The Experts below are selected from a list of 11547 Experts worldwide ranked by ideXlab platform
Henning Hermjakob - One of the best experts on this subject based on the ideXlab platform.
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the ontology lookup service more data and better tools for Controlled Vocabulary queries
Nucleic Acids Research, 2008Co-Authors: Richard G Cote, Philip Jones, Rolf Apweiler, Lennart Martens, Henning HermjakobAbstract:The Ontology Lookup Service (OLS) (http://www.ebi.ac.uk/ols) provides interactive and programmatic interfaces to query, browse and navigate an ever increasing number of biomedical ontologies and Controlled vocabularies. The volume of data available for querying has more than quadrupled since it went into production and OLS functionality has been integrated into several high-usage databases and data entry tools. Improvements have been made to both OLS query interfaces, based on user feedback and requirements, to improve usability and service interoperability and provide novel ways to perform queries.
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the ontology lookup service a lightweight cross platform tool for Controlled Vocabulary queries
BMC Bioinformatics, 2006Co-Authors: Richard G Cote, Philip Jones, Rolf Apweiler, Henning HermjakobAbstract:With the vast amounts of biomedical data being generated by high-throughput analysis methods, Controlled vocabularies and ontologies are becoming increasingly important to annotate units of information for ease of search and retrieval. Each scientific community tends to create its own locally available ontology. The interfaces to query these ontologies tend to vary from group to group. We saw the need for a centralized location to perform Controlled Vocabulary queries that would offer both a lightweight web-accessible user interface as well as a consistent, unified SOAP interface for automated queries. The Ontology Lookup Service (OLS) was created to integrate publicly available biomedical ontologies into a single database. All modified ontologies are updated daily. A list of currently loaded ontologies is available online. The database can be queried to obtain information on a single term or to browse a complete ontology using AJAX. Auto-completion provides a user-friendly search mechanism. An AJAX-based ontology viewer is available to browse a complete ontology or subsets of it. A programmatic interface is available to query the webservice using SOAP. The service is described by a WSDL descriptor file available online. A sample Java client to connect to the webservice using SOAP is available for download from SourceForge. All OLS source code is publicly available under the open source Apache Licence. The OLS provides a user-friendly single entry point for publicly available ontologies in the Open Biomedical Ontology (OBO) format. It can be accessed interactively or programmatically at http://www.ebi.ac.uk/ontology-lookup/ .
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the ontology lookup service a lightweight cross platform tool for Controlled Vocabulary queries
BMC Bioinformatics, 2006Co-Authors: Richard G Cote, Philip Jones, Rolf Apweiler, Henning HermjakobAbstract:Background With the vast amounts of biomedical data being generated by high-throughput analysis methods, Controlled vocabularies and ontologies are becoming increasingly important to annotate units of information for ease of search and retrieval. Each scientific community tends to create its own locally available ontology. The interfaces to query these ontologies tend to vary from group to group. We saw the need for a centralized location to perform Controlled Vocabulary queries that would offer both a lightweight web-accessible user interface as well as a consistent, unified SOAP interface for automated queries.
Joachim Bendiek - One of the best experts on this subject based on the ideXlab platform.
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gmo genetic elements thesaurus gmo get a Controlled Vocabulary for the consensus designation of introduced or modified genetic elements in genetically modified organisms
BMC Bioinformatics, 2021Co-Authors: P Adamse, Emilie Dagand, Karen Bohmerttatarev, Daniela Wahler, Manoela Miranda, Esther J Kok, Joachim BendiekAbstract:Various databases on genetically modified organisms (GMOs) exist, all with their specific focus to facilitate access to information needed for, e. g., the assistance in risk assessment, the development of detection and identification strategies or inspection and control activities. Each database has its unique approach towards the subject. Often these databases use different terminology to describe the GMOs. For adequate GMO addressing and identification and exchange of GMO-related information it is necessary to use commonly agreed upon concepts and terminology. A hierarchically structured Controlled Vocabulary describing the genetic elements inserted into conventional GMOs, and GMOs developed by the use of gen(om)e-editing is presented: the GMO genetic element thesaurus (GMO-GET). GMO-GET can be used for GMO-related documentation, including GMO-related databases. It has initially been developed on the basis of two GMO databases, i.e. the Biosafety Clearing-House and the EUginius database. The use of GMO-GET will enable consistent and compatible information (harmonisation), also allowing an accurate exchange of information between the different data systems and thereby facilitating their interoperability. GMO-GET can also be used to describe genetic elements that are altered in organisms obtained through current targeted genome-editing techniques.
Martin M Sachs - One of the best experts on this subject based on the ideXlab platform.
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the plant ontology database a community resource for plant structure and developmental stages Controlled Vocabulary and annotations
Nucleic Acids Research, 2008Co-Authors: Shulamit Avraham, Pankaj Jaiswal, Katica Ilic, Elizabeth A Kellogg, Susan R Mccouch, Anuradha Pujar, Leonore Reiser, Seung Y Rhee, Chihwei Tung, Martin M SachsAbstract:The Plant Ontology Consortium (POC, http://www.plantontology.org) is a collaborative effort among model plant genome databases and plant researchers that aims to create, maintain and facilitate the use of a Controlled Vocabulary (ontology) for plants. The ontology allows users to ascribe attributes of plant structure (anatomy and morphology) and developmental stages to data types, such as genes and phenotypes, to provide a semantic framework to make meaningful cross-species and database comparisons. The POC builds upon groundbreaking work by the Gene Ontology Consortium (GOC) by adopting and extending the GOC's principles, existing software and database structure. Over the past year, POC has added hundreds of ontology terms to associate with thousands of genes and gene products from Arabidopsis, rice and maize, which are available through a newly updated web-based browser (http://www.plantontology.org/amigo/go.cgi) for viewing, searching and querying. The Consortium has also implemented new functionalities to facilitate the application of PO in genomic research and updated the website to keep the contents current. In this report, we present a brief description of resources available from the website, changes to the interfaces, data updates, community activities and future enhancement.
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plant ontology po a Controlled Vocabulary of plant structures and growth stages
Comparative and Functional Genomics, 2005Co-Authors: Pankaj Jaiswal, Shulamit Avraham, Katica Ilic, Elizabeth A Kellogg, Susan R Mccouch, Anuradha Pujar, Leonore Reiser, Seung Y Rhee, Martin M SachsAbstract:The Plant Ontology Consortium (POC) (www.plantontology.org) is a collaborative effort among several plant databases and experts in plant systematics, botany and genomics. A primary goal of the POC is to develop simple yet robust and extensible Controlled vocabularies that accurately reflect the biology of plant structures and developmental stages. These provide a network of vocabularies linked by relationships (ontology) to facilitate queries that cut across datasets within a database or between multiple databases. The current version of the ontology integrates diverse vocabularies used to describe Arabidopsis, maize and rice (Oryza sp.) anatomy, morphology and growth stages. Using the ontology browser, over 3500 gene annotations from three species-specific databases, The Arabidopsis Information Resource (TAIR) for Arabidopsis, Gramene for rice and MaizeGDB for maize, can now be queried and retrieved.
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plant ontology po a Controlled Vocabulary of plant structures and growth stages research articles
Comparative and Functional Genomics, 2005Co-Authors: Pankaj Jaiswal, Shulamit Avraham, Katica Ilic, Elizabeth A Kellogg, Susan R Mccouch, Anuradha Pujar, Leonore Reiser, Seung Y Rhee, Martin M Sachs, Mary L SchaefferAbstract:The Plant Ontology Consortium (POC) () is a collaborative effort among several plant databases and experts in plant systematics, botany and genomics. A primary goal of the POC is to develop simple yet robust and extensible Controlled vocabularies that accurately reflect the biology of plant structures and developmental stages. These provide a network of vocabularies linked by relationships (ontology) to facilitate queries that cut across datasets within a database or between multiple databases. The current version of the ontology integrates diverse vocabularies used to describe Arabidopsis, maize and rice (Oryza sp.) anatomy, morphology and growth stages. Using the ontology browser, over 3500 gene annotations from three species-specific databases, The Arabidopsis Information Resource (TAIR) for Arabidopsis, Gramene for rice and MaizeGDB for maize, can now be queried and retrieved. Copyright © 2006 John Wiley & Sons, Ltd.
Richard G Cote - One of the best experts on this subject based on the ideXlab platform.
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the ontology lookup service more data and better tools for Controlled Vocabulary queries
Nucleic Acids Research, 2008Co-Authors: Richard G Cote, Philip Jones, Rolf Apweiler, Lennart Martens, Henning HermjakobAbstract:The Ontology Lookup Service (OLS) (http://www.ebi.ac.uk/ols) provides interactive and programmatic interfaces to query, browse and navigate an ever increasing number of biomedical ontologies and Controlled vocabularies. The volume of data available for querying has more than quadrupled since it went into production and OLS functionality has been integrated into several high-usage databases and data entry tools. Improvements have been made to both OLS query interfaces, based on user feedback and requirements, to improve usability and service interoperability and provide novel ways to perform queries.
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the ontology lookup service a lightweight cross platform tool for Controlled Vocabulary queries
BMC Bioinformatics, 2006Co-Authors: Richard G Cote, Philip Jones, Rolf Apweiler, Henning HermjakobAbstract:With the vast amounts of biomedical data being generated by high-throughput analysis methods, Controlled vocabularies and ontologies are becoming increasingly important to annotate units of information for ease of search and retrieval. Each scientific community tends to create its own locally available ontology. The interfaces to query these ontologies tend to vary from group to group. We saw the need for a centralized location to perform Controlled Vocabulary queries that would offer both a lightweight web-accessible user interface as well as a consistent, unified SOAP interface for automated queries. The Ontology Lookup Service (OLS) was created to integrate publicly available biomedical ontologies into a single database. All modified ontologies are updated daily. A list of currently loaded ontologies is available online. The database can be queried to obtain information on a single term or to browse a complete ontology using AJAX. Auto-completion provides a user-friendly search mechanism. An AJAX-based ontology viewer is available to browse a complete ontology or subsets of it. A programmatic interface is available to query the webservice using SOAP. The service is described by a WSDL descriptor file available online. A sample Java client to connect to the webservice using SOAP is available for download from SourceForge. All OLS source code is publicly available under the open source Apache Licence. The OLS provides a user-friendly single entry point for publicly available ontologies in the Open Biomedical Ontology (OBO) format. It can be accessed interactively or programmatically at http://www.ebi.ac.uk/ontology-lookup/ .
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the ontology lookup service a lightweight cross platform tool for Controlled Vocabulary queries
BMC Bioinformatics, 2006Co-Authors: Richard G Cote, Philip Jones, Rolf Apweiler, Henning HermjakobAbstract:Background With the vast amounts of biomedical data being generated by high-throughput analysis methods, Controlled vocabularies and ontologies are becoming increasingly important to annotate units of information for ease of search and retrieval. Each scientific community tends to create its own locally available ontology. The interfaces to query these ontologies tend to vary from group to group. We saw the need for a centralized location to perform Controlled Vocabulary queries that would offer both a lightweight web-accessible user interface as well as a consistent, unified SOAP interface for automated queries.
Rolf Apweiler - One of the best experts on this subject based on the ideXlab platform.
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the ontology lookup service more data and better tools for Controlled Vocabulary queries
Nucleic Acids Research, 2008Co-Authors: Richard G Cote, Philip Jones, Rolf Apweiler, Lennart Martens, Henning HermjakobAbstract:The Ontology Lookup Service (OLS) (http://www.ebi.ac.uk/ols) provides interactive and programmatic interfaces to query, browse and navigate an ever increasing number of biomedical ontologies and Controlled vocabularies. The volume of data available for querying has more than quadrupled since it went into production and OLS functionality has been integrated into several high-usage databases and data entry tools. Improvements have been made to both OLS query interfaces, based on user feedback and requirements, to improve usability and service interoperability and provide novel ways to perform queries.
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the ontology lookup service a lightweight cross platform tool for Controlled Vocabulary queries
BMC Bioinformatics, 2006Co-Authors: Richard G Cote, Philip Jones, Rolf Apweiler, Henning HermjakobAbstract:With the vast amounts of biomedical data being generated by high-throughput analysis methods, Controlled vocabularies and ontologies are becoming increasingly important to annotate units of information for ease of search and retrieval. Each scientific community tends to create its own locally available ontology. The interfaces to query these ontologies tend to vary from group to group. We saw the need for a centralized location to perform Controlled Vocabulary queries that would offer both a lightweight web-accessible user interface as well as a consistent, unified SOAP interface for automated queries. The Ontology Lookup Service (OLS) was created to integrate publicly available biomedical ontologies into a single database. All modified ontologies are updated daily. A list of currently loaded ontologies is available online. The database can be queried to obtain information on a single term or to browse a complete ontology using AJAX. Auto-completion provides a user-friendly search mechanism. An AJAX-based ontology viewer is available to browse a complete ontology or subsets of it. A programmatic interface is available to query the webservice using SOAP. The service is described by a WSDL descriptor file available online. A sample Java client to connect to the webservice using SOAP is available for download from SourceForge. All OLS source code is publicly available under the open source Apache Licence. The OLS provides a user-friendly single entry point for publicly available ontologies in the Open Biomedical Ontology (OBO) format. It can be accessed interactively or programmatically at http://www.ebi.ac.uk/ontology-lookup/ .
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the ontology lookup service a lightweight cross platform tool for Controlled Vocabulary queries
BMC Bioinformatics, 2006Co-Authors: Richard G Cote, Philip Jones, Rolf Apweiler, Henning HermjakobAbstract:Background With the vast amounts of biomedical data being generated by high-throughput analysis methods, Controlled vocabularies and ontologies are becoming increasingly important to annotate units of information for ease of search and retrieval. Each scientific community tends to create its own locally available ontology. The interfaces to query these ontologies tend to vary from group to group. We saw the need for a centralized location to perform Controlled Vocabulary queries that would offer both a lightweight web-accessible user interface as well as a consistent, unified SOAP interface for automated queries.