of the historical and political context of Amerasian resettlement and a review of the scant available research on coping and adaptation with this…

  10. Radiocarbon Dating: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Fortine, Suellen

    This selective annotated bibliography covers various sources of information on the radiocarbon dating method, including journal articles, conference proceedings, and reports, reflecting the most important and useful sources of the last 25 years. The bibliography is divided into five parts--general background on radiocarbon, radiocarbon dating,…

  11. Instructional Materials Centers; Annotated Bibliography.

    ERIC Educational Resources Information Center

    Poli, Rosario, Comp.

    An annotated bibliography lists 74 articles and reports on instructional materials centers (IMC) which appeared from 1967-70. The articles deal with such topics as the purposes of an IMC, guidelines for setting up an IMC, and the relationship of an IMC to technology. Most articles deal with use of an IMC on an elementary or secondary level, but…

  12. BIBLIOTHERAPY--AN ANNOTATED BIBLIOGRAPHY.

    ERIC Educational Resources Information Center

    RIGGS, CORINNE W.

    THIS ANNOTATED BIBLIOGRAPHY ON BIBLIOTHERAPY IS COMPOSED OF 138 CITATIONS RANGING IN DATE FROM 1936 TO 1967. IT IS DESIGNED TO AID TEACHERS AND LIBRARIANS IN MODIFYING THE ATTITUDES AND BEHAVIOR OF BOYS AND GIRLS. ITS LISTINGS ARE ARRANGED ALPHABETICALLY ACCORDING TO AUTHOR UNDER THE GENERAL DIVISIONS OF BOOKS, PERIODICALS, AND UNPUBLISHED…

  13. MSDAC Resource Library Annotated Bibliography.

    ERIC Educational Resources Information Center

    Watson, Cristel; And Others

    This annotated bibliography lists books, films, filmstrips, recordings, and booklets on sex equity. Entries are arranged according to the following topics: career resources, curriculum resources, management, sex equity, sex roles, women's studies, student activities, and sex-fair fiction. Included in each entry are name of author, editor or…

  14. Teacher Evaluation: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    McKenna, Bernard H.; And Others

    In his introduction to the 86-item annotated bibliography by Mueller and Poliakoff, McKenna discusses his views on teacher evaluation and his impressions of the documents cited. He observes, in part, that the current concern is with the process of evaluation and that most researchers continue to believe that student achievement is the most…

  15. Workforce Reductions. An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Hickok, Thomas A.; Hickok, Thomas A.

    This report, which is based on a review of practitioner-oriented sources and scholarly journals, uses a three-part framework to organize annotated bibliographies that, together, list a total of 104 sources that provide the following three perspectives on work force reduction issues: organizational, organizational-individual relationship, and…

  16. Annotated Bibliography, Grades K-6.

    ERIC Educational Resources Information Center

    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…

  17. Appalachian Women. An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Hamm, Mary Margo

    This bibliography compiles annotations of 178 books, journal articles, ERIC documents, and dissertations on Appalachian women and their social, cultural, and economic environment. Entries were published 1966-93 and are listed in the following categories: (1) authors and literary criticism; (2) bibliographies and resource guides; (3) economics,…

  18. Service Integration: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Chaudry, Ajay; And Others

    This annotated bibliography describes 53 books, papers, and articles written about efforts toward integrating and improving human services for children, youth, and families living in poverty. The bibliography has been developed for individuals working on and interested in service integration, including policymakers, program administrators,…

  19. Annotation and Classification of Argumentative Writing Revisions

    ERIC Educational Resources Information Center

    Zhang, Fan; Litman, Diane

    2015-01-01

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

  20. Alcohol Education Materials; An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Milgram, Gail Gleason

    This 873-item annotated bibliography cites books, pamphlets, leaflets, and other materials produced for education about alcohol from 1950 to May 1973. The major part of each annotation is a brief summary of the contents. The annotation also contains a statement of orientation or type of presentation and evaluative comments. Each item is classified…

  1. Automatic annotation of organellar genomes with DOGMA

    SciTech Connect

    Wyman, Stacia; Jansen, Robert K.; Boore, Jeffrey L.

    2004-06-01

    Dual Organellar GenoMe Annotator (DOGMA) automates the annotation of extra-nuclear organellar (chloroplast and animal mitochondrial) genomes. It is a web-based package that allows the use of comparative BLAST searches to identify and annotate genes in a genome. DOGMA presents a list of putative genes to the user in a graphical format for viewing and editing. Annotations are stored on our password-protected server. Complete annotations can be extracted for direct submission to GenBank. Furthermore, intergenic regions of specified length can be extracted, as well the nucleotide sequences and amino acid sequences of the genes.

  2. Cancer markers: integratively annotated classification.

    PubMed

    Orsini, M; Travaglione, A; Capobianco, E

    2013-11-10

    Translational cancer genomics research aims to ensure that experimental knowledge is subject to computational analysis, and integrated with a variety of records from omics and clinical sources. The data retrieval from such sources is not trivial, due to their redundancy and heterogeneity, and the presence of false evidence. In silico marker identification, therefore, remains a complex task that is mainly motivated by the impact that target identification from the elucidation of gene co-expression dynamics and regulation mechanisms, combined with the discovery of genotype-phenotype associations, may have for clinical validation. Based on the reuse of publicly available gene expression data, our aim is to propose cancer marker classification by integrating the prediction power of multiple annotation sources. In particular, with reference to the functional annotation for colorectal markers, we indicate a classification of markers into diagnostic and prognostic classes combined with susceptibility and risk factors. PMID:23928109

  3. Quality of Computationally Inferred Gene Ontology Annotations

    PubMed Central

    Škunca, Nives; Altenhoff, Adrian; Dessimoz, Christophe

    2012-01-01

    Gene Ontology (GO) has established itself as the undisputed standard for protein function annotation. Most annotations are inferred electronically, i.e. without individual curator supervision, but they are widely considered unreliable. At the same time, we crucially depend on those automated annotations, as most newly sequenced genomes are non-model organisms. Here, we introduce a methodology to systematically and quantitatively evaluate electronic annotations. By exploiting changes in successive releases of the UniProt Gene Ontology Annotation database, we assessed the quality of electronic annotations in terms of specificity, reliability, and coverage. Overall, we not only found that electronic annotations have significantly improved in recent years, but also that their reliability now rivals that of annotations inferred by curators when they use evidence other than experiments from primary literature. This work provides the means to identify the subset of electronic annotations that can be relied upon—an important outcome given that >98% of all annotations are inferred without direct curation. PMID:22693439

  4. Computational algorithms to predict Gene Ontology annotations

    PubMed Central

    2015-01-01

    Background Gene function annotations, which are associations between a gene and a term of a controlled vocabulary describing gene functional features, are of paramount importance in modern biology. Datasets of these annotations, such as the ones provided by the Gene Ontology Consortium, are used to design novel biological experiments and interpret their results. Despite their importance, these sources of information have some known issues. They are incomplete, since biological knowledge is far from being definitive and it rapidly evolves, and some erroneous annotations may be present. Since the curation process of novel annotations is a costly procedure, both in economical and time terms, computational tools that can reliably predict likely annotations, and thus quicken the discovery of new gene annotations, are very useful. Methods We used a set of computational algorithms and weighting schemes to infer novel gene annotations from a set of known ones. We used the latent semantic analysis approach, implementing two popular algorithms (Latent Semantic Indexing and Probabilistic Latent Semantic Analysis) and propose a novel method, the Semantic IMproved Latent Semantic Analysis, which adds a clustering step on the set of considered genes. Furthermore, we propose the improvement of these algorithms by weighting the annotations in the input set. Results We tested our methods and their weighted variants on the Gene Ontology annotation sets of three model organism genes (Bos taurus, Danio rerio and Drosophila melanogaster ). The methods showed their ability in predicting novel gene annotations and the weighting procedures demonstrated to lead to a valuable improvement, although the obtained results vary according to the dimension of the input annotation set and the considered algorithm. Conclusions Out of the three considered methods, the Semantic IMproved Latent Semantic Analysis is the one that provides better results. In particular, when coupled with a proper

  5. TriAnnot: A Versatile and High Performance Pipeline for the Automated Annotation of Plant Genomes.

    PubMed

    Leroy, Philippe; Guilhot, Nicolas; Sakai, Hiroaki; Bernard, Aurélien; Choulet, Frédéric; Theil, Sébastien; Reboux, Sébastien; Amano, Naoki; Flutre, Timothée; Pelegrin, Céline; Ohyanagi, Hajime; Seidel, Michael; Giacomoni, Franck; Reichstadt, Mathieu; Alaux, Michael; Gicquello, Emmanuelle; Legeai, Fabrice; Cerutti, Lorenzo; Numa, Hisataka; Tanaka, Tsuyoshi; Mayer, Klaus; Itoh, Takeshi; Quesneville, Hadi; Feuillet, Catherine

    2012-01-01

    In support of the international effort to obtain a reference sequence of the bread wheat genome and to provide plant communities dealing with large and complex genomes with a versatile, easy-to-use online automated tool for annotation, we have developed the TriAnnot pipeline. Its modular architecture allows for the annotation and masking of transposable elements, the structural, and functional annotation of protein-coding genes with an evidence-based quality indexing, and the identification of conserved non-coding sequences and molecular markers. The TriAnnot pipeline is parallelized on a 712 CPU computing cluster that can run a 1-Gb sequence annotation in less than 5 days. It is accessible through a web interface for small scale analyses or through a server for large scale annotations. The performance of TriAnnot was evaluated in terms of sensitivity, specificity, and general fitness using curated reference sequence sets from rice and wheat. In less than 8 h, TriAnnot was able to predict more than 83% of the 3,748 CDS from rice chromosome 1 with a fitness of 67.4%. On a set of 12 reference Mb-sized contigs from wheat chromosome 3B, TriAnnot predicted and annotated 93.3% of the genes among which 54% were perfectly identified in accordance with the reference annotation. It also allowed the curation of 12 genes based on new biological evidences, increasing the percentage of perfect gene prediction to 63%. TriAnnot systematically showed a higher fitness than other annotation pipelines that are not improved for wheat. As it is easily adaptable to the annotation of other plant genomes, TriAnnot should become a useful resource for the annotation of large and complex genomes in the future. PMID:22645565

  6. Omics data management and annotation.

    PubMed

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

    2011-01-01

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

  7. BioBuilder as a database development and functional annotation platform for proteins

    PubMed Central

    Navarro, J Daniel; Talreja, Naveen; Peri, Suraj; Vrushabendra, BM; Rashmi, BP; Padma, N; Surendranath, Vineeth; Jonnalagadda, Chandra Kiran; Kousthub, PS; Deshpande, Nandan; Shanker, K; Pandey, Akhilesh

    2004-01-01

    Background The explosion in biological information creates the need for databases that are easy to develop, easy to maintain and can be easily manipulated by annotators who are most likely to be biologists. However, deployment of scalable and extensible databases is not an easy task and generally requires substantial expertise in database development. Results BioBuilder is a Zope-based software tool that was developed to facilitate intuitive creation of protein databases. Protein data can be entered and annotated through web forms along with the flexibility to add customized annotation features to protein entries. A built-in review system permits a global team of scientists to coordinate their annotation efforts. We have already used BioBuilder to develop Human Protein Reference Database , a comprehensive annotated repository of the human proteome. The data can be exported in the extensible markup language (XML) format, which is rapidly becoming as the standard format for data exchange. Conclusions As the proteomic data for several organisms begins to accumulate, BioBuilder will prove to be an invaluable platform for functional annotation and development of customizable protein centric databases. BioBuilder is open source and is available under the terms of LGPL. PMID:15099404

  8. Citizen Participation in Education: Annotated Bibliography.

    ERIC Educational Resources Information Center

    Davies, Don

    The emphasis in this annotated bibliography is citizen participation in education in the areas of decision making, policy development, and school governance. The focus is on the public school and school system rather than on private and parochial schools. One hundred fifty books, parts of books, and published reports are annotated, together with…

  9. Effects of Multimedia Annotations on Vocabulary Acquisition.

    ERIC Educational Resources Information Center

    Chun, Dorothy M.; Plass, Jan L.

    1996-01-01

    Discusses studies of German students using "CyberBuch," a hypermedia application for reading German texts that contains annotations for words in the form of text, pictures, and video. The article examines incidental vocabulary learning, the effectiveness of different types of annotations for vocabulary acquisition, and the effect of look-up…

  10. Harnessing Collaborative Annotations on Online Formative Assessments

    ERIC Educational Resources Information Center

    Lin, Jian-Wei; Lai, Yuan-Cheng

    2013-01-01

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

  11. Annotated Catalog of Bilingual Vocational Training Materials.

    ERIC Educational Resources Information Center

    Miranda (L.) and Associates, Bethesda, MD.

    This catalog contains annotations for 170 bilingual vocational training materials. Most of the materials are written in English, but materials written in 13 source languages and directed toward speakers of 17 target languages are provided. Annotations are provided for the following different types of documents: administrative, assessment and…

  12. Automatic multilevel medical image annotation and retrieval.

    PubMed

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

    2008-09-01

    Image retrieval at the semantic level mostly depends on image annotation or image classification. Image annotation performance largely depends on three issues: (1) automatic image feature extraction; (2) a semantic image concept modeling; (3) algorithm for semantic image annotation. To address first issue, multilevel features are extracted to construct the feature vector, which represents the contents of the image. To address second issue, domain-dependent concept hierarchy is constructed for interpretation of image semantic concepts. To address third issue, automatic multilevel code generation is proposed for image classification and multilevel image annotation. We make use of the existing image annotation to address second and third issues. Our experiments on a specific domain of X-ray images have given encouraging results. PMID:17846834

  13. Concept annotation in the CRAFT corpus

    PubMed Central

    2012-01-01

    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 freely available at http

  14. Facilitating functional annotation of chicken microarray data

    PubMed Central

    2009-01-01

    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 will be updated on regular

  15. Genome Annotation and Curation Using MAKER and MAKER-P

    PubMed Central

    Campbell, Michael S.; Holt, Carson; Moore, Barry; Yandell, Mark

    2014-01-01

    This unit describes how to use the genome annotation and curation tools MAKER and MAKER-P to annotate protein coding and non-coding RNA genes in newly assembled genomes, update/combine legacy annotations in light of new evidence, add quality metrics to annotations from other pipelines, and map existing annotations to a new assembly. MAKER and MAKER-P can rapidly annotate genomes of any size, and scale to match available computational resources. PMID:25501943

  16. Making web annotations persistent over time

    SciTech Connect

    Sanderson, Robert; Van De Sompel, Herbert

    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.

  17. Genotator: a workbench for sequence annotation.

    PubMed

    Harris, N L

    1997-07-01

    Sequencing centers such as the Human Genome Center at LBNL are producing an ever-increasing flood of genetic data. Annotation can greatly enhance the biological value of these sequences. Useful annotations include possible gene locations, homologies to known genes, and gene signal such as promoters and splice sites. Genotator is a workbench for automated sequence annotation and annotation browsing. The back end runs a series of sequence analysis tools on a DNA sequence, handling the various input and output formats required by the tools. Genotator currently runs five different gene-finding programs, three homology searches, and searches for promoters, splice sites, and ORFs. The results of the analyses run by Genotator can be viewed with the interactive graphical browser. The browser displays color-coded sequence annotations on a canvas that can be scrolled and zoomed, allowing the annotated sequence to be explored at multiple levels of detail. The user can view the actual DNA sequence in a separate window; when a region is selected in the map display, it is highlighted automatically in the sequence display, and vice versa. By displaying the output of all of the sequence analyses, Genotator provides an intuitive way to identify the significant regions (for example, probable exons) in a sequence. Users can interactively add personal annotations to label regions of interest. Additional capabilities of Genotator include primer design and pattern searching. PMID:9253604

  18. Emergency management: An annotated bibliography

    SciTech Connect

    Not Available

    1988-03-01

    Training Resources and Data Exchange (TRADE) is an organization designed to increase communication and exchange of ideas, information, and resources among US Department of Energy contractors and DOE personnel. Oak Ridge Associated Universities, located in Oak Ridge, Tennessee, manages TRADE for the DOE. The Emergency Preparedness Special Interest Group (EP SIG) is a group formed within TRADE for emergency preparedness coordinators and trainers to share information about emergency preparedness training and other EP resources. This bibliography was prepared for the EP SIG as a resource for EP training and planning activities.

  19. Annotating user-defined abstractions for optimization

    SciTech Connect

    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.

  20. Automated Knowledge Annotation for Dynamic Collaborative Environments

    SciTech Connect

    Cowell, Andrew J.; Gregory, Michelle L.; Marshall, Eric J.; McGrath, Liam R.

    2009-05-19

    This paper describes the Knowledge Encapsulation Framework (KEF), a suite of tools to enable automated knowledge annotation for modeling and simulation projects. This framework can be used to capture evidence (e.g., facts extracted from journal articles and government reports), discover new evidence (from similar peer-reviewed material as well as social media), enable discussions surrounding domain-specific topics and provide automatically generated semantic annotations for improved corpus investigation. The current KEF implementation is presented within a wiki environment, providing a simple but powerful collaborative space for team members to review, annotate, discuss and align evidence with their modeling frameworks.

  1. SASL: A Semantic Annotation System for Literature

    NASA Astrophysics Data System (ADS)

    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.

  2. Annotation and retrieval in protein interaction databases

    NASA Astrophysics Data System (ADS)

    Cannataro, Mario; Hiram Guzzi, Pietro; Veltri, Pierangelo

    2014-06-01

    Biological databases have been developed with a special focus on the efficient retrieval of single records or the efficient computation of specialized bioinformatics algorithms against the overall database, such as in sequence alignment. The continuos production of biological knowledge spread on several biological databases and ontologies, such as Gene Ontology, and the availability of efficient techniques to handle such knowledge, such as annotation and semantic similarity measures, enable the development on novel bioinformatics applications that explicitly use and integrate such knowledge. After introducing the annotation process and the main semantic similarity measures, this paper shows how annotations and semantic similarity can be exploited to improve the extraction and analysis of biologically relevant data from protein interaction databases. As case studies, the paper presents two novel software tools, OntoPIN and CytoSeVis, both based on the use of Gene Ontology annotations, for the advanced querying of protein interaction databases and for the enhanced visualization of protein interaction networks.

  3. GRADUATE AND PROFESSIONAL EDUCATION, AN ANNOTATED BIBLIOGRAPHY.

    ERIC Educational Resources Information Center

    HEISS, ANN M.; AND OTHERS

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

  4. Genepi: a blackboard framework for genome annotation

    PubMed Central

    Descorps-Declère, Stéphane; Ziébelin, Danielle; Rechenmann, François; Viari, Alain

    2006-01-01

    Background Genome annotation can be viewed as an incremental, cooperative, data-driven, knowledge-based process that involves multiple methods to predict gene locations and structures. This process might have to be executed more than once and might be subjected to several revisions as the biological (new data) or methodological (new methods) knowledge evolves. In this context, although a lot of annotation platforms already exist, there is still a strong need for computer systems which take in charge, not only the primary annotation, but also the update and advance of the associated knowledge. In this paper, we propose to adopt a blackboard architecture for designing such a system Results We have implemented a blackboard framework (called Genepi) for developing automatic annotation systems. The system is not bound to any specific annotation strategy. Instead, the user will specify a blackboard structure in a configuration file and the system will instantiate and run this particular annotation strategy. The characteristics of this framework are presented and discussed. Specific adaptations to the classical blackboard architecture have been required, such as the description of the activation patterns of the knowledge sources by using an extended set of Allen's temporal relations. Although the system is robust enough to be used on real-size applications, it is of primary use to bioinformatics researchers who want to experiment with blackboard architectures. Conclusion In the context of genome annotation, blackboards have several interesting features related to the way methodological and biological knowledge can be updated. They can readily handle the cooperative (several methods are implied) and opportunistic (the flow of execution depends on the state of our knowledge) aspects of the annotation process. PMID:17038181

  5. JGI Plant Genomics Gene Annotation Pipeline

    SciTech Connect

    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.

  6. IFA - INTELLIGENT FRONT ANNOTATION PROGRAM

    NASA Technical Reports Server (NTRS)

    Burke, G. R.

    1994-01-01

    An important aspect of an ASIC (Application Specific Integrated Circuit) design process is verification. The design must not only be functionally accurate, but it must also maintain the correct timing. After a circuit has been laid out, one can utilize the Back Annotation (BA) method to simulate the design and obtain an accurate estimate of performance. However, this can lead to major design changes. It is therefore preferable to eliminate potential problems early in this process. IFA, the Intelligent Front Annotation program, assists in verifying the timing of the ASIC early in the design process. Many difficulties can arise during ASIC design. In a synchronous design, both long path and short path problems can be present. In modern ASIC technologies, the delay through a gate is very dependent on loading. This loading has two main components, the capacitance of the gates being driven and the capacitance of the metal tracks (wires). When using GaAs gate arrays, the metal line capacitance is often the dominating factor. Additionally, the RC delay through the wire itself is significant in sub-micron technologies. Since the wire lengths are unknown before place and route of the entire chip, this would seem to postpone any realistic timing verification until towards the end of the design process, obviously an undesirable situation. The IFA program estimates the delays in an ASIC before layout. Currently the program is designed for Vitesse GaAs gate arrays and, for input, requires the expansion file which is output by the program GED; however, the algorithm is appropriate for many different ASIC types and CAE platforms. IFA is especially useful for devices whose delay is extremely dependent on the interconnection wiring. It estimates the length of the interconnects using information supplied by the user and information in the netlist. The resulting wire lengths are also used to constrain the Place and Route program, ensuring reasonable results. IFA takes locality into

  7. The Annotation of RNA Motifs

    PubMed Central

    2002-01-01

    The recent deluge of new RNA structures, including complete atomic-resolution views of both subunits of the ribosome, has on the one hand literally overwhelmed our individual abilities to comprehend the diversity of RNA structure, and on the other hand presented us with new opportunities for comprehensive use of RNA sequences for comparative genetic, evolutionary and phylogenetic studies. Two concepts are key to understanding RNA structure: hierarchical organization of global structure and isostericity of local interactions. Global structure changes extremely slowly, as it relies on conserved long-range tertiary interactions. Tertiary RNA–RNA and quaternary RNA–protein interactions are mediated by RNA motifs, defined as recurrent and ordered arrays of non-Watson–Crick base-pairs. A single RNA motif comprises a family of sequences, all of which can fold into the same three-dimensional structure and can mediate the same interaction(s). The chemistry and geometry of base pairing constrain the evolution of motifs in such a way that random mutations that occur within motifs are accepted or rejected insofar as they can mediate a similar ordered array of interactions. The steps involved in the analysis and annotation of RNA motifs in 3D structures are: (a) decomposition of each motif into non-Watson–Crick base-pairs; (b) geometric classification of each basepair; (c) identification of isosteric substitutions for each basepair by comparison to isostericity matrices; (d) alignment of homologous sequences using the isostericity matrices to identify corresponding positions in the crystal structure; (e) acceptance or rejection of the null hypothesis that the motif is conserved. PMID:18629252

  8. Annotated checklist of Georgia birds

    USGS Publications Warehouse

    Beaton, G.; Sykes, P.W., Jr.; Parrish, J.W., Jr.

    2003-01-01

    This edition of the checklist includes 446 species, of which 407 are on the Regular Species List, 8 on the Provisional, and 31 on the Hypothetical. This new publication has been greatly expanded and much revised over the previous checklist (GOS Occasional Publ. No. 10, 1986, 48 pp., 6x9 inches) to a 7x10-inch format with an extensive Literature Cited section added, 22 species added to the Regular List, 2 to the Provisional List, and 9 to the Hypothetical List. Each species account is much more comprehensive over all previous editions of the checklist. Among some of the new features are citations for sources of most information used, high counts of individuals for each species on the Regular List, extreme dates of occurrence within physiographic regions, a list of abbreviations and acronyms, and for each species the highest form of verifiable documentation given with its repository institution with a catalog number. This checklist is helpful for anyone working with birds in the Southeastern United States or birding in that region. Sykes' contribution to this fifth edition of the Annotated Checklist of Georgia Birds includes: suggestion of the large format and spiral binding, use of Richard A. Parks' painting of the Barn Owl on the front cover, use of literature citations throughout, and inclusion of high counts for each species. Sykes helped plan all phases of the publication, wrote about 90% of the Introduction and 84 species accounts (Osprey through Red Phalarope), designed the four maps in the introduction section and format for the Literature Cited, and with Giff Beaton designed the layout of the title page.

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

    PubMed Central

    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 PMID:26994912

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

    PubMed

    Akhondi, Saber A; Klenner, Alexander G; Tyrchan, Christian; Manchala, Anil K; Boppana, Kiran; Lowe, Daniel; Zimmermann, Marc; Jagarlapudi, Sarma A R P; Sayle, Roger; Kors, Jan A; Muresan, Sorel

    2014-01-01

    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. PMID:25268232

  11. Non-Formal Education and Radio: A Selected, Annotated Bibliography. Annotated Bibliography #14.

    ERIC Educational Resources Information Center

    Vergeldt, Vicki; And Others

    Materials concerning the use of radio and mass communications for non-formal education and development are listed in a selected annotated bibliography, intended for those actively involved in non-formal education and development. Three sections contain annotated entries (which range from 1972-1983), each of which includes source information and…

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

    PubMed

    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. PMID:25826378

  13. Gene and alternative splicing annotation with AIR

    PubMed Central

    Florea, Liliana; Di Francesco, Valentina; Miller, Jason; Turner, Russell; Yao, Alison; Harris, Michael; Walenz, Brian; Mobarry, Clark; Merkulov, Gennady V.; Charlab, Rosane; Dew, Ian; Deng, Zuoming; Istrail, Sorin; Li, Peter; Sutton, Granger

    2005-01-01

    Designing effective and accurate tools for identifying the functional and structural elements in a genome remains at the frontier of genome annotation owing to incompleteness and inaccuracy of the data, limitations in the computational models, and shifting paradigms in genomics, such as alternative splicing. We present a methodology for the automated annotation of genes and their alternatively spliced mRNA transcripts based on existing cDNA and protein sequence evidence from the same species or projected from a related species using syntenic mapping information. At the core of the method is the splice graph, a compact representation of a gene, its exons, introns, and alternatively spliced isoforms. The putative transcripts are enumerated from the graph and assigned confidence scores based on the strength of sequence evidence, and a subset of the high-scoring candidates are selected and promoted into the annotation. The method is highly selective, eliminating the unlikely candidates while retaining 98% of the high-quality mRNA evidence in well-formed transcripts, and produces annotation that is measurably more accurate than some evidence-based gene sets. The process is fast, accurate, and fully automated, and combines the traditionally distinct gene annotation and alternative splicing detection processes in a comprehensive and systematic way, thus considerably aiding in the ensuing manual curation efforts. PMID:15632090

  14. Real-time computerized annotation of pictures.

    PubMed

    Li, Jia; Wang, James Z

    2008-06-01

    Developing effective methods for automated annotation of digital pictures continues to challenge computer scientists. The capability of annotating pictures by computers can lead to breakthroughs in a wide range of applications, including Web image search, online picture-sharing communities, and scientific experiments. In this work, the authors developed new optimization and estimation techniques to address two fundamental problems in machine learning. These new techniques serve as the basis for the Automatic Linguistic Indexing of Pictures - Real Time (ALIPR) system of fully automatic and high speed annotation for online pictures. In particular, the D2-clustering method, in the same spirit as k-means for vectors, is developed to group objects represented by bags of weighted vectors. Moreover, a generalized mixture modeling technique (kernel smoothing as a special case) for non-vector data is developed using the novel concept of Hypothetical Local Mapping (HLM). ALIPR has been tested by thousands of pictures from an Internet photo-sharing site, unrelated to the source of those pictures used in the training process. Its performance has also been studied at an online demo site where arbitrary users provide pictures of their choices and indicate the correctness of each annotation word. The experimental results show that a single computer processor can suggest annotation terms in real-time and with good accuracy. PMID:18421105

  15. Pathway Analysis Software: Annotation Errors and Solutions

    PubMed Central

    Henderson-MacLennan, Nicole K.; Papp, Jeanette C.; Talbot, C. Conover; McCabe, Edward R.B.; Presson, Angela P.

    2010-01-01

    Genetic databases contain a variety of annotation errors that often go unnoticed due to the large size of modern genetic data sets. Interpretation of these data sets requires bioinformatics tools that may contribute to this problem. While providing gene symbol annotations for identifiers (IDs) such as microarray probeset, RefSeq, GenBank and Entrez Gene is seemingly trivial, the accuracy is fundamental to any subsequent conclusions. We examine gene symbol annotations and results from three commercial pathway analysis software (PAS) packages: Ingenuity Pathways Analysis, GeneGO and Pathway Studio. We compare gene symbol annotations and canonical pathway results over time and among different input ID types. We find that PAS results can be affected by variation in gene symbol annotations across software releases and the input ID type analyzed. As a result, we offer suggestions for using commercial PAS and reporting microarray results to improve research quality. We propose a wiki type website to facilitate communication of bioinformatics software problems within the scientific community. PMID:20663702

  16. Automated analysis and annotation of basketball video

    NASA Astrophysics Data System (ADS)

    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.

  17. MPEG-7 based video annotation and browsing

    NASA Astrophysics Data System (ADS)

    Hoeynck, Michael; Auweiler, Thorsten; Wellhausen, Jens

    2003-11-01

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

  18. Quantitative measures for the management and comparison of annotated genomes

    PubMed Central

    Eilbeck, Karen; Moore, Barry; Holt, Carson; Yandell, Mark

    2009-01-01

    Background The ever-increasing number of sequenced and annotated genomes has made management of their annotations a significant undertaking, especially for large eukaryotic genomes containing many thousands of genes. Typically, changes in gene and transcript numbers are used to summarize changes from release to release, but these measures say nothing about changes to individual annotations, nor do they provide any means to identify annotations in need of manual review. Results In response, we have developed a suite of quantitative measures to better characterize changes to a genome's annotations between releases, and to prioritize problematic annotations for manual review. We have applied these measures to the annotations of five eukaryotic genomes over multiple releases – H. sapiens, M. musculus, D. melanogaster, A. gambiae, and C. elegans. Conclusion Our results provide the first detailed, historical overview of how these genomes' annotations have changed over the years, and demonstrate the usefulness of these measures for genome annotation management. PMID:19236712

  19. Quantifying Variability of Manual Annotation in Cryo-Electron Tomograms.

    PubMed

    Hecksel, Corey W; Darrow, Michele C; Dai, Wei; Galaz-Montoya, Jesús G; Chin, Jessica A; Mitchell, Patrick G; Chen, Shurui; Jakana, Jemba; Schmid, Michael F; Chiu, Wah

    2016-06-01

    Although acknowledged to be variable and subjective, manual annotation of cryo-electron tomography data is commonly used to answer structural questions and to create a "ground truth" for evaluation of automated segmentation algorithms. Validation of such annotation is lacking, but is critical for understanding the reproducibility of manual annotations. Here, we used voxel-based similarity scores for a variety of specimens, ranging in complexity and segmented by several annotators, to quantify the variation among their annotations. In addition, we have identified procedures for merging annotations to reduce variability, thereby increasing the reliability of manual annotation. Based on our analyses, we find that it is necessary to combine multiple manual annotations to increase the confidence level for answering structural questions. We also make recommendations to guide algorithm development for automated annotation of features of interest. PMID:27225525

  20. Corpus annotation for mining biomedical events from literature

    PubMed Central

    Kim, Jin-Dong; Ohta, Tomoko; Tsujii, Jun'ichi

    2008-01-01

    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. PMID:18182099

  1. Critical Assessment of Function Annotation Meeting, 2011

    SciTech Connect

    Friedberg, Iddo

    2015-01-21

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

  2. Motion lecture annotation system to learn Naginata performances

    NASA Astrophysics Data System (ADS)

    Kobayashi, Daisuke; Sakamoto, Ryota; Nomura, Yoshihiko

    2013-12-01

    This paper describes a learning assistant system using motion capture data and annotation to teach "Naginata-jutsu" (a skill to practice Japanese halberd) performance. There are some video annotation tools such as YouTube. However these video based tools have only single angle of view. Our approach that uses motion-captured data allows us to view any angle. A lecturer can write annotations related to parts of body. We have made a comparison of effectiveness between the annotation tool of YouTube and the proposed system. The experimental result showed that our system triggered more annotations than the annotation tool of YouTube.

  3. Annotating images by mining image search results.

    PubMed

    Wang, Xin-Jing; Zhang, Lei; Li, Xirong; Ma, Wei-Ying

    2008-11-01

    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. Some 2.4 million images with their surrounding text are collected from a few photo forums to support this approach. The entire process is formulated in a divide-and-conquer framework where a query keyword is provided along with the uncaptioned image to improve both the effectiveness and efficiency. This is helpful when the collected data set is not dense everywhere. In this sense, our approach contains three steps: 1) the search process to discover visually and semantically similar search results, 2) the mining process to identify salient terms from textual descriptions of the search results, and 3) the annotation rejection process to filter out noisy terms yielded by Step 2. To ensure real-time annotation, two key techniques are leveraged-one is to map the high-dimensional image visual features into hash codes, the other is to implement it as a distributed system, of which the search and mining processes are provided as Web services. As a typical result, the entire process finishes in less than 1 second. Since no training data set is required, our approach enables annotating with unlimited vocabulary and is highly scalable and robust to outliers. Experimental results on both real Web images and a benchmark image data set show the effectiveness and efficiency of the proposed algorithm. It is also worth noting that, although the entire approach is illustrated within the divide-and conquer framework, a query keyword is not crucial to our current implementation. We provide experimental results to prove this. PMID:18787241

  4. Solar Tutorial and Annotation Resource (STAR)

    NASA Astrophysics Data System (ADS)

    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

  5. Computer systems for annotation of single molecule fragments

    DOEpatents

    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.

  6. Food for Thought: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Bennett, Susan G., Ed.

    Most of the 24 books reviewed in this annotated bibliography concern writing and are recent publications (1980-1985). Titles and authors are as follows: "Teacher" (Sylvia Ashton-Warner); "What Did I Write? Beginning Writing Behavior" (Marie M. Clay); "Composing: Writing as a Self-Creating Process" (William E. Coles); "Right Brain...Write On!…

  7. Skin Cancer Education Materials: Selected Annotations.

    ERIC Educational Resources Information Center

    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. A Partially Annotated Political Communication Bibliography.

    ERIC Educational Resources Information Center

    Thornton, Barbara C.

    This 63-page annotated bibliography contains available materials in the area of political communication, a relatively new field of political science. Political communication includes facets of the election process and interaction between political parties and the voter. A variety of materials dating from 1960 to 1972 include books, pamphlets,…

  9. Annotated Psychodynamic Bibliography for Residents in Psychiatry

    PubMed Central

    CALIGOR, EVE

    1996-01-01

    The author provides an annotated bibliography to introduce psychodynamic psychotherapy and psychoanalysis to residents in psychiatry. The emphasis of the selection is on relevance to practice. The entries are grouped by topic, levels of difficulty are noted, and readings are identified as being of either current or historic relevance. PMID:22700303

  10. Staff Differentiation; An Annotated Bibliography Addendum.

    ERIC Educational Resources Information Center

    Marin County Public Schools, Corte Madera, CA.

    Differentiated staffing has emphasized development of teacher leadership roles, the importance of shared decision making in schools, and the constructive ways in which paid instructional aides and volunteer aides can support the professional teaching staff. Eighteen annotated bibliographic citations concerning the various aspects of differentiated…

  11. Revenue Producing Athletes: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Ervin, Leroy; And Others

    An annotated bibliography on revenue producing sports is presented, with attention to: Proposition 48, exploitation of athletes, legal proceedings, research related to athletes and academic performance, psychological characteristics of athletes, and counseling programs for athletes. Introductions to each of the six topics are included. The section…

  12. Intellectual Freedom and Censorship: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Hoffmann, Frank

    Intended to act as a general introduction for high school and college students, this book presents an annotated bibliography of books, periodical articles, legal materials, and other documents dealing with the subject of intellectual freedom and censorship. The book is divided into five parts: (1) "The Theoretical Foundations of Censorship and…

  13. Annotated Bibliography of EDGE2D Use

    SciTech Connect

    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.

  14. Research: Annotated Bibliography of New Canadian Studies.

    ERIC Educational Resources Information Center

    Toronto Board of Education (Ontario). Research Dept.

    This annotated bibliography of twenty-one research reports that provide knowledge about various cultures and educational experiences of the major ethnic groups in the Toronto schools is designed to present information for not only special English teachers, but other school personnel as well. The bibliography consists of reports that aim to: 1)…

  15. Alaskan Rural Justice: A Selected Annotated Bibliography.

    ERIC Educational Resources Information Center

    Alaska Judicial Council, Anchorage.

    This annotated bibliography lists approximately 300 documents and source materials directly or indirectly related to the problem of access to justice in rural Alaska. Written materials about the state's history, geography, economics, and culture have often touched upon the justice system and its role in the development of the state. Other works…

  16. Women and World Development: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Buvinic, Mayra; And Others

    This annotated bibliography focuses on the effects of socioeconomic development and cultural change on women and on women's reactions to these changes. It is an expanded version of one which was prepared for the American Association of Science Seminar on Women in Development held in Mexico City in June 1975. The objectives were to disseminate this…

  17. An Annotated Bibliography of Small Town Research.

    ERIC Educational Resources Information Center

    Smith, Suzanne M.

    The purpose of this annotated bibliography is to list books, articles, and bulletins (written from 1900 to 1968) related to small towns in the United States. The work contributes to the project "Population Changes in Small Towns," sponsored by the Division of Social Sciences of the National Science Foundation and by the University of Wisconsin…

  18. Human object annotation for surveillance video forensics

    NASA Astrophysics Data System (ADS)

    Fraz, Muhammad; Zafar, Iffat; Tzanidou, Giounona; Edirisinghe, Eran A.; Sarfraz, Muhammad Saquib

    2013-10-01

    A system that can automatically annotate surveillance video in a manner useful for locating a person with a given description of clothing is presented. Each human is annotated based on two appearance features: primary colors of clothes and the presence of text/logos on clothes. The annotation occurs after a robust foreground extraction stage employing a modified Gaussian mixture model-based approach. The proposed pipeline consists of a preprocessing stage where color appearance of an image is improved using a color constancy algorithm. In order to annotate color information for human clothes, we use the color histogram feature in HSV space and find local maxima to extract dominant colors for different parts of a segmented human object. To detect text/logos on clothes, we begin with the extraction of connected components of enhanced horizontal, vertical, and diagonal edges in the frames. These candidate regions are classified as text or nontext on the basis of their local energy-based shape histogram features. Further, to detect humans, a novel technique has been proposed that uses contourlet transform-based local binary pattern (CLBP) features. In the proposed method, we extract the uniform direction invariant LBP feature descriptor for contourlet transformed high-pass subimages from vertical and diagonal directional bands. In the final stage, extracted CLBP descriptors are classified by a trained support vector machine. Experimental results illustrate the superiority of our method on large-scale surveillance video data.

  19. Chemical Principles Revisited: Annotating Reaction Equations.

    ERIC Educational Resources Information Center

    Tykodi, R. J.

    1987-01-01

    Urges chemistry teachers to have students annotate the chemical reactions in aqueous-solutions that they see in their textbooks and witness in the laboratory. Suggests this will help students recognize the reaction type more readily. Examples are given for gas formation, precipitate formation, redox interaction, acid-base interaction, and…

  20. Librarian-Teacher Partnerships: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Avino, Catherine

    This annotated list of 23 journal articles and documents provided focuses on faculty-librarian collaboration in bibliographic instruction (BI) at academic libraries. Topics including the following: BI for developmental and English-as-a-Second-Language (ESL) students; faculty and librarian collaboration on the design of BI assignments; the teaching…

  1. Music, Higher Education, and Technology. Annotated Bibliography.

    ERIC Educational Resources Information Center

    Reitenour, Steve

    An annotated bibliography on music, higher education, and technology includes 27 journal articles and 6 books, most dated 1980 or later. The following topics are covered: resource groups with expertise in the music educational application of computers, manufacturers dealing with educational technology products, information on the National…

  2. Labor and Migration; An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Brooks, Thomas R.

    This annotated bibliography is intended to contribute toward an understanding of labor and migration, both of which have helped to shape our nation. A total of 131 works, including a few periodicals and newspapers, focus on immigration and internal migration as it affects organized and unorganized labor. (BH)

  3. An Annotated Publications List on Homelessness.

    ERIC Educational Resources Information Center

    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…

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

    ERIC Educational Resources Information Center

    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";…

  5. An Annotated Bibliography of Nonsexist Resources.

    ERIC Educational Resources Information Center

    Miles Coll., Eutaw, AL. West Alabama Curriculum and Materials Resource Center.

    The result of a thorough search, review, and compilation of resources on women's equity, the annotated bibliography represents a sample of print materials, games and kits, photos and posters, and audiovisual aids now available on sexism that should prove useful to counselors, instructors, school administrators, parents, and elementary and…

  6. Communication and Sexuality: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Buley, Jerry, Comp.; And Others

    The entries in this annotated bibliography represent books, educational journals, dissertations, popular magazines, and research studies that deal with the topic of communication and sexuality. Arranged alphabetically by author and also indexed according to subject matter, the titles span a variety of topics, including the following: sex and…

  7. SEF Annotated Bibliography on Informal Education.

    ERIC Educational Resources Information Center

    Metropolitan Toronto School Board (Ontario). Study of Educational Facilities.

    This bibliography on informal education grew out of a concern to understand the kinds of programs possible in open plan schools. The annotations are reading notes generally more descriptive than evaluative. Citations are grouped under nine headings: (1) general, (2) description of British informal education by British writers, (3) description of…

  8. Teleconferencing, an annotated bibliography, volume 3

    NASA Technical Reports Server (NTRS)

    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.

  9. An Annotated Bibliography of Migrant Related Materials.

    ERIC Educational Resources Information Center

    Florida Atlantic Univ., Boca Raton.

    Over 1,000 annotated entries in this bibliography present a wide variety of materials related to the teaching and understanding of the migrant and culturally deprived student. Materials are divided into 6 major content areas: (1) health, (2) information on migrants and culturally disadvantaged, (3) curriculum materials, (4) guidance, (5)…

  10. Annotated bibliography of psychomotor testing. Technical report

    SciTech Connect

    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.

  11. Sexually Transmitted Diseases: A Selective, Annotated Bibliography.

    ERIC Educational Resources Information Center

    Planned Parenthood Federation of America, Inc., New York, NY. Education Dept.

    This document contains a reference sheet and an annotated bibliography concerned with sexually transmitted diseases (STD). The reference sheet provides a brief, accurate overview of STDs which includes both statistical and background information. The bibliography contains 83 entries, listed alphabetically, that deal with STDs. Books and articles…

  12. Genome Annotation of Five Mycoplasma canis Strains

    PubMed Central

    May, M.; Michaels, D. L.; Barbet, A. F.

    2012-01-01

    To understand its potential to cause invasive disease, the genome of Mycoplasma canis strain PG14T from a dog's throat was compared to those of isolates from the genital tract or brain of dogs. The average nucleotide identity between strain pairs is 98%, and their genome annotations are similar. PMID:22815452

  13. Document Delivery: An Annotated Selective Bibliography.

    ERIC Educational Resources Information Center

    Khalil, Mounir A.; Katz, Suzanne R.

    1992-01-01

    Presents a selective annotated bibliography of 61 items that deal with topics related to document delivery, including networks; hypertext; interlibrary loan; computer security; electronic publishing; copyright; online catalogs; resource sharing; electronic mail; electronic libraries; optical character recognition; microcomputers; liability issues;…

  14. SPEED READING--AN ANNOTATED BIBLIOGRAPHY.

    ERIC Educational Resources Information Center

    BERGER, ALLEN

    APPROXIMATELY 125 REFERENCES TO SPEED READING APPEARING DURING THE PAST 40 YEARS ARE INCLUDED IN THIS ANNOTATED BIBLIOGRAPHY. THEY ARE GROUPED INTO THE CATEGORIES OF TACHISTOSCOPIC AND CONTROLLED PACING, PAPERBACK SCANNING, RETENTION OF GAINS, FLEXIBILITY, PERCEPTION, PROCESSING INFORMATION, SEX DIFFERENCES, AND MEASUREMENT. MORE THAN 35 JOURNALS…

  15. INDIVIDUALIZED READING--AN ANNOTATED BIBLIOGRAPHY.

    ERIC Educational Resources Information Center

    SARTAIN, HARRY

    THIS ANNOTATED BIBLIOGRAPHY ON INDIVIDUALIZED READING IS COMPOSED OF 62 CITATIONS RANGING IN DATE FROM 1952 TO 1964. MAJOR EMPHASIS IS PLACED ON RECENT BOOKS AND WIDELY CIRCULATED PERIODICALS WHICH ARE EASILY ACCESSIBLE. LISTINGS REPRESENT VARIED PRACTICES AND POINTS OF VIEW. THEY INCLUDE ARGUMENTS FOR AND AGAINST INDIVIDUALIZED READING,…

  16. READABILITY AND READING--AN ANNOTATED BIBLIOGRAPHY.

    ERIC Educational Resources Information Center

    DALE, EDGAR; SEELS, BARBARA

    THIS ANNOTATED BIBLIOGRAPHY COVERS THE FIELD OF READABILITY AND READING. THE SELECTED WORKS ARE ORGANIZED INTO NINE SECTIONS--(1) GENERAL REFERENCES ON READABILITY, (2) MEASURING OF READABILITY, (3) READABILITY AND SENTENCE STRUCTURE, (4) READABILITY AND VOCABULARY, (5) READABILITY AND LITERARY STYLE, (6) READABILITY IN SUBJECT AREA MATERIALS, (7)…

  17. Annotated Bibliography of Literature on Narcotic Addiction.

    ERIC Educational Resources Information Center

    Bowden, R. Renee

    Nearly 150 abstracts have been included in this annotated bibliography; its purpose has been to scan the voluminous number of documents on the problem of drug addiction in order to summarize the present state of knowledge on narcotic addiction and on methods for its treatment and control. The literature reviewed has been divided into the following…

  18. Studies of Scientific Disciplines. An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Weisz, Diane; Kruytbosch, Carlos

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

  19. The Mentally Retarded Offender: Annotated Bibliography.

    ERIC Educational Resources Information Center

    Schilit, Jeffrey; And Others

    An annotated bibliography of approximately 150 books and articles on the mentally retarded offender as well as 30 nonannotated entries are provided. Topics covered include such areas as characteristics of mentally retarded delinquents, rehabilitation of the retarded offender, community services for retarded persons, rights of the mentally…

  20. Health Economics Research: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Dillard, Carole D.; And Others

    This annotated bibliography lists books and journal articles published since 1976 which deal with health economics and which are based on health services research supported by the National Center for Health Services Research (NCHSR). Articles prepared by NCHSR staff are listed as intramural. All other articles cite the NCHSR grant or contract…

  1. Food Habits: A Selected Annotated Bibliography

    ERIC Educational Resources Information Center

    Wilson, Christine S.

    1973-01-01

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

  2. Higher Education Literature: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    White, Jane N., Ed.; Burnett, Collins W., Ed.

    An annotated bibliography on higher education is presented that is limited to programs and phenomena in two- and four-year accredited degree-granting colleges and universities. The following sections and topics are covered: (1) Historical Background and Nature and Scope of American Higher Education (ancient, medieval, and U.S. education,…

  3. Annotation Technologies: A Software and Research Review.

    ERIC Educational Resources Information Center

    Wolfe, Joanna

    2002-01-01

    Describes a range of currently available and developing technologies for creating and presenting annotations, glosses, and other comments on digital documents. Discusses the potential applications of these tools for providing feedback to student writers, supporting extended group discussions around digital texts, and facilitating research and…

  4. Law in the Classroom. An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Carsello, Carmen J.

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

  5. Children and Poetry: A Selective, Annotated Bibliography.

    ERIC Educational Resources Information Center

    Haviland, Virginia; Smith, William Jay

    This annotated bibliography of over 120 books was compiled to call attention to poetry for children that is both pleasing and rewarding. Omitted are traditional materials such as Mother Goose rhymes, textbooks, and collections designed especially for the classroom. Sample illustrations from the books noted and lines from poems are reproduced…

  6. Evaluating Image Browsers Using Structured Annotation.

    ERIC Educational Resources Information Center

    Muller, Wolfgang; Marchand-Mailet, Stephane; Muller, Henning; Squire, David McG.; Pun, Thierry

    2001-01-01

    Addresses the problem of benchmarking image browsers. Existence of different search paradigms for image browsers makes it difficult to compare them. Currently, the only admissible evaluation method involves conducting large-scale user studies. An automatic image browser benchmark is proposed that uses structured text annotation of the image…

  7. Annotated Bibliography of Products/Materials.

    ERIC Educational Resources Information Center

    Lee, Carolyn S., Comp.; Jennings, Mark B., Comp.; Mayo, Linda P., Comp.; Young, Debra A., Comp.

    This document, which is intended for teachers, program directors, researchers, businesspeople, and students, is an annotated bibliography of more than 600 programs and resources that were developed with funds from the Office of Vocational and Adult Education in fiscal years 1987-1998. The document is divided into two parts. Part 1 is a summary of…

  8. Organizational and Intercultural Communication: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    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,…

  9. Science Fiction Criticism: An Annotated Checklist.

    ERIC Educational Resources Information Center

    Clareson, Thomas

    An expansion of the list published in "Extrapolation" between May 1970 and May 1971, this book contains approximately 800 entries of science fiction criticism. Divided into special categories, all items are annotated and explicitly discuss science fiction. The nine categories of science fiction criticism are Literary Studies; Book Reviews; the…

  10. Teachers and Research: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Griffee, Dale T.

    The annotated bibliography consists of reviews, of three to seven paragraphs each, of nine books focusing on classroom research and the teacher's role in conducting and publishing it. Eight of the books relate specifically to research on English-as-a-Second-Language teaching and learning. Each review provides basic bibliographic information,…

  11. The Alaska Eskimos. A Selected, Annotated Bibliography.

    ERIC Educational Resources Information Center

    Hippler, Arthur E.; Wood, John R.

    This annotated bibliography, containing approximately 732 entries, provides a general overview of English literature concerning Alaska Eskimos and cities. Although the earliest date of publication is 1843, the majority of the works have been done since 1900; there are no entries published later than 1975. Section I lists the works alphabetically…

  12. Counseling American Indians: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Tisdale, Elizabeth; Thomason, Timothy C.

    This bibliography presents 75 annotated entries on counseling and psychotherapy with American Indians. Entries include journal articles, books, book chapters, newspaper and newsletter articles, and conference papers, published 1964-96. Topics covered include counseling approaches and techniques, mental health services for Native Americans,…

  13. Realistic Portrayal of Aging. An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Dodson, Anita E.; Hause, Judith B.

    This annotated bibliography cites selected reading materials for all age levels that present aging and the aged realistically with a full range of human behaviors. The listing is meant to serve as a resource to educators who wish to develop positive attitudes in children and in adolescents about the elderly and about themselves. Educators should…

  14. Suggested Books for Children: An Annotated Bibliography

    ERIC Educational Resources Information Center

    NHSA Dialog, 2008

    2008-01-01

    This article provides an annotated bibliography of various children's books. It includes listings of books that illustrate the dynamic relationships within the natural environment, economic context, racial and cultural identities, cross-group similarities and differences, gender, different abilities and stories of injustice and resistance.

  15. Greeks in Canada (an Annotated Bibliography).

    ERIC Educational Resources Information Center

    Bombas, Leonidas C.

    This bibliography on Greeks in Canada includes annotated references to both published and (mostly) unpublished works. Among the 70 entries (arranged in alphabetical order by author) are articles, reports, papers, and theses that deal either exclusively with or include a separate section on Greeks in the various Canadian provinces. (GC)

  16. Multicultural Education: A Selected Annotated Bibliography.

    ERIC Educational Resources Information Center

    Mathieson, Moira B.; Tatis, Rita M.

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

  17. Environment and the Community: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Department of Housing and Urban Development, Washington, DC.

    Three hundred and nine citations of books, reports, and articles dating from 1964 to 1971 are included in this annotated bibliography, intended as a selection tool for concerned citizens, architects, builders, and city planners emphasizing the environment of American cities and communities. It is topically arranged into sixteen broad sections with…

  18. Project for Global Education: Annotated Bibliography.

    ERIC Educational Resources Information Center

    Institute for World Order, New York, NY.

    Over 260 books, textbooks, articles, pamphlets, periodicals, films, and multi-media packages appropriate for the analysis of global issues at the college level are briefly annotated. Entries include classic books and articles as well as a number of recent (1976-1981) publications. The purpose is to assist students and educators in developing a…

  19. Annotated Bibliography of Autism 1943-1983.

    ERIC Educational Resources Information Center

    Tari, Andor J.; And Others

    The annotated bibliography of over 1,200 citations published between 1943 and 1983 is intended as a comprehensive reference guide to the scientific study of infantile autism. After a search of the literature was conducted, the information was organized by format and subject, first for journal articles (19 topics are concerned with general…

  20. Kwanzaa: A Selective Annotated Bibliography for Teachers.

    ERIC Educational Resources Information Center

    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…

  1. Mulligan Concept manual therapy: standardizing annotation.

    PubMed

    McDowell, Jillian Marie; Johnson, Gillian Margaret; Hetherington, Barbara Helen

    2014-10-01

    Quality technique documentation is integral to the practice of manual therapy, ensuring uniform application and reproducibility of treatment. Manual therapy techniques are described by annotations utilizing a range of acronyms, abbreviations and universal terminology based on biomechanical and anatomical concepts. The various combinations of therapist and patient generated forces utilized in a variety of weight-bearing positions, which are synonymous with Mulligan Concept, challenge practitioners existing annotational skills. An annotation framework with recording rules adapted to the Mulligan Concept is proposed in which the abbreviations incorporate established manual therapy tenets and are detailed in the following sequence of; starting position, side, joint/s, method of application, glide/s, Mulligan technique, movement (or function), whether an assistant is used, overpressure (and by whom) and numbers of repetitions or time and sets. Therapist or patient application of overpressure and utilization of treatment belts or manual techniques must be recorded to capture the complete description. The adoption of the Mulligan Concept annotation framework in this way for documentation purposes will provide uniformity and clarity of information transfer for the future purposes of teaching, clinical practice and audit for its practitioners. PMID:24491791

  2. College Students in Transition: An Annotated Bibliography

    ERIC Educational Resources Information Center

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

    2013-01-01

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

  3. Selected Annotated Bibliography on Costume History.

    ERIC Educational Resources Information Center

    Weisfeld, Zelma H.

    This annotated bibliography, designed for secondary and postsecondary teachers and practitioners of theatre costuming, contains a basic listing of recent and reprinted works on costume history. Most of the books included in this bibliography are in print, are easily obtainable, and contain reproductions of contemporary art and garments.…

  4. Health Communication and Literacy: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Beveridge, Jennifer

    This annotated bibliography lists publications and World Wide Web sites dealing with health communication and literacy. The 51 publications, which were all published between 1982 and 1998, contain information about and/or for use in the following areas: assessment, assessment tools, elderly adults, empowerment, maternal and child health, patient…

  5. Measures of Infant Development: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Guthrie, P. D.; Horne, Eleanor V.

    Annotations of tests measuring motor development, cognitive growth, intelligence, mental health, social maturity, and concept attainment in infants from birth to 24 months of age are presented. Information is given concerning test purpose; intended groups; test subdivisions or tested skills, behaviors, or competencies; administration; scoring;…

  6. Teaching Family History: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Mintz, Steven

    2001-01-01

    Provides an annotated bibliography on teaching family history, organized by eight approaches to the topic: (1) chronological; (2) multicultural families (comparative); (3) the life-cycle (4) gender; (5) impact of major historical events on families; (6) family and public policy; (7) family rituals; and (8) genealogical. (CMK)

  7. The Career Education Resource Center Annotated Catalog.

    ERIC Educational Resources Information Center

    Lawhead, Jeanie; And Others

    This catalog provides an annotated list of the career education materials which may be borrowed for previewing from the Career Education Resource Center in Colorado. Covering materials of interest to educators in kindergarten through postsecondary programs, the catalog includes items produced by classroom teachers, commercial publishers, business…

  8. Sex and Proxemics: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Nelson, Audrey A.

    This annotated bibliography focuses on the sex differences and similarities in two proxemic variables, physical distance and orientation of the body. The majority of the more than 90 titles, dating from 1965 to the present, are selected from the following sources: dissertation abstracts, social-psychology journals, communication journals, and…

  9. Reflective Annotations: On Becoming a Scholar

    ERIC Educational Resources Information Center

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

    2012-01-01

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

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

    ERIC Educational Resources Information Center

    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…

  11. Statistical mechanics of ontology based annotations

    NASA Astrophysics Data System (ADS)

    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.

  12. Automating Ontological Annotation with WordNet

    SciTech Connect

    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.

  13. Ontological Annotation with WordNet

    SciTech Connect

    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.

  14. MEETING: Chlamydomonas Annotation Jamboree - October 2003

    SciTech Connect

    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

  15. Representing annotation compositionality and provenance for the Semantic Web

    PubMed Central

    2013-01-01

    Background Though the annotation of digital artifacts with metadata has a long history, the bulk of that work focuses on the association of single terms or concepts to single targets. As annotation efforts expand to capture more complex information, annotations will need to be able to refer to knowledge structures formally defined in terms of more atomic knowledge structures. Existing provenance efforts in the Semantic Web domain primarily focus on tracking provenance at the level of whole triples and do not provide enough detail to track how individual triple elements of annotations were derived from triple elements of other annotations. Results We present a task- and domain-independent ontological model for capturing annotations and their linkage to their denoted knowledge representations, which can be singular concepts or more complex sets of assertions. We have implemented this model as an extension of the Information Artifact Ontology in OWL and made it freely available, and we show how it can be integrated with several prominent annotation and provenance models. We present several application areas for the model, ranging from linguistic annotation of text to the annotation of disease-associations in genome sequences. Conclusions With this model, progressively more complex annotations can be composed from other annotations, and the provenance of compositional annotations can be represented at the annotation level or at the level of individual elements of the RDF triples composing the annotations. This in turn allows for progressively richer annotations to be constructed from previous annotation efforts, the precise provenance recording of which facilitates evidence-based inference and error tracking. PMID:24268021

  16. Functional Annotation Analytics of Rhodopseudomonas palustris Genomes

    PubMed Central

    Simmons, Shaneka S.; Isokpehi, Raphael D.; Brown, Shyretha D.; McAllister, Donee L.; Hall, Charnia C.; McDuffy, Wanaki M.; Medley, Tamara L.; Udensi, Udensi K.; Rajnarayanan, Rajendram V.; Ayensu, Wellington K.; Cohly, Hari H.P.

    2011-01-01

    Rhodopseudomonas palustris, a nonsulphur purple photosynthetic bacteria, has been extensively investigated for its metabolic versatility including ability to produce hydrogen gas from sunlight and biomass. The availability of the finished genome sequences of six R. palustris strains (BisA53, BisB18, BisB5, CGA009, HaA2 and TIE-1) combined with online bioinformatics software for integrated analysis presents new opportunities to determine the genomic basis of metabolic versatility and ecological lifestyles of the bacteria species. The purpose of this investigation was to compare the functional annotations available for multiple R. palustris genomes to identify annotations that can be further investigated for strain-specific or uniquely shared phenotypic characteristics. A total of 2,355 protein family Pfam domain annotations were clustered based on presence or absence in the six genomes. The clustering process identified groups of functional annotations including those that could be verified as strain-specific or uniquely shared phenotypes. For example, genes encoding water/glycerol transport were present in the genome sequences of strains CGA009 and BisB5, but absent in strains BisA53, BisB18, HaA2 and TIE-1. Protein structural homology modeling predicted that the two orthologous 240 aa R. palustris aquaporins have water-specific transport function. Based on observations in other microbes, the presence of aquaporin in R. palustris strains may improve freeze tolerance in natural conditions of rapid freezing such as nitrogen fixation at low temperatures where access to liquid water is a limiting factor for nitrogenase activation. In the case of adaptive loss of aquaporin genes, strains may be better adapted to survive in conditions of high-sugar content such as fermentation of biomass for biohydrogen production. Finally, web-based resources were developed to allow for interactive, user-defined selection of the relationship between protein family annotations and the R

  17. VideoANT: Extending Online Video Annotation beyond Content Delivery

    ERIC Educational Resources Information Center

    Hosack, Bradford

    2010-01-01

    This paper expands the boundaries of video annotation in education by outlining the need for extended interaction in online video use, identifying the challenges faced by existing video annotation tools, and introducing Video-ANT, a tool designed to create text-based annotations integrated within the time line of a video hosted online. Several…

  18. The Father's Role in Family Systems: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Wisconsin Univ., Madison. School of Family Resources and Consumer Sciences.

    This bibliography contains more than 400 annotated references on the topic of the father's role in family systems. In addition to the standard bibliographic citation, each entry includes an annotation which summarizes, discusses, or evaluates the item. The annotations range in length from a few sentences to several paragraphs. An alpha-numeric…

  19. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

    SciTech Connect

    Brettin, Thomas; Davis, James J.; Disz, Terry; Edwards, Robert A.; Gerdes, Svetlana; Olsen, Gary J.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Shukla, Maulik; Thomason, III, James A.; Stevens, Rick; Vonstein, Veronika; Wattam, Alice R.; Xia, Fangfang

    2015-02-10

    The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.

  20. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

    PubMed Central

    Brettin, Thomas; Davis, James J.; Disz, Terry; Edwards, Robert A.; Gerdes, Svetlana; Olsen, Gary J.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; Shukla, Maulik; Thomason, James A.; Stevens, Rick; Vonstein, Veronika; Wattam, Alice R.; Xia, Fangfang

    2015-01-01

    The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offers a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception. PMID:25666585

  1. Model and Interoperability using Meta Data Annotations

    NASA Astrophysics Data System (ADS)

    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

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

    ERIC Educational Resources Information Center

    Wolfe, Joanna

    2008-01-01

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

  3. Cadec: A corpus of adverse drug event annotations.

    PubMed

    Karimi, Sarvnaz; Metke-Jimenez, Alejandro; Kemp, Madonna; Wang, Chen

    2015-06-01

    CSIRO Adverse Drug Event Corpus (Cadec) is a new rich annotated corpus of medical forum posts on patient-reported Adverse Drug Events (ADEs). The corpus is sourced from posts on social media, and contains text that is largely written in colloquial language and often deviates from formal English grammar and punctuation rules. Annotations contain mentions of concepts such as drugs, adverse effects, symptoms, and diseases linked to their corresponding concepts in controlled vocabularies, i.e., SNOMED Clinical Terms and MedDRA. The quality of the annotations is ensured by annotation guidelines, multi-stage annotations, measuring inter-annotator agreement, and final review of the annotations by a clinical terminologist. This corpus is useful for studies in the area of information extraction, or more generally text mining, from social media to detect possible adverse drug reactions from direct patient reports. The corpus is publicly available at https://data.csiro.au.(1). PMID:25817970

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

    PubMed

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

    2003-02-01

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

  5. Analysis and Annotation of Nucleic Acid Sequence

    SciTech Connect

    States, David J.

    2004-07-28

    The aims of this project were to develop improved methods for computational genome annotation and to apply these methods to improve the annotation of genomic sequence data with a specific focus on human genome sequencing. The project resulted in a substantial body of published work. Notable contributions of this project were the identification of basecalling and lane tracking as error processes in genome sequencing and contributions to improved methods for these steps in genome sequencing. This technology improved the accuracy and throughput of genome sequence analysis. Probabilistic methods for physical map construction were developed. Improved methods for sequence alignment, alternative splicing analysis, promoter identification and NF kappa B response gene prediction were also developed.

  6. Analysis and Annotation of Nucleic Acid Sequence

    SciTech Connect

    David J. States

    1998-08-01

    The aims of this project were to develop improved methods for computational genome annotation and to apply these methods to improve the annotation of genomic sequence data with a specific focus on human genome sequencing. The project resulted in a substantial body of published work. Notable contributions of this project were the identification of basecalling and lane tracking as error processes in genome sequencing and contributions to improved methods for these steps in genome sequencing. This technology improved the accuracy and throughput of genome sequence analysis. Probabilistic methods for physical map construction were developed. Improved methods for sequence alignment, alternative splicing analysis, promoter identification and NF kappa B response gene prediction were also developed.

  7. Cognition inspired framework for indoor scene annotation

    NASA Astrophysics Data System (ADS)

    Ye, Zhipeng; Liu, Peng; Zhao, Wei; Tang, Xianglong

    2015-09-01

    We present a simple yet effective scene annotation framework based on a combination of bag-of-visual words (BoVW), three-dimensional scene structure estimation, scene context, and cognitive theory. From a macroperspective, the proposed cognition-based hybrid motivation framework divides the annotation problem into empirical inference and real-time classification. Inspired by the inference ability of human beings, common objects of indoor scenes are defined for experience-based inference, while in the real-time classification stage, an improved BoVW-based multilayer abstract semantics labeling method is proposed by introducing abstract semantic hierarchies to narrow the semantic gap and improve the performance of object categorization. The proposed framework was evaluated on a variety of common data sets and experimental results proved its effectiveness.

  8. Annotating Large Genomes With Exact Word Matches

    PubMed Central

    Healy, John; Thomas, Elizabeth E.; Schwartz, Jacob T.; Wigler, Michael

    2003-01-01

    We have developed a tool for rapidly determining the number of exact matches of any word within large, internally repetitive genomes or sets of genomes. Thus we can readily annotate any sequence, including the entire human genome, with the counts of its constituent words. We create a Burrows-Wheeler transform of the genome, which together with auxiliary data structures facilitating counting, can reside in about one gigabyte of RAM. Our original interest was motivated by oligonucleotide probe design, and we describe a general protocol for defining unique hybridization probes. But our method also has applications for the analysis of genome structure and assembly. We demonstrate the identification of chromosome-specific repeats, and outline a general procedure for finding undiscovered repeats. We also illustrate the changing contents of the human genome assemblies by comparing the annotations built from different genome freezes. PMID:12975312

  9. Deburring: an annotated bibliography. Volume VI

    SciTech Connect

    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.

  10. Effective function annotation through catalytic residue conservation.

    PubMed

    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. PMID:16037208

  11. Jannovar: a java library for exome annotation.

    PubMed

    Jäger, Marten; Wang, Kai; Bauer, Sebastian; Smedley, Damian; Krawitz, Peter; Robinson, Peter N

    2014-05-01

    Transcript-based annotation and pedigree analysis are two basic steps in the computational analysis of whole-exome sequencing experiments in genetic diagnostics and disease-gene discovery projects. Here, we present Jannovar, a stand-alone Java application as well as a Java library designed to be used in larger software frameworks for exome and genome analysis. Jannovar uses an interval tree to identify all transcripts affected by a given variant, and provides Human Genome Variation Society-compliant annotations both for variants affecting coding sequences and splice junctions as well as untranslated regions and noncoding RNA transcripts. Jannovar can also perform family-based pedigree analysis with Variant Call Format (VCF) files with data from members of a family segregating a Mendelian disorder. Using a desktop computer, Jannovar requires a few seconds to annotate a typical VCF file with exome data. Jannovar is freely available under the BSD2 license. Source code as well as the Java application and library file can be downloaded from http://compbio.charite.de (with tutorial) and https://github.com/charite/jannovar. PMID:24677618

  12. UCSC Data Integrator and Variant Annotation Integrator

    PubMed Central

    Hinrichs, Angie S.; Raney, Brian J.; Speir, Matthew L.; Rhead, Brooke; Casper, Jonathan; Karolchik, Donna; Kuhn, Robert M.; Rosenbloom, Kate R.; Zweig, Ann S.; Haussler, David; Kent, W. James

    2016-01-01

    Summary: Two new tools on the UCSC Genome Browser web site provide improved ways of combining information from multiple datasets, optionally including the user's own custom track data and/or data from track hubs. The Data Integrator combines columns from multiple data tracks, showing all items from the first track along with overlapping items from the other tracks. The Variant Annotation Integrator is tailored to adding functional annotations to variant calls; it offers a more restricted set of underlying data tracks but adds predictions of each variant's consequences for any overlapping or nearby gene transcript. When available, it optionally adds additional annotations including effect prediction scores from dbNSFP for missense mutations, ENCODE regulatory summary tracks and conservation scores. Availability and implementation: The web tools are freely available at http://genome.ucsc.edu/ and the underlying database is available for download at http://hgdownload.cse.ucsc.edu/. The software (written in C and Javascript) is available from https://genome-store.ucsc.edu/ and is freely available for academic and non-profit usage; commercial users must obtain a license. Contact: angie@soe.ucsc.edu Supplementary information: Supplementary data are available at Bioinformatics online. PMID:26740527

  13. CART—a chemical annotation retrieval toolkit

    PubMed Central

    Deghou, Samy; Zeller, Georg; Iskar, Murat; Driessen, Marja; Castillo, Mercedes; van Noort, Vera; Bork, Peer

    2016-01-01

    Motivation: Data on bioactivities of drug-like chemicals are rapidly accumulating in public repositories, creating new opportunities for research in computational systems pharmacology. However, integrative analysis of these data sets is difficult due to prevailing ambiguity between chemical names and identifiers and a lack of cross-references between databases. Results: To address this challenge, we have developed CART, a Chemical Annotation Retrieval Toolkit. As a key functionality, it matches an input list of chemical names into a comprehensive reference space to assign unambiguous chemical identifiers. In this unified space, bioactivity annotations can be easily retrieved from databases covering a wide variety of chemical effects on biological systems. Subsequently, CART can determine annotations enriched in the input set of chemicals and display these in tabular format and interactive network visualizations, thereby facilitating integrative analysis of chemical bioactivity data. Availability and Implementation: CART is available as a Galaxy web service (cart.embl.de). Source code and an easy-to-install command line tool can also be obtained from the web site. Contact: bork@embl.de Supplementary information: Supplementary data are available at Bioinformatics online. PMID:27256313

  14. Video data annotation, archiving, and access

    NASA Astrophysics Data System (ADS)

    Wilkin, D.; Connor, J.; Stout, N. J.; Walz, K.; Schlining, K.; Graybeal, J.

    2002-12-01

    Scientifically useful, high-quality video data can be challenging to integrate with other data, and to analyze and archive for use in ocean science. The Monterey Bay Aquarium Research Institute (MBARI) uses high-resolution video equipment to record over 300 remotely operated vehicle dives per year. Over the past 14 years, 13,000 videotapes have been archived and maintained as a centralized institutional resource. MBARI has developed a set of software applications to annotate and access video data. Users can identify the location of video sequences using a data query component; complex queries can be made by constraining temporal, spatial, or physical parameters (e.g., season, location, or depth). The applications reference a knowledge base of over 3,000 biological, geological and technical terms, providing consistent hierarchical information about objects and associated descriptions for annotating video at sea or on shore. The annotation, knowledge base, and query components together provide a comprehensive video archive software system that can be applied to a variety of scientific disciplines. Also in development, using the XML data format, is an interactive reference interface to explore MBARI's deep-sea knowledge base. When complete, the full software system will be disseminated to the research community via the web or CD, to help meet the challenges inherent in archiving video data.

  15. WebMedSA: a web-based framework for segmenting and annotating medical images using biomedical ontologies

    NASA Astrophysics Data System (ADS)

    Vega, Francisco; Pérez, Wilson; Tello, Andrés.; Saquicela, Victor; Espinoza, Mauricio; Solano-Quinde, Lizandro; Vidal, Maria-Esther; La Cruz, Alexandra

    2015-12-01

    Advances in medical imaging have fostered medical diagnosis based on digital images. Consequently, the number of studies by medical images diagnosis increases, thus, collaborative work and tele-radiology systems are required to effectively scale up to this diagnosis trend. We tackle the problem of the collaborative access of medical images, and present WebMedSA, a framework to manage large datasets of medical images. WebMedSA relies on a PACS and supports the ontological annotation, as well as segmentation and visualization of the images based on their semantic description. Ontological annotations can be performed directly on the volumetric image or at different image planes (e.g., axial, coronal, or sagittal); furthermore, annotations can be complemented after applying a segmentation technique. WebMedSA is based on three main steps: (1) RDF-ization process for extracting, anonymizing, and serializing metadata comprised in DICOM medical images into RDF/XML; (2) Integration of different biomedical ontologies (using L-MOM library), making this approach ontology independent; and (3) segmentation and visualization of annotated data which is further used to generate new annotations according to expert knowledge, and validation. Initial user evaluations suggest that WebMedSA facilitates the exchange of knowledge between radiologists, and provides the basis for collaborative work among them.

  16. Genome-wide metabolic (re-) annotation of Kluyveromyces lactis

    PubMed Central

    2012-01-01

    Background Even before having its genome sequence published in 2004, Kluyveromyces lactis had long been considered a model organism for studies in genetics and physiology. Research on Kluyveromyces lactis is quite advanced and this yeast species is one of the few with which it is possible to perform formal genetic analysis. Nevertheless, until now, no complete metabolic functional annotation has been performed to the proteins encoded in the Kluyveromyces lactis genome. Results In this work, a new metabolic genome-wide functional re-annotation of the proteins encoded in the Kluyveromyces lactis genome was performed, resulting in the annotation of 1759 genes with metabolic functions, and the development of a methodology supported by merlin (software developed in-house). The new annotation includes novelties, such as the assignment of transporter superfamily numbers to genes identified as transporter proteins. Thus, the genes annotated with metabolic functions could be exclusively enzymatic (1410 genes), transporter proteins encoding genes (301 genes) or have both metabolic activities (48 genes). The new annotation produced by this work largely surpassed the Kluyveromyces lactis currently available annotations. A comparison with KEGG’s annotation revealed a match with 844 (~90%) of the genes annotated by KEGG, while adding 850 new gene annotations. Moreover, there are 32 genes with annotations different from KEGG. Conclusions The methodology developed throughout this work can be used to re-annotate any yeast or, with a little tweak of the reference organism, the proteins encoded in any sequenced genome. The new annotation provided by this study offers basic knowledge which might be useful for the scientific community working on this model yeast, because new functions have been identified for the so-called metabolic genes. Furthermore, it served as the basis for the reconstruction of a compartmentalized, genome-scale metabolic model of Kluyveromyces lactis, which is

  17. Semi-automatic conversion of BioProp semantic annotation to PASBio annotation

    PubMed Central

    Tsai, Richard Tzong-Han; Dai, Hong-Jie; Huang, Chi-Hsin; Hsu, Wen-Lian

    2008-01-01

    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 domain. In the biomedical field, however, more detailed and restrictive PAS annotation formats such as PASBio are popular. Unfortunately, due to the lack of an annotated PASBio corpus, no publicly available machine-learning (ML) based SRL systems based on PASBio have been developed. In previous work, we constructed a biomedical corpus based on the PropBank standard called BioProp, on which we developed an ML-based SRL system, BIOSMILE. In this paper, we aim to build a system to convert BIOSMILE's BioProp annotation output to PASBio annotation. Our system consists of BIOSMILE in combination with a BioProp-PASBio rule-based converter, and an additional semi-automatic rule generator. Results Our first experiment evaluated our rule-based converter's performance independently from BIOSMILE performance. The converter achieved an F-score of 85.29%. The second experiment evaluated combined system (BIOSMILE + rule-based converter). The system achieved an F-score of 69.08% for PASBio's 29 verbs. Conclusion Our approach allows PAS conversion between BioProp and PASBio annotation using BIOSMILE alongside our newly developed semi-automatic rule generator and rule-based converter. Our system can match the performance of other state-of-the-art domain-specific ML-based SRL systems and can be easily customized for PASBio application development. PMID:19091017

  18. Annotation and visualization of endogenous retroviral sequences using the Distributed Annotation System (DAS) and eBioX

    PubMed Central

    Martínez Barrio, Álvaro; Lagercrantz, Erik; Sperber, Göran O; Blomberg, Jonas; Bongcam-Rudloff, Erik

    2009-01-01

    Background The Distributed Annotation System (DAS) is a widely used network protocol for sharing biological information. The distributed aspects of the protocol enable the use of various reference and annotation servers for connecting biological sequence data to pertinent annotations in order to depict an integrated view of the data for the final user. Results An annotation server has been devised to provide information about the endogenous retroviruses detected and annotated by a specialized in silico tool called RetroTector. We describe the procedure to implement the DAS 1.5 protocol commands necessary for constructing the DAS annotation server. We use our server to exemplify those steps. Data distribution is kept separated from visualization which is carried out by eBioX, an easy to use open source program incorporating multiple bioinformatics utilities. Some well characterized endogenous retroviruses are shown in two different DAS clients. A rapid analysis of areas free from retroviral insertions could be facilitated by our annotations. Conclusion The DAS protocol has shown to be advantageous in the distribution of endogenous retrovirus data. The distributed nature of the protocol is also found to aid in combining annotation and visualization along a genome in order to enhance the understanding of ERV contribution to its evolution. Reference and annotation servers are conjointly used by eBioX to provide visualization of ERV annotations as well as other data sources. Our DAS data source can be found in the central public DAS service repository, , or at . PMID:19534743

  19. Protein Sequence Annotation Tool (PSAT): A centralized web-based meta-server for high-throughput sequence annotations

    DOE PAGESBeta

    Leung, Elo; Huang, Amy; Cadag, Eithon; Montana, Aldrin; Soliman, Jan Lorenz; Zhou, Carol L. Ecale

    2016-01-20

    In this study, we introduce the Protein Sequence Annotation Tool (PSAT), a web-based, sequence annotation meta-server for performing integrated, high-throughput, genome-wide sequence analyses. Our goals in building PSAT were to (1) create an extensible platform for integration of multiple sequence-based bioinformatics tools, (2) enable functional annotations and enzyme predictions over large input protein fasta data sets, and (3) provide a web interface for convenient execution of the tools. In this paper, we demonstrate the utility of PSAT by annotating the predicted peptide gene products of Herbaspirillum sp. strain RV1423, importing the results of PSAT into EC2KEGG, and using the resultingmore » functional comparisons to identify a putative catabolic pathway, thereby distinguishing RV1423 from a well annotated Herbaspirillum species. This analysis demonstrates that high-throughput enzyme predictions, provided by PSAT processing, can be used to identify metabolic potential in an otherwise poorly annotated genome. Lastly, PSAT is a meta server that combines the results from several sequence-based annotation and function prediction codes, and is available at http://psat.llnl.gov/psat/. PSAT stands apart from other sequencebased genome annotation systems in providing a high-throughput platform for rapid de novo enzyme predictions and sequence annotations over large input protein sequence data sets in FASTA. PSAT is most appropriately applied in annotation of large protein FASTA sets that may or may not be associated with a single genome.« less

  20. Genomic Data and Annotation from the SEED

    DOE Data Explorer

    Fonstein, Michael; Kogan, Yakov; Osterman, Andrei; Overbeek, Ross; Vonstein, Veronika The Fellowship for Interpretation of Genomes (FIG)

    The SEED Project is a cooperative effort to annotate ever-expanding genomic data so researchers can conduct effective comparative analyses of genomes. Launched in 2003 by the Fellowship for Interpretation of Genomes (FIG), the project is one of several initiatives in ongoing development of data curation systems. SEED is designed to be used by scientists from numerous centers and with varied research objectives. As such, several institutions have since joined FIG in a consortium, including the University of Chicago, DOE’s Argonne National Laboratory (ANL), the University of Illinois at Urbana-Champaign, and others. As one example, ANL has used SEED to develop the National Microbial Pathogen Data Resource. Other agencies and institutions have used the project to discover genome components and clarify gene functions such as metabolism. SEED also has enabled researchers to conduct comparative analyses of closely related genomes and has supported derivation of stoichiometric models to understand metabolic processes. The SEED Project has been extended to support metagenomic samples and concomitant analytical tools. Moreover, the number of genomes being introduced into SEED is growing very rapidly. Building a framework to support this growth while providing highly accurate annotations is centrally important to SEED. The project’s subsystem-based annotation strategy has become the technological foundation for addressing these challenges.(copied from Appendix 7 of Systems Biology Knowledgebase for a New Era in Biology, A Genomics:GTL Report from the May 2008 Workshop, DOE/SC-0113, Grequrick, S; Fredrickson, J.K.; Stevens, R., Pub March 1, 2009.)

  1. Annotated bibliography of Software Engineering Laboratory literature

    NASA Technical Reports Server (NTRS)

    Morusiewicz, Linda; Valett, Jon D.

    1991-01-01

    An annotated bibliography of technical papers, documents, and memorandums produced by or related to the Software Engineering Laboratory is given. More than 100 publications are summarized. These publications cover many areas of software engineering and range from research reports to software documentation. All materials have been grouped into eight general subject areas for easy reference: The Software Engineering Laboratory; The Software Engineering Laboratory: Software Development Documents; Software Tools; Software Models; Software Measurement; Technology Evaluations; Ada Technology; and Data Collection. Subject and author indexes further classify these documents by specific topic and individual author.

  2. Annotated bibliography of Software Engineering Laboratory literature

    NASA Technical Reports Server (NTRS)

    Morusiewicz, Linda; Valett, Jon

    1993-01-01

    This document is an annotated bibliography of technical papers, documents, and memorandums produced by or related to the Software Engineering Laboratory. Nearly 200 publications are summarized. These publications cover many areas of software engineering and range from research reports to software documentation. This document has been updated and reorganized substantially since the original version (SEL-82-006, November 1982). All materials have been grouped into eight general subject areas for easy reference: the Software Engineering Laboratory; the Software Engineering Laboratory: software development documents; software tools; software models; software measurement; technology evaluations; Ada technology; and data collection. This document contains an index of these publications classified by individual author.

  3. Film annotation system for a space experiment

    NASA Technical Reports Server (NTRS)

    Browne, W. R.; Johnson, S. S.

    1989-01-01

    This microprocessor system was designed to control and annotate a Nikon 35 mm camera for the purpose of obtaining photographs and data at predefined time intervals. The single STD BUSS interface card was designed in such a way as to allow it to be used in either a stand alone application with minimum features or installed in a STD BUSS computer allowing for maximum features. This control system also allows the exposure of twenty eight alpha/numeric characters across the bottom of each photograph. The data contains such information as camera identification, frame count, user defined text, and time to .01 second.

  4. Expressed sequence tags: analysis and annotation.

    PubMed

    Parkinson, John; Blaxter, Mark

    2004-01-01

    Expressed sequence tags (ESTs) present a special set of problems for bioinformatic analysis. They are partial and error-prone, and large datasets can have significant internal redundancy. To facilitate analysis of small EST datasets from in-house projects, we present an integrated "pipeline" of tools that take EST data from sequence trace to database submission. These tools also can be used to provide clustering of ESTs into putative genes and to annotate these genes with preliminary sequence similarity searches. The systems are written to use the public-domain LINUX environment and other openly available analytical tools. PMID:15153624

  5. Annotated bibliography of Software Engineering Laboratory literature

    NASA Technical Reports Server (NTRS)

    1985-01-01

    An annotated bibliography of technical papers, documents, and memorandums produced by or related to the Software Engineering Laboratory is presented. More than 100 publications are summarized. These publications are summarized. These publications cover many areas of software engineering and range from research reports to software documentation. This document has been updated and reorganized substantially since the original version (SEL-82-006, November 1982). All materials are grouped into five general subject areas for easy reference: (1) the software engineering laboratory; (2) software tools; (3) models and measures; (4) technology evaluations; and (5) data collection. An index further classifies these documents by specific topic.

  6. Annotated bibliography of software engineering laboratory literature

    NASA Technical Reports Server (NTRS)

    Buhler, Melanie; Valett, Jon

    1989-01-01

    An annotated bibliography is presented of technical papers, documents, and memorandums produced by or related to the Software Engineering Laboratory. The bibliography was updated and reorganized substantially since the original version (SEL-82-006, November 1982). All materials were grouped into eight general subject areas for easy reference: (1) The Software Engineering Laboratory; (2) The Software Engineering Laboratory: Software Development Documents; (3) Software Tools; (4) Software Models; (5) Software Measurement; (6) Technology Evaluations; (7) Ada Technology; and (8) Data Collection. Subject and author indexes further classify these documents by specific topic and individual author.

  7. Annotated bibliography of software engineering laboratory literature

    NASA Technical Reports Server (NTRS)

    Groves, Paula; Valett, Jon

    1990-01-01

    An annotated bibliography of technical papers, documents, and memorandums produced by or related to the Software Engineering Laboratory is given. More than 100 publications are summarized. These publications cover many areas of software engineering and range from research reports to software documentation. This document has been updated and reorganized substantially since the original version (SEL-82-006, November 1982). All materials have been grouped into eight general subject areas for easy reference: the Software Engineering Laboratory; the Software Engineering Laboratory-software development documents; software tools; software models; software measurement; technology evaluations; Ada technology; and data collection. Subject and author indexes further classify these documents by specific topic and individual author.

  8. Human disturbances of waterfowl: an annotated bibliography

    USGS Publications Warehouse

    Dahlgren, R.B.; Korschgen, C.E.

    1992-01-01

    The expansion of outdoor recreation greatly increased the interaction between the public, waterfowl, and waterfowl habitat. The effects of these interactions on waterfowl habitats are visible and obvious, whereas the effects of interactions that disrupt the normal behavior of waterfowl are subtle and often overlooked, but perhaps no less harmful than destruction of habitat. Resource managers and administrators require information on the types, magnitude, and effects of disturbances from human contact with wildlife. This bibliography contains annotations for 211 articles with information about effects of human disturbances on waterfowl. Indexes are provided by subject or key words, geographic locations, species of waterfowl, and authors.

  9. Human disturbances of waterfowl: An annotated bibliography

    USGS Publications Warehouse

    Dahlgren, R.B.; Korschgen, C.E.

    1992-01-01

    The expansion of outdoor recreation greatly increased the interaction between the public, waterfowl, and waterfowl habitat. The effects of these interactions on waterfowl habitats are visible and obvious, whereas the effects of interactions that disrupt the normal behavior of waterfowl are subtle and often overlooked, but perhaps no less harmful than destruction of habitat. Resource managers and administrators require information on the types, magnitude, and effect of disturbances from human contact with wildlife. This bibliography contains annotations for 211 articles with information about effects of human disturbances on waterfowl. Indexes are provided by subject or key words, geographic locations, species of waterfowl, and authors.

  10. Literacy and Basic Education: A Selected, Annotated Bibliography. Annotated Bibliography #3.

    ERIC Educational Resources Information Center

    Michigan State Univ., East Lansing. Non-Formal Education Information Center.

    A selected annotated bibliography on literacy and basic education, including contributions from practitioners in the worldwide non-formal education network and compiled for them, has three interrelated themes: integration of literacy programs with broader development efforts; the learner-centered or "psycho-social" approach to literacy, often with…

  11. Projects, Training, and Strategies for Generating Income: A Selected Annotated Bibliography. Annotated Bibliography #4.

    ERIC Educational Resources Information Center

    Michigan State Univ., East Lansing. Non-Formal Education Information Center.

    A selected annotated bibliography on projects, training, and strategies for generating income, intended for persons actively engaged in non-formal education for development, reflects a growing number of projects on income generation by and for women's groups, and a reliance upon indigenous associations and group action. Documents dating from 1969…

  12. Correction of the Caulobacter crescentus NA1000 Genome Annotation

    PubMed Central

    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%. PMID:24621776

  13. Gene Ontology annotation quality analysis in model eukaryotes

    PubMed Central

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

    2008-01-01

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

  14. A Framework for Comparing Phenotype Annotations of Orthologous Genes

    PubMed Central

    Bodenreider, Olivier; Burgun, Anita

    2015-01-01

    Objectives Animal models are a key resource for the investigation of human diseases. In contrast to functional annotation, phenotype annotation is less standard, and comparing phenotypes across species remains challenging. The objective of this paper is to propose a framework for comparing phenotype annotations of orthologous genes based on the Medical Subject Headings (MeSH) indexing of biomedical articles in which these genes are discussed. Methods 17,769 pairs of orthologous genes (mouse and human) are downloaded from the Mouse Genome Informatics (MGI) system and linked to biomedical articles through Entrez Gene. MeSH index terms corresponding to diseases are extracted from Medline. Results 11,111 pairs of genes exhibited at least one phenotype annotation for each gene in the pair. Among these, 81% have at least one phenotype annotation in common, 80% have at least one annotation specific to the human gene and 84% have at least one annotation specific to the mouse gene. Four disease categories represent 54% of all phenotype annotations. Conclusions This framework supports the curation of phenotype annotation and the generation of research hypotheses based on comparative studies. PMID:20841896

  15. Learning from partially annotated OPT images by contextual relevance ranking.

    PubMed

    Li, Wenqi; Zhang, Jianguo; Zheng, Wei-Shi; Coats, Maria; Carey, Frank A; McKenna, Stephen J

    2013-01-01

    Annotations delineating regions of interest can provide valuable information for training medical image classification and segmentation methods. However the process of obtaining annotations is tedious and time-consuming, especially for high-resolution volumetric images. In this paper we present a novel learning framework to reduce the requirement of manual annotations while achieving competitive classification performance. The approach is evaluated on a dataset with 59 3D optical projection tomography images of colorectal polyps. The results show that the proposed method can robustly infer patterns from partially annotated images with low computational cost. PMID:24505790

  16. Interactive annotation of textures in thoracic CT scans

    NASA Astrophysics Data System (ADS)

    Kockelkorn, Thessa T. J. P.; de Jong, Pim A.; Gietema, Hester A.; Grutters, Jan C.; Prokop, Mathias; van Ginneken, Bram

    2010-03-01

    This study describes a system for interactive annotation of thoracic CT scans. Lung volumes in these scans are segmented and subdivided into roughly spherical volumes of interest (VOIs) with homogeneous texture using a clustering procedure. For each 3D VOI, 72 features are calculated. The observer inspects the scan to determine which textures are present and annotates, with mouse clicks, several VOIs of each texture. Based on these annotations, a k-nearest-neighbor classifier is trained, which classifies all remaining VOIs in the scan. The algorithm then presents a slice with suggested annotations to the user, in which the user can correct mistakes. The classifier is retrained, taking into account these new annotations, and the user is presented another slice for correction. This process continues until at least 50% of all lung voxels in the scan have been classified. The remaining VOIs are classified automatically. In this way, the entire lung volume is annotated. The system has been applied to scans of patients with usual and non-specific interstitial pneumonia. The results of interactive annotation are compared to a setup in which the user annotates all predefined VOIs manually. The interactive system is 3.7 times as fast as complete manual annotation of VOIs and differences between the methods are similar to interobserver variability. This is a first step towards precise volumetric quantitation of texture patterns in thoracic CT in clinical research and in clinical practice.

  17. The UniProt-GO Annotation database in 2011.

    PubMed

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

    2012-01-01

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

  18. African American Literature, 1989-94: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Miller, R. Baxter; Butts, Tracy; Jones, Sharon

    1997-01-01

    Contains an annotated bibliography of African American literature (published between 1989 and 1994), including anthologies, fiction, poetry, drama, criticism, cultural studies, biography, interviews, and letters. (TB)

  19. The UniProt-GO Annotation database in 2011

    PubMed Central

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

    2012-01-01

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

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

    SciTech Connect

    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.

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

    SciTech Connect

    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.

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

    PubMed

    Kim, J

    2001-03-01

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

  3. Sonoran Pronghorn Literature: An Annotated Bibliography

    USGS Publications Warehouse

    Krausman, Paul R.; Morgart, John R.; Harris, Lisa K.; O'Brien, Chantal S.; Cain, James W.; Rosenstock, Steve S.

    2005-01-01

    EXECUTIVE SUMMARY The Sonoran pronghorn (Antilocapra americana sonoriensis) is 1 of 5 subspecies of pronghorn in North America. Sonoran pronghorn historically ranged from eastern California into southeastern Arizona and south to Sonora, Mexico. Sonoran pronghorn currently inhabit the Sonoran Desert in Southwestern Arizona and northern Sonora, Mexico. Unfortunately, their future in North America is uncertain. In the United States, as of December 2004, there were <51 freeranging individual Sonoran pronghorn. This subspecies has been listed as endangered by the United States Fish and Wildlife Service since 1967. Because of the rapid decline in population size, biologists and managers increased management efforts to reverse the downward spiral to extinction. To assist with enhanced management we have compiled an annotated bibliography of most of the works published on Sonoran pronghorn including peer-reviewed papers (n = 31, including submitted manuscripts), books (n = 26), theses and dissertations (n = 5), conferences, proceedings and symposiums (n = 31), reports (n = 84), abstracts (n = 14), popular articles (n = 41), and others (n = 4). These are the same categories under which we list annotations. Most of the articles involve A. a. sonoriensis. We present the scientific name of other pronghorn when clarification is needed.

  4. Transcriptome annotation using tandem SAGE tags

    PubMed Central

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

    2007-01-01

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

  5. HEAT EXCHANGER

    DOEpatents

    Fox, T.H. III; Richey, T. Jr.; Winders, G.R.

    1962-10-23

    A heat exchanger is designed for use in the transfer of heat between a radioactive fiuid and a non-radioactive fiuid. The exchanger employs a removable section containing the non-hazardous fluid extending into the section designed to contain the radioactive fluid. The removable section is provided with a construction to cancel out thermal stresses. The stationary section is pressurized to prevent leakage of the radioactive fiuid and to maintain a safe, desirable level for this fiuid. (AEC)

  6. DEVELOPMENT OF AN ANNOTATION SCHEME FOR STANDARDIZED DESCRIPTION OF MATHEMATICAL MODELS IN THE FIELD OF PLANT PROTECTION.

    PubMed

    Günther, T; Büttner, C; Käsbohrer, A; Filter, M

    2015-01-01

    Mathematical models on properties and behavior of harmful organisms in the food chain are an increas- ingly relevant approach of the agriculture and food industry. As a consequence, there are many efforts to develop biological models in science, economics and risk assessment nowadays. However, there is a lack of international harmonized standards on model annotation and model formats, which would be neces- sary to set up efficient tools supporting broad model application and information exchange. There are some established standards in the field of systems biology, but there is currently no corresponding provi- sion in the area of plant protection. This work therefore aimed at the development of an annotation scheme using domain-specific metadata. The proposed scheme has been validated in a prototype implementation of a web-database model repository. This prototypic community resource currently contains models on aflatoxin secreting fungal Aspergillus flavus in maize, as these models have a high relevance to food safety and economic impact. Specifically, models describing biological processes of the fungus (growth, Aflatoxin secreting), as well as dose-response- and carry over models were included. Furthermore, phenological models for maize were integrated as well. The developed annotation scheme is based on the well-established data exchange format SBML, which is broadly applied in the field of systems biology. The identified example models were annotated according to the developed scheme and entered into a Web-table (Google Sheets), which was transferred to a web based demonstrator available at https://sites.google.com/site/test782726372685/. By implementation of a software demonstrator it became clear that the proposed annotation scheme can be applied to models on plant pathogens and that broad adoption within the domain could promote communication and application of mathematical models. PMID:27141756

  7. ASAP, a systematic annotation package for community analysis of genomes.

    PubMed

    Glasner, Jeremy D; Liss, Paul; Plunkett, Guy; Darling, Aaron; Prasad, Tejasvini; Rusch, Michael; Byrnes, Alexis; Gilson, Michael; Biehl, Bryan; Blattner, Frederick R; Perna, Nicole T

    2003-01-01

    ASAP (a systematic annotation package for community analysis of genomes) is a relational database and web interface developed to store, update and distribute genome sequence data and functional characterization (https://asap.ahabs.wisc.edu/annotation/php/ASAP1.htm). ASAP facilitates ongoing community annotation of genomes and tracking of information as genome projects move from preliminary data collection through post-sequencing functional analysis. The ASAP database includes multiple genome sequences at various stages of analysis, corresponding experimental data and access to collections of related genome resources. ASAP supports three levels of users: public viewers, annotators and curators. Public viewers can currently browse updated annotation information for Escherichia coli K-12 strain MG1655, genome-wide transcript profiles from more than 50 microarray experiments and an extensive collection of mutant strains and associated phenotypic data. Annotators worldwide are currently using ASAP to participate in a community annotation project for the Erwinia chrysanthemi strain 3937 genome. Curation of the E. chrysanthemi genome annotation as well as those of additional published enterobacterial genomes is underway and will be publicly accessible in the near future. PMID:12519969

  8. A Factor Graph Approach to Automated GO Annotation.

    PubMed

    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

  9. The RAST server : rapid annotations using subsystems technology.

    SciTech Connect

    Aziz, R. K.; Bartels, D.; Best, A. A.; DeJongh, M.; Disz, T.; Edwards, R. A.; Formsma, K.; Gerdes, S.; Glass, E. M.; Kubal, M.; Meyer, F.; Olsen, G. J.; Olson, R.; Osterman, A. L.; Overbeek, R. A.; McNeil, L. K.; Paarmann, D.; Paczian, T.; Parrello, B.; Pusch, G. D.; Reich, C.; Stevens, R.; Vassieva, O.; Vonstein, V.; Wilke, A.; Zagnitko, O.; Mathematics and Computer Science; Fellowship for Interpretation of Genomes; Univ. of Chicago; Univ. of Illinois; The Burnham Inst.; Hope Coll.; Univ. of Tenn.; Cairo Univ.

    2008-02-08

    The number of prokaryotic genome sequences becoming available is growing steadily and is growing faster than our ability to accurately annotate them. We describe a fully automated service for annotating bacterial and archaeal genomes. The service identifies protein-encoding, rRNA and tRNA genes, assigns functions to the genes, predicts which subsystems are represented in the genome, uses this information to reconstruct the metabolic network and makes the output easily downloadable for the user. In addition, the annotated genome can be browsed in an environment that supports comparative analysis with the annotated genomes maintained in the SEED environment. The service normally makes the annotated genome available within 12-24 hours of submission, but ultimately the quality of such a service will be judged in terms of accuracy, consistency, and completeness of the produced annotations. We summarize our attempts to address these issues and discuss plans for incrementally enhancing the service. By providing accurate, rapid annotation freely to the community we have created an important community resource. The service has now been utilized by over 120 external users annotating over 350 distinct genomes.

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

    PubMed

    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

  11. Annotated Bibliography of Research in the Teaching of English

    ERIC Educational Resources Information Center

    Beach, Richard; Bigelow, Martha; Dillon, Deborah; Dockter, Jessie; Galda, Lee; Helman, Lori; Kalnin, Julie; Ngo, Bic; O'Brien, David; Sato, Mistilina; Scharber, Cassandra; Jorgensen, Karen; Liang, Lauren; Braaksma, Martine; Janssen, Tanja

    2008-01-01

    This article presents an annotated bibliography of research in the teaching of English. This annotated bibliography addresses the following topics: (1) discourse/cultural analysis; (2) literacy; (3) literary response/literature/narrative; (4) professional development/teacher education; (5) reading; (6) second language literacy; (7)…

  12. K-Nearest Neighbors Relevance Annotation Model for Distance Education

    ERIC Educational Resources Information Center

    Ke, Xiao; Li, Shaozi; Cao, Donglin

    2011-01-01

    With the rapid development of Internet technologies, distance education has become a popular educational mode. In this paper, the authors propose an online image automatic annotation distance education system, which could effectively help children learn interrelations between image content and corresponding keywords. Image automatic annotation is…

  13. Annotated selected references on natural resources investigations, Collier County, Florida

    USGS Publications Warehouse

    Swayze, L.J.

    1981-01-01

    A data base for future natural resources investigations in Collier County, Fla., was initiated by compiling a selected annotated bibliography. This report provides references and annotations for selected reports released between 1950 and 1978. The references are presented by subject material as follows: biologic, ecologic, geologic, geochemical, and hydrologic. (USGS)

  14. Developing Annotation Solutions for Online Data Driven Learning

    ERIC Educational Resources Information Center

    Perez-Paredes, Pascual; Alcaraz-Calero, Jose M.

    2009-01-01

    Although "annotation" is a widely-researched topic in Corpus Linguistics (CL), its potential role in Data Driven Learning (DDL) has not been addressed in depth by Foreign Language Teaching (FLT) practitioners. Furthermore, most of the research in the use of DDL methods pays little attention to annotation in the design and implementation of…

  15. Grade 10 to Grade 12 Mathematics Resources: Annotated Bibliography.

    ERIC Educational Resources Information Center

    Western Canadian Protocol for Collaboration in Basic Education, Edmonton (Alberta).

    This annotated bibliography identifies English language resources endorsed by all Western Canadian Protocol (WCP) jurisdictions implementing The Common Curriculum Framework for K-12 Mathematics Grade 10 to Grade 12. Resources in this annotated bibliography were selected through a collaborative review process based on their high level of fidelity…

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

    ERIC Educational Resources Information Center

    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.…

  17. PROVIDING CLINICAL SERVICES IN READING--AN ANNOTATED BIBLIOGRAPHY.

    ERIC Educational Resources Information Center

    JOHNSON, MARJORIE S.; KRESS, ROY A.

    THIS ANNOTATED BIBLIOGRAPHY IS COMPOSED OF 55 CITATIONS RANGING IN DATE FROM 1932 TO 1965. IT IS DESIGNED TO AID THOSE INTERESTED IN SETTING UP A READING CLINIC AND IS DIVIDED INTO TWO SECTIONS--THE ANNOTATED REVIEWS OF THE ARTICLES SELECTED AND A LIST OF PUBLICATIONS DEALING PRIMARILY WITH A CLINICAL APPROACH TO THE DIAGNOSIS AND TREATMENT OF…

  18. International Development and the Human Environment. An Annotated Bibliography.

    ERIC Educational Resources Information Center

    1974

    Most of the material in this annotated bibliography has been selected from the literature published between 1968 and 1972. Each annotation and citation is indexed by author, subject, and publisher. Entries are organized into 11 chapters: Environment, Development, and Conservation of Natural Resources; The Third World: Development and Economic…

  19. Attitudes & Disability: An Annotated Bibliography, 1975-1981.

    ERIC Educational Resources Information Center

    Makas, Elaine, Comp.

    The annotated bibliography contains approximately 1,000 citations (1975-1981) dealing with attitudes related to disability. In addition to a brief annotation, entries include information on author, title, source, date, and pagination. Citations are classified according to the following topics: specific disabilities (cardiovascular impairment,…

  20. Behavioral Contributions to Teaching of Psychology: An Annotated Bibliography

    PubMed Central

    Karsten, Amanda M; Carr, James 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. PMID:22478500

  1. Computer Applications in Marketing. An Annotated Bibliography of Computer Software.

    ERIC Educational Resources Information Center

    Burrow, Jim; Schwamman, Faye

    This bibliography contains annotations of 95 items of educational and business software with applications in seven marketing and business functions. The annotations, which appear in alphabetical order by title, provide this information: category (related application), title, date, source and price, equipment, supplementary materials, description…

  2. Puerto Rican Literature, 1988-96: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Ortiz-Marquez, Maribel

    1996-01-01

    Presents a 108-item annotated bibliography of works by Puerto Ricans born and raised in the United States to complement and update Edna Acosta-Belen's "The Literature of Puerto Rican Migration in the United States: An Annotated Bibliography." Includes sections on anthologies, prose fiction, poetry, drama, autobiographies, criticism, and journals.…

  3. Orienteering: An Annotated Bibliography = Orientierungslauf: Eine kommentierte Bibliographie.

    ERIC Educational Resources Information Center

    Seiler, Roland, Ed.; Hartmann, Wolfgang, Ed.

    1994-01-01

    Annotated bibliography of 220 books, monographs, and journal articles on orienteering published 1984-94, from SPOLIT database of the Federal Institute of Sport Science (Cologne, Germany). Annotations in English or German. Ten sections including psychological, physiological, health, sociological, and environmental aspects; training and coaching;…

  4. A User-Driven Annotation Framework for Scientific Data

    ERIC Educational Resources Information Center

    Li, Qinglan

    2013-01-01

    Annotations play an increasingly crucial role in scientific exploration and discovery, as the amount of data and the level of collaboration among scientists increases. There are many systems today focusing on annotation management, querying, and propagation. Although all such systems are implemented to take user input (i.e., the annotations…

  5. Evaluating techniques for metagenome annotation using simulated sequence data

    PubMed Central

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

    2016-01-01

    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

  6. Using Annotation Services in a Ubiquitous Jigsaw Cooperative Learning Environment

    ERIC Educational Resources Information Center

    Huang, Yueh-Min; Huang, Tien-Chi; Hsieh, Meng-Yeh

    2008-01-01

    This study describes the development of a ubiquitous cooperative learning environment using proposed annotation services, wireless communication devices, and the Jigsaw method of cooperative learning. The purpose of the study is to investigate the potential benefits of studying digital course materials with embedded annotations. The SQ3R study…

  7. Collaborative Paper-Based Annotation of Lecture Slides

    ERIC Educational Resources Information Center

    Steimle, Jurgen; Brdiczka, Oliver; Muhlhauser, Max

    2009-01-01

    In a study of notetaking in university courses, we found that the large majority of students prefer paper to computer-based media like Tablet PCs for taking notes and making annotations. Based on this finding, we developed CoScribe, a concept and system which supports students in making collaborative handwritten annotations on printed lecture…

  8. Maize - GO annotation methods, evaluation, and review (Maize-GAMER)

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Making a genome sequence accessible and useful involves three basic steps: genome assembly, structural annotation, and functional annotation. The quality of data generated at each step influences the accuracy of inferences that can be made, with high-quality analyses produce better datasets resultin...

  9. Applying negative rule mining to improve genome annotation

    PubMed Central

    Artamonova, Irena I; Frishman, Goar; Frishman, Dmitrij

    2007-01-01

    Background Unsupervised annotation of proteins by software pipelines suffers from very high error rates. Spurious functional assignments are usually caused by unwarranted homology-based transfer of information from existing database entries to the new target sequences. We have previously demonstrated that data mining in large sequence annotation databanks can help identify annotation items that are strongly associated with each other, and that exceptions from strong positive association rules often point to potential annotation errors. Here we investigate the applicability of negative association rule mining to revealing erroneously assigned annotation items. Results Almost all exceptions from strong negative association rules are connected to at least one wrong attribute in the feature combination making up the rule. The fraction of annotation features flagged by this approach as suspicious is strongly enriched in errors and constitutes about 0.6% of the whole body of the similarity-transferred annotation in the PEDANT genome database. Positive rule mining does not identify two thirds of these errors. The approach based on exceptions from negative rules is much more specific than positive rule mining, but its coverage is significantly lower. Conclusion Mining of both negative and positive association rules is a potent tool for finding significant trends in protein annotation and flagging doubtful features for further inspection. PMID:17659089

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

    ERIC Educational Resources Information Center

    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,…

  11. A Factor Graph Approach to Automated GO Annotation

    PubMed Central

    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

  12. The GATO gene annotation tool for research laboratories.

    PubMed

    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

  13. Automatic Annotation Method on Learners' Opinions in Case Method Discussion

    ERIC Educational Resources Information Center

    Samejima, Masaki; Hisakane, Daichi; Komoda, Norihisa

    2015-01-01

    Purpose: The purpose of this paper is to annotate an attribute of a problem, a solution or no annotation on learners' opinions automatically for supporting the learners' discussion without a facilitator. The case method aims at discussing problems and solutions in a target case. However, the learners miss discussing some of problems and solutions.…

  14. MitoFish and MitoAnnotator: A Mitochondrial Genome Database of Fish with an Accurate and Automatic Annotation Pipeline

    PubMed Central

    Iwasaki, Wataru; Fukunaga, Tsukasa; Isagozawa, Ryota; Yamada, Koichiro; Maeda, Yasunobu; Satoh, Takashi P.; Sado, Tetsuya; Mabuchi, Kohji; Takeshima, Hirohiko; Miya, Masaki; Nishida, Mutsumi

    2013-01-01

    Mitofish is a database of fish mitochondrial genomes (mitogenomes) that includes powerful and precise de novo annotations for mitogenome sequences. Fish occupy an important position in the evolution of vertebrates and the ecology of the hydrosphere, and mitogenomic sequence data have served as a rich source of information for resolving fish phylogenies and identifying new fish species. The importance of a mitogenomic database continues to grow at a rapid pace as massive amounts of mitogenomic data are generated with the advent of new sequencing technologies. A severe bottleneck seems likely to occur with regard to mitogenome annotation because of the overwhelming pace of data accumulation and the intrinsic difficulties in annotating sequences with degenerating transfer RNA structures, divergent start/stop codons of the coding elements, and the overlapping of adjacent elements. To ease this data backlog, we developed an annotation pipeline named MitoAnnotator. MitoAnnotator automatically annotates a fish mitogenome with a high degree of accuracy in approximately 5 min; thus, it is readily applicable to data sets of dozens of sequences. MitoFish also contains re-annotations of previously sequenced fish mitogenomes, enabling researchers to refer to them when they find annotations that are likely to be erroneous or while conducting comparative mitogenomic analyses. For users who need more information on the taxonomy, habitats, phenotypes, or life cycles of fish, MitoFish provides links to related databases. MitoFish and MitoAnnotator are freely available at http://mitofish.aori.u-tokyo.ac.jp/ (last accessed August 28, 2013); all of the data can be batch downloaded, and the annotation pipeline can be used via a web interface. PMID:23955518

  15. MitoFish and MitoAnnotator: a mitochondrial genome database of fish with an accurate and automatic annotation pipeline.

    PubMed

    Iwasaki, Wataru; Fukunaga, Tsukasa; Isagozawa, Ryota; Yamada, Koichiro; Maeda, Yasunobu; Satoh, Takashi P; Sado, Tetsuya; Mabuchi, Kohji; Takeshima, Hirohiko; Miya, Masaki; Nishida, Mutsumi

    2013-11-01

    Mitofish is a database of fish mitochondrial genomes (mitogenomes) that includes powerful and precise de novo annotations for mitogenome sequences. Fish occupy an important position in the evolution of vertebrates and the ecology of the hydrosphere, and mitogenomic sequence data have served as a rich source of information for resolving fish phylogenies and identifying new fish species. The importance of a mitogenomic database continues to grow at a rapid pace as massive amounts of mitogenomic data are generated with the advent of new sequencing technologies. A severe bottleneck seems likely to occur with regard to mitogenome annotation because of the overwhelming pace of data accumulation and the intrinsic difficulties in annotating sequences with degenerating transfer RNA structures, divergent start/stop codons of the coding elements, and the overlapping of adjacent elements. To ease this data backlog, we developed an annotation pipeline named MitoAnnotator. MitoAnnotator automatically annotates a fish mitogenome with a high degree of accuracy in approximately 5 min; thus, it is readily applicable to data sets of dozens of sequences. MitoFish also contains re-annotations of previously sequenced fish mitogenomes, enabling researchers to refer to them when they find annotations that are likely to be erroneous or while conducting comparative mitogenomic analyses. For users who need more information on the taxonomy, habitats, phenotypes, or life cycles of fish, MitoFish provides links to related databases. MitoFish and MitoAnnotator are freely available at http://mitofish.aori.u-tokyo.ac.jp/ (last accessed August 28, 2013); all of the data can be batch downloaded, and the annotation pipeline can be used via a web interface. PMID:23955518

  16. Inter-Annotator Reliability of Medical Events, Coreferences and Temporal Relations in Clinical Narratives by Annotators with Varying Levels of Clinical Expertise

    PubMed Central

    Raghavan, Preethi; Fosler-Lussier, Eric; Lai, Albert M.

    2012-01-01

    The manual annotation of clinical narratives is an important step for training and validating the performance of automated systems that utilize these clinical narratives. We build an annotation specification to capture medical events, and coreferences and temporal relations between medical events in clinical text. Unfortunately, the process of clinical data annotation is both time consuming and costly. Many annotation efforts have used physicians to annotate the data. We investigate using annotators that are current students or graduates from diverse clinical backgrounds with varying levels of clinical experience. In spite of this diversity, the annotation agreement across our team of annotators is high; the average inter-annotator kappa statistic for medical events, coreferences, temporal relations, and medical event concept unique identifiers was 0.843, 0.859, 0.833, and 0.806, respectively. We describe methods towards leveraging the annotations to support temporal reasoning with medical events. PMID:23304416

  17. Interpretation Errors related to the GO Annotation File Format

    PubMed Central

    Moreira, Dilvan A.; Shah, Nigam H.; Musen, Mark A.

    2007-01-01

    The Gene Ontology (GO) is the most widely used ontology for creating biomedical annotations. GO annotations are statements associating a biological entity with a GO term. These statements comprise a large dataset of biological knowledge that is used widely in biomedical research. GO Annotations are available as “gene association files” from the GO website in a tab-delimited file format (GO Annotation File Format) composed of rows of 15 tab-delimited fields. This simple format lacks the knowledge representation (KR) capabilities to represent unambiguously semantic relationships between each field. This paper demonstrates that this KR shortcoming leads users to interpret the files in ways that can be erroneous. We propose a complementary format to represent GO annotation files as knowledge bases using the W3C recommended Web Ontology Language (OWL). PMID:18693894

  18. Efficient similarity search on 3D bounding box annotations

    NASA Astrophysics Data System (ADS)

    Kriegel, Hans-Peter; Petri, Marisa; Schubert, Matthias; Shekelyan, Michael; Stockerl, Michael

    2012-02-01

    Searching for similar image regions in medical databases yields valuable information for diagnosis. However, most of the current approaches are restricted to special cases or they are only available for rather small data stores. In this paper, we propose a fast query pipeline for 3D similarity queries on large databases of computed tomography (CT) scans consisting of minimum bounding box annotations. As these box annotations also contain background information which is not part of the item that was actually annotated, we employ approximate segmentation approaches for distinguishing between within-object texture and background texture in order to correctly describe the annotated objects. Our method allows a compact form of object description. In our framework, we exploit this advantage for enabling very fast query times. We have validated our method on data sets of 111 and 1293 bounding box lesion annotations within the liver and other organs. Our experiments show a significant performance improvement over previous approaches in both runtime and precision.

  19. Meeting report: a workshop on Best Practices in Genome Annotation

    PubMed Central

    Madupu, Ramana; Brinkac, Lauren M.; Harrow, Jennifer; Wilming, Laurens G.; Böhme, Ulrike; Lamesch, Philippe; Hannick, Linda I.

    2010-01-01

    Efforts to annotate the genomes of a wide variety of model organisms are currently carried out by sequencing centers, model organism databases and academic/institutional laboratories around the world. Different annotation methods and tools have been developed over time to meet the needs of biologists faced with the task of annotating biological data. While standardized methods are essential for consistent curation within each annotation group, methods and tools can differ between groups, especially when the groups are curating different organisms. Biocurators from several institutes met at the Third International Biocuration Conference in Berlin, Germany, April 2009 and hosted the ‘Best Practices in Genome Annotation: Inference from Evidence’ workshop to share their strategies, pipelines, standards and tools. This article documents the material presented in the workshop. PMID:20428316

  20. Global probabilistic annotation of metabolic networks enables enzyme discovery

    PubMed Central

    Plata, Germán; Fuhrer, Tobias; Hsiao, Tzu-Lin; Sauer, Uwe; Vitkup, Dennis

    2013-01-01

    Annotation of organism-specific metabolic networks is one of the main challenges of systems biology. Importantly, due to inherent uncertainty of computational annotations, predictions of biochemical function need to be treated probabilistically. We present a global probabilistic approach to annotate genome-scale metabolic networks that integrates sequence homology and context-based correlations under a single principled framework. The developed method for Global Biochemical reconstruction Using Sampling (GLOBUS) not only provides annotation probabilities for each functional assignment, but also suggests likely alternative functions. GLOBUS is based on statistical Gibbs sampling of probable metabolic annotations and is able to make accurate functional assignments even in cases of remote sequence identity to known enzymes. We apply GLOBUS to genomes of Bacillus subtilis and Staphylococcus aureus, and validate the method predictions by experimentally demonstrating the 6-phosphogluconolactonase activity of ykgB and the role of the sps pathway for rhamnose biosynthesis in B. subtilis. PMID:22960854

  1. Genome and proteome annotation: organization, interpretation and integration

    PubMed Central

    Reeves, Gabrielle A.; Talavera, David; Thornton, Janet M.

    2008-01-01

    Recent years have seen a huge increase in the generation of genomic and proteomic data. This has been due to improvements in current biological methodologies, the development of new experimental techniques and the use of computers as support tools. All these raw data are useless if they cannot be properly analysed, annotated, stored and displayed. Consequently, a vast number of resources have been created to present the data to the wider community. Annotation tools and databases provide the means to disseminate these data and to comprehend their biological importance. This review examines the various aspects of annotation: type, methodology and availability. Moreover, it puts a special interest on novel annotation fields, such as that of phenotypes, and highlights the recent efforts focused on the integrating annotations. PMID:19019817

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

    PubMed

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

    2012-01-01

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

  3. Semantator: Annotating Clinical Narratives with Semantic Web Ontologies

    PubMed Central

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

    2012-01-01

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

  4. Annotated bibliography of software engineering laboratory literature

    NASA Technical Reports Server (NTRS)

    Kistler, David; Bristow, John; Smith, Don

    1994-01-01

    This document is an annotated bibliography of technical papers, documents, and memorandums produced by or related to the Software Engineering Laboratory. Nearly 200 publications are summarized. These publications cover many areas of software engineering and range from research reports to software documentation. This document has been updated and reorganized substantially since the original version (SEL-82-006, November 1982). All materials have been grouped into eight general subject areas for easy reference: (1) The Software Engineering Laboratory; (2) The Software Engineering Laboratory: Software Development Documents; (3) Software Tools; (4) Software Models; (5) Software Measurement; (6) Technology Evaluations; (7) Ada Technology; and (8) Data Collection. This document contains an index of these publications classified by individual author.

  5. Desert tortoise annotated bibliography, 1991-2015

    USGS Publications Warehouse

    Berry, Kristin H.; Lyren, Lisa M.; Mack, Jeremy S.; Brand, L. Arriana; Wood, Dustin A.

    2016-01-01

    Agassiz’s Desert Tortoise (hereinafter called desert tortoise) is a state- and federally-listed threatened species (U.S. Fish and Wildlife Service, 1990; California Department of Fish and Game, 2015). The first population federally listed as threatened occurred on the Beaver Dam Slope, Utah (U.S. Fish and Wildlife Service, 1980). In 1990, the entire geographic range north and west of the Colorado River was federally listed as threatened (U.S. Fish and Wildlife Service, 1990), with the exception being a small population in northwestern Arizona. The purpose of this annotated bibliography is to support recovery efforts for the species, because populations have continued to decline in spite of designation of critical habitat and publication of a recovery plan (U.S. Fish and Wildlife Service, 1994). For example, between 2005 and 2014, populations in critical habitats declined about 50% (U.S. Fish and Wildlife Service, 2015).

  6. Prediction in Annotation Based Guideline Encoding

    PubMed Central

    Hagerty, C. Greg; Pickens, David S.; Chang, Jaime; Kulikowski, Casimir A.; Sonnenberg, Frank A.

    2006-01-01

    The encoding of clinical practice guidelines into machine operable representations poses numerous challenges and will require considerable human intervention for the foreseeable future. To assist and potentially speed up this process, we have developed an incremental approach to guideline encoding which begins with the annotation of the original guideline text using markup techniques. A modular and flexible sequence of subtasks results in increasingly inter-operable representations while maintaining the connections to all prior source representations and supporting knowledge. To reduce the encoding bottleneck we also employ a number of machine-assisted learning and prediction techniques within a knowledge-based software environment. Promising results with a straightforward incremental learning algorithm illustrate the feasibility of such an approach. PMID:17238354

  7. Science exchanges

    NASA Astrophysics Data System (ADS)

    Richman, Barbara T.

    Dwindling scientific and technical exchange between the United States and the Soviet Union and prospects for enhancing such exchanges were discussed at an August 2 hearing by the Foreign Affairs Committee of the U.S. House of Representatives. The committee also heard overviews on the United States' approach to international exchange of science and technology. The hearing was the first in a series on current and future international science and technology programs.Four of eight science and technology agreements with the USSR that have expired in the last 15 months, including one on space, have not been renewed. The remaining four agreements have been extended into 1987 and 1988. Two others, including one on oceanography, are scheduled to run out in 1984.

  8. Annotation methods to develop and evaluate an expert system based on natural language processing in electronic medical records.

    PubMed

    Gicquel, Quentin; Tvardik, Nastassia; Bouvry, Côme; Kergourlay, Ivan; Bittar, André; Segond, Frédérique; Darmoni, Stefan; Metzger, Marie-Hélène

    2015-01-01

    The objective of the SYNODOS collaborative project was to develop a generic IT solution, combining a medical terminology server, a semantic analyser and a knowledge base. The goal of the project was to generate meaningful epidemiological data for various medical domains from the textual content of French medical records. In the context of this project, we built a care pathway oriented conceptual model and corresponding annotation method to develop and evaluate an expert system's knowledge base. The annotation method is based on a semi-automatic process, using a software application (MedIndex). This application exchanges with a cross-lingual multi-termino-ontology portal. The annotator selects the most appropriate medical code proposed for the medical concept in question by the multi-termino-ontology portal and temporally labels the medical concept according to the course of the medical event. This choice of conceptual model and annotation method aims to create a generic database of facts for the secondary use of electronic health records data. PMID:26262366

  9. Journals and Newsletters on Non-Formal Education and Development: A Selected, Annotated Bibliography. Annotated Bibliography #12.

    ERIC Educational Resources Information Center

    Sullivan, Karen Collamore; And Others

    An annotated bibliography of journals and newsletters on non-formal education and development, intended for those actively involved in the field, updates an earlier bibliography on the subject. This bibliography contains 609 entries, each annotated and with information on availability. Cross-references are provided for publications which may be…

  10. RASTtk: A modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes

    DOE PAGESBeta

    Brettin, Thomas; Davis, James J.; Disz, Terry; Edwards, Robert A.; Gerdes, Svetlana; Olsen, Gary J.; Olson, Robert; Overbeek, Ross; Parrello, Bruce; Pusch, Gordon D.; et al

    2015-02-10

    The RAST (Rapid Annotation using Subsystem Technology) annotation engine was built in 2008 to annotate bacterial and archaeal genomes. It works by offering a standard software pipeline for identifying genomic features (i.e., protein-encoding genes and RNA) and annotating their functions. Recently, in order to make RAST a more useful research tool and to keep pace with advancements in bioinformatics, it has become desirable to build a version of RAST that is both customizable and extensible. In this paper, we describe the RAST tool kit (RASTtk), a modular version of RAST that enables researchers to build custom annotation pipelines. RASTtk offersmore » a choice of software for identifying and annotating genomic features as well as the ability to add custom features to an annotation job. RASTtk also accommodates the batch submission of genomes and the ability to customize annotation protocols for batch submissions. This is the first major software restructuring of RAST since its inception.« less

  11. Heat exchanger

    SciTech Connect

    Drury, C.R.

    1988-02-02

    A heat exchanger having primary and secondary conduits in heat-exchanging relationship is described comprising: at least one serpentine tube having parallel sections connected by reverse bends, the serpentine tube constituting one of the conduits; a group of open-ended tubes disposed adjacent to the parallel sections, the open-ended tubes constituting the other of the conduits, and forming a continuous mass of contacting tubes extending between and surrounding the serpentine tube sections; and means securing the mass of tubes together to form a predetermined cross-section of the entirety of the mass of open-ended tubes and tube sections.

  12. ProteoAnnotator--open source proteogenomics annotation software supporting PSI standards.

    PubMed

    Ghali, Fawaz; Krishna, Ritesh; Perkins, Simon; Collins, Andrew; Xia, Dong; Wastling, Jonathan; Jones, Andrew R

    2014-12-01

    The recent massive increase in capability for sequencing genomes is producing enormous advances in our understanding of biological systems. However, there is a bottleneck in genome annotation--determining the structure of all transcribed genes. Experimental data from MS studies can play a major role in confirming and correcting gene structure--proteogenomics. However, there are some technical and practical challenges to overcome, since proteogenomics requires pipelines comprising a complex set of interconnected modules as well as bespoke routines, for example in protein inference and statistics. We are introducing a complete, open source pipeline for proteogenomics, called ProteoAnnotator, which incorporates a graphical user interface and implements the Proteomics Standards Initiative mzIdentML standard for each analysis stage. All steps are included as standalone modules with the mzIdentML library, allowing other groups to re-use the whole pipeline or constituent parts within other tools. We have developed new modules for pre-processing and combining multiple search databases, for performing peptide-level statistics on mzIdentML files, for scoring grouped protein identifications matched to a given genomic locus to validate that updates to the official gene models are statistically sound and for mapping end results back onto the genome. ProteoAnnotator is available from http://www.proteoannotator.org/. All MS data have been deposited in the ProteomeXchange with identifiers PXD001042 and PXD001390 (http://proteomecentral.proteomexchange.org/dataset/PXD001042; http://proteomecentral.proteomexchange.org/dataset/PXD001390). PMID:25297486

  13. Detection of gene annotations and protein-protein interaction associated disorders through transitive relationships between integrated annotations

    PubMed Central

    2015-01-01

    Background Increasingly high amounts of heterogeneous and valuable controlled biomolecular annotations are available, but far from exhaustive and scattered in many databases. Several annotation integration and prediction approaches have been proposed, but these issues are still unsolved. We previously created a Genomic and Proteomic Knowledge Base (GPKB) that efficiently integrates many distributed biomolecular annotation and interaction data of several organisms, including 32,956,102 gene annotations, 273,522,470 protein annotations and 277,095 protein-protein interactions (PPIs). Results By comprehensively leveraging transitive relationships defined by the numerous association data integrated in GPKB, we developed a software procedure that effectively detects and supplement consistent biomolecular annotations not present in the integrated sources. According to some defined logic rules, it does so only when the semantic type of data and of their relationships, as well as the cardinality of the relationships, allow identifying molecular biology compliant annotations. Thanks to controlled consistency and quality enforced on data integrated in GPKB, and to the procedures used to avoid error propagation during their automatic processing, we could reliably identify many annotations, which we integrated in GPKB. They comprise 3,144 gene to pathway and 21,942 gene to biological function annotations of many organisms, and 1,027 candidate associations between 317 genetic disorders and 782 human PPIs. Overall estimated recall and precision of our approach were 90.56 % and 96.61 %, respectively. Co-functional evaluation of genes with known function showed high functional similarity between genes with new detected and known annotation to the same pathway; considering also the new detected gene functional annotations enhanced such functional similarity, which resembled the one existing between genes known to be annotated to the same pathway. Strong evidence was also found in

  14. Structural and functional annotation of the porcine immunome

    PubMed Central

    2013-01-01

    Background The domestic pig is known as an excellent model for human immunology and the two species share many pathogens. Susceptibility to infectious disease is one of the major constraints on swine performance, yet the structure and function of genes comprising the pig immunome are not well-characterized. The completion of the pig genome provides the opportunity to annotate the pig immunome, and compare and contrast pig and human immune systems. Results The Immune Response Annotation Group (IRAG) used computational curation and manual annotation of the swine genome assembly 10.2 (Sscrofa10.2) to refine the currently available automated annotation of 1,369 immunity-related genes through sequence-based comparison to genes in other species. Within these genes, we annotated 3,472 transcripts. Annotation provided evidence for gene expansions in several immune response families, and identified artiodactyl-specific expansions in the cathelicidin and type 1 Interferon families. We found gene duplications for 18 genes, including 13 immune response genes and five non-immune response genes discovered in the annotation process. Manual annotation provided evidence for many new alternative splice variants and 8 gene duplications. Over 1,100 transcripts without porcine sequence evidence were detected using cross-species annotation. We used a functional approach to discover and accurately annotate porcine immune response genes. A co-expression clustering analysis of transcriptomic data from selected experimental infections or immune stimulations of blood, macrophages or lymph nodes identified a large cluster of genes that exhibited a correlated positive response upon infection across multiple pathogens or immune stimuli. Interestingly, this gene cluster (cluster 4) is enriched for known general human immune response genes, yet contains many un-annotated porcine genes. A phylogenetic analysis of the encoded proteins of cluster 4 genes showed that 15% exhibited an accelerated

  15. Heat exchanger

    DOEpatents

    Daman, Ernest L.; McCallister, Robert A.

    1979-01-01

    A heat exchanger is provided having first and second fluid chambers for passing primary and secondary fluids. The chambers are spaced apart and have heat pipes extending from inside one chamber to inside the other chamber. A third chamber is provided for passing a purge fluid, and the heat pipe portion between the first and second chambers lies within the third chamber.

  16. Comparison of concept recognizers for building the Open Biomedical Annotator.

    PubMed

    Shah, Nigam H; Bhatia, Nipun; Jonquet, Clement; Rubin, Daniel; Chiang, Annie P; Musen, Mark A

    2009-01-01

    The National Center for Biomedical Ontology (NCBO) is developing a system for automated, ontology-based access to online biomedical resources (Shah NH, et al.: Ontology-driven indexing of public datasets for translational bioinformatics. BMC Bioinformatics 2009, 10(Suppl 2):S1). The system's indexing workflow processes the text metadata of diverse resources such as datasets from GEO and ArrayExpress to annotate and index them with concepts from appropriate ontologies. This indexing requires the use of a concept-recognition tool to identify ontology concepts in the resource's textual metadata. In this paper, we present a comparison of two concept recognizers - NLM's MetaMap and the University of Michigan's Mgrep. We utilize a number of data sources and dictionaries to evaluate the concept recognizers in terms of precision, recall, speed of execution, scalability and customizability. Our evaluations demonstrate that Mgrep has a clear edge over MetaMap for large-scale service oriented applications. Based on our analysis we also suggest areas of potential improvements for Mgrep. We have subsequently used Mgrep to build the Open Biomedical Annotator service. The Annotator service has access to a large dictionary of biomedical terms derived from the United Medical Language System (UMLS) and NCBO ontologies. The Annotator also leverages the hierarchical structure of the ontologies and their mappings to expand annotations. The Annotator service is available to the community as a REST Web service for creating ontology-based annotations of their data. PMID:19761568

  17. Fuzzy emotional semantic analysis and automated annotation of scene images.

    PubMed

    Cao, Jianfang; Chen, Lichao

    2015-01-01

    With the advances in electronic and imaging techniques, the production of digital images has rapidly increased, and the extraction and automated annotation of emotional semantics implied by images have become issues that must be urgently addressed. To better simulate human subjectivity and ambiguity for understanding scene images, the current study proposes an emotional semantic annotation method for scene images based on fuzzy set theory. A fuzzy membership degree was calculated to describe the emotional degree of a scene image and was implemented using the Adaboost algorithm and a back-propagation (BP) neural network. The automated annotation method was trained and tested using scene images from the SUN Database. The annotation results were then compared with those based on artificial annotation. Our method showed an annotation accuracy rate of 91.2% for basic emotional values and 82.4% after extended emotional values were added, which correspond to increases of 5.5% and 8.9%, respectively, compared with the results from using a single BP neural network algorithm. Furthermore, the retrieval accuracy rate based on our method reached approximately 89%. This study attempts to lay a solid foundation for the automated emotional semantic annotation of more types of images and therefore is of practical significance. PMID:25838818

  18. The caBIG annotation and image Markup project.

    PubMed

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

    2010-04-01

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

  19. Considerations to improve functional annotations in biological databases.

    PubMed

    Benítez-Páez, Alfonso

    2009-12-01

    Despite the great effort to design efficient systems allowing the electronic indexation of information concerning genes, proteins, structures, and interactions published daily in scientific journals, some problems are still observed in specific tasks such as functional annotation. The annotation of function is a critical issue for bioinformatic routines, such as for instance, in functional genomics and the further prediction of unknown protein function, which are highly dependent of the quality of existing annotations. Some information management systems evolve to efficiently incorporate information from large-scale projects, but often, annotation of single records from the literature is difficult and slow. In this short report, functional characterizations of a representative sample of the entire set of uncharacterized proteins from Escherichia coli K12 was compiled from Swiss-Prot, PubMed, and EcoCyc and demonstrate a functional annotation deficit in biological databases. Some issues are postulated as causes of the lack of annotation, and different solutions are evaluated and proposed to avoid them. The hope is that as a consequence of these observations, there will be new impetus to improve the speed and quality of functional annotation and ultimately provide updated, reliable information to the scientific community. PMID:20050264

  20. Scoring consensus of multiple ECG annotators by optimal sequence alignment.

    PubMed

    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

  1. eXamine: Exploring annotated modules in networks

    PubMed Central

    2014-01-01

    Background Biological networks have a growing importance for the interpretation of high-throughput “omics” data. Integrative network analysis makes use of statistical and combinatorial methods to extract smaller subnetwork modules, and performs enrichment analysis to annotate the modules with ontology terms or other available knowledge. This process results in an annotated module, which retains the original network structure and includes enrichment information as a set system. A major bottleneck is a lack of tools that allow exploring both network structure of extracted modules and its annotations. Results This paper presents a visual analysis approach that targets small modules with many set-based annotations, and which displays the annotations as contours on top of a node-link diagram. We introduce an extension of self-organizing maps to lay out nodes, links, and contours in a unified way. An implementation of this approach is freely available as the Cytoscape app eXamine Conclusions eXamine accurately conveys small and annotated modules consisting of several dozens of proteins and annotations. We demonstrate that eXamine facilitates the interpretation of integrative network analysis results in a guided case study. This study has resulted in a novel biological insight regarding the virally-encoded G-protein coupled receptor US28. PMID:25002203

  2. Open semantic annotation of scientific publications using DOMEO

    PubMed Central

    2012-01-01

    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. PMID:22541592

  3. A semantic analysis of the annotations of the human genome.

    PubMed

    Khatri, Purvesh; Done, Bogdan; Rao, Archana; Done, Arina; Draghici, Sorin

    2005-08-15

    The correct interpretation of any biological experiment depends in an essential way on the accuracy and consistency of the existing annotation databases. Such databases are ubiquitous and used by all life scientists in most experiments. However, it is well known that such databases are incomplete and many annotations may also be incorrect. In this paper we describe a technique that can be used to analyze the semantic content of such annotation databases. Our approach is able to extract implicit semantic relationships between genes and functions. This ability allows us to discover novel functions for known genes. This approach is able to identify missing and inaccurate annotations in existing annotation databases, and thus help improve their accuracy. We used our technique to analyze the current annotations of the human genome. From this body of annotations, we were able to predict 212 additional gene-function assignments. A subsequent literature search found that 138 of these gene-functions assignments are supported by existing peer-reviewed papers. An additional 23 assignments have been confirmed in the meantime by the addition of the respective annotations in later releases of the Gene Ontology database. Overall, the 161 confirmed assignments represent 75.95% of the proposed gene-function assignments. Only one of our predictions (0.4%) was contradicted by the existing literature. We could not find any relevant articles for 50 of our predictions (23.58%). The method is independent of the organism and can be used to analyze and improve the quality of the data of any public or private annotation database. PMID:15955782

  4. Comparative Omics-Driven Genome Annotation Refinement: Application across Yersiniae

    SciTech Connect

    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 pathogen, thus

  5. An annotation system for 3D fluid flow visualization

    NASA Technical Reports Server (NTRS)

    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.

  6. Gene ontology annotation by density and gravitation models.

    PubMed

    Hou, Wen-Juan; Lin, Kevin Hsin-Yih; Chen, Hsin-Hsi

    2006-01-01

    Gene Ontology (GO) is developed to provide standard vocabularies of gene products in different databases. The process of annotating GO terms to genes requires curators to read through lengthy articles. Methods for speeding up or automating the annotation process are thus of great importance. We propose a GO annotation approach using full-text biomedical documents for directing more relevant papers to curators. This system explores word density and gravitation relationships between genes and GO terms. Different density and gravitation models are built and several evaluation criteria are employed to assess the effects of the proposed methods. PMID:17503384

  7. A defeasible deontic reasoning system based on annotated logic programming

    NASA Astrophysics Data System (ADS)

    Nakamatsu, Kazumi; Abe, Jair Minoro; Suzuki, Atsuyuki

    2001-06-01

    In this paper, we provide a theoretical framework for a defeasible deontic reasoning system based on annotated logic programming, we propose an annotated logic program called an EVALPSN (Extended Vector Annotated Logic Program with Strong Negation) to formulate a defeasible deontic reasoning proposed by D. Nute. We also propose a translation rule from defeasible deontic theory into EVALPSN and show that the derivability of defeasible deontic theory can be translated into the satisfiability of EVALPSN stable model. The combination of a translation system from defeasible deontic theories into EVALPSNs and a computing system of EVALPSN stable models can easily provide a theoretical framework for an automated defeasible deontic reasoning system.

  8. Investigating heterogeneous protein annotations toward cross-corpora utilization

    PubMed Central

    2009-01-01

    Background The number of corpora, collections of structured texts, has been increasing, as a result of the growing interest in the application of natural language processing methods to biological texts. Many named entity recognition (NER) systems have been developed based on these corpora. However, in the biomedical community, there is yet no general consensus regarding named entity annotation; thus, the resources are largely incompatible, and it is difficult to compare the performance of systems developed on resources that were divergently annotated. On the other hand, from a practical application perspective, it is desirable to utilize as many existing annotated resources as possible, because annotation is costly. Thus, it becomes a task of interest to integrate the heterogeneous annotations in these resources. Results We explore the potential sources of incompatibility among gene and protein annotations that were made for three common corpora: GENIA, GENETAG and AIMed. To show the inconsistency in the corpora annotations, we first tackle the incompatibility problem caused by corpus integration, and we quantitatively measure the effect of this incompatibility on protein mention recognition. We find that the F-score performance declines tremendously when training with integrated data, instead of training with pure data; in some cases, the performance drops nearly 12%. This degradation may be caused by the newly added heterogeneous annotations, and cannot be fixed without an understanding of the heterogeneities that exist among the corpora. Motivated by the result of this preliminary experiment, we further qualitatively analyze a number of possible sources for these differences, and investigate the factors that would explain the inconsistencies, by performing a series of well-designed experiments. Our analyses indicate that incompatibilities in the gene/protein annotations exist mainly in the following four areas: the boundary annotation conventions, the scope of

  9. Enhanced Acylcarnitine Annotation in High-Resolution Mass Spectrometry Data: Fragmentation Analysis for the Classification and Annotation of Acylcarnitines

    PubMed Central

    van der Hooft, Justin J. J.; Ridder, Lars; Barrett, Michael P.; Burgess, Karl E. V.

    2015-01-01

    Metabolite annotation and identification are primary challenges in untargeted metabolomics experiments. Rigorous workflows for reliable annotation of mass features with chemical structures or compound classes are needed to enhance the power of untargeted mass spectrometry. High-resolution mass spectrometry considerably improves the confidence in assigning elemental formulas to mass features in comparison to nominal mass spectrometry, and embedding of fragmentation methods enables more reliable metabolite annotations and facilitates metabolite classification. However, the analysis of mass fragmentation spectra can be a time-consuming step and requires expert knowledge. This study demonstrates how characteristic fragmentations, specific to compound classes, can be used to systematically analyze their presence in complex biological extracts like urine that have undergone untargeted mass spectrometry combined with data dependent or targeted fragmentation. Human urine extracts were analyzed using normal phase liquid chromatography (hydrophilic interaction chromatography) coupled to an Ion Trap-Orbitrap hybrid instrument. Subsequently, mass chromatograms and collision-induced dissociation and higher-energy collisional dissociation (HCD) fragments were annotated using the freely available MAGMa software1. Acylcarnitines play a central role in energy metabolism by transporting fatty acids into the mitochondrial matrix. By filtering on a combination of a mass fragment and neutral loss designed based on the MAGMa fragment annotations, we were able to classify and annotate 50 acylcarnitines in human urine extracts, based on high-resolution mass spectrometry HCD fragmentation spectra at different energies for all of them. Of these annotated acylcarnitines, 31 are not described in HMDB yet and for only 4 annotated acylcarnitines the fragmentation spectra could be matched to reference spectra. Therefore, we conclude that the use of mass fragmentation filters within the context

  10. Annotation and curation of uncharacterized proteins- challenges

    PubMed Central

    Ijaq, Johny; Chandrasekharan, Mohanalatha; Poddar, Rajdeep; Bethi, Neeraja; Sundararajan, Vijayaraghava S.

    2015-01-01

    Hypothetical proteins (HPs) are the proteins predicted to be expressed from an open reading frame, making 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 enlist various methods linking annotation to structural and functional prediction of HPs that assist in the discovery of new structures and functions serving as markers and pharmacological targets for drug designing, discovery, and screening. Further we give an overview of how mass spectrometry as an analytical technique is used to validate protein characterisation. We discuss how 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. Finally, we articulate challenges on how next generation sequencing methods have accelerated multiple areas of genomics with special focus on uncharacterized proteins. PMID:25873935

  11. Annotating Human P-Glycoprotein Bioassay Data

    PubMed Central

    Zdrazil, Barbara; Pinto, Marta; Vasanthanathan, Poongavanam; Williams, Antony J; Balderud, Linda Zander; Engkvist, Ola; Chichester, Christine; Hersey, Anne; Overington, John P; Ecker, Gerhard F

    2012-01-01

    Abstract Huge amounts of small compound bioactivity data have been entering the public domain as a consequence of open innovation initiatives. It is now the time to carefully analyse existing bioassay data and give it a systematic structure. Our study aims to annotate prominent in vitro assays used for the determination of bioactivities of human P-glycoprotein inhibitors and substrates as they are represented in the ChEMBL and TP-search open source databases. Furthermore, the ability of data, determined in different assays, to be combined with each other is explored. As a result of this study, it is suggested that for inhibitors of human P-glycoprotein it is possible to combine data coming from the same assay type, if the cell lines used are also identical and the fluorescent or radiolabeled substrate have overlapping binding sites. In addition, it demonstrates that there is a need for larger chemical diverse datasets that have been measured in a panel of different assays. This would certainly alleviate the search for other inter-correlations between bioactivity data yielded by different assay setups. PMID:23293680

  12. Semantic Annotation for Biological Information Retrieval System

    PubMed Central

    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. PMID:25737720

  13. Cancer Survivorship for Primary Care Annotated Bibliography

    PubMed Central

    Westfall, Matthew Y.; Overholser, Linda; Zittleman, Linda; Westfall, John M.

    2015-01-01

    Long-term cancer survivorship care is a relatively new and rapidly advancing field of research. Increasing cancer survivorship rates have created a huge population of long-term cancer survivors whose cancer-specific needs challenge healthcare infrastructure and highlight a significant deficit of knowledge and guidelines in transitional care from treatment to normalcy/prolonged survivorship. As the paradigm of cancer care has changed from a fixation on the curative to the maintenance on long-term overall quality of life, so to, has the delineation of responsibility between oncologists and primary care physicians (PCPs). As more patients enjoy long-term survival, PCPs play a more comprehensive role in cancer care following acute treatment. To this end, this annotated bibliography was written to provide PCPs and other readers with an up-to-date and robust base of knowledge on long-term cancer survivorship, including definitions and epidemiological information as well as specific considerations and recommendations on physical, psychosocial, sexual, and comorbidity needs of survivors. Additionally, significant information is included on survivorship care, specifically Survivorship Care Plans (SPCs) and their evolution, utilization by oncologists and PCPs, and current gaps, as well as an introduction to patient navigation programs. Given rapid advancements in cancer research, this bibliography is meant to serve as current baseline reference outlining the state of the science. PMID:26114091

  14. ECOSYSTEM MONITORING AND ECOLOGICAL INDICATORS: AN ANNOTATED BIBLIOGRAPHY

    EPA Science Inventory

    The annotated bibliography serves as the initial literature base for ecological indicators for regional monitoring within the U.S. EPA's Environmental Monitoring and Assessment Program (EMAP). ive hundred fifty six (556) citations were obtained through a combination of computeriz...

  15. Civil War Resources on the Internet: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Vincenti, William; Sielaff, McKinley

    1997-01-01

    Presents an annotated bibliography of online resources on the Civil War from the Abolition movement through Reconstruction, drawn from Rutgers University's (New Jersey) Web page. Lists primary resources, secondary sources, online bibliographies and indexes, general sites, and listservs. (AEF)

  16. An analysis on the entity annotations in biological corpora

    PubMed Central

    Neves, Mariana

    2014-01-01

    Collection of documents annotated with semantic entities and relationships are crucial resources to support development and evaluation of text mining solutions for the biomedical domain. Here I present an overview of 36 corpora and show an analysis on the semantic annotations they contain. Annotations for entity types were classified into six semantic groups and an overview on the semantic entities which can be found in each corpus is shown. Results show that while some semantic entities, such as genes, proteins and chemicals are consistently annotated in many collections, corpora available for diseases, variations and mutations are still few, in spite of their importance in the biological domain. PMID:25254099

  17. Annotated Bibliography of Research in the Teaching of English.

    ERIC Educational Resources Information Center

    Brown, Deborah; Kalman, Judith; Gomez, Macrina; Rijlaarsdam, Gert; Stinson, Anne D'Antonio; Whiting, Melissa E.

    2001-01-01

    Presents 36 annotations of journal articles (published between January and June, 2001) dealing with assessment, bilingual/foreign language education, literacy, professional development, reading, teaching and learning of literature, teaching and learning of writing, and technology and literacy. (SG)

  18. Geothermal wetlands: an annotated bibliography of pertinent literature

    SciTech Connect

    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)

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

    NASA Technical Reports Server (NTRS)

    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.

  20. Analysis of Annotation on Documents for Recycling Information

    NASA Astrophysics Data System (ADS)

    Nakai, Tomohiro; Kondo, Nobuyuki; Kise, Koichi; Matsumoto, Keinosuke

    In order to make collaborative business activities fruitful, it is essential to know characteristics of organizations and persons in more details and to gather information relevant to the activities. In this paper, we describe a notion of “information recycle" that actualizes these requirements by analyzing documents. The key of recycling information is to utilize annotations on documents as clues for generating users' profiles and for weighting contents in the context of the activities. We also propose a method of extracting annotations on paper documents just by pressing one button with the help of techniques of camera-based document image analysis. Experimental results demonstrate that it is fundamentally capable of acquiring annotations on paper documents on condition that their electronic versions without annotations are available for the processing.

  1. BEHAVIORAL AND PHYSIOLOGICAL CORRELATES OF VARYING NOISE ENVIRONMENTS: ANNOTATED BIBLIOGRAPHY

    EPA Science Inventory

    The annotated bibliography contains 365 references related to the behavioral and physiological effects of noise. References to research articles, texts, other literature reviews and symposia are provided. The review covers the period 1968 thru 1974. Some foreign research publishe...

  2. The Integration of Baseball: An Annotated Bibliography of Nonfiction Books.

    ERIC Educational Resources Information Center

    Kaplan, Ron

    2002-01-01

    This annotated bibliography of nonfiction books on the integration of baseball focuses on the Negro leagues, books for young readers, individual teams, autobiographies and biographies of the pioneers, and autobiographies and biographies of the African American major leaguers. (SM)

  3. Annotated Bibliography of Recent Research Related to Academic Advising

    ERIC Educational Resources Information Center

    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.

  4. Freedom of Speech: A Selected, Annotated Basic Bibliography.

    ERIC Educational Resources Information Center

    Tedford, Thomas L.

    This bibliography lists 36 books related to problems of freedom of speech. General sources (history, analyses, texts, and anthologies) are listed separately from those dealing with censorship of obscenity and pornography. Each entry is briefly annotated. (AA)

  5. Managing and Querying Image Annotation and Markup in XML

    PubMed Central

    Wang, Fusheng; Pan, Tony; Sharma, Ashish; Saltz, Joel

    2010-01-01

    Proprietary approaches for representing annotations and image markup are serious barriers for researchers to share image data and knowledge. The Annotation and Image Markup (AIM) project is developing a standard based information model for image annotation and markup in health care and clinical trial environments. The complex hierarchical structures of AIM data model pose new challenges for managing such data in terms of performance and support of complex queries. In this paper, we present our work on managing AIM data through a native XML approach, and supporting complex image and annotation queries through native extension of XQuery language. Through integration with xService, AIM databases can now be conveniently shared through caGrid. PMID:21218167

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

    ERIC Educational Resources Information Center

    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)

  7. Hymenoptera Genome Database: integrating genome annotations in HymenopteraMine

    PubMed Central

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

    2016-01-01

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

  8. 102. Photocopy of 1882 plan of Smithsonian grounds annotated through ...

    Library of Congress Historic Buildings Survey, Historic Engineering Record, Historic Landscapes Survey

    102. Photocopy of 1882 plan of Smithsonian grounds annotated through 1891. Displayed in Great Hall of 'Castle.' SMITHSONIAN PARK - Smithsonian Institution Building, 1000 Jefferson Drive, between Ninth & Twelfth Streets, Southwest, Washington, District of Columbia, DC

  9. Statement-Based Semantic Annotation of Media Resources

    NASA Astrophysics Data System (ADS)

    Weiss, Wolfgang; Bürger, Tobias; Villa, Robert; Punitha, P.; Halb, Wolfgang

    Currently the media production domain lacks efficient ways to organize and search for media assets. Ontology-based applications have been identified as a viable solution to this problem, however, sometimes being too complex for non-experienced users. We present a fast and easy to use approach to create semantic annotations and relationships of media resources. The approach is implemented in the SALERO Intelligent Media Annotation & Search system. It combines the simplicity of free text tagging and the power of semantic technologies and by that makes a compromise in the complexity of full semantic annotations. We present the implementation of the approach in the system and an evaluation of different user interface techniques for creating annotations.

  10. Ethics in Oncology: An Annotated Bibliography of Important Literature

    PubMed Central

    Tenner, Laura L.; Helft, Paul R.

    2013-01-01

    The aim of this annotated bibliography about important articles in the field of ethics and oncology is to provide the practicing hematologist/oncologist with a brief overview of some of the important literature in this crucial area. PMID:23942932

  11. Annotated Bibliography of Global Resources Information Systems Related Publications

    NASA Technical Reports Server (NTRS)

    Estes, J. E.; Star, J. L. (Principal Investigator); Cosentino, M. J.; Mann, L. J.

    1984-01-01

    An annotated bibliography of work concerning geophysical data management systems is presented. Major topics under investigation include data acquisition, data storage, long term data preservation, architecture, preprocessing, hydrology, land resources, geology, meteorology, and applications of remote sensing techniques.

  12. Articles Pertinent to the Campus Press: A Selected Annotated Bibliography

    ERIC Educational Resources Information Center

    Ardoin, Birthney

    1974-01-01

    Contains a selected annotated bibliography of 51 items covering articles published from January through August, 1974, organized under the following categories: advertising, broadcasting, media criticism, editorial policy, graphics, job opportunities, pedagogy, and photography. (RB)

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

    PubMed

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

    2016-01-01

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

  14. GIFtS: annotation landscape analysis with GeneCards

    PubMed Central

    Harel, Arye; Inger, Aron; Stelzer, Gil; Strichman-Almashanu, Liora; Dalah, Irina; Safran, Marilyn; Lancet, Doron

    2009-01-01

    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 given gene measured by

  15. EGASP: the human ENCODE Genome Annotation Assessment Project

    PubMed Central

    Guigó, Roderic; Flicek, Paul; Abril, Josep F; Reymond, Alexandre; Lagarde, Julien; Denoeud, France; Antonarakis, Stylianos; Ashburner, Michael; Bajic, Vladimir B; Birney, Ewan; Castelo, Robert; Eyras, Eduardo; Ucla, Catherine; Gingeras, Thomas R; Harrow, Jennifer; Hubbard, Tim; Lewis, Suzanna E; Reese, Martin G

    2006-01-01

    Background We present the results of EGASP, a community experiment to assess the state-of-the-art in genome annotation within the ENCODE regions, which span 1% of the human genome sequence. The experiment had two major goals: the assessment of the accuracy of computational methods to predict protein coding genes; and the overall assessment of the completeness of the current human genome annotations as represented in the ENCODE regions. For the computational prediction assessment, eighteen groups contributed gene predictions. We evaluated these submissions against each other based on a 'reference set' of annotations generated as part of the GENCODE project. These annotations were not available to the prediction groups prior to the submission deadline, so that their predictions were blind and an external advisory committee could perform a fair assessment. Results The best methods had at least one gene transcript correctly predicted for close to 70% of the annotated genes. Nevertheless, the multiple transcript accuracy, taking into account alternative splicing, reached only approximately 40% to 50% accuracy. At the coding nucleotide level, the best programs reached an accuracy of 90% in both sensitivity and specificity. Programs relying on mRNA and protein sequences were the most accurate in reproducing the manually curated annotations. Experimental validation shows that only a very small percentage (3.2%) of the selected 221 computationally predicted exons outside of the existing annotation could be verified. Conclusion This is the first such experiment in human DNA, and we have followed the standards established in a similar experiment, GASP1, in Drosophila melanogaster. We believe the results presented here contribute to the value of ongoing large-scale annotation projects and should guide further experimental methods when being scaled up to the entire human genome sequence. PMID:16925836

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

    SciTech Connect

    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.

  17. AmiGO: online access to ontology and annotation data

    SciTech Connect

    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.

  18. From Paper-and-Pen Annotations to Artefact-Based Mobile Learning

    ERIC Educational Resources Information Center

    Hoff, C.; Wehling, U.; Rothkugel, S.

    2009-01-01

    Making annotations on books and learning materials is part of students' everyday life. Although there are many computer-based annotation systems, many people prefer to print digital documents and make annotations on physical paper. We introduce a classification scheme for computer-based annotation systems and provide an overview of different…

  19. Annotation of SBML models through rule-based semantic integration

    PubMed Central

    2010-01-01

    Background The creation of accurate quantitative Systems Biology Markup Language (SBML) models is a time-intensive, manual process often complicated by the many data sources and formats required to annotate even a small and well-scoped model. Ideally, the retrieval and integration of biological knowledge for model annotation should be performed quickly, precisely, and with a minimum of manual effort. Results Here we present rule-based mediation, a method of semantic data integration applied to systems biology model annotation. The heterogeneous data sources are first syntactically converted into ontologies, which are then aligned to a small domain ontology by applying a rule base. We demonstrate proof-of-principle of this application of rule-based mediation using off-the-shelf semantic web technology through two use cases for SBML model annotation. Existing tools and technology provide a framework around which the system is built, reducing development time and increasing usability. Conclusions Integrating resources in this way accommodates multiple formats with different semantics, and provides richly-modelled biological knowledge suitable for annotation of SBML models. This initial work establishes the feasibility of rule-based mediation as part of an automated SBML model annotation system. Availability Detailed information on the project files as well as further information on and comparisons with similar projects is available from the project page at http://cisban-silico.cs.ncl.ac.uk/RBM/. PMID:20626923

  20. A semi-automatic annotation tool for cooking video

    NASA Astrophysics Data System (ADS)

    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.

  1. GENCODE: The reference human genome annotation for The ENCODE Project

    PubMed Central

    Harrow, Jennifer; Frankish, Adam; Gonzalez, Jose M.; Tapanari, Electra; Diekhans, Mark; Kokocinski, Felix; Aken, Bronwen L.; Barrell, Daniel; Zadissa, Amonida; Searle, Stephen; Barnes, If; Bignell, Alexandra; Boychenko, Veronika; Hunt, Toby; Kay, Mike; Mukherjee, Gaurab; Rajan, Jeena; Despacio-Reyes, Gloria; Saunders, Gary; Steward, Charles; Harte, Rachel; Lin, Michael; Howald, Cédric; Tanzer, Andrea; Derrien, Thomas; Chrast, Jacqueline; Walters, Nathalie; Balasubramanian, Suganthi; Pei, Baikang; Tress, Michael; Rodriguez, Jose Manuel; Ezkurdia, Iakes; van Baren, Jeltje; Brent, Michael; Haussler, David; Kellis, Manolis; Valencia, Alfonso; Reymond, Alexandre; Gerstein, Mark; Guigó, Roderic; Hubbard, Tim J.

    2012-01-01

    The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented in UCSC genes and RefSeq. It also has the most comprehensive annotation of long noncoding RNA (lncRNA) loci publicly available with the predominant transcript form consisting of two exons. We have examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites. Over one-third of GENCODE protein-coding genes are supported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas. New models derived from the Illumina Body Map 2.0 RNA-seq data identify 3689 new loci not currently in GENCODE, of which 3127 consist of two exon models indicating that they are possibly unannotated long noncoding loci. GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers. PMID:22955987

  2. Metagenomic gene annotation by a homology-independent approach

    SciTech Connect

    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.

  3. GENCODE: the reference human genome annotation for The ENCODE Project.

    PubMed

    Harrow, Jennifer; Frankish, Adam; Gonzalez, Jose M; Tapanari, Electra; Diekhans, Mark; Kokocinski, Felix; Aken, Bronwen L; Barrell, Daniel; Zadissa, Amonida; Searle, Stephen; Barnes, If; Bignell, Alexandra; Boychenko, Veronika; Hunt, Toby; Kay, Mike; Mukherjee, Gaurab; Rajan, Jeena; Despacio-Reyes, Gloria; Saunders, Gary; Steward, Charles; Harte, Rachel; Lin, Michael; Howald, Cédric; Tanzer, Andrea; Derrien, Thomas; Chrast, Jacqueline; Walters, Nathalie; Balasubramanian, Suganthi; Pei, Baikang; Tress, Michael; Rodriguez, Jose Manuel; Ezkurdia, Iakes; van Baren, Jeltje; Brent, Michael; Haussler, David; Kellis, Manolis; Valencia, Alfonso; Reymond, Alexandre; Gerstein, Mark; Guigó, Roderic; Hubbard, Tim J

    2012-09-01

    The GENCODE Consortium aims to identify all gene features in the human genome using a combination of computational analysis, manual annotation, and experimental validation. Since the first public release of this annotation data set, few new protein-coding loci have been added, yet the number of alternative splicing transcripts annotated has steadily increased. The GENCODE 7 release contains 20,687 protein-coding and 9640 long noncoding RNA loci and has 33,977 coding transcripts not represented in UCSC genes and RefSeq. It also has the most comprehensive annotation of long noncoding RNA (lncRNA) loci publicly available with the predominant transcript form consisting of two exons. We have examined the completeness of the transcript annotation and found that 35% of transcriptional start sites are supported by CAGE clusters and 62% of protein-coding genes have annotated polyA sites. Over one-third of GENCODE protein-coding genes are supported by peptide hits derived from mass spectrometry spectra submitted to Peptide Atlas. New models derived from the Illumina Body Map 2.0 RNA-seq data identify 3689 new loci not currently in GENCODE, of which 3127 consist of two exon models indicating that they are possibly unannotated long noncoding loci. GENCODE 7 is publicly available from gencodegenes.org and via the Ensembl and UCSC Genome Browsers. PMID:22955987

  4. Heat exchanger

    DOEpatents

    Brackenbury, Phillip J.

    1986-04-01

    A heat exchanger comparising a shell attached at its open end to one side of a tube sheet and a detachable head connected to the other side of said tube sheet. The head is divided into a first and second chamber in fluid communication with a nozzle inlet and nozzle outlet, respectively, formed in said tube sheet. A tube bundle is mounted within said shell and is provided with inlets and outlets formed in said tube sheet in communication with said first and second chambers, respectively.

  5. Deep Question Answering for protein annotation

    PubMed Central

    Gobeill, Julien; Gaudinat, Arnaud; Pasche, Emilie; Vishnyakova, Dina; Gaudet, Pascale; Bairoch, Amos; Ruch, Patrick

    2015-01-01

    Biomedical professionals have access to a huge amount of literature, but when they use a search engine, they often have to deal with too many documents to efficiently find the appropriate information in a reasonable time. In this perspective, question-answering (QA) engines are designed to display answers, which were automatically extracted from the retrieved documents. Standard QA engines in literature process a user question, then retrieve relevant documents and finally extract some possible answers out of these documents using various named-entity recognition processes. In our study, we try to answer complex genomics questions, which can be adequately answered only using Gene Ontology (GO) concepts. Such complex answers cannot be found using state-of-the-art dictionary- and redundancy-based QA engines. We compare the effectiveness of two dictionary-based classifiers for extracting correct GO answers from a large set of 100 retrieved abstracts per question. In the same way, we also investigate the power of GOCat, a GO supervised classifier. GOCat exploits the GOA database to propose GO concepts that were annotated by curators for similar abstracts. This approach is called deep QA, as it adds an original classification step, and exploits curated biological data to infer answers, which are not explicitly mentioned in the retrieved documents. We show that for complex answers such as protein functional descriptions, the redundancy phenomenon has a limited effect. Similarly usual dictionary-based approaches are relatively ineffective. In contrast, we demonstrate how existing curated data, beyond information extraction, can be exploited by a supervised classifier, such as GOCat, to massively improve both the quantity and the quality of the answers with a +100% improvement for both recall and precision. Database URL: http://eagl.unige.ch/DeepQA4PA/ PMID:26384372

  6. Deep Question Answering for protein annotation.

    PubMed

    Gobeill, Julien; Gaudinat, Arnaud; Pasche, Emilie; Vishnyakova, Dina; Gaudet, Pascale; Bairoch, Amos; Ruch, Patrick

    2015-01-01

    Biomedical professionals have access to a huge amount of literature, but when they use a search engine, they often have to deal with too many documents to efficiently find the appropriate information in a reasonable time. In this perspective, question-answering (QA) engines are designed to display answers, which were automatically extracted from the retrieved documents. Standard QA engines in literature process a user question, then retrieve relevant documents and finally extract some possible answers out of these documents using various named-entity recognition processes. In our study, we try to answer complex genomics questions, which can be adequately answered only using Gene Ontology (GO) concepts. Such complex answers cannot be found using state-of-the-art dictionary- and redundancy-based QA engines. We compare the effectiveness of two dictionary-based classifiers for extracting correct GO answers from a large set of 100 retrieved abstracts per question. In the same way, we also investigate the power of GOCat, a GO supervised classifier. GOCat exploits the GOA database to propose GO concepts that were annotated by curators for similar abstracts. This approach is called deep QA, as it adds an original classification step, and exploits curated biological data to infer answers, which are not explicitly mentioned in the retrieved documents. We show that for complex answers such as protein functional descriptions, the redundancy phenomenon has a limited effect. Similarly usual dictionary-based approaches are relatively ineffective. In contrast, we demonstrate how existing curated data, beyond information extraction, can be exploited by a supervised classifier, such as GOCat, to massively improve both the quantity and the quality of the answers with a +100% improvement for both recall and precision. Database URL: http://eagl.unige.ch/DeepQA4PA/. PMID:26384372

  7. COGNIZER: A Framework for Functional Annotation of Metagenomic Datasets

    PubMed Central

    Bose, Tungadri; Haque, Mohammed Monzoorul; Reddy, CVSK; Mande, Sharmila S.

    2015-01-01

    Background Recent advances in sequencing technologies have resulted in an unprecedented increase in the number of metagenomes that are being sequenced world-wide. Given their volume, functional annotation of metagenomic sequence datasets requires specialized computational tools/techniques. In spite of having high accuracy, existing stand-alone functional annotation tools necessitate end-users to perform compute-intensive homology searches of metagenomic datasets against "multiple" databases prior to functional analysis. Although, web-based functional annotation servers address to some extent the problem of availability of compute resources, uploading and analyzing huge volumes of sequence data on a shared public web-service has its own set of limitations. In this study, we present COGNIZER, a comprehensive stand-alone annotation framework which enables end-users to functionally annotate sequences constituting metagenomic datasets. The COGNIZER framework provides multiple workflow options. A subset of these options employs a novel directed-search strategy which helps in reducing the overall compute requirements for end-users. The COGNIZER framework includes a cross-mapping database that enables end-users to simultaneously derive/infer KEGG, Pfam, GO, and SEED subsystem information from the COG annotations. Results Validation experiments performed with real-world metagenomes and metatranscriptomes, generated using diverse sequencing technologies, indicate that the novel directed-search strategy employed in COGNIZER helps in reducing the compute requirements without significant loss in annotation accuracy. A comparison of COGNIZER's results with pre-computed benchmark values indicate the reliability of the cross-mapping database employed in COGNIZER. Conclusion The COGNIZER framework is capable of comprehensively annotating any metagenomic or metatranscriptomic dataset from varied sequencing platforms in functional terms. Multiple search options in COGNIZER provide

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

    PubMed Central

    2011-01-01

    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 information to be specified as

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

    PubMed Central

    Thompson, Paul; Iqbal, Syed A; McNaught, John; Ananiadou, Sophia

    2009-01-01

    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 viably be used to train IE

  10. Comprehensive comparative homeobox gene annotation in human and mouse

    PubMed Central

    Wilming, Laurens G.; Boychenko, Veronika; Harrow, Jennifer L.

    2015-01-01

    Homeobox genes are a group of genes coding for transcription factors with a DNA-binding helix-turn-helix structure called a homeodomain and which play a crucial role in pattern formation during embryogenesis. Many homeobox genes are located in clusters and some of these, most notably the HOX genes, are known to have antisense or opposite strand long non-coding RNA (lncRNA) genes that play a regulatory role. Because automated annotation of both gene clusters and non-coding genes is fraught with difficulty (over-prediction, under-prediction, inaccurate transcript structures), we set out to manually annotate all homeobox genes in the mouse and human genomes. This includes all supported splice variants, pseudogenes and both antisense and flanking lncRNAs. One of the areas where manual annotation has a significant advantage is the annotation of duplicated gene clusters. After comprehensive annotation of all homeobox genes and their antisense genes in human and in mouse, we found some discrepancies with the current gene set in RefSeq regarding exact gene structures and coding versus pseudogene locus biotype. We also identified previously un-annotated pseudogenes in the DUX, Rhox and Obox gene clusters, which helped us re-evaluate and update the gene nomenclature in these regions. We found that human homeobox genes are enriched in antisense lncRNA loci, some of which are known to play a role in gene or gene cluster regulation, compared to their mouse orthologues. Of the annotated set of 241 human protein-coding homeobox genes, 98 have an antisense locus (41%) while of the 277 orthologous mouse genes, only 62 protein coding gene have an antisense locus (22%), based on publicly available transcriptional evidence. PMID:26412852

  11. Segmented heat exchanger

    DOEpatents

    Baldwin, Darryl Dean; Willi, Martin Leo; Fiveland, Scott Byron; Timmons, Kristine Ann

    2010-12-14

    A segmented heat exchanger system for transferring heat energy from an exhaust fluid to a working fluid. The heat exchanger system may include a first heat exchanger for receiving incoming working fluid and the exhaust fluid. The working fluid and exhaust fluid may travel through at least a portion of the first heat exchanger in a parallel flow configuration. In addition, the heat exchanger system may include a second heat exchanger for receiving working fluid from the first heat exchanger and exhaust fluid from a third heat exchanger. The working fluid and exhaust fluid may travel through at least a portion of the second heat exchanger in a counter flow configuration. Furthermore, the heat exchanger system may include a third heat exchanger for receiving working fluid from the second heat exchanger and exhaust fluid from the first heat exchanger. The working fluid and exhaust fluid may travel through at least a portion of the third heat exchanger in a parallel flow configuration.

  12. Integrative annotation of chromatin elements from ENCODE data

    PubMed Central

    Hoffman, Michael M.; Ernst, Jason; Wilder, Steven P.; Kundaje, Anshul; Harris, Robert S.; Libbrecht, Max; Giardine, Belinda; Ellenbogen, Paul M.; Bilmes, Jeffrey A.; Birney, Ewan; Hardison, Ross C.; Dunham, Ian; Kellis, Manolis; Noble, William Stafford

    2013-01-01

    The ENCODE Project has generated a wealth of experimental information mapping diverse chromatin properties in several human cell lines. Although each such data track is independently informative toward the annotation of regulatory elements, their interrelations contain much richer information for the systematic annotation of regulatory elements. To uncover these interrelations and to generate an interpretable summary of the massive datasets of the ENCODE Project, we apply unsupervised learning methodologies, converting dozens of chromatin datasets into discrete annotation maps of regulatory regions and other chromatin elements across the human genome. These methods rediscover and summarize diverse aspects of chromatin architecture, elucidate the interplay between chromatin activity and RNA transcription, and reveal that a large proportion of the genome lies in a quiescent state, even across multiple cell types. The resulting annotation of non-coding regulatory elements correlate strongly with mammalian evolutionary constraint, and provide an unbiased approach for evaluating metrics of evolutionary constraint in human. Lastly, we use the regulatory annotations to revisit previously uncharacterized disease-associated loci, resulting in focused, testable hypotheses through the lens of the chromatin landscape. PMID:23221638

  13. Dizeez: an online game for human gene-disease annotation.

    PubMed

    Loguercio, Salvatore; Good, Benjamin M; Su, Andrew I

    2013-01-01

    Structured gene annotations are a foundation upon which many bioinformatics and statistical analyses are built. However the structured annotations available in public databases are a sparse representation of biological knowledge as a whole. The rate of biomedical data generation is such that centralized biocuration efforts struggle to keep up. New models for gene annotation need to be explored that expand the pace at which we are able to structure biomedical knowledge. Recently, online games have emerged as an effective way to recruit, engage and organize large numbers of volunteers to help address difficult biological challenges. For example, games have been successfully developed for protein folding (Foldit), multiple sequence alignment (Phylo) and RNA structure design (EteRNA). Here we present Dizeez, a simple online game built with the purpose of structuring knowledge of gene-disease associations. Preliminary results from game play online and at scientific conferences suggest that Dizeez is producing valid gene-disease annotations not yet present in any public database. These early results provide a basic proof of principle that online games can be successfully applied to the challenge of gene annotation. Dizeez is available at http://genegames.org. PMID:23951102

  14. Metadata and Annotations for Multi-scale Electrophysiological Data

    PubMed Central

    Bower, Mark R.; Stead, Matt; Brinkmann, Benjamin H.; Dufendach, Kevin; Worrell, Gregory A.

    2010-01-01

    The increasing use of high-frequency (kHz), long-duration (days) intracranial monitoring from multiple electrodes during pre-surgical evaluation for epilepsy produces large amounts of data that are challenging to store and maintain. Descriptive metadata and clinical annotations of these large data sets also pose challenges to simple, often manual, methods of data analysis. The problems of reliable communication of metadata and annotations between programs, the maintenance of the meanings within that information over long time periods, and the flexibility to re-sort data for analysis place differing demands on data structures and algorithms. Solutions to these individual problem domains (communication, storage and analysis) can be configured to provide easy translation and clarity across the domains. The Multi-scale Annotation Format (MAF) provides an integrated metadata and annotation environment that maximizes code reuse, minimizes error probability and encourages future changes by reducing the tendency to over-fit information technology solutions to current problems. An example of a graphical utility for generating and evaluating metadata and annotations for “big data” files is presented. PMID:19964266

  15. Dizeez: An Online Game for Human Gene-Disease Annotation

    PubMed Central

    Loguercio, Salvatore; Good, Benjamin M.; Su, Andrew I.

    2013-01-01

    Structured gene annotations are a foundation upon which many bioinformatics and statistical analyses are built. However the structured annotations available in public databases are a sparse representation of biological knowledge as a whole. The rate of biomedical data generation is such that centralized biocuration efforts struggle to keep up. New models for gene annotation need to be explored that expand the pace at which we are able to structure biomedical knowledge. Recently, online games have emerged as an effective way to recruit, engage and organize large numbers of volunteers to help address difficult biological challenges. For example, games have been successfully developed for protein folding (Foldit), multiple sequence alignment (Phylo) and RNA structure design (EteRNA). Here we present Dizeez, a simple online game built with the purpose of structuring knowledge of gene-disease associations. Preliminary results from game play online and at scientific conferences suggest that Dizeez is producing valid gene-disease annotations not yet present in any public database. These early results provide a basic proof of principle that online games can be successfully applied to the challenge of gene annotation. Dizeez is available at http://genegames.org. PMID:23951102

  16. Annotations of Mexican bullfighting videos for semantic index

    NASA Astrophysics Data System (ADS)

    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.

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

    NASA Astrophysics Data System (ADS)

    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.

  18. The Rice Annotation Project Database (RAP-DB): 2008 update.

    PubMed

    Tanaka, Tsuyoshi; Antonio, Baltazar A; Kikuchi, Shoshi; Matsumoto, Takashi; Nagamura, Yoshiaki; Numa, Hisataka; Sakai, Hiroaki; Wu, Jianzhong; Itoh, Takeshi; Sasaki, Takuji; Aono, Ryo; Fujii, Yasuyuki; Habara, Takuya; Harada, Erimi; Kanno, Masako; Kawahara, Yoshihiro; Kawashima, Hiroaki; Kubooka, Hiromi; Matsuya, Akihiro; Nakaoka, Hajime; Saichi, Naomi; Sanbonmatsu, Ryoko; Sato, Yoshiharu; Shinso, Yuji; Suzuki, Mami; Takeda, Jun-ichi; Tanino, Motohiko; Todokoro, Fusano; Yamaguchi, Kaori; Yamamoto, Naoyuki; Yamasaki, Chisato; Imanishi, Tadashi; Okido, Toshihisa; Tada, Masahito; Ikeo, Kazuho; Tateno, Yoshio; Gojobori, Takashi; Lin, Yao-Cheng; Wei, Fu-Jin; Hsing, Yue-ie; Zhao, Qiang; Han, Bin; Kramer, Melissa R; McCombie, Richard W; Lonsdale, David; O'Donovan, Claire C; Whitfield, Eleanor J; Apweiler, Rolf; Koyanagi, Kanako O; Khurana, Jitendra P; Raghuvanshi, Saurabh; Singh, Nagendra K; Tyagi, Akhilesh K; Haberer, Georg; Fujisawa, Masaki; Hosokawa, Satomi; Ito, Yukiyo; Ikawa, Hiroshi; Shibata, Michie; Yamamoto, Mayu; Bruskiewich, Richard M; Hoen, Douglas R; Bureau, Thomas E; Namiki, Nobukazu; Ohyanagi, Hajime; Sakai, Yasumichi; Nobushima, Satoshi; Sakata, Katsumi; Barrero, Roberto A; Sato, Yutaka; Souvorov, Alexandre; Smith-White, Brian; Tatusova, Tatiana; An, Suyoung; An, Gynheung; OOta, Satoshi; Fuks, Galina; Fuks, Galina; Messing, Joachim; Christie, Karen R; Lieberherr, Damien; Kim, HyeRan; Zuccolo, Andrea; Wing, Rod A; Nobuta, Kan; Green, Pamela J; Lu, Cheng; Meyers, Blake C; Chaparro, Cristian; Piegu, Benoit; Panaud, Olivier; Echeverria, Manuel

    2008-01-01

    The Rice Annotation Project Database (RAP-DB) was created to provide the genome sequence assembly of the International Rice Genome Sequencing Project (IRGSP), manually curated annotation of the sequence, and other genomics information that could be useful for comprehensive understanding of the rice biology. Since the last publication of the RAP-DB, the IRGSP genome has been revised and reassembled. In addition, a large number of rice-expressed sequence tags have been released, and functional genomics resources have been produced worldwide. Thus, we have thoroughly updated our genome annotation by manual curation of all the functional descriptions of rice genes. The latest version of the RAP-DB contains a variety of annotation data as follows: clone positions, structures and functions of 31 439 genes validated by cDNAs, RNA genes detected by massively parallel signature sequencing (MPSS) technology and sequence similarity, flanking sequences of mutant lines, transposable elements, etc. Other annotation data such as Gnomon can be displayed along with those of RAP for comparison. We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/. PMID:18089549

  19. Anatomical annotation on vascular structure in volume rendered images.

    PubMed

    Jiang, Zhengang; Nimura, Yukitaka; Hayashi, Yuichiro; Kitasaka, Takayuki; Misawa, Kazunari; Fujiwara, Michitaka; Kajita, Yasukazu; Wakabayashi, Toshihiko; Mori, Kensaku

    2013-03-01

    The precise annotation of vascular structure is desired in computer-assisted systems to help surgeons identify each vessel branch. This paper proposes a method that annotates vessels on volume rendered images by rendering their names on them using a two-pass rendering process. In the first rendering pass, vessel surface models are generated using such properties as centerlines, radii, and running directions. Then the vessel names are drawn on the vessel surfaces. Finally, the vessel name images and the corresponding depth buffer are generated by a virtual camera at the viewpoint. In the second rendering pass, volume rendered images are generated by a ray casting volume rendering algorithm that considers the depth buffer generated in the first rendering pass. After the two-pass rendering is finished, an annotated image is generated by blending the volume rendered image with the surface rendered image. To confirm the effectiveness of our proposed method, we performed a computer-assisted system for the automated annotation of abdominal arteries. The experimental results show that vessel names can be drawn on the corresponding vessel surface in the volume rendered images at a computing cost that is nearly the same as that by volume rendering only. The proposed method has enormous potential to be adopted to annotate the vessels in the 3D medical images in clinical applications, such as image-guided surgery. PMID:23562139

  20. WEGO: a web tool for plotting GO annotations.

    PubMed

    Ye, Jia; Fang, Lin; Zheng, Hongkun; Zhang, Yong; Chen, Jie; Zhang, Zengjin; Wang, Jing; Li, Shengting; Li, Ruiqiang; Bolund, Lars; Wang, Jun

    2006-07-01

    Unified, structured vocabularies and classifications freely provided by the Gene Ontology (GO) Consortium are widely accepted in most of the large scale gene annotation projects. Consequently, many tools have been created for use with the GO ontologies. WEGO (Web Gene Ontology Annotation Plot) is a simple but useful tool for visualizing, comparing and plotting GO annotation results. Different from other commercial software for creating chart, WEGO is designed to deal with the directed acyclic graph structure of GO to facilitate histogram creation of GO annotation results. WEGO has been used widely in many important biological research projects, such as the rice genome project and the silkworm genome project. It has become one of the daily tools for downstream gene annotation analysis, especially when performing comparative genomics tasks. WEGO, along with the two other tools, namely External to GO Query and GO Archive Query, are freely available for all users at http://wego.genomics.org.cn. There are two available mirror sites at http://wego2.genomics.org.cn and http://wego.genomics.com.cn. Any suggestions are welcome at wego@genomics.org.cn. PMID:16845012

  1. APPRIS: annotation of principal and alternative splice isoforms.

    PubMed

    Rodriguez, Jose Manuel; Maietta, Paolo; Ezkurdia, Iakes; Pietrelli, Alessandro; Wesselink, Jan-Jaap; Lopez, Gonzalo; Valencia, Alfonso; Tress, Michael L

    2013-01-01

    Here, we present APPRIS (http://appris.bioinfo.cnio.es), a database that houses annotations of human splice isoforms. APPRIS has been designed to provide value to manual annotations of the human genome by adding reliable protein structural and functional data and information from cross-species conservation. The visual representation of the annotations provided by APPRIS for each gene allows annotators and researchers alike to easily identify functional changes brought about by splicing events. In addition to collecting, integrating and analyzing reliable predictions of the effect of splicing events, APPRIS also selects a single reference sequence for each gene, here termed the principal isoform, based on the annotations of structure, function and conservation for each transcript. APPRIS identifies a principal isoform for 85% of the protein-coding genes in the GENCODE 7 release for ENSEMBL. Analysis of the APPRIS data shows that at least 70% of the alternative (non-principal) variants would lose important functional or structural information relative to the principal isoform. PMID:23161672

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

    ERIC Educational Resources Information Center

    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…

  3. Semantic Reasoning with Image Annotations for Tumor Assessment

    PubMed Central

    Levy, Mia A.; O’Connor, Martin J.; Rubin, Daniel L.

    2009-01-01

    Identifying, tracking and reasoning about tumor lesions is a central task in cancer research and clinical practice that could potentially be automated. However, information about tumor lesions in imaging studies is not easily accessed by machines for automated reasoning. The Annotation and Image Markup (AIM) information model recently developed for the cancer Biomedical Informatics Grid provides a method for encoding the semantic information related to imaging findings, enabling their storage and transfer. However, it is currently not possible to apply automated reasoning methods to image information encoded in AIM. We have developed a methodology and a suite of tools for transforming AIM image annotations into OWL, and an ontology for reasoning with the resulting image annotations for tumor lesion assessment. Our methods enable automated inference of semantic information about cancer lesions in images. PMID:20351880

  4. CRISPRdigger: detecting CRISPRs with better direct repeat annotations

    PubMed Central

    Ge, Ruiquan; Mai, Guoqin; Wang, Pu; Zhou, Manli; Luo, Youxi; Cai, Yunpeng; Zhou, Fengfeng

    2016-01-01

    Clustered regularly interspaced short palindromic repeats (CRISPRs) are important genetic elements in many bacterial and archaeal genomes, and play a key role in prokaryote immune systems’ fight against invasive foreign elements. The CRISPR system has also been engineered to facilitate target gene editing in eukaryotic genomes. Using the common features of mis-annotated CRISPRs in prokaryotic genomes, this study proposed an accurate de novo CRISPR annotation program CRISPRdigger, which can take a partially assembled genome as its input. A comprehensive comparison with the three existing programs demonstrated that CRISPRdigger can recover more Direct Repeats (DRs) for CRISPRs and achieve a higher accuracy for a query genome. The program was implemented by Perl and all the parameters had default values, so that a user could annotate CRISPRs in a query genome by supplying only a genome sequence in the FASTA format. All the supplementary data are available at http://www.healthinformaticslab.org/supp/. PMID:27596864

  5. Annotation of the Protein Coding Regions of the Equine Genome

    PubMed Central

    Hestand, Matthew S.; Kalbfleisch, Theodore S.; Coleman, Stephen J.; Zeng, Zheng; Liu, Jinze; Orlando, Ludovic; MacLeod, James N.

    2015-01-01

    Current gene annotation of the horse genome is largely derived from in silico predictions and cross-species alignments. Only a small number of genes are annotated based on equine EST and mRNA sequences. To expand the number of equine genes annotated from equine experimental evidence, we sequenced mRNA from a pool of forty-three different tissues. From these, we derived the structures of 68,594 transcripts. In addition, we identified 301,829 positions with SNPs or small indels within these transcripts relative to EquCab2. Interestingly, 780 variants extend the open reading frame of the transcript and appear to be small errors in the equine reference genome, since they are also identified as homozygous variants by genomic DNA resequencing of the reference horse. Taken together, we provide a resource of equine mRNA structures and protein coding variants that will enhance equine and cross-species transcriptional and genomic comparisons. PMID:26107351

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

    PubMed

    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

  7. Micro-structural tissue analysis for automatic histopathological image annotation.

    PubMed

    Díaz, Gloria; Romero, Eduardo

    2012-03-01

    This article presents a new approach for extracting high level semantic concepts from digital histopathological images. This strategy provides not only annotation of several biological concepts, but also a coarse location of these concepts. The proposed approach is composed of five main steps: (1) a stain decomposition stage, which separates the contribution of hematoxylin and eosin dyes, (2) a color standardization that corrects color image differences, (3) a part-based representation, which describes the image in terms of the conditional probability of relevant local patches, selected by their stain contributions, (4) a discriminative classification model, which bridges out the found patterns and the biological concepts, (5) a block-based annotation strategy that identifies the multiple biological concepts within an image. A set of 655 skin images, containing 10 biological concepts of skin tissues were used for assessing the proposed approach, obtaining a sensitivity of 84% and a specificity of 67% when annotating images with multiple concepts. PMID:21997952

  8. Comparative genomics and functional annotation of bacterial transporters

    NASA Astrophysics Data System (ADS)

    Gelfand, Mikhail S.; Rodionov, Dmitry A.

    2008-03-01

    Transport proteins are difficult to study experimentally, and because of that their functional characterization trails that of enzymes. The comparative genomic analysis is a powerful approach to functional annotation of proteins, which makes it possible to utilize the genomic sequence data from thousands of organisms. The use of computational techniques allows one to identify candidate transporters, predict their structure and localization in the membrane, and perform detailed functional annotation, which includes substrate specificity and cellular role. We overview the main techniques of analysis of transporters' structure and function. We consider the most popular algorithms to identify transmembrane segments in protein sequences and to predict topology of multispanning proteins. We describe the main approaches of the comparative genomics, and how they may be applied to the analysis of transporters, and provide examples showing how combinations of these techniques is used for functional annotation of new transporter specificities in known families, characterization of new families, and prediction of novel transport mechanisms.

  9. Use of Annotations for Component and Framework Interoperability

    NASA Astrophysics Data System (ADS)

    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

  10. Functional annotation of hypothetical proteins – A review

    PubMed Central

    Sivashankari, Selvarajan; Shanmughavel, Piramanayagam

    2006-01-01

    The complete human genome sequences in the public database provide ways to understand the blue print of life. As of June 29, 2006, 27 archaeal, 326 bacterial and 21 eukaryotes is complete genomes are available and the sequencing for 316 bacterial, 24 archaeal, 126 eukaryotic genomes are in progress. The traditional biochemical/molecular experiments can assign accurate functions for genes in these genomes. However, the process is time-consuming and costly. Despite several efforts, only 50-60 % of genes have been annotated in most completely sequenced genomes. Automated genome sequence analysis and annotation may provide ways to understand genomes. Thus, determination of protein function is one of the challenging problems of the post-genome era. This demands bioinformatics to predict functions of un-annotated protein sequences by developing efficient tools. Here, we discuss some of the recent and popular approaches developed in Bioinformatics to predict functions for hypothetical proteins. PMID:17597916

  11. Linking genome-scale metabolic modeling and genome annotation

    PubMed Central

    Blais, Edik M.; Chavali, Arvind K.; Papin, Jason A.

    2014-01-01

    Summary Genome-scale metabolic network reconstructions, assembled from annotated genomes, serve as a platform for integrating data from heterogeneous sources and generating hypotheses for further experimental validation. Implementing constraint-based modeling techniques such as Flux Balance Analysis (FBA) on network reconstructions allow for interrogating metabolism at a systems-level, which aids in identifying and rectifying gaps in knowledge. With genome sequences for various organisms from prokaryotes to eukaryotes becoming increasingly available, a significant bottleneck lies in the structural and functional annotation of these sequences. Using topologically-based and biologically-inspired metabolic network refinement, we can better characterize enzymatic functions present in an organism and link annotation of these functions to candidate transcripts, both steps that can be experimentally validated. PMID:23417799

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

    PubMed

    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

  13. Scripps Genome ADVISER: Annotation and Distributed Variant Interpretation SERver

    PubMed Central

    Pham, Phillip H.; Shipman, William J.; Erikson, Galina A.; Schork, Nicholas J.; Torkamani, Ali

    2015-01-01

    Interpretation of human genomes is a major challenge. We present the Scripps Genome ADVISER (SG-ADVISER) suite, which aims to fill the gap between data generation and genome interpretation by performing holistic, in-depth, annotations and functional predictions on all variant types and effects. The SG-ADVISER suite includes a de-identification tool, a variant annotation web-server, and a user interface for inheritance and annotation-based filtration. SG-ADVISER allows users with no bioinformatics expertise to manipulate large volumes of variant data with ease – without the need to download large reference databases, install software, or use a command line interface. SG-ADVISER is freely available at genomics.scripps.edu/ADVISER. PMID:25706643

  14. CRISPRdigger: detecting CRISPRs with better direct repeat annotations.

    PubMed

    Ge, Ruiquan; Mai, Guoqin; Wang, Pu; Zhou, Manli; Luo, Youxi; Cai, Yunpeng; Zhou, Fengfeng

    2016-01-01

    Clustered regularly interspaced short palindromic repeats (CRISPRs) are important genetic elements in many bacterial and archaeal genomes, and play a key role in prokaryote immune systems' fight against invasive foreign elements. The CRISPR system has also been engineered to facilitate target gene editing in eukaryotic genomes. Using the common features of mis-annotated CRISPRs in prokaryotic genomes, this study proposed an accurate de novo CRISPR annotation program CRISPRdigger, which can take a partially assembled genome as its input. A comprehensive comparison with the three existing programs demonstrated that CRISPRdigger can recover more Direct Repeats (DRs) for CRISPRs and achieve a higher accuracy for a query genome. The program was implemented by Perl and all the parameters had default values, so that a user could annotate CRISPRs in a query genome by supplying only a genome sequence in the FASTA format. All the supplementary data are available at http://www.healthinformaticslab.org/supp/. PMID:27596864

  15. Incorporating Non-Coding Annotations into Rare Variant Analysis

    PubMed Central

    Richardson, Tom G.; Campbell, Colin; Timpson, Nicholas J; Gaunt, Tom R.

    2016-01-01

    Background The success of collapsing methods which investigate the combined effect of rare variants on complex traits has so far been limited. The manner in which variants within a gene are selected prior to analysis has a crucial impact on this success, which has resulted in analyses conventionally filtering variants according to their consequence. This study investigates whether an alternative approach to filtering, using annotations from recently developed bioinformatics tools, can aid these types of analyses in comparison to conventional approaches. Methods & Results We conducted a candidate gene analysis using the UK10K sequence and lipids data, filtering according to functional annotations using the resource CADD (Combined Annotation-Dependent Depletion) and contrasting results with ‘nonsynonymous’ and ‘loss of function’ consequence analyses. Using CADD allowed the inclusion of potentially deleterious intronic variants, which was not possible when filtering by consequence. Overall, different filtering approaches provided similar evidence of association, although filtering according to CADD identified evidence of association between ANGPTL4 and High Density Lipoproteins (P = 0.02, N = 3,210) which was not observed in the other analyses. We also undertook genome-wide analyses to determine how filtering in this manner compared to conventional approaches for gene regions. Results suggested that filtering by annotations according to CADD, as well as other tools known as FATHMM-MKL and DANN, identified association signals not detected when filtering by variant consequence and vice versa. Conclusion Incorporating variant annotations from non-coding bioinformatics tools should prove to be a valuable asset for rare variant analyses in the future. Filtering by variant consequence is only possible in coding regions of the genome, whereas utilising non-coding bioinformatics annotations provides an opportunity to discover unknown causal variants in non

  16. Determining similarity of scientific entities in annotation datasets.

    PubMed

    Palma, Guillermo; Vidal, Maria-Esther; Haag, Eric; Raschid, Louiqa; Thor, Andreas

    2015-01-01

    Linked Open Data initiatives have made available a diversity of scientific collections where scientists have annotated entities in the datasets with controlled vocabulary terms from ontologies. Annotations encode scientific knowledge, which is captured in annotation datasets. Determining relatedness between annotated entities becomes a building block for pattern mining, e.g. identifying drug-drug relationships may depend on the similarity of the targets that interact with each drug. A diversity of similarity measures has been proposed in the literature to compute relatedness between a pair of entities. Each measure exploits some knowledge including the name, function, relationships with other entities, taxonomic neighborhood and semantic knowledge. We propose a novel general-purpose annotation similarity measure called 'AnnSim' that measures the relatedness between two entities based on the similarity of their annotations. We model AnnSim as a 1-1 maximum weight bipartite match and exploit properties of existing solvers to provide an efficient solution. We empirically study the performance of AnnSim on real-world datasets of drugs and disease associations from clinical trials and relationships between drugs and (genomic) targets. Using baselines that include a variety of measures, we identify where AnnSim can provide a deeper understanding of the semantics underlying the relatedness of a pair of entities or where it could lead to predicting new links or identifying potential novel patterns. Although AnnSim does not exploit knowledge or properties of a particular domain, its performance compares well with a variety of state-of-the-art domain-specific measures. Database URL: http://www.yeastgenome.org/ PMID:25725057

  17. Determining similarity of scientific entities in annotation datasets

    PubMed Central

    Palma, Guillermo; Vidal, Maria-Esther; Haag, Eric; Raschid, Louiqa; Thor, Andreas

    2015-01-01

    Linked Open Data initiatives have made available a diversity of scientific collections where scientists have annotated entities in the datasets with controlled vocabulary terms from ontologies. Annotations encode scientific knowledge, which is captured in annotation datasets. Determining relatedness between annotated entities becomes a building block for pattern mining, e.g. identifying drug–drug relationships may depend on the similarity of the targets that interact with each drug. A diversity of similarity measures has been proposed in the literature to compute relatedness between a pair of entities. Each measure exploits some knowledge including the name, function, relationships with other entities, taxonomic neighborhood and semantic knowledge. We propose a novel general-purpose annotation similarity measure called ‘AnnSim’ that measures the relatedness between two entities based on the similarity of their annotations. We model AnnSim as a 1–1 maximum weight bipartite match and exploit properties of existing solvers to provide an efficient solution. We empirically study the performance of AnnSim on real-world datasets of drugs and disease associations from clinical trials and relationships between drugs and (genomic) targets. Using baselines that include a variety of measures, we identify where AnnSim can provide a deeper understanding of the semantics underlying the relatedness of a pair of entities or where it could lead to predicting new links or identifying potential novel patterns. Although AnnSim does not exploit knowledge or properties of a particular domain, its performance compares well with a variety of state-of-the-art domain-specific measures. Database URL: http://www.yeastgenome.org/ PMID:25725057

  18. Finding seed points for organ segmentation using example annotations

    NASA Astrophysics Data System (ADS)

    Joyseeree, Ranveer; Müller, Henning

    2014-03-01

    Organ segmentation is important in diagnostic medicine to make current decision-support tools more effective and efficient. Performing it automatically can save time and labor. In this paper, a method to perform automatic identification of seed points for the segmentation of organs in three-dimensional (3D) non-annotated, full- body magnetic resonance (MR) and computed tomography (CT) volumes is presented. It uses 3D MR and CT acquisitions along with corresponding organ annotations from the Visual Concept Extraction Challenge in Radiology (VISCERAL) banchmark. A training MR or CT volume is first registered affinely with a carefully-chosen reference volume. The registration transform obtained is then used to warp the annotations accompanying that training volume. The process is repeated for several other training volumes. For each organ of interest, an overlap volume is created by merging the warped training annotations corresponding to it. Next, a 3D probability map for organ location on the reference volume is derived from each overlap volume. The centroid of each probability map is determined and it represents a suitable seed point for segmentation of each organ. Afterwards, the reference volume can be affinely mapped onto any non-annotated volume and the mapping applied to the pre-computed volume containing the centroid and the probability distribution for an organ of interest. Segmentation on the non-annotated volume may then be started using existing region-growing segmentation algorithms with the warped centroid as the seed point and the warped probability distribution as an aid to the stopping criterion. The approach yields very promising results.

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

    PubMed

    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

  20. 3D annotation and manipulation of medical anatomical structures

    NASA Astrophysics Data System (ADS)

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

    2009-02-01

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

  1. Educator Exchange Resource Guide.

    ERIC Educational Resources Information Center

    Garza, Cris; Rodriguez, Victor

    This resource guide was developed for teachers and administrators interested in participating in intercultural and international exchange programs or starting an exchange program. An analysis of an exchange program's critical elements discusses exchange activities; orientation sessions; duration of exchange; criteria for participation; travel,…

  2. Ontology-Based Annotation of Brain MRI Images

    PubMed Central

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

    2008-01-01

    This paper describes a hybrid system for annotating anatomical structures in brain Magnetic Resonance Images. The system involves both numerical knowledge from an atlas and symbolic knowledge represented in a rule-extended ontology, written in standard web languages, and symbolic constraints. The system combines this knowledge with graphical data automatically extracted from the images. The annotations of the parts of sulci and of gyri located in a region of interest selected by the user are obtained with a reasoning based on a Constraint Satisfaction Problem solving combined with Description Logics inference services. The first results obtained with both normal and pathological data are promising. PMID:18998967

  3. MICROTASK CROWDSOURCING FOR DISEASE MENTION ANNOTATION IN PUBMED ABSTRACTS

    PubMed Central

    Good, Benjamin M; Nanis, Max; Wu, Chunlei; Su, Andrew I

    2014-01-01

    Identifying concepts and relationships in biomedical text enables knowledge to be applied in computational analyses. Many biological natural language processing (BioNLP) projects attempt to address this challenge, but the state of the art still leaves much room for improvement. Progress in BioNLP research depends on large, annotated corpora for evaluating information extraction systems and training machine learning models. Traditionally, such corpora are created by small numbers of expert annotators often working over extended periods of time. Recent studies have shown that workers on microtask crowdsourcing platforms such as Amazon’s Mechanical Turk (AMT) can, in aggregate, generate high-quality annotations of biomedical text. Here, we investigated the use of the AMT in capturing disease mentions in PubMed abstracts. We used the NCBI Disease corpus as a gold standard for refining and benchmarking our crowdsourcing protocol. After several iterations, we arrived at a protocol that reproduced the annotations of the 593 documents in the ‘training set’ of this gold standard with an overall F measure of 0.872 (precision 0.862, recall 0.883). The output can also be tuned to optimize for precision (max = 0.984 when recall = 0.269) or recall (max = 0.980 when precision = 0.436). Each document was completed by 15 workers, and their annotations were merged based on a simple voting method. In total 145 workers combined to complete all 593 documents in the span of 9 days at a cost of $.066 per abstract per worker. The quality of the annotations, as judged with the F measure, increases with the number of workers assigned to each task; however minimal performance gains were observed beyond 8 workers per task. These results add further evidence that microtask crowdsourcing can be a valuable tool for generating well-annotated corpora in BioNLP. Data produced for this analysis are available at http://figshare.com/articles/Disease_Mention_Annotation

  4. Biocuration of functional annotation at the European nucleotide archive

    PubMed Central

    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

  5. Knowledge Representation and Management. From Ontology to Annotation

    PubMed Central

    Darmoni, S.J.

    2015-01-01

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

  6. Protein function annotation using protein domain family resources.

    PubMed

    Das, Sayoni; Orengo, Christine A

    2016-01-15

    As a result of the genome sequencing and structural genomics initiatives, we have a wealth of protein sequence and structural data. However, only about 1% of these proteins have experimental functional annotations. As a result, computational approaches that can predict protein functions are essential in bridging this widening annotation gap. This article reviews the current approaches of protein function prediction using structure and sequence based classification of protein domain family resources with a special focus on functional families in the CATH-Gene3D resource. PMID:26434392

  7. ONEMercury: Towards Automatic Annotation of Earth Science Metadata

    NASA Astrophysics Data System (ADS)

    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. Application of Annotated Logic Program to Pipeline Process Safety Verification

    NASA Astrophysics Data System (ADS)

    Nakamatsu, Kazumi

    We have developed a paraconsistent annotated logic program called Extended Vector Annotated Logic Program with Strong Negation (abbr. EVALPSN), which can deal with defeasible deontic reasoning and contradiction, and we have already applied it to safety verification and control such as railway interlocking safety verification and traffic signal control. In this paper, we introduce process safety verification as an application of EVALPSN with a small example for brewery pipeline valve control. The safety verification control is based on EVALPSN defeasible deontic reasoning to avoid unexpected mix of different sorts of liquid in pipeline networks.

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

    PubMed Central

    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 bookmarking. The CATMAID interface enables synchronized navigation through multiple registered datasets even at vastly different scales such as in comparisons between optical and electron microscopy. Availability: http://fly.mpi-cbg.de/catmaid Contact: tomancak@mpi-cbg.de PMID:19376822

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

    PubMed

    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. Efficient assembly and annotation of the transcriptome of catfish by RNA-seq analysis of a doubled haploid homozygote

    Technology Transfer Automated Retrieval System (TEKTRAN)

    Upon the completion of whole genome sequencing, thorough genome annotation that associates genome sequences with biological meanings is essential. Genome annotation depends on the availability of transcript information as well as orthology information. In teleost fish, genome annotation is seriousl...

  12. Corrosive resistant heat exchanger

    DOEpatents

    Richlen, Scott L.

    1989-01-01

    A corrosive and errosive resistant heat exchanger which recovers heat from a contaminated heat stream. The heat exchanger utilizes a boundary layer of innocuous gas, which is continuously replenished, to protect the heat exchanger surface from the hot contaminated gas. The innocuous gas is conveyed through ducts or perforations in the heat exchanger wall. Heat from the heat stream is transferred by radiation to the heat exchanger wall. Heat is removed from the outer heat exchanger wall by a heat recovery medium.

  13. Asynchronous multimedia annotations for web-based collaboration in biology education

    NASA Astrophysics Data System (ADS)

    Petkovic, Dragutin; Lank, E.; Ramirez, F. A.; Raghavendra, S.; Chen, F.; Pekiner, C.; Fregoso, A.; Marquez, A.

    2004-12-01

    The focus of this paper is on the design, implementation, and validation of asynchronous multimedia annotations designed for Web-based collaboration in educational and research settings. The two key questions we explore in this paper are: How useful are such annotations and what purpose do annotations serve? What is the ease of use of our specific implementation of annotations? The context of our project has been in the area of multimedia information usage and collaboration in the biological sciences. We have developed asynchronous annotations for HTML and image data. Our annotations can be executed via any browser and require no downloads. They are stored in a central database allowing search and asynchronous access by all registered users. An easy to use user interface allows users to add, view and search annotations. We also performed a usability study that showed that our implementation of text annotations to validate our implementation.

  14. Asynchronous multimedia annotations for web-based collaboration in biology education

    NASA Astrophysics Data System (ADS)

    Petkovic, Dragutin; Lank, E.; Ramirez, F. A.; Raghavendra, S.; Chen, F.; Pekiner, C.; Fregoso, A.; Marquez, A.

    2005-01-01

    The focus of this paper is on the design, implementation, and validation of asynchronous multimedia annotations designed for Web-based collaboration in educational and research settings. The two key questions we explore in this paper are: How useful are such annotations and what purpose do annotations serve? What is the ease of use of our specific implementation of annotations? The context of our project has been in the area of multimedia information usage and collaboration in the biological sciences. We have developed asynchronous annotations for HTML and image data. Our annotations can be executed via any browser and require no downloads. They are stored in a central database allowing search and asynchronous access by all registered users. An easy to use user interface allows users to add, view and search annotations. We also performed a usability study that showed that our implementation of text annotations to validate our implementation.

  15. An Annotated Bibliography of the Chisanbop Method of Finger Calculation.

    ERIC Educational Resources Information Center

    Dougherty, Mary K.

    The term Chisanbop is the trademark for the finger calculation method originally developed by a Korean, Sung Jin Pai. It was refined and simplified by his son, Hang Young Pai, who introduced the technique to the United States in 1976. This annotated bibliography has been organized in five categories. Readings in the first category, Historical…

  16. An Annotated Bibliography of Games and Simulations in Consumer Education.

    ERIC Educational Resources Information Center

    Blucker, Gwen

    Thirty-two games and simulations relating to consumer education comprise this annotated bibliography designed to aid the teacher of adult basic education students and others in their search for teaching devices. Topics covered in the various simulations include money management, insurance, credit, credit unions, consumer law, consumer frauds,…

  17. Annotated Filmography of Selected Films with Lesbian/Gay Content.

    ERIC Educational Resources Information Center

    Council on Social Work Education, New York, NY.

    Intended to provide social work educators, practitioners, and students with a resource for identifying films which depict varying aspects of homosexuality and society's responses to it, this annotated filmography lists over 100 films, most of which were produced between 1967 and 1983. Divided into three sections, films listed in Part I are…

  18. Developing a Resource Center in Consumer Education: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Garman, E. Thomas; And Others

    The rationale behind this annotated bibliography of over 1300 items is that every consumer education teacher needs numerous classroom resources to provide for the individual needs of his students, and these resources should be balanced in representing all content areas. The resource materials included, mostly booklets and pamphlets for classroom…

  19. Feeling Expression Using Avatars and Its Consistency for Subjective Annotation

    NASA Astrophysics Data System (ADS)

    Ito, Fuyuko; Sasaki, Yasunari; Hiroyasu, Tomoyuki; Miki, Mitsunori

    Consumer Generated Media(CGM) is growing rapidly and the amount of content is increasing. However, it is often difficult for users to extract important contents and the existence of contents recording their experiences can easily be forgotten. As there are no methods or systems to indicate the subjective value of the contents or ways to reuse them, subjective annotation appending subjectivity, such as feelings and intentions, to contents is needed. Representation of subjectivity depends on not only verbal expression, but also nonverbal expression. Linguistically expressed annotation, typified by collaborative tagging in social bookmarking systems, has come into widespread use, but there is no system of nonverbally expressed annotation on the web. We propose the utilization of controllable avatars as a means of nonverbal expression of subjectivity, and confirmed the consistency of feelings elicited by avatars over time for an individual and in a group. In addition, we compared the expressiveness and ease of subjective annotation between collaborative tagging and controllable avatars. The result indicates that the feelings evoked by avatars are consistent in both cases, and using controllable avatars is easier than collaborative tagging for representing feelings elicited by contents that do not express meaning, such as photos.

  20. Annotated bibliography on decision analysis with applications to project management

    SciTech Connect

    Booker, J.M.; Bryson, M.C.

    1984-02-01

    The results of an extensive literature survey on decision analysis, with specific application to problems in research and development project management, are summarized in bibliographic form. Approximately 215 references are organized by subject matter and also summarized and annotated (several lines per reference) in a separate listing.

  1. Annotated Bibliography for 6th Grade Science and Social Studies.

    ERIC Educational Resources Information Center

    Randolph, Margo

    Designed to support curriculum and to facilitate instruction and learning at the sixth grade level, this annotated bibliography contains materials found in the library at the Brawley Middle School in Scotland Neck, North Carolina. To foster cooperative planning between teacher and librarian, the bibliography provides sample activities and lessons…

  2. Extension to distributed annotation system: Summary and summaryplot commands.

    PubMed

    Chrysostomou, Charalambos; Brookes, Anthony J

    2015-08-01

    In recent years, the development of high-throughput sequencing technologies provided an effective way to generate data from entire genomes and test variants from thousands of individuals. The information acquired from analysing the data generated from high-throughput sequencing technologies provided useful insights into applications like whole-exome sequencing and targeted sequencing to discover the genetic cause of complex diseases and drug responses. The Distributed Annotation System (DAS) is one of the proposed solution developed to share and unify biological data from multiple local and remote DAS annotation servers. The researchers can use DAS to request data from federated or centralised databases and integrate them into a unified view. Furthermore, with the use of Reference DAS servers, structural and sequence data can be used to accompany annotation data, for the pursue of new knowledge for a particular feature or region. In this paper, two additional commands, summary and summary-plot commands, to the existing DAS protocol are proposed and implemented. The proposed commands were created in order to give the users the capabilities to request a summary of features for a particular region of interest. The summary command was created in order to extend the capabilities of the current DAS protocol, while the summaryplot command was created to provide a more user-friendly alternative to standard XML DAS responses. Finally, three examples are presented based on the GENCODE annotation data. PMID:26738065

  3. Global Climate Change. Selected Annotated Bibliography. Second Edition.

    ERIC Educational Resources Information Center

    Jones, Douglas E.

    This annotated bibliography on global climate change contains 27 articles designed to expand the breadth and depth of information presented in the Global Change Information Packet. Most articles were chosen from journals likely to be available in most medium-sized public or college libraries. The articles cover a variety of topics related to…

  4. Education Packet, 1972. (Annotated Bibliography of Classroom Materials on Asia.)

    ERIC Educational Resources Information Center

    Committee of Concerned Asian Scholars, Stanford, CA.

    Three major sections comprise this annotated bibliography of recent books and classroom materials compiled to help teachers plan secondary Asian studies courses. The first section lists books, many of which are available in paperback, providing teachers with sources for background reading on Asia in general, Indochina, Japan, Korea, and China.…

  5. Annotated Bibliography of Wayne Dennis, Ph.D.

    ERIC Educational Resources Information Center

    Kraft, William A.; Rodolfa, Emil R.

    The major works of the child/developmental psychologist and educator Wayne Dennis are listed in this annotated bibliography. (One-hundred-twenty-one citations are included.) For ease of use, the bibliography has been subdivided into the major headings of aging (7 citations); animistic thinking (9 citations); cross-cultural studies (8 citations);…

  6. AN ANNOTATED BIBLIOGRAPHY ON THE DESIGN OF INSTRUCTIONAL SYSTEMS.

    ERIC Educational Resources Information Center

    SMITH, ROBERT G., JR.

    THIS BIBLIOGRAPHY OF 449 ANNOTATED ENTRIES SUPPLEMENTS AN EARLIER HUMAN RESOURCES RESEARCH OFFICE REPORT, "THE DESIGN OF INSTRUCTIONAL SYSTEMS" (TECHNICAL REPORT 66-18, NOVEMBER, 1966). IT SERVES AS A GUIDE TO MANY OF THE STUDIES CONDUCTED ON THE DEVELOPMENT OF TRAINING METHODS AND TOTAL INSTRUCTIONAL SYSTEMS. AN INSTRUCTIONAL SYSTEM INCLUDES…

  7. Picture Books That Teach Language: An Annotated Booklist.

    ERIC Educational Resources Information Center

    Gerstein, Leonore, Comp.

    This annotated booklist for parents and child caregivers is intended as a guide for using picture books to help children develop language skills. It differs from other lists which emphasize learning to listen; here the purpose is to facilitate talking. Each listed title is followed by a description of how the book might be used to teach a specific…

  8. Annotated Bibliography on Offender Job Training and Placement. Second Edition.

    ERIC Educational Resources Information Center

    Clem, Constance, Ed.

    This second edition of an annotated bibliography on offender job training and placement lists nearly 400 items from the collection of the National Institute of Corrections (NIC) Information Center in Longmont, Colorado, including 85 items added since the first edition in 1997. Items new to this edition are marked with an asterisk. Citations have…

  9. Cartel: Annotated Bibliography of Bilingual Bicultural Materials, No. 11.

    ERIC Educational Resources Information Center

    Dissemination and Assessment Center for Bilingual Education, Austin, TX.

    This booklet contains an annotated listing of instructional materials for use in bilingual-bicultural programs. Each entry includes the following information: title, author or developing agency, name and address of the publisher, publication date, number of pages, language(s) used, intended audience or level, and a descriptive statement. Any…

  10. [Cartel]: Monthly Annotated Bibliography of Bilingual Bicultural Materials, No. 1.

    ERIC Educational Resources Information Center

    Dissemination and Assessment Center for Bilingual Education, Austin, TX.

    This booklet contains an annotated listing of instructional materials for use in bilingual-bicultural programs. Each entry includes the following information: title, author or developing agency, name and address of the publisher, publication date, number of pages, language(s) used, intended audience or level, and a descriptive statement. Any…

  11. Cartel: Annotated Bibliography of Bilingual Bicultural Materials, No. 3.

    ERIC Educational Resources Information Center

    Dissemination and Assessment Center for Bilingual Education, Austin, TX.

    This booklet contains an annotated listing of instructional materials for use in bilingual-bicultural programs. Each entry includes the following information: title, author or developing agency, name and address of the publisher, publication date, number of pages, language(s) used, intended audience or level, and a descriptive statement. Any…

  12. Cartel: Annotated Bibliography of Bilingual Bicultural Materials, No. 2.

    ERIC Educational Resources Information Center

    Dissemination and Assessment Center for Bilingual Education, Austin, TX.

    This booklet contains an annotated listing of instructional materials for use in bilingual-bicultural programs. Each entry includes the following information: title, author or developing agency, name and address of the publisher, publication date, number of pages, language(s) used, intended audience or level, and a descriptive statement. Any…

  13. Cartel: Annotated Bibliography of Bilingual Bicultural Materials, No. 6.

    ERIC Educational Resources Information Center

    Dissemination and Assessment Center for Bilingual Education, Austin, TX.

    This booklet contains an annotated listing of instructional materials for use in bilingual-bicultural programs. Each entry includes the following information: title, author or developing agency, name and address of the publisher, publication date, number of pages, language(s) used, intended audience or level, and a descriptive statement. Any…

  14. Cartel: Annotated Bibliography of Bilingual Bicultural Materials, No. 7.

    ERIC Educational Resources Information Center

    Dissemination and Assessment Center for Bilingual Education, Austin, TX.

    This booklet contains an annotated listing of instructional materials for use in bilingual-bicultural programs. Each entry includes the following information: title, author or developing agency, name and address of the publisher, publication date, number of pages, language(s) used, intended audience or level, and a descriptive statement. Any…

  15. Cartel: Annotated Bibliography of Bilingual Bicultural Materials, No. 5.

    ERIC Educational Resources Information Center

    Dissemination and Assessment Center for Bilingual Education, Austin, TX.

    This booklet contains an annotated listing of instructional materials for use in bilingual-bicultural programs. Each entry includes the following information: title, author or developing agency, name and address of the publisher, publication date, number of pages, language(s) used, intended audience or level, and a descriptive statement. Any…

  16. Cartel: Annotated Bibliography of Bilingual Bicultural Materials, No. 9.

    ERIC Educational Resources Information Center

    Dissemination and Assessment Center for Bilingual Education, Austin, TX.

    This booklet contains an annotated listing of instructional materials for use in bilingual-bicultural programs. Each entry includes the following information: title, author or developing agency, name and address of the publisher, publication date, number of pages, language(s) used, intended audience or level, and a descriptive statement. Any…

  17. Cartel: Annotated Bibliography of Bilingual Bicultural Materials, No. 10.

    ERIC Educational Resources Information Center

    Dissemination and Assessment Center for Bilingual Education, Austin, TX.

    This booklet contains an annotated listing of instructional materials for use in bilingual-bicultural programs. Each entry includes the following information: title, author or developing agency, name and address of the publisher, publication date, number of pages, language(s) used, intended audience or level, and a descriptive statement. Any…

  18. Cartel: Annotated Bibliography of Bilingual Bicultural Materials, No. 8.

    ERIC Educational Resources Information Center

    Dissemination and Assessment Center for Bilingual Education, Austin, TX.

    This booklet contains an annotated listing of instructional materials for use in bilingual-bicultural programs. Each entry includes the following information: title, author or developing agency, name and address of the publisher, publication date, number of pages, language(s) used, intended audience or level, and a descriptive statement. Any…

  19. Annotated Bibliography on the Teaching of Psychology: 2006

    ERIC Educational Resources Information Center

    Johnson, David E.; Schroder, Simone I.

    2007-01-01

    This article presents an annotated bibliography of books, articles and other documents published in 2006, which is a continuation of those published in "Teaching of Psychology" (e.g., Berry & Daniel, 1984; Fulkerson & Wise, 1987; Johnson & Schroder, 1997; Wise & Fulkerson, 1996). It maintains similar search methods and criteria for inclusion that…

  20. ACOUSTICS IN ARCHITECTURAL DESIGN, AN ANNOTATED BIBLIOGRAPHY ON ARCHITECTURAL ACOUSTICS.

    ERIC Educational Resources Information Center

    DOELLE, LESLIE L.

    THE PURPOSE OF THIS ANNOTATED BIBLIOGRAPHY ON ARCHITECTURAL ACOUSTICS WAS--(1) TO COMPILE A CLASSIFIED BIBLIOGRAPHY, INCLUDING MOST OF THOSE PUBLICATIONS ON ARCHITECTURAL ACOUSTICS, PUBLISHED IN ENGLISH, FRENCH, AND GERMAN WHICH CAN SUPPLY A USEFUL AND UP-TO-DATE SOURCE OF INFORMATION FOR THOSE ENCOUNTERING ANY ARCHITECTURAL-ACOUSTIC DESIGN…

  1. Thermal Environment in School Facilities. A Selected and Annotated Bibliography.

    ERIC Educational Resources Information Center

    Hartman, Robert R.

    Contains a selected and annotated listing of source material concerning the thermal environment in school facilities. It is directed toward the school planner, architect, or administrator concerned with developing a more functional classroom environment. Topical coverage includes--(1) The Thermal Environment and Learning, (2) Physiological Factors…

  2. Folklore of the North American Indians. An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Ullom, Judith C., Comp.

    Intended for compilers or retellers of folktales, for storytellers or librarians serving children, or for children themselves, the annotated bibliography contains references to 152 sources of North American Indian folktales. Sources in the non-comprehensive bibliography were selected on the basis of (1) a statement of sources and faithfulness to…

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

    ERIC Educational Resources Information Center

    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…

  4. Appropriate Technology--A Selected, Annotated Bibliography No. 8.

    ERIC Educational Resources Information Center

    Andree, Carolyn

    Presented is an annotated bibliography of "appropriate technology" (AT) publications. The bibliography is divided into the following sections. Philosophy and overview section includes works describing the interrelationship of technology with other facets of development; place of technology in international relations; criteria for…

  5. Autism and Childhood Psychosis: Annotated Bibliography 1969-1974.

    ERIC Educational Resources Information Center

    Erskine, Richard G.; And Others

    The annotated bibliography contains approximately 400 citations of articles (1969-1974) on autism and childhood psychosis. It is explained that material was drawn from medical, psychological, social service and educational sources. Entries are arranged in separate sections for autism and childhood psychosis and are presented alphabetically by…

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

    ERIC Educational Resources Information Center

    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…

  7. Portfolio Assessment: An Annotated Bibliography of Selected Resources.

    ERIC Educational Resources Information Center

    Hayes, Betty, Comp.; Kretschmann, Karen Johnson, Comp.

    This annotated bibliography lists and summarizes the key points of 33 resource materials that focus specifically on portfolio assessment. Compiled in Spring 1993 as part of a demonstration project funded by the Wisconsin State Board of Vocational, Technical, and Adult Education, the bibliography is intended to serve as a tool for use in developing…

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

    ERIC Educational Resources Information Center

    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…

  9. Minority Access and Persistence Study: A Working Bibliography with Annotations.

    ERIC Educational Resources Information Center

    Cowart, Vinette; And Others

    One of the working papers in the final report of the Arizona Board of Regents' Task Force on Excellence, Efficiency and Competitiveness, this contribution offers an annotated bibliography on minority access and persistence. It cites the following: nine books (e.g., "Student Outcome Questionnaires: An Implementation Handbook" by P. Ewell and…

  10. Personnel Development for Career Education: A Selected Annotated Bibliography.

    ERIC Educational Resources Information Center

    Ohio State Univ., Columbus. Center for Vocational and Technical Education.

    The purpose of this document is to provide a selected, annotated bibliography in staff development for career education for the years 1970-73. It is expected that this document may be of assistance to those planning and/or working in the career education movement who have responsibility for preparing and utilizing staff effectively. The selections…

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

    ERIC Educational Resources Information Center

    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,…

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

    ERIC Educational Resources Information Center

    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…

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

    PubMed

    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. PMID:25313296

  14. Selective, annotated bibliography on current south Asian issues. Final report

    SciTech Connect

    Blood, P.; Ross, R.; Levy, R.; Makeig, D.

    1987-03-01

    This bibliography provides selective annotations of open-source material on two current issues: nuclear developments in South Asia, and tactics and organization of Afghan resistance groups. The monthly bibliography incorporates serials and monographs arranged alphabetically by author and title within each section.

  15. Selective, annotated bibliography on current south Asian issues. Final report

    SciTech Connect

    Blood, P.R.; Curtiss, E.R.; Heitzman, J.; LePoer, B.A.; Levy, R.J.

    1985-10-01

    This bibliography provides selective annotations of open-source material on two current issues: nuclear developments in South Asia, and tactics and organization of Afghan resistance groups. The monthly bibliography incorporates serials and monographs arranged alphabetically by author and title within each section.

  16. Selective, annotated bibliography on current south Asian issues. Final report

    SciTech Connect

    Blood, P.; Ross, R.; LePoer, B.; Levy, R.; Curtiss, E.

    1987-08-01

    This bibliography provides selective annotations of open-source material on two current issues: nuclear developments in South Asia, and tactics and organization of Afghan resistance groups. The monthly bibliography incorporates serials and monographs arranged alphabetically by author and title within each section.

  17. Selective, annotated bibliography on current south Asian issues. Final report

    SciTech Connect

    Blood, P.; Curtiss, E.; Heitzman, J.; LePoer, B.; Levy, R.

    1985-09-01

    This bibliography provides selective annotations of open-source material on two current issues: nuclear developments in South Asia and tactics and organization of Afghan resistance groups. The monthly bibliography incorporates serials and monographs arranged alphabetically by author and title within each section.

  18. Selective, annotated bibliography on current south Asian issues. Final report

    SciTech Connect

    Blood, P.R.; Curtiss, E.R.; Heitzman, J.; LePoer, B.A.; Levy, R.J.

    1986-01-01

    This bibliography provides selective annotations of open source material on two current issues: nuclear developments in South Asia, and tactics and organization of Afghan resistance groups. The monthly bibliography incorporates serials and monographs arranged alphabetically by author and title within each section.

  19. Selective, annotated bibliography on current south Asian issues. Final report

    SciTech Connect

    Blood, P.R.; Levy, R.J.; Heitzman, J.; LePoer, B.; Ross, R.

    1986-11-01

    This bibliography provides selective annotations of open-source material on two current issues: nuclear developments in South Asia, and tactics and organization of Afghan resistance groups. The monthly bibliography incorporates serials and monographs arranged alphabetically by author and title within each section.

  20. Selective, annotated bibliography on current south Asian issues. Final report

    SciTech Connect

    Blood, P.R.; Curtiss, E.R.; Heitzman, J.; LePoer, B.A.; Levy, R.J.

    1985-12-01

    This bibliography provides selective annotations of open-source material on two current issues: nuclear developments in South Asia, and tactics and organization of Afghan resistance groups. The monthly bibliography incorporates serials and monographs arranged alphabetically by author and title within each section.

  1. Selective, annotated bibliography on current south Asian issues. Final report

    SciTech Connect

    Blood, P.R.; Curtiss, E.R.; Heitzman, J.; LePoer, B.A.; Levy, R.J.

    1985-07-01

    This bibliography procides selective annotations of open-source material on two current issues: nuclear developments in South Asia and tactics and organization of Afghan resistance groups. The monthly bibliography incorporates serials and monographs arranged alphabetically by author and title within each section.

  2. Selective, annotated bibliography on current south Asian issues. Final report

    SciTech Connect

    Blood, P.R.; Levy, R.J.; Heitzman, J.; Ross, R.; Curtiss, E.

    1987-01-01

    This bibliography provides selective annotations of open source material on two current issues: nuclear developments in South Asia, and tactics and organization of Afghan resistance groups. The monthly bibliography incorporates serials and monographs arranged alphabetically by author and title within each section.

  3. Selective, annotated bibliography on current south Asian issues. Final report

    SciTech Connect

    Blood, P.R.; Curtiss, E.R.; Hietzman, J.; LePoer, B.A.; Levy, R.J.

    1985-11-01

    This bibliography provides selective annotations of open-source material on two current issues: nuclear developments in South Asia, and tactics and organization of Afghan resistance groups. The monthly bibliography incorporates serials and monographs arranged alphabetically by author and title within each section.

  4. Selective, annotated bibliography on current south Asian issues. Final report

    SciTech Connect

    Ross, R.R.; Blood, P.; Curtiss, E.; Heitzman, J.; LePoer, B.

    1986-05-01

    This bibliography provides selective annotations of open-source material on two current issues: nuclear developments in South Asia, and tactics and organization of Afghan resistance groups. The monthly bibliography incorporates serials and monographs arranged alphabetically by author and title within each section.

  5. Selective, annotated bibliography on current south Asian issues. Final report

    SciTech Connect

    Blood, P.; Heitzman, J.; Levy, R.; Ross, R.; Curtiss, E.

    1986-12-01

    This bibliography provides selective annotations of open-source material on two current issues: nuclear developments in South Asia and tactics and organization of Afghan resistance groups. The monthly bibliography incorporates serials and monographs arranged alphabetically by author and title within each section.

  6. Selective, annotated bibliography on current south Asian issues. Final report

    SciTech Connect

    Blood, P.; Curtiss, E.; Heitzman, J.; LePoer, B.; Levy, R.

    1985-08-01

    This bibliography provides selective annotations of open-source material on two current issues: nuclear developments in South Asia and tactics and organization of Afghan resistance groups. The monthly bibliography incorporates serials and monographs arranged alphabetically by author and title within each section.

  7. Selective, annotated bibliography on current south Asian issues. Final report

    SciTech Connect

    Blood, P.; Heitzman, J.; Levy, R.; Ross, R.; Curtiss, E.

    1986-03-01

    This bibliography provides selective annotations of open-source material on two current issues: nuclear developments in South Asia, and tactics and organization of Afghan resistance groups. The monthly bibliography incorporates serials and monographs arranged alphabetically by author and title within each section.

  8. Selective, annotated bibliography on current south Asian issues. Final report

    SciTech Connect

    Blood, P.; Heitzman, J.; Levy, R.; Ross, R.; Curtiss, E.

    1986-04-01

    This bibliography provides selective annotations of open-source material on two current issues: nuclear developments in South Asia and tactics and organization of Afghan resistance groups. The monthly bibliography incorporates serials and monographs arranged alphabetically by author and title within each section.

  9. Selective, annotated bibliography on current south Asian issues. Final report

    SciTech Connect

    Blood, P.; Makeig, D.C.; Heitzman, J.; Ross, R.; Curtiss, E.

    1986-10-01

    This bibliography provides selective annotations of open-source material on two current issues: nuclear developments in South Asia, and tactics and organization of Afghan resistance groups. The monthly bibliography incorporates serials and monographs arranged alphabetically by author and title within each section.

  10. Selective, annotated bibliography on current south Asian issues. Final report

    SciTech Connect

    Blood, P.; Curtiss, E.; Heitzman, J.; LePoer, B.; Levy, R.

    1987-02-01

    This bibliography provides selective annotations of open source material on two current issues: nuclear developments in South Asia and tactics and organization of Afghan resistance groups. The monthly bibliography incorporates serials and monographs arranged alphabetically by author and title within each section.

  11. Selective, annotated bibliography on current south Asian issues. Final report

    SciTech Connect

    Blood, P.; Heitzman, J.; Levy, R.; Levy, R.; Ross, R.

    1986-09-01

    This bibliography provides selective annotations of open-source material on two current issues: nuclear developments in South Asia, and tactics and organization of Afghan resistance groups. The monthly bibliography incorporates serials and monographs arranged alphabetically by author and title within each section.

  12. Selective, annotated bibliography on current south Asian issues. Final report

    SciTech Connect

    Blood, P.; Heitzman, J.; Levy, R.; Ross, R.; Curtiss, E.

    1986-06-01

    This bibliography provides selective annotations of open-source material on two current issues: nuclear developments in South Asia and tactics and organization of Afghan resistance groups. The monthly bibliography incorporates serials and monographs arranged alphabetically by author and title within each section.

  13. Selective, annotated bibliography on current south Asian issues. Final report

    SciTech Connect

    Blood, P.; Curtiss, E.; Heitzman, J.; LePoer, B.; Levy, R.

    1987-09-01

    This bibliography provides selective annotations of open-source material on two current issues: nuclear developments in South Asia, and tactics and organization of Afghan resistance groups. The monthly bibliography incorporates serials and monographs arranged alphabetically by author and title within each section.

  14. Selective, annotated bibliography on current south Asian issues. Final report

    SciTech Connect

    Blood, P.; Curtiss, E.; Heitzman, J.; LePoer, B.; Levy, R.

    1986-02-01

    This bibliography provides selective annotations of open-source material on two current issues: nuclear developments in South Asia and tactics and organization of Afghan resistance groups. The monthly bibliography incorporates serials and monographs arranged alphabetically by author and title within each section.

  15. Selective, annotated bibliography on current south Asian issues. Final report

    SciTech Connect

    Blood, P.; Heitzman, J.; Levy, R.; Ross, R.; Curtiss, E.

    1986-07-01

    This bibliography provides selective annotations of open-source material on two current issues: nuclear developments in South Asia, and tactics and organization of Afghan resistance groups. The monthly bibliography incorporates serials and monographs arranged alphabetically by author and title within each section.

  16. Annotated Bibliography of Research in the Teaching of English

    ERIC Educational Resources Information Center

    Beach, Richard; Bigelow, Martha; Dillon, Deborah; Dockter, Jessie; Galda, Lee; Helman, Lori; Kapoor, Richa; Ngo, Bic; O'Brien, David; Sato, Mistilina; Scharber, Cassie; Jorgensen, Karen; Liang, Lauren; Braaksma, Martine; Janssen, Tanja

    2009-01-01

    This article presents an annotated bibliography of research works about digital/technology tools for literacy instruction, discourse/cultural analysis, literacy, literary response/literature/narrative, media-information literacy/media use, professional development/teacher education related to English/language arts, reading, second language…

  17. Visual Detection, Identification, and Localization: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Lyman, Bernard

    This annotated bibliography containing research on visual perception executed at photopic levels in artificial laboratory situations has been compiled to make information available that can be applied to scotopic perception of natural objects in natural situations. There are 407 reports or studies, published from 1945 through 1964, cited in this…

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

    ERIC Educational Resources Information Center

    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…

  19. A Novel Method for Learner Assessment Based on Learner Annotations

    ERIC Educational Resources Information Center

    Noorbehbahani, Fakhroddin; Samani, Elaheh Biglar Beigi; Jazi, Hossein Hadian

    2013-01-01

    Assessment is one of the most essential parts of any instructive learning process which aims to evaluate a learner's knowledge about learning concepts. In this work, a new method for learner assessment based on learner annotations is presented. The proposed method exploits the M-BLEU algorithm to find the most similar reference annotations…

  20. Annotated Football Bibliography. An Applied Project in Physical Education.

    ERIC Educational Resources Information Center

    Clemence, William J., Jr.; Pitts, James Walter

    This annotated bibliography was compiled to assist physical education majors, especially those having a major interest in football and football coaching. The bibliography is limited to the areas of coaching techniques and philosophy, fundamentals, offense, defense, injuries, and conditioning at the high school and college level. These broader…

  1. Collaborative Annotation of a Hyperbook on Hypermedia Design.

    ERIC Educational Resources Information Center

    Jonassen, David H.; Wang, Sherwood

    This report describes the process and results of a collaborative annotation process for inserting internal, conceptual linking in a book about hypertext design and the implications of that process for designing collaborative hypertext environments. The book was the product of a NATO (North Atlantic Treaty Organization)-sponsored Advanced Research…

  2. Annotation in School English: A Social Semiotic Historical Account

    ERIC Educational Resources Information Center

    Jewitt, Carey; Bezemer, Jeff; Kress, Gunther

    2011-01-01

    What exactly has changed in the production of secondary school English over the last decade? To provide one part of an answer to that question, this paper takes the practice of annotation--a defining activity of the subject English in the UK seldom researched--and uses it as a device for uncovering aspects of changes in the subject. The…

  3. Canadian Doctoral Dissertations in Reading Education: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Narang, H. L.

    This annotated bibliography lists 27 Canadian doctoral dissertations in reading instruction written from 1928 through April 1971. Each citation describes the research investigations involved and the conclusions drawn. Some of the topics covered include: (1) remedial reading, (2) reading achievement, (3) perceptual skills, (4) parental…

  4. Gender, Science, and Technology: A Selected Annotated Bibliography.

    ERIC Educational Resources Information Center

    Eldredge, Mary; And Others

    1990-01-01

    Presents 196 annotated listings of works on science, technology, and gender, under 9 headings: Biography and History; Women Scientists; Science Education; Feminists Look at Science and Technology; Effects of Technology on Women; Medicine and Reproductive Technologies in Women's Lives; Women and Evolution; Women and Agriculture; and Gender,…

  5. Latin America: Books for High Schools. An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Farrell, Robert V., Comp.; Hohenstein, John F., Comp.

    This bibliography, intended for use as a selection tool for social studies programs and libraries in order to supply secondary students and teachers with recent Latin American books, contains 171 annotated bibliographic citations prepared by the center for Inter-American Relations after examination of more than 1200 books for comprehensiveness,…

  6. An Annotated Bibliography of Isotonic Weight-Training Methods.

    ERIC Educational Resources Information Center

    Wysong, John V.

    This literature study was conducted to compare and evaluate various types and techniques of weight lifting so that a weight lifting program could be selected or devised for a secondary school. Annotations of 32 research reports, journal articles, and monographs on isotonic strength training are presented. The literature in the first part of the…

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

    ERIC Educational Resources Information Center

    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…

  8. Educational Leadership: A Selective Annotated Bibliography, 1981-1985.

    ERIC Educational Resources Information Center

    1985

    This bibliography consists of annotations of selected journal articles, magazine articles, books, and unpublished doctoral dissertations pertinent to the topic of educational leadership. The selections encompass a time frame ranging from 1981 to 1985. "Education Index" and "Psychological Abstracts" were the primary sources for journal and magazine…

  9. Annotated Bibliography on the Teaching of Psychology: 1999.

    ERIC Educational Resources Information Center

    Johnson, David E.; Schroder, Simone I.

    2000-01-01

    Presents an annotated bibliography covering awards, computers and technology, critical thinking, developmental psychology and aging, ethics, graduate education and training issues, high school psychology, history, introductory psychology, learning and cognition, perception/physiological/comparative psychology, research methods and research-related…

  10. Cognitive Approaches to Writing: An Introductory Annotated Bibliography.

    ERIC Educational Resources Information Center

    Puma, Vincent; And Others

    The annotated titles in this bibliography are intended to introduce the novice to current or significant work on the application of cognitive psychology methodologies to the writing process. The bibliography is arranged in four sections: (1) an overview of the topic that includes anthologies, essays and papers; (2) relevant publications of Linda…

  11. Annotated Bibliography of Research in the Teaching of English.

    ERIC Educational Resources Information Center

    Brown, Deborah; Beavis, Catherine; Kalman, Judith; Stinson, Anne D'Antonio; Whiting, Melissa E.

    2002-01-01

    Presents annotations of 37 selected recent research in the teaching of English and related fields. Addresses bilingual/foreign language education, discourse processes, literacy, professional development, reading, teaching and learning of literature, teaching and learning of writing, and technology and literacy. Notes that most of the studies…

  12. Annotated Bibliography of Research in the Teaching of English.

    ERIC Educational Resources Information Center

    Brown, Deborah; Kalman, Judy; Stinson, Anne D'Antonio; Whiting, Melissa E.

    2001-01-01

    Presents 34-item annotated bibliography of journal articles addressing issues such as: bilingual/foreign language/second language education; classroom discourse; literacy; reading; and writing. Notes that most of the studies appeared during the six-month period from June to December, 2000 but some studies that appeared earlier are occasionally…

  13. Annotated Bibliography of Selected Publications on the Adolescent Years.

    ERIC Educational Resources Information Center

    Schoff, Linda L.

    1993-01-01

    An annotated bibliography includes publications on adolescent issues such as school-community collaboration, pregnancy prevention, decision making, health promotion, injury prevention, music, violence prevention, health care, African-American adolescents, sexuality education, futures planning, policy, and health service delivery. (SM)

  14. Resources for Achieving Sex Equity: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Miller, Susan W., Comp.

    This annotated bibliography provides a list of resources dealing with sex equity in vocational education. The bibliography first provides operational definitions of "sexism,""sex fair,""sex affirmative,""sex bias," and "affirmative action." It then lists resources under the following topics and/or bibliographic forms: (1) sex role definition, (2)…

  15. COMMUNITY COLLEGE BOARDS OF TRUSTEES, AN ANNOTATED BIBLIOGRAPHY. OCCASIONAL PAPERS.

    ERIC Educational Resources Information Center

    GILES, FREDERIC T.; OLSON, OMAR L.

    ENTRIES IN THIS ANNOTATED LISTING OF PUBLISHED AND UNPUBLISHED MATERIALS ABOUT COMMUNITY AND JUNIOR COLLEGE BOARDS OF TRUSTEES ARE ARRANGED IN THREE GROUPS--(1) REFERENCES OF PARTICULAR RELEVANCE TO THE NEW TRUSTEE OR ADMINISTRATOR, (2) REFERENCES WHICH SPECIFICALLY RELATE TO OR DEAL PRIMARILY WITH THE ROLE OF THE TRUSTEE AND THE BOARD AT THE…

  16. An Assessment of Reliability of Dialogue-Annotation Instructions.

    ERIC Educational Resources Information Center

    Mann, William C.; And Others

    This report is part of ongoing research engaged in transforming knowledge of how human communication works into improvements in man-machine communication of existing and planned computer systems. The methodology includes having a trained "Observer" annotate transcripts of human communication in a prescribed manner. One of the issues, therefore, in…

  17. The Netherlands in Fifty Maps: An Annotated Atlas.

    ERIC Educational Resources Information Center

    Tamsma, R.

    1988-01-01

    Statistical data relating to The Netherlands is presented in 50 maps that were originally published in the "Journal of Economic and Social Geography" between 1977 and 1986. Lengthy annotations accompanying each map provide important background information on the issues depicted. These elucidations were written with the foreign reader in mind, who…

  18. Annotated Bibliography of Multi-Ethnic Curriculum Materials, Sixth Supplement.

    ERIC Educational Resources Information Center

    Midwest Center for Equal Educational Opportunity, Columbia, MO.

    This annotated bibliography cites 132 multiethnic curriculum materials for grades K through 12. It is designed to be used by students, teachers, and administrators. Some of the materials focus on specific groups, such as Blacks, American Indians, Puerto Ricans, Italian Americans, Chinese Americans, Slavs, Scandinavians, and women. Other materials…

  19. Job Creation in Rural Areas: A Select Annotated Bibliography.

    ERIC Educational Resources Information Center

    Pankratz, John

    1989-01-01

    This annotated bibliography is designed to assist rural leaders seeking ways to effectively structure successful job development projects in their communities. The 120 entries are listed in the main body alphabetically by author, and are grouped in the index into categories reflecting Thomas's "seven hallmarks of successful rural development": (1)…

  20. Genome Annotation in a Community College Cell Biology Lab

    ERIC Educational Resources Information Center

    Beagley, C. Timothy

    2013-01-01

    The Biology Department at Salt Lake Community College has used the IMG-ACT toolbox to introduce a genome mapping and annotation exercise into the laboratory portion of its Cell Biology course. This project provides students with an authentic inquiry-based learning experience while introducing them to computational biology and contemporary learning…

  1. Postsecondary Peer Cooperative Learning Programs: Annotated Bibliography 2016

    ERIC Educational Resources Information Center

    Arendale, David R., Comp.

    2016-01-01

    Purpose: This 2016 annotated bibliography reviews seven postsecondary peer cooperative learning programs that have been implemented nationally to increase student achievement. Methodology: An extensive literature search was conducted of published journal articles, newspaper accounts, book chapters, books, ERIC documents, thesis and dissertations,…

  2. Assessing the quality of annotations in asthma gene expression experiments

    PubMed Central

    2010-01-01

    Background The amount of data deposited in the Gene Expression Omnibus (GEO) has expanded significantly. It is important to ensure that these data are properly annotated with clinical data and descriptions of experimental conditions so that they can be useful for future analysis. This study assesses the adequacy of documented asthma markers in GEO. Three objective measures (coverage, consistency and association) were used for evaluation of annotations contained in 17 asthma studies. Results There were 918 asthma samples with 20,640 annotated markers. Of these markers, only 10,419 had documented values (50% coverage). In one study carefully examined for consistency, there were discrepancies in drug name usage, with brand name and generic name used in different sections to refer to the same drug. Annotated markers showed adequate association with other relevant variables (i.e. the use of medication only when its corresponding disease state was present). Conclusions There is inadequate variable coverage within GEO and usage of terms lacks consistency. Association between relevant variables, however, was adequate. PMID:21044366

  3. Chicano Perspectives in Literature--A Critical and Annotated Bibliography.

    ERIC Educational Resources Information Center

    Lomeli, Francisco A.; Urioste, Donaldo W.

    As an effort to define and explore the horizons of Chicano literature, this annotated and critical bibliography provides bibliographical data and critical evaluations and judgments regarding the quality, importance, and impact of 131 literary works by Chicanos. The commentaries are intended to be taken as opinions with the objective for promoting…

  4. Variobox: automatic detection and annotation of human genetic variants.

    PubMed

    Gaspar, Paulo; Lopes, Pedro; Oliveira, Jorge; Santos, Rosário; Dalgleish, Raymond; Oliveira, José Luís

    2014-02-01

    Triggered by the sequencing of the human genome, personalized medicine has been one of the fastest growing research areas in the last decade. Multiple software and hardware technologies have been developed by several projects, culminating in the exponential growth of genetic data. Considering the technological developments in this field, it is now fairly easy and inexpensive to obtain genetic profiles for unique individuals, such as those performed by several genetic analysis companies. The availability of computational tools that simplify genetic data analysis and the disclosure of biomedical evidences are of utmost importance. We present Variobox, a desktop tool to annotate, analyze, and compare human genes. Variobox obtains variant annotation data from WAVe, protein metadata annotations from Protein Data Bank, and sequences are obtained from Locus Reference Genomic or RefSeq databases. To explore the data, Variobox provides an advanced sequence visualization that enables agile navigation through genetic regions. DNA sequencing data can be compared with reference sequences retrieved from LRG or RefSeq records, identifying and automatically annotating new potential variants. These features and data, ranging from patient sequences to HGVS-compliant variant descriptions, are combined in an intuitive interface to analyze genes and variants. Variobox is a Java application, available at http://bioinformatics.ua.pt/variobox. PMID:24186831

  5. Coleoptera of the Idaho National Engineering Laboratory: an annotated checklist

    SciTech Connect

    Stafford, M.P.; Barr, W.F.; Johnson, J.B.

    1986-04-30

    An insect survey was conducted on the Idaho National Engineering Laboratory during the summers of 1981-1983. This site is on the Snake River Plains in southeastern Idaho. Presented here is an annotated checklist of the Coleoptera collected. Successful collecting methods, dates of adult occurrence, and relative abundance are given for each species. Relevant biological information is also presented for some species.

  6. Sequence-based feature prediction and annotation of proteins

    PubMed Central

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

    2009-01-01

    A recent trend in computational methods for annotation of protein function is that many prediction tools are combined in complex workflows and pipelines to facilitate the analysis of feature combinations, for example, the entire repertoire of kinase-binding motifs in the human proteome. PMID:19226438

  7. Annotation of Korean Learner Corpora for Particle Error Detection

    ERIC Educational Resources Information Center

    Lee, Sun-Hee; Jang, Seok Bae; Seo, Sang-Kyu

    2009-01-01

    In this study, we focus on particle errors and discuss an annotation scheme for Korean learner corpora that can be used to extract heuristic patterns of particle errors efficiently. We investigate different properties of particle errors so that they can be later used to identify learner errors automatically, and we provide resourceful annotation…

  8. Television and Sex Roles: A Selected Annotated Bibliography.

    ERIC Educational Resources Information Center

    Kear, Lynn

    Thirty-five books and articles about television and sex roles that were published between l954 and l983 are listed in this annotated bibliography. Among the topics covered in the articles and books are female stereotypes, the influence of television on children's perception of sex roles, a survey and summary of the research on sex roles and mass…

  9. Censorship of Sexual Materials: A Selected, Annotated Basic Bibliography.

    ERIC Educational Resources Information Center

    Tedford, Thomas L.

    The 37 references in this annotated bibliography are compiled for researchers of information on the censorship of sexual materials from ancient times to present. The materials include case studies, histories, essays, and opinion pieces about the use and regulation of "obscenity" in literature, pictorial art, radio broadcasting, the mail, film, and…

  10. Rapid reconstruction and annotation of vaccinium macrocarpon organellar genomes

    Technology Transfer Automated Retrieval System (TEKTRAN)

    The mitochondria genome of the American cranberry (Vaccinium macrocarpon Ait.) cultivar “HyRed” is being reconstructed using sequence 454 shotgun data and in silico procedures. We previously reconstructed and annotated a putative plastid cranberry genome with an approximate length of 176kb. The reli...

  11. An Annotated Bibliography of Migrant Related Materials. Third Edition.

    ERIC Educational Resources Information Center

    Tuttle, Lester E., Jr., Ed.; Hooker, Dennis A., Ed.

    Instructional materials and reference materials applicable to migratory children and youth are compiled in this revised annotated bibliography containing over 800 entries. Materials listed are coded by content area (health, information on migrants and culturally disadvantaged, curriculum materials, guidance, occupational, supplementary…

  12. Resources for Exceptional Adult Education: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Beltran, Alejandro C.; And Others

    This annotated bibliography describes materials that can be helpful to adult educators working with exceptional adults. The bibliography includes 186 citations of resource materials, assessment materials, training guides, curriculum guides, research findings, films, and general information. The opening section consists of citations of general…

  13. Classic Religious Books for Children: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Campbell, Carol, Comp.

    This annotated bibliography of religious books for children contains approximately 450 books, one-fifth of which are Judaic. The books' current availability has been verified using Web sites such as those of individual publishers, the Library of Congress, Amazon.com, or Barnes&Noble.com. New subject headings have been added, such as Kwanza,…

  14. Machine learning and genome annotation: a match meant to be?

    PubMed Central

    2013-01-01

    By its very nature, genomics produces large, high-dimensional datasets that are well suited to analysis by machine learning approaches. Here, we explain some key aspects of machine learning that make it useful for genome annotation, with illustrative examples from ENCODE. PMID:23731483

  15. Chemical Geology: An Annotated Bibliography. CEGS Programs Publication Number 11.

    ERIC Educational Resources Information Center

    Billings, Gale K.

    The annotated bibliography is intended to aid geologists whose primary background is not in geochemistry. The references thus range from chemistry texts to papers on complex geochemical applications. The emphasis has been on those books and papers concerned with the application of chemical concepts to geology. Citations are arranged topically to…

  16. Building Blocks. An Annotated Bibliography for Single Parent Programming.

    ERIC Educational Resources Information Center

    Wiley-Thomas, Cheryl, Comp.; Norden, Tamara, Ed.

    This booklet lists 645 books, articles, curriculum materials, computer software, and videos that educational professionals can use to develop programs for single parents (especially teen parents). Many of the listings are annotated; all contain information on author, title, publisher name and city, and date of publication or production. The…

  17. "Books" Annotated by American Council for Elementary School Industrial Arts.

    ERIC Educational Resources Information Center

    Stunard, E. Arthur, Ed.

    Prepared by the American Council for Elementary School Industrial Arts, (ACESIA), this annotated bibliography of books is a result of their commitment to publish materials that might be useful to the profession. For use in elementary school industrial arts activities, this list was compiled over a period of years with the help of many colleagues.…

  18. CLASSROOM ORGANIZATION FOR READING INSTRUCTION--AN ANNOTATED BIBLIOGRAPHY.

    ERIC Educational Resources Information Center

    SPACHE, GEORGE D.

    THIS ANNOTATED BIBLIOGRAPHY ON CLASSROOM ORGANIZATION FOR READING INSTRUCTION IS COMPOSED OF 112 CITATIONS RANGING IN DATE FROM 1948 TO 1964. ITS DIVISIONS INCLUDE GENERAL SOURCES, GROUP DYNAMICS, HOMOGENEOUS VERSUS HETEROGENEOUS, CROSS-CLASS GROUPING, NONGRADED SCHOOLS AND THE UPGRADED PRIMARY, PROGRAMED INSTRUCTION, TEAM TEACHING AND EDUCATIONAL…

  19. LINGUISTICS AND THE TEACHING OF READING--AN ANNOTATED BIBLIOGRAPHY.

    ERIC Educational Resources Information Center

    GOODMAN, KENNETH S.; GOODMAN, YETTA M.

    ONE OF THE INTERNATIONAL READING ASSOCIATION'S ANNOTATED BIBLIOGRAPHY SERIES IS CONCERNED WITH THE APPLICATION OF LINGUISTICS TO READING INSTRUCTION AND WAS PREPARED TO SERVE A WIDE RANGE OF USERS. IT CONTAINS ABOUT 100 CITATIONS OF BOOKS, RESEARCH REPORTS, DOCTORAL DISSERTATIONS, AND ARTICLES FROM PERIODICALS, YEARBOOKS, AND CONFERENCE…

  20. The Middle East: An Annotated Bibliography of Literature for Children.

    ERIC Educational Resources Information Center

    Maehr, Jane

    This is an annotated bibliography of folklore, fiction and nonfiction about the Middle East, written in English for children aged 5 and older. There are eleven chapters - one which focuses on the entire Middle Eastern region, and ten which deal with individual countries: Iran, Iraq, Israel, Jordan, Kuwait, Lebanon, Saudi Arabia, Syria, Turkey, and…

  1. Intra-species sequence comparisons for annotating genomes

    SciTech Connect

    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.

  2. BioDEAL: community generation of biological annotations

    PubMed Central

    Breimyer, Paul; Green, Nathan; Kumar, Vinay; Samatova, Nagiza F

    2009-01-01

    Background Publication databases in biomedicine (e.g., PubMed, MEDLINE) are growing rapidly in size every year, as are public databases of experimental biological data and annotations derived from the data. Publications often contain evidence that confirm or disprove annotations, such as putative protein functions, however, it is increasingly difficult for biologists to identify and process published evidence due to the volume of papers and the lack of a systematic approach to associate published evidence with experimental data and annotations. Natural Language Processing (NLP) tools can help address the growing divide by providing automatic high-throughput detection of simple terms in publication text. However, NLP tools are not mature enough to identify complex terms, relationships, or events. Results In this paper we present and extend BioDEAL, a community evidence annotation system that introduces a feedback loop into the database-publication cycle to allow scientists to connect data-driven biological concepts to publications. Conclusion BioDEAL may change the way biologists relate published evidence with experimental data. Instead of biologists or research groups searching and managing evidence independently, the community can collectively build and share this knowledge. PMID:19891799

  3. Bibliographies and Annotations from Speakers and Class Participants.

    ERIC Educational Resources Information Center

    California Univ., Berkeley. Office of Resources for International and Area Studies.

    This annotated bibliography focuses on recent children's literature that deals with other cultures. The books in the bibliography are set in or about Africa (29 selections), Ancient Egypt (3 selections), East Asia (20 selections), India (7 selections), Latin America (3 selections), Middle East (5 selections), and Russia (9 selections). The…

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

    ERIC Educational Resources Information Center

    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…

  5. Automatic image annotation and retrieval using group sparsity.

    PubMed

    Zhang, Shaoting; Huang, Junzhou; Li, Hongsheng; Metaxas, Dimitris N

    2012-06-01

    Automatically assigning relevant text keywords to images is an important problem. Many algorithms have been proposed in the past decade and achieved good performance. Efforts have focused upon model representations of keywords, whereas properties of features have not been well investigated. In most cases, a group of features is preselected, yet important feature properties are not well used to select features. In this paper, we introduce a regularization-based feature selection algorithm to leverage both the sparsity and clustering properties of features, and incorporate it into the image annotation task. Using this group-sparsity-based method, the whole group of features [e.g., red green blue (RGB) or hue, saturation, and value (HSV)] is either selected or removed. Thus, we do not need to extract this group of features when new data comes. A novel approach is also proposed to iteratively obtain similar and dissimilar pairs from both the keyword similarity and the relevance feedback. Thus, keyword similarity is modeled in the annotation framework. We also show that our framework can be employed in image retrieval tasks by selecting different image pairs. Extensive experiments are designed to compare the performance between features, feature combinations, and regularization-based feature selection methods applied on the image annotation task, which gives insight into the properties of features in the image annotation task. The experimental results demonstrate that the group-sparsity-based method is more accurate and stable than others. PMID:22249744

  6. French Readers for Primary Schools: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Naylor, J. W., Comp.

    Teachers of elementary school children will find this annotated bibliography of 39 readers considers 10 relevant factors for each entry. They cover: (1) components and bibliographical details (including pagination, cost, publisher, and book size), (2) general description, (3) content, (4) notes for the teacher, (5) presentation, (6) illustrations,…

  7. Higher Education in the People's Republic of China: Annotated Bibliography.

    ERIC Educational Resources Information Center

    Parker, Franklin

    An annotated bibliography of publications on every aspect of higher education in China, before and since the creation of the People's Republic of China, is presented. The 125 publications include journal articles, articles from major newspapers, and books produced in China, Japan, the United States, and Europe, including the U.S.S.R. Most of the…

  8. Issues Affecting Teaching On-Line: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Thompson, Kelvin

    This annotated bibliography identifies issues affecting the on-line teaching environment by assembling a variety of quantitative and qualitative studies. Studies in the bibliography are divided into two major categories: (1) topical studies, which contain papers that focus primarily on one issue affecting teaching on-line (student…

  9. Population Education: A Selective Annotated Bibliography for United States Schools.

    ERIC Educational Resources Information Center

    Leighton, Andrew J.

    This selective, annotated bibliography provides elementary, secondary, and undergraduate teachers, students, and curriculum designers with 47 references on population education. The bibliography is divided into four sections listing citations on basic reference data for the study of population, specific population education materials, points of…

  10. Africa: An Annotated List of Printed Materials Suitable for Children.

    ERIC Educational Resources Information Center

    State Univ. of New York, Ithaca. School of Hotel Administration at Cornell Univ.

    This joint project of the American Library Association, Children's Services Division, and the African American Institute is intended to provide kindergarten through ninth grade children with an annotated listing of appropriate works concerning the land and peoples of the African continent. The listings are presented by country and include…

  11. KNOWING AND EDUCATING THE DISADVANTAGED, AN ANNOTATED BIBLIOGRAPHY.

    ERIC Educational Resources Information Center

    POTTS, ALFRED M., 2D

    "KNOWING AND EDUCATING THE DISADVANTAGED" IS AN ANNOTATED BIBLIOGRAPHY OF MATERIALS RELATED TO THE EDUCATION OF MIGRANTS OR THE ECONOMICALLY DISADVANTAGED. IT IS ARRANGED BY BOTH TOPIC AND TITLE INDEXES. TOPICS INCLUDE AGRICULTURE, AMERICAN CULTURE, DIRECTORIES, BIBLIOGRAPHIES, GUIDES, HANDBOOKS, ADMINISTRATION AND ORGANIZATION OF EDUCATION, ADULT…

  12. Religious Books for Children: An Annotated Bibliography. Revised Edition.

    ERIC Educational Resources Information Center

    Pearl, Patricia.

    This bibliography is intended to serve primarily as a guide for the selection of children's religious books and secondarily for the evaluation of this area in library collections. The 442 annotated citations are arranged by seven major subject areas: (1) Bible, (2) Old Testament, (3) New Testament and Jesus, (4) Christianity, (5) Judaism, (6)…

  13. Using 360-Degree Feedback in Organizations: An Annotated Bibliography.

    ERIC Educational Resources Information Center

    Fleenor, John W.; Prince, Jeffrey Michael

    Noting that the use of multi-rater assessment tools (also called 360-degree feedback) in organizations has increased dramatically in recent years, this booklet provides an introduction to this growing practical literature. In addition to annotations of 56 books and journal articles published between 1990 and 1997, the booklet answers frequently…

  14. Systematic Functional Annotation and Visualization of Biological Networks.

    PubMed

    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

  15. Annotated Bibliography; Freedom of Information Center Reports and Summary Papers.

    ERIC Educational Resources Information Center

    Freedom of Information Center, Columbia, MO.

    This bibliography lists and annotates almost 400 information reports, opinion papers, and summary papers dealing with freedom of information. Topics covered include the nature of press freedom and increased press efforts toward more open access to information; the press situation in many foreign countries, including France, Sweden, Communist…

  16. Functional Annotations of Paralogs: A Blessing and a Curse.

    PubMed

    Zallot, Rémi; Harrison, Katherine J; Kolaczkowski, Bryan; de Crécy-Lagard, Valérie

    2016-01-01

    Gene duplication followed by mutation is a classic mechanism of neofunctionalization, producing gene families with functional diversity. In some cases, a single point mutation is sufficient to change the substrate specificity and/or the chemistry performed by an enzyme, making it difficult to accurately separate enzymes with identical functions from homologs with different functions. Because sequence similarity is often used as a basis for assigning functional annotations to genes, non-isofunctional gene families pose a great challenge for genome annotation pipelines. Here we describe how integrating evolutionary and functional information such as genome context, phylogeny, metabolic reconstruction and signature motifs may be required to correctly annotate multifunctional families. These integrative analyses can also lead to the discovery of novel gene functions, as hints from specific subgroups can guide the functional characterization of other members of the family. We demonstrate how careful manual curation processes using comparative genomics can disambiguate subgroups within large multifunctional families and discover their functions. We present the COG0720 protein family as a case study. We also discuss strategies to automate this process to improve the accuracy of genome functional annotation pipelines. PMID:27618105

  17. Annotated List of Periodicals for Canadian School and Public Libraries.

    ERIC Educational Resources Information Center

    Galler, Anne M., Comp.

    This annotated list of periodicals is intended for both public libraries and school libraries in Canada. While focusing on Canadian magazines, this publication also cites some non-Canadian material suitable for Canadian school and public library collections. Most of the material is suitable for the average child or youngster, although there are…

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

    ERIC Educational Resources Information Center

    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…

  19. Supervised learning of semantic classes for image annotation and retrieval.

    PubMed

    Carneiro, Gustavo; Chan, Antoni B; Moreno, Pedro J; Vasconcelos, Nuno

    2007-03-01

    A probabilistic formulation for semantic image annotation and retrieval is proposed. Annotation and retrieval are posed as classification problems where each class is defined as the group of database images labeled with a common semantic label. It is shown that, by establishing this one-to-one correspondence between semantic labels and semantic classes, a minimum probability of error annotation and retrieval are feasible with algorithms that are 1) conceptually simple, 2) computationally efficient, and 3) do not require prior semantic segmentation of training images. In particular, images are represented as bags of localized feature vectors, a mixture density estimated for each image, and the mixtures associated with all images annotated with a common semantic label pooled into a density estimate for the corresponding semantic class. This pooling is justified by a multiple instance learning argument and performed efficiently with a hierarchical extension of expectation-maximization. The benefits of the supervised formulation over the more complex, and currently popular, joint modeling of semantic label and visual feature distributions are illustrated through theoretical arguments and extensive experiments. The supervised formulation is shown to achieve higher accuracy than various previously published methods at a fraction of their computational cost. Finally, the proposed method is shown to be fairly robust to parameter tuning. PMID:17224611

  20. Annotated Bibliography on the Teaching of Psychology: 2007

    ERIC Educational Resources Information Center

    Johnson, David E.; Schroder, Simone I.; Erickson, Jonathan P.; Grimes, Katherine N.

    2008-01-01

    This annotated bibliography is a continuation of those previously published in "Teaching of Psychology" (e.g., Berry & Daniel, 1984; Fulkerson & Wise, 1987; Johnson & Schroder, 1997; Wise & Fulkerson, 1996). In this paper, the authors maintained similar search methods and criteria for inclusion that were used in previous bibliographies. They also…