User:Schnagglepuss/sandbox
| Content | |
|---|---|
| Description | Biomedical ontology |
| Data types captured | Experimental and sample variables |
| Organisms | Multiple |
| Contact | |
| Research center | European Molecular Biology Laboratory |
| Laboratory |  European Bioinformatics Institute |
| Primary citation | [1] |
| Access | |
| Website | EFO |
| Download URL | Download ontology |
| Sparql endpoint | EBI RDF Platform |
| Tools | |
| Web | http://www.ebi.ac.uk/efo |
| Miscellaneous | |
| Data release frequency | monthly |
| Curation policy | Manually curated, text mining |
The Experimental Factor Ontology, also known as EFO,[1] is an ontology of experimental variables particularly those used in molecular biology. The ontology covers a very wide range of variables which include concepts such as disease, anatomy, cell type, cell lines, chemical compounds and assay information. EFO is developed and maintained primarily at the EMBL-EBI as a cross-cutting resource for curation, querying and data integration in resources such as Ensembl, ChEMBL and Expression Atlas[2].
Scope and Access
[edit]The original aim of EFO was to describe experimental variables in the EBI's Expression Atlas resource. This consisted primarily of disease, anatomical regions and cell types. More recently the scope has grown to include several other EMBL-EBI resources and several external projects including cell lines from the ENCODE project.
EFO makes extensive use of existing biomedical ontologies from the Open Biomedical Ontologies collection in order to improve interoperability with other resources which may also use these same ontologies.
All data in the database is non-proprietary or is derived from a non-proprietary source. It is thus freely accessible and available to anyone. In addition, each data item is fully traceable and explicitly referenced to the original source.
The EFO data is available through a public web interface, Web Service and downloads.
See also
[edit]References
[edit]- ^ a b Malone, J.; Holloway, E.; Adamusiak, T.; Kapushesky, M.; Zheng, J.; Kolesnikov, N.; Zhukova, A.; Brazma, A.; Parkinson, H. (2010). "Modeling sample variables with an Experimental Factor Ontology". Bioinformatics. 26: 1112–8. doi:10.1093/bioinformatics/btq099. PMC 2853691. PMID 20200009.
{{cite journal}}: Invalid|display-authors=9(help) - ^ Brooksbank, C.; Bergman, M.T.; Apweiler, A.; Birney, E.; Thornton, J. = (2014). "The European Bioinformatics Institute's data resources 2014". Nucleic Acids Research. 42: D18 – D25. doi:10.1093/nar/gkt1206. PMC 3964968. PMID 24271396.
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External links
[edit]
Category:Biological databases
Category:Ontology (information science)
Category:Biology terminology