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

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dc.contributor.authorO'Neill, Kieranen_ZA
dc.contributor.authorGarcia, Alexanderen_ZA
dc.contributor.authorSchwegmann, Anitaen_ZA
dc.contributor.authorJimenez, Rafaelen_ZA
dc.contributor.authorJacobson, Danen_ZA
dc.contributor.authorHermjakob, Henningen_ZA
dc.date.accessioned2015-10-28T07:01:13Z
dc.date.available2015-10-28T07:01:13Z
dc.date.issued2008en_ZA
dc.description.abstractBACKGROUND: 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.zaen_ZA
dc.identifier.apacitationO'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/11427/14451en_ZA
dc.identifier.chicagocitationO'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/11427/14451en_ZA
dc.identifier.citationO'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.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
dc.identifier.urihttp://hdl.handle.net/11427/14451
dc.identifier.urihttp://dx.doi.org/10.1186/1471-2105-9-437
dc.identifier.vancouvercitationO'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.language.isoengen_ZA
dc.publisherBioMed Central Ltden_ZA
dc.publisher.departmentInstitute of Infectious Disease and Molecular Medicineen_ZA
dc.publisher.facultyFaculty of Health Sciencesen_ZA
dc.publisher.institutionUniversity of Cape Town
dc.rightsThis is an Open Access article distributed under the terms of the Creative Commons Attribution Licenseen_ZA
dc.rights.holder2008 O'Neill et al; licensee BioMed Central Ltd.en_ZA
dc.rights.urihttp://creativecommons.org/licenses/by/2.0en_ZA
dc.sourceBMC Bioinformaticsen_ZA
dc.source.urihttp://www.biomedcentral.com/bmcbioinformatics/en_ZA
dc.subject.otherGene Ontologyen_ZA
dc.titleOntoDas - a tool for facilitating the construction of complex queries to the Gene Ontologyen_ZA
dc.typeJournal Articleen_ZA
uct.type.filetypeText
uct.type.filetypeImage
uct.type.publicationResearchen_ZA
uct.type.resourceArticleen_ZA
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