Experimental Factor Ontology(EFO)
Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N, Zhukova A, Brazma A, Parkinson H: Modeling Sample Variables with an Experimental Factor Ontology. Bioinformatics 2010, 26(8):1112-1118
The Experimental Factor Ontology (EFO) provides a systematic description of many experimental variables available in EBI databases, and for external projects such as the NHGRI GWAS catalogue. It combines parts of several biological ontologies, such as anatomy, disease and chemical compounds. The scope of EFO is to support the annotation, analysis and visualization of data handled by many groups at the EBI and as the core ontology for OpenTargets.org
Experimental factors are essentially the variable aspects of an experiment design which can be used to describe an experiment, or set of experiments, in an increasingly detailed manner. The factors are modelled as classes (i.e. types) within the ontology and properties are used to add information about each type such as a textual definition and synonyms for that term label as well as axiomatic class descriptions such as whether the entity being described is part_of another entity or a subclass of it.
As an application focused ontology, we attempt to import and reuse classes where they exist in external, reference ontologies.
- External Ontology and Resource Mapping List
The full list of ontologies and external resources currently imported or mapped into EFO is as follows:
The Monarch Disease Ontology (MONDO)
Orphanet Rare Disease (version 2.0)
UBERON anatomy ontology Chemical entities of biological interest (CHEBI)
Cell type ontology (CL)
Cell Line Ontology (CLO)
Mammalian phenotype (MP) ver1.309
Human Phenotype (HP)
Medical Subject Headings (MSH) ver2009_2009_02_13
International Classification of Diseases (ICD-9) ver9
Phenotypic quality (PATO) ver1.188
CRISP Thesaurus Version 2.5.2.0
Mosquito gross anatomy (TGMA) ver1.10
Human disease (DOID) ver1.88
Drosophila gross anatomy (FBbt) ver1.30
Foundational Model of Anatomy (FMA) ver3.0
The Arabidopsis Information Resource (TAIR) (various dates)
The Jackson Lab mouse database (various dates)
SNOMED Clinical Terms (SNOMEDCT) ver2009_01_31
Ontology for Biomedical Investigations (OBI)
Units of measurement (UO) ver1.21
Microarray experimental conditions (MO) ver1.3.1.1
Plant structure (PO)
Minimal anatomical terminology (MAT) ver1.1
NIFSTD (nif) ver1.4
NCI Thesaurus (NCIt) ver09.07
Zebrafish anatomy and development (ZFA) ver1.23
BRENDA tissue / enzyme source (BTO) ver1.3
Relation Ontology
网友评论