OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology

 

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dc.contributor.author O'Neill, Kieran en_ZA
dc.contributor.author Garcia, Alexander en_ZA
dc.contributor.author Schwegmann, Anita en_ZA
dc.contributor.author Jimenez, Rafael en_ZA
dc.contributor.author Jacobson, Dan en_ZA
dc.contributor.author Hermjakob, Henning en_ZA
dc.date.accessioned 2015-10-28T07:01:13Z
dc.date.available 2015-10-28T07:01:13Z
dc.date.issued 2008 en_ZA
dc.identifier.citation O'Neill, K., Garcia, A., Schwegmann, A., Jimenez, R. C., Jacobson, D., & Hermjakob, H. (2008). OntoDas–a tool for facilitating the construction of complex queries to the Gene Ontology. BMC bioinformatics, 9(1), 437. en_ZA
dc.identifier.uri http://hdl.handle.net/11427/14451
dc.identifier.uri http://dx.doi.org/10.1186/1471-2105-9-437
dc.description.abstract BACKGROUND: Ontologies such as the Gene Ontology can enable the construction of complex queries over biological information in a conceptual way, however existing systems to do this are too technical. Within the biological domain there is an increasing need for software that facilitates the flexible retrieval of information. OntoDas aims to fulfil this need by allowing the definition of queries by selecting valid ontology terms. RESULTS: OntoDas is a web-based tool that uses information visualisation techniques to provide an intuitive, interactive environment for constructing ontology-based queries against the Gene Ontology Database. Both a comprehensive use case and the interface itself were designed in a participatory manner by working with biologists to ensure that the interface matches the way biologists work. OntoDas was further tested with a separate group of biologists and refined based on their suggestions. CONCLUSION: OntoDas provides a visual and intuitive means for constructing complex queries against the Gene Ontology. It was designed with the participation of biologists and compares favourably with similar tools. It is available at http://ontodas.nbn.ac.za en_ZA
dc.language.iso eng en_ZA
dc.publisher BioMed Central Ltd en_ZA
dc.rights This is an Open Access article distributed under the terms of the Creative Commons Attribution License en_ZA
dc.rights.uri http://creativecommons.org/licenses/by/2.0 en_ZA
dc.source BMC Bioinformatics en_ZA
dc.source.uri http://www.biomedcentral.com/bmcbioinformatics/ en_ZA
dc.subject.other Gene Ontology en_ZA
dc.title OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology en_ZA
dc.type Journal Article en_ZA
dc.rights.holder 2008 O'Neill et al; licensee BioMed Central Ltd. en_ZA
uct.type.publication Research en_ZA
uct.type.resource Article en_ZA
dc.publisher.institution University of Cape Town
dc.publisher.faculty Faculty of Health Sciences en_ZA
dc.publisher.department Institute of Infectious Disease and Molecular Medicine en_ZA
uct.type.filetype Text
uct.type.filetype Image
dc.identifier.apacitation O'Neill, K., Garcia, A., Schwegmann, A., Jimenez, R., Jacobson, D., & Hermjakob, H. (2008). OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology. <i>BMC Bioinformatics</i>, http://hdl.handle.net/11427/14451 en_ZA
dc.identifier.chicagocitation O'Neill, Kieran, Alexander Garcia, Anita Schwegmann, Rafael Jimenez, Dan Jacobson, and Henning Hermjakob "OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology." <i>BMC Bioinformatics</i> (2008) http://hdl.handle.net/11427/14451 en_ZA
dc.identifier.vancouvercitation O'Neill K, Garcia A, Schwegmann A, Jimenez R, Jacobson D, Hermjakob H. OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology. BMC Bioinformatics. 2008; http://hdl.handle.net/11427/14451. en_ZA
dc.identifier.ris TY - Journal Article AU - O'Neill, Kieran AU - Garcia, Alexander AU - Schwegmann, Anita AU - Jimenez, Rafael AU - Jacobson, Dan AU - Hermjakob, Henning AB - BACKGROUND: Ontologies such as the Gene Ontology can enable the construction of complex queries over biological information in a conceptual way, however existing systems to do this are too technical. Within the biological domain there is an increasing need for software that facilitates the flexible retrieval of information. OntoDas aims to fulfil this need by allowing the definition of queries by selecting valid ontology terms. RESULTS: OntoDas is a web-based tool that uses information visualisation techniques to provide an intuitive, interactive environment for constructing ontology-based queries against the Gene Ontology Database. Both a comprehensive use case and the interface itself were designed in a participatory manner by working with biologists to ensure that the interface matches the way biologists work. OntoDas was further tested with a separate group of biologists and refined based on their suggestions. CONCLUSION: OntoDas provides a visual and intuitive means for constructing complex queries against the Gene Ontology. It was designed with the participation of biologists and compares favourably with similar tools. It is available at http://ontodas.nbn.ac.za DA - 2008 DB - OpenUCT DO - 10.1186/1471-2105-9-437 DP - University of Cape Town J1 - BMC Bioinformatics LK - https://open.uct.ac.za PB - University of Cape Town PY - 2008 T1 - OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology TI - OntoDas - a tool for facilitating the construction of complex queries to the Gene Ontology UR - http://hdl.handle.net/11427/14451 ER - en_ZA


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