VIVO Documentation
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Background
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
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Integrated Semantic Framework
The VIVO ontology incorporates classses and properties from several other well-known ontologies, including the following:ISF ontology leverages the following ontologies in a unified, semantic structure:
- VIVO – http://vivoweb.org/ontology/core
- eagle-i Resource Ontology (ERO) – https://open.med.harvard.edu/wiki/display/eaglei/Ontology
- Basic Formal Ontology (BFO) – http://www.ifomis.org/bfo
- Bibliographic Ontology (BIBO) – http://bibliographic-ontology.org/
- Cell Ontology (CL) – http://cellontology.org/?q=download
- Event Ontology – http://motools.sourceforge.net/event/event.html
- The Bibliographic Ontology (BIBO, namespace bibo)
- BIBO includes the Event Ontology
- eagle-i, the research resource ontology developed by the NIH-funded eagle-i Consortium
- Friend of a Friend (FOAF) – http://www.foaf-project.org/
- Gene Ontology (GO) – http://geneontology.sourceforge.net/#code
- Geopolitical.owl, from the U.N. Food and Agriculture Organization
- Information Artifact Ontology (IAO) – https://github.com/information-artifact-ontology/IAO/
- Ontology for Biomedical Investigations (OBI) – http://obi.sourceforge.net/ontologyInformation/
- 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://obofoundry.org/ro/
- Software Ontology (SWO) – http://theswo.sourceforge.net/
- Sequence Ontology (SO) – http://www.sequenceontology.org/
- 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/