List of Ontologies in the model_v1

This table has a list of all the ontologies used in the CDE semantic model. The first column has links to either download the ontology or to browse it. The prefix links are not all resolvable. Some comments on the usage of ontologies or the prefixes of the ontologies as used in the model are also given.

Disclaimer: This table is outdated (version from 2020) and it will be updated in 2022.

Ontology name	Prefix link	Prefix	Comments
Ontology for Biomedical Investigations (OBI)	http://purl.obolibrary.org/obo/	obo
RDConnect Ontology	http://rdf.biosemantics.org/ontologies/rd-connect/	rdc-meta, rdc	In the images the prefix is rdc-meta but in the ShEx and Turtle files the prefix is rdc.
NCBI Taxon	http://purl.obolibrary.org/obo/	ncbi, obo	In the images the prefix is ncbi but in the ShEx and Turtle files the prefix is obo.
National Cancer Institute Thesaurus (NCIT)	http://purl.obolibrary.org/obo/	ncit, obo	In the images the prefix is ncit but in the ShEx and Turtle files the prefix is obo.
SNOMED CT	http://purl.bioontology.org/ontology/SNOMEDCT/	snomedct
HL7	http://purl.bioontology.org/ontology/HL7/	hl7
The Phenotype and Trait Ontology (PATO)	http://purl.obolibrary.org/obo/	pato, obo	In the images the prefix is pato but in the ShEx and Turtle files the prefix is obo.
Orphanet Rare Disease Ontology (ORDO)	http://www.orpha.net/ORDO/	orpha	ORDO is only used in the image and not in the ShEx and Turtle files.
Logical Observation Identifier Names and codes (LOINC)	http://purl.bioontology.org/ontology/LNC/	loinc
Semantic science Ontology (SIO)	http://semanticscience.org/resource/	sio
Experimental Factor Ontology (EFO)	http://www.ebi.ac.uk/efo/	efo
Variation Ontology (VariO)	http://purl.obolibrary.org/obo/	vario, obo	In the images the prefix is vario but in the ShEx and Turtle files the prefix is obo.
Ontology for miRNA Target (OMIT)	http://purl.obolibrary.org/obo/	omit	OMIT is the ‘Disease history and diagnosis’ module image, but is not in ShEx or Turtle files
Human Phenotype Ontology (HP)	http://purl.obolibrary.org/obo/	hp, obo	In the images the prefix is hp but in the ShEx and Turtle files the prefix is obo.
Informed Consent Ontology (ICO)	http://purl.obolibrary.org/obo/	ico, obo	In the images the prefix is ico but in the ShEx and Turtle files the prefix is obo.
Ontologized Minimum Information About BIobank data Sharing (OMIABIS)	http://purl.obolibrary.org/obo/	omiabis	OMIABIS is not in the whole model figure, is part of the ‘Biobank’ module ShEx file.
EDAM Ontology	http://edamontology.org/	edam	EDAM is not in the whole model figure, is part of the module ‘Pseudonym’ ShEx file.
Genotype Ontology (GENO)	http://purl.obolibrary.org/obo/	obo	GENO is not in the whole model figure, is part of the module ‘Undiagnosis’ ShEx file.
RDF Concepts Vocabulary	https://www.w3.org/1999/02/22-rdf-syntax-ns#	rdf
Relation Ontology (RO)	http://purl.obolibrary.org/obo/	ro, obo	In the images the prefix is ro but in the ShEx and Turtle files the prefix is obo.
Information Artifact Ontology (IAO)	http://purl.obolibrary.org/obo/	iao, obo	In the images the prefix is iao but in the ShEx and Turtle files the prefix is obo.
Dublin Core (DCT)	http://purl.org/dc/terms/	dct
Eagle-I Research Resource (ERO)	http://purl.obolibrary.org/obo/	ero, obo	In the images the prefix is ero but in the ShEx and Turtle files the prefix is obo.
WikiData	https://www.wikidata.org/wiki/	wiki, wdp	In the images the prefix is wiki but in the ShEx and Turtle files the prefix is wdp. We also need to discuss if we need to use this since it is not an ontology
Provenance Ontology (PROV-O)	http://www.w3.org/ns/prov#	prov
XML Schema Definition (XSD)	http://www.w3.org/2001/XMLSchema#	xsd

Notes

In some cases the prefixes on ontologies are tied to the OBO foundry. In these cases we make a decision to use readable prefixes for the images and keep it obo for the files.

In cases where the term ids are numbers we could also use (human-readable) labels for the images and the identifiers for the ShEx and Turtle files.