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 (originally on Google code and now 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

As documented on the CTSAconnect website ontologies page, the ISF ontology leverages the following ontologies in a unified, semantic structure:

• VIVO – http://vivoweb.org/ontology/core
• eagle-i Resource Ontology (ERO) – http://code.google.com/p/eagle-i

• Basic Formal Ontology (BFO) – http://www.ifomis.org/bfo
• Bibliographic Ontology (BIBO) – http://code.google.com/p/bibotools
• 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/#code
• Geopolitical.owl, from the U.N. Food and Agriculture Organization
• Information Artifact Ontology (IAO) – http://code.google.com/p/information-artifact-ontology/
• 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/

Many of these ontologies are part of The Open Biological and Biomedical Ontologies organization, known as the OBO Foundry