License information for the list of ontologies used in the model

Licence information

This page is meant to list all the current licensing state for the list of ontologies used within the CDE semantic models.

Metadata on license

Table Fields description:

• 'Ontology name' (Ontology name term),
• 'Ontology prefix' (Ontology prefix),
• 'Model prefix' (Ontology prefix used in the models (RDF/ShEx),
• 'Source IRI' (Ontology source IRI or website URL where the license information was found),
• 'Accessed at' (TimeStamp when the license information was checked),
• 'Licence IRI' (License identifier),
• 'Comments' (Additional notes).

Data on license

Ontology name	Ontology prefix	Model prefix	Source IRI	Accessed at	License IRI	Comments
Ontology for Biomedical Investigations	obi	obo	https://raw.githubusercontent.com/obi-ontology/obi/v2019-11-12/obi.owl	03-Sep-20	http://creativecommons.org/licenses/by/4.0/	Attribution 4.0 International (CC BY 4.0): You are free to share and adapt, under the term attribution
RDConnect Ontology	rdc-meta	rdc	https://raw.githubusercontent.com/LUMC-BioSemantics/Rare-Disease-Semantic-Model/master/ontologies/rdc-meta.owl	03-Sep-20	Unknown	In the OWL ontology file there is no metadata information regarding license. Nothing found neither in the RDConnect website https://rd-connect.eu/what-we-do/data-linkage/ontologies-in-rare-disease-registries/
NCBI Taxon	ncbitaxon	obo	http://obofoundry.org/ontology/ncbitaxon.html	03-Sep-20	https://creativecommons.org/publicdomain/zero/1.0/	CC0 1.0 Universal (CC0 1.0) Public Domain Dedication : No Copyright
National Cancer Institute Thesaurus	ncit	obo	https://bioportal.bioontology.org/ontologies/NCIT	04-Sep-20	https://creativecommons.org/licenses/by/4.0/legalcode	Attribution 4.0 International (CC BY 4.0): You are free to share and adapt, under the term attribution
SNOMED CT	snomedct	snomedct	http://bioportal.bioontology.org/ontologies/SNOMEDCT?p=summary	04-Sep-20	https://uts.nlm.nih.gov/license.html	This ontology is made available via the UMLS. Relevant in the UMLS License APPENDIX 2: 2.2.4 in the Licensee's systems (including browsers and data analysis systems) made available to the general public for accessing and/or retrieving any part of the International Release and/or data encoded using the foregoing, provided that users of those systems are not able to extract any substantial portion of SNOMED CT and provided further that no fee is charged for access to those systems except where access is incidental to the provision of training or consulting services. See the license doc in this folder.
HL7	hl7	hl7	http://bioportal.bioontology.org/ontologies/HL7?p=summary	04-Sep-20	Unknown or https://www.hl7.org/fhir/license.html	No License mention neither in the source IRI from the NCBO nor in the RDF/TTL file, BUT HL7 has its own license (CC). In the RDF file: RDF Version of the UMLS ontology HL7V3.0; converted with the UMLS2RDF tool (https://github.com/ncbo/umls2rdf), developed by the NCBO project. It may be that the UMLS applies to this derived product. The UMLS ontology HL7V3.0 is offered under the UMLS License - restriction Level 0. (view this license infomation about the UMLS ontology IRI in the metadata section: https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/HL7V3.0/metadata.html). See the license doc in this folder. I am not an expert but in principle only get the UMLS license (free fees) and include attribution to NLM publicly.
The Phenotype and Trait Ontology	pato	obo	https://raw.githubusercontent.com/pato-ontology/pato/master/pato.owl	04-Sep-20	https://creativecommons.org/licenses/by/3.0/	Attribution 3.0 Unported (CC BY 3.0): you are free to share and adapt, you must give Attribution — You must give appropriate credit, provide a link to the license, and indicate if changes were made. You may do so in any reasonable manner, but not in any way that suggests the licensor endorses you or your use.
Orphanet Rare Disease Ontology	ordo	orpha	http://data.bioontology.org/ontologies/ORDO/submissions/20/download?apikey=8b5b7825-538d-40e0-9e9e-5ab9274a9aeb	04-Sep-20	https://creativecommons.org/licenses/by/4.0/	Attribution 4.0 International (CC BY 4.0). NB in the EJP wiki: ORDO is only used in the image and not in the ShEx and Turtle files.
Logical Observation Identifier Names and Codes	loinc	loinc	http://bioportal.bioontology.org/ontologies/LOINC?p=summary	04-Sep-20	https://uts.nlm.nih.gov/license.html	This ontology is made available via the UMLS. Users of all UMLS ontologies must abide by the terms of the UMLS license, available at https://uts.nlm.nih.gov/license.html. Like HL7, LOINC is made available though level 0 restriction (https://www.nlm.nih.gov/research/umls/sourcereleasedocs/current/LNC/metadata.html). LOINC license: https://loinc.org/kb/license/
Semantic science Ontology	sio	sio	https://raw.githubusercontent.com/micheldumontier/semanticscience/master/ontology/sio/release/sio-release.owl	04-Sep-20	http://creativecommons.org/licenses/by/4.0/	Attribution 4.0 International (CC BY 4.0) : free to use,share,modify. modify with attribution
Experimental Factor Ontology	efo	efo	https://www.ebi.ac.uk/efo/	04-Sep-20	https://www.apache.org/licenses/LICENSE-2.0	EMBL-EBI no restrictions but expects attribution: http://www.ebi.ac.uk/about/terms-of-use/
Variation Ontology	vario	obo	http://www.obofoundry.org/ontology/vario.html	04-Sep-20	Unknown	I checked the OWL file, the OBO vario page, and the VARIO website, ncbo portal, and fairshairing and there is no license information available
Ontology for miRNA Target	omit	is it actually used in the models (see comments field)? as obo??	http://www.obofoundry.org/ontology/omit.html	04-Sep-20	https://creativecommons.org/licenses/by/3.0/	Attribution 3.0 Unported (CC BY 3.0). NB Claimed in EJP wiki: OMIT is the ‘Disease history and diagnosis’ module image, but is not in ShEx or Turtle files
Human Phenotype Ontology	hp	obo	https://raw.githubusercontent.com/obophenotype/human-phenotype-ontology/master/hp.owl	04-Sep-20	https://hpo.jax.org/app/license	license restrictions: The HPO vocabularies, annotation files, tools and documentation are freely available. Users of the HPO should add the following statement to their online presence.
Informed Consent Ontology	ico	obo	https://raw.githubusercontent.com/ICO-ontology/ICO/master/ico.owl	04-Sep-20	http://creativecommons.org/licenses/by/3.0/	Attribution 3.0 Unported (CC BY 3.0).
Ontologized Minimum Information About BIobank data Sharing	omiabis	omiabis	http://www.obofoundry.org/ontology/omiabis.html	04-Sep-20	https://creativecommons.org/licenses/by/3.0/	Attribution 3.0 Unported (CC BY 3.0). NB Claimed in EJP wiki: OMIABIS is not in the whole model figure, is part of the ‘Biobank’ module ShEx file.
EDAM Ontology	edam	edam	http://edamontology.org/page	04-Sep-20	http://creativecommons.org/licenses/by-sa/4.0/	Attribution-ShareAlike 4.0 International License (CC BY-SA 4.0). Free: share and adapt; Restricted to: Attribution and ShareAlike. NB in the EJP wiki: EDAM is not in the whole model figure, is part of the module ‘Pseudonym’ ShEx file.
Genotype Ontology	geno	obo	http://www.obofoundry.org/ontology/geno.html	04-Sep-20	https://creativecommons.org/licenses/by-sa/2.0/	Attribution-ShareAlike 2.0 Generic (CC BY-SA 2.0). Free to: share and adapt. Restricted to: Attribution and ShareAlike.NB in the EJP wiki: GENO is not in the whole model figure, is part of the module ‘Undiagnosis’ ShEx file.
RDF Concepts Vocabulary	rdf	rdf	https://www.w3.org/TR/rdf-concepts/	04-Sep-20	https://www.w3.org/Consortium/Legal/2015/doc-license	W3C Document License: Permission to copy, and distribute the contents of this document, or the W3C document from which this statement is linked, in any medium for any purpose and without fee or royalty is hereby granted, provided that you include the following on ALL copies of the document, or portions thereof, that you use
Relation Ontology	ro	obo	https://raw.githubusercontent.com/oborel/obo-relations/master/ro.owl	04-Sep-20	https://creativecommons.org/publicdomain/zero/1.0/	"CC0 1.0 Universal (CC0 1.0) Public Domain Dedication "
Information Artifact Ontology	iao	obo	https://raw.githubusercontent.com/information-artifact-ontology/IAO/v2020-06-10/iao.owl	05-Sep-20	http://creativecommons.org/licenses/by/4.0/	Attribution 4.0 International (CC BY 4.0) : free to use,share,modify. modify with attribution
Dublin Core	dct	dct	https://dublincore.org/specifications/dublin-core/dcmi-terms/	05-Sep-20	http://creativecommons.org/licenses/by/3.0/	Attribution 3.0 Unported (CC BY 3.0).
Eagle-I Research Resource	ero	obo	http://www.obofoundry.org/ontology/ero.html	05-Sep-20	https://creativecommons.org/licenses/by/2.0/	Attribution 2.0 Generic (CC BY 2.0) : free to share and adapt, you must give attribution
Wikidata	wd	wdp	https://www.wikidata.org/wiki/Wikidata:Main_Page	05-Sep-20	https://creativecommons.org/publicdomain/zero/1.0/	CC0 NB in the ejp wiki: We also need to discuss if we need to use this since it is not an ontology
Provenance Ontology	provo	prov	https://www.w3.org/ns/prov	05-Sep-20	https://www.w3.org/Consortium/Legal/2015/doc-license	W3C Document License
XML Schema Definition	xsd	xsd	https://www.w3.org/TR/xmlschema11-1/	05-Sep-20	https://www.w3.org/Consortium/Legal/2015/doc-license	W3C Document License