Ontologies in the VCI and GCI
Wherever possible the VCI and GCI ensures rigorous and standardized data capture of specific evidence types by the use of ontologies and controlled vocabularies (examples shown in table below).
Most ontologies can be searched using the EMBL-EBI Ontology Lookup Service. We provide detailed guidance on how to look up MONDO disease terms and HPO phenotypes.
| Ontology/Vocabulary System | Topic Covered | Resource Information |
|---|---|---|
HUGO Gene Nomenclature Committee (HGNC) | gene nomenclature | |
Human Genome Variation Society (HGVS) | variant nomenclature | |
Monarch Disease Ontology (MonDO) | disease descriptions | |
Online Mendelian Inheritance in Man (OMIM) | disease descriptions | |
Human Phenotype Ontology (HPO) | phenotypic descriptions | |
ClinGen Allele Registry (CAR) | canonical alleles | |
Gene Ontology (GO) | cell processes and interactions | |
Sequence Ontology (SO) | molecular consequences | |
Uber-anatomy Ontology (UBERON) | anatomy (organs/tissues) | |
NCBI Organismal Taxonomy (NCBITAXON) | organism descriptions | |
BioAssay Ontology (BAO) | functional data | |
Cell Ontology (CL) | cell lines and cell culture models | |
Experimental Factor Ontology (EFO) | cell lines and cell culture models | |
Mammalian Phenotype Ontology (MP) | non human model organisms | |
Measurement Method Ontology (MMO) | clinical and phenotypic measurement methods | |
Molecular Interactions Controlled Vocabulary (MI) | protein-protein interactions | |
Scientific Evidence & Provenance Ontology (SEPIO) | provenance of scientific claims |
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