VIVO Documentation
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Source ontologies may be imported in their entirety or included selectively through the MIREOT approach – minimum information to reference an external ontology term – used when importing an entire ontology would include unnecessary classes, properties, or axioms.
Imports vs. modules
The Integrated Semantic Framework is maintained in a file repository on GitHub [full ISF] [VIVO-ISF]) that reflects the source ontologies while creating distribution modules grouping classes and properties more by function, such as grants, agents, education, etc.
Ontologies Integrated into the Integrated Semantic Framework
by importing terms and the terms required to support the required terms.
Ontologies Used in the VIVO Ontology
The VIVO Ontology The ISF ontology leverages the following ontologies in a unified, semantic structure:
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- eagle-i Resource Ontology (ERO) – https – http://openwww.medobofoundry.harvard.eduorg/wiki/display/eaglei/Ontologyontology/ero.html
- Basic Formal Ontology (BFO) – http://www.ifomisobofoundry.org/ontology/bfo.html
- Bibliographic Ontology (BIBO) – http://bibliographic-ontologybibliontology.orgcom/
- Cell Ontology (CL) – http://cellontology.org/?q=download
- Event Ontology – http://motools.sourceforge.net/event/event.html
- Friend of a Friend (FOAF) – http://www.foaf-project.org/
- Gene Ontology (GO) – http://geneontology.sourceforge.net/#codeobofoundry.org/ontology/go.html
- Geopolitical.owl, from the U.N. Food and Agriculture Organization
- Information Artifact Ontology (IAO) – httpshttp://githubwww.obofoundry.comorg/information-artifact-ontology/IAO/iao.html
- Ontology for Biomedical Investigations (OBI) – – http://obiwww.sourceforgeobofoundry.netorg/ontologyInformationontology/obi.html
- Ontology of Clinical Research (OCRe) – http://code.google.com/p/ontology-of-clinical-research/
- Reagent Ontology (ReO) – http://code.google.com/p/reagent-ontology/
- Relations Ontology (RO) – http://www.obofoundry.org/ontology/ro/.html
- Software Ontology (SWO) – – http://theswowww.sourceforgeobofoundry.net/Sequence Ontology (SO) – http://www.sequenceontology.org/org/ontology/swo.html
- SKOS (Simple Knowledge Organization System) – http://www.w3.org/2004/02/skos/
- Uberon (Uber anatomy ontology) – http://obo.svn.sourceforge.net/viewvc/obo/uberon/releases/
- vCard – http://www.w3.org/TR/vcard-rdf/
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- SPAR ontologies, including FABIO, CiTO, and C4O: https://purl.org/spar/fabio