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  1. External Tools

Ontologies in the VCI and GCI

PreviousGCI APINextMONDO Search Help

Last updated 1 year ago

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 . We provide detailed guidance on how to look up and .

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

EMBL-EBI Ontology Lookup Service
MONDO disease terms
HPO phenotypes
https://www.genenames.org/
https://hgvs-nomenclature.org/
https://mondo.monarchinitiative.org/
https://omim.org/
https://hpo.jax.org/
https://reg.clinicalgenome.org/
http://geneontology.org/
http://www.sequenceontology.org/
http://obophenotype.github.io/uberon/
https://www.ncbi.nlm.nih.gov/taxonomy
http://bioassayontology.org/
https://obophenotype.github.io/cell-ontology/
https://www.ebi.ac.uk/efo/
http://www.informatics.jax.org/vocab/mp_ontology/
https://obofoundry.org/ontology/mmo
https://github.com/HUPO-PSI/psi-mi-CV
https://github.com/monarch-initiative/SEPIO-ontology/wiki