Experimental factor ontology
{{Use dmy dates|date=December 2015}}
{{infobox biodatabase
|title = Experimental Factor Ontology
|logo = Logo of the Experimental Factor Ontlogy.gif
|description = Biomedical ontology
|scope = Experimental and sample variables
|organism = Multiple
|center = European Molecular Biology Laboratory
|laboratory = European Bioinformatics Institute
|author =
|released =
|standard =
|format =
|url = [http://www.ebi.ac.uk/efo/ EFO]
|download = [http://www.ebi.ac.uk/efo/efo.owl Download ontology]
|sparql = [http://www.ebi.ac.uk/rdf/services/atlas/sparql EBI RDF Platform]
|webapp = http://www.ebi.ac.uk/efo
|standalone =
|license =
|versioning =
|frequency = monthly
|curation = Manually curated, text mining
}}
Experimental factor ontology, also known as EFO, is an open-access ontology of experimental variables particularly those used in molecular biology. The ontology covers variables which include aspects of disease, anatomy, cell type, cell lines, chemical compounds and assay information. EFO is developed and maintained at the EMBL-EBI as a cross-cutting resource for the purposes of curation, querying and data integration{{cite journal |pages=D18–D25 |doi= 10.1093/nar/gkt1206 |title=The European Bioinformatics Institute's data resources 2014 |year=2014 |last1=Brooksbank|first1=C. |last2=Bergman |first2=M.T. |last3=Apweiler |first3=A. |last4=Birney |first4=E. |last5=Thornton |first5=J. = |journal=Nucleic Acids Research |volume=42 |issue= Database issue |pmid=24271396 |pmc=3964968 }} in resources such as Ensembl,{{cite journal |pages=D749–D755 |doi=10.1093/nar/gkt1196 |title=Ensembl 2014| year=2014 |last1=Flicek |first1=P. |journal=Nucleic Acids Research |volume= 42|issue=Database issue |pmid=24316576 | pmc=3964975}} ChEMBL and Expression Atlas.{{cite journal |pages=D690–D698 |doi=10.1093/nar/gkp936 |title=Gene Expression Atlas at the European Bioinformatics Institute| year=2010 |last1=Kapushesky|first1=M. | last2=Emam| first2=I | last3=Holloway| first3=E | last4=Kurnosov | first4=P| last5=Zorin|first5=A|last6=Malone | first6=J | last7=Rustici| first7=G |last8=Williams| first8=E |last9=Parkinson| first9=H |last10=Brazma| first10=A | journal=Nucleic Acids Research |volume=38 |issue=Database issue |pmid=19906730 | pmc=2808905}}
Scope and access
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. By December 2013 the scope had grown to include several other EMBL-EBI resources and several external projects including CellFinder,{{cite journal | title=CELDA – an ontology for the comprehensive representation of cells in complex systems | pages=228 | volume=14 | journal=BMC Bioinformatics| last1=Seltmann |first1=S. | year=2014 | doi=10.1186/1471-2105-14-228 | pmid=23865855 | pmc=3722091 | doi-access=free }} cell lines from the ENCODE project and phenotype to SNP information in the NHGRI's Catalog of Published Genome-Wide Association Studies.{{cite journal |pages=D1001–D1006 |doi=10.1093/nar/gkt1229 |title=The NHGRI GWAS Catalog, a curated resource of SNP-trait associations| year=2014 |last1=Welter |first1=D. |journal=Nucleic Acids Research |volume=42 |issue=Database issue |pmid=24316577 | pmc=3965119}}
EFO makes 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, such as ChEBI{{cite journal |pages=D249–54 |doi=10.1093/nar/gkp886 |title=Chemical Entities of Biological Interest: An update |year=2009 |last1=De Matos |first1=P. |last2=Alcantara |first2=R. |last3=Dekker |first3=A. |last4=Ennis |first4=M. |last5=Hastings |first5=J. |last6=Haug |first6=K. |last7=Spiteri |first7=I. |last8=Turner |first8=S. |last9=Steinbeck |first9=C. |journal=Nucleic Acids Research |volume=38 |pmid=19854951 |issue=Database issue |pmc=2808869 }} and the Ontology for Biomedical Investigations.
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, BioPortal Web Service hosted at the National Centre for Biomedical Ontology (NCBO){{cite web |url=http://bioportal.bioontology.org/ |title= NCBO BioPortal | publisher=Stanford University |access-date=4 April 2014}} and downloads.
See also
References
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