Modeling sample variables with an Experimental Factor Ontology
| العنوان: | Modeling sample variables with an Experimental Factor Ontology |
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| المؤلفون: | James Malone, Jie Zheng, Alvis Brazma, Nikolay Kolesnikov, Tomasz Adamusiak, Helen Parkinson, Anna Zhukova, Misha Kapushesky, Ele Holloway |
| المساهمون: | European Bioinforrmatics Institute (UK) (EBI), École de biologie industrielle (EBI), European Bioinformatics Institute [Hinxton] (EMBL-EBI), EMBL Heidelberg |
| المصدر: | Bioinformatics; Vol 26 Bioinformatics Bioinformatics, Oxford University Press (OUP), 2010, 26 (8), pp.1112-8. ⟨10.1093/bioinformatics/btq099⟩ |
| بيانات النشر: | Oxford University Press, 2010. |
| سنة النشر: | 2010 |
| مصطلحات موضوعية: | Statistics and Probability, Ontology Inference Layer, Databases, Factual, Experimental factor ontology, Computer science, Process ontology, Databases and Ontologies, Interoperability, Ontology (information science), Biochemistry, Open Biomedical Ontologies, 03 medical and health sciences, 0302 clinical medicine, Text mining, Ontology components, Upper ontology, IDEF5, Molecular Biology, 030304 developmental biology, 0303 health sciences, Information retrieval, business.industry, Gene Expression Profiling, Ontology-based data integration, Suggested Upper Merged Ontology, Computational Biology, Original Papers, [SDV.BIBS]Life Sciences [q-bio]/Quantitative Methods [q-bio.QM], Computer Science Applications, Computational Mathematics, Computational Theory and Mathematics, Ontology, ComputingMethodologies_GENERAL, [INFO.INFO-BI]Computer Science [cs]/Bioinformatics [q-bio.QM], business, Ontology alignment, Algorithms, 030217 neurology & neurosurgery |
| الوصف: | Motivation: Describing biological sample variables with ontologies is complex due to the cross-domain nature of experiments. Ontologies provide annotation solutions; however, for cross-domain investigations, multiple ontologies are needed to represent the data. These are subject to rapid change, are often not interoperable and present complexities that are a barrier to biological resource users. Results: We present the Experimental Factor Ontology, designed to meet cross-domain, application focused use cases for gene expression data. We describe our methodology and open source tools used to create the ontology. These include tools for creating ontology mappings, ontology views, detecting ontology changes and using ontologies in interfaces to enhance querying. The application of reference ontologies to data is a key problem, and this work presents guidelines on how community ontologies can be presented in an application ontology in a data-driven way. Availability: http://www.ebi.ac.uk/efoTest Contact: malone@ebi.ac.uk Supplementary information: Supplementary data are available at Bioinformatics online. |
| اللغة: | English |
| تدمد: | 1367-4803 1367-4811 |
| DOI: | 10.1093/bioinformatics/btq099 |
| الوصول الحر: | https://explore.openaire.eu/search/publication?articleId=doi_dedup___::d5d323e99793c014b250cbabf9f67ea2Test |
| حقوق: | OPEN |
| رقم الانضمام: | edsair.doi.dedup.....d5d323e99793c014b250cbabf9f67ea2 |
| قاعدة البيانات: | OpenAIRE |
| تدمد: | 13674803 13674811 |
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| DOI: | 10.1093/bioinformatics/btq099 |