Old Release

This documentation relates to an old version of VIVO, version 1.9.x. Looking for another version? See all documentation.

Overview

VIVO stores its information in graphs – named collections of triples.  Graphs keep data organized by kind, and provide the opportunity for different access rights and management practices to be applied at the graph level.  All graphs are available to the VIVO SPARQL query interface.  When using SPARQL to query the VIVO data, one does not need to know the graph the data is contained in.  Triples in all graphs are available to the query.  When updating data in VIVO using CONSTRUCT or UPDATE, knowledge of the graph may be necessary.

Here we show how to list the graphs in a VIVO, and provide a reference for the purpose of each graph.

Listing the graphs used by VIVO

To list the graphs being used by your VIVO, you can run the SPARQL query shown below.  Caution:  If you have a significant amount of data in your VIVO, the query may take quite a while to run.  With tens of thousands of entities in your VIVO, the query should complete in a few minutes.

SPARQL query to list the graphs in a VIVO
SELECT ?g
WHERE
{
    GRAPH ?g {
        ?s ?p ?o .
    }
}
GROUP BY ?g
ORDER BY ?g

To list the triples in a named graph, use the query below, substituting the name of the graph you wish to list.  Caution:  listing the triples in larger graphs may take significant time.

SPARQL query to list the triples in a named graph
SELECT ?s ?p ?o
WHERE
{
    GRAPH <http://vitro.mannlib.cornell.edu/filegraph/tbox/sameAs.n3> {
        ?s ?p ?o .
    }
}

The graphs used by VIVO

Graph nameContents
http://vitro.mannlib.cornell.edu/default/asserted-tboxAll ontology triples as asserted
http://vitro.mannlib.cornell.edu/default/inferred-tboxTriples infered from the asserted ontology triples
http://vitro.mannlib.cornell.edu/default/vitro-kb-2The main triple store for content
http://vitro.mannlib.cornell.edu/default/vitro-kb-applicationMetadataTriples controlling the application
http://vitro.mannlib.cornell.edu/default/vitro-kb-infTriples created by the inferencer
http://vitro.mannlib.cornell.edu/filegraph/abox/academicDegree.rdfControlled vocabulary for academic degrees
http://vitro.mannlib.cornell.edu/filegraph/abox/continents.n3Data provided regarding the continents
http://vitro.mannlib.cornell.edu/filegraph/abox/dateTimeValuePrecision.owlControlled vocabulary for dateTimePrecision
http://vitro.mannlib.cornell.edu/filegraph/abox/documentStatus.owlControlled vocabulary for documentStatus
http://vitro.mannlib.cornell.edu/filegraph/abox/geopolitical.abox.ver1.1-11-18-11.owlData provided regarding geopolitical entities
http://vitro.mannlib.cornell.edu/filegraph/abox/grid.n3Example of a data package. Grid data regarding organizations
http://vitro.mannlib.cornell.edu/filegraph/abox/us-states.rdfData provided regarding US states and territories
http://vitro.mannlib.cornell.edu/filegraph/abox/validation.n3Data regarding validated ORCiD identifiers
http://vitro.mannlib.cornell.edu/filegraph/abox/vocabularySource.n3Data regarding external vocabulary services
http://vitro.mannlib.cornell.edu/filegraph/tbox/agent.owlOntology assertions regarding agents
http://vitro.mannlib.cornell.edu/filegraph/tbox/appControls-temp.n3?
http://vitro.mannlib.cornell.edu/filegraph/tbox/bfo-bridge.owlOntology assertions relating VIVO entities to BFO
http://vitro.mannlib.cornell.edu/filegraph/tbox/bfo.owlOntology assertions regarding Basic Formal Ontology (BFO)
http://vitro.mannlib.cornell.edu/filegraph/tbox/classes-additional.owlOntology assertions regarding classes used in VIVO
http://vitro.mannlib.cornell.edu/filegraph/tbox/clinical.owlOntology assertions regarding clinical trials
http://vitro.mannlib.cornell.edu/filegraph/tbox/contact-vcard.owlOntology assertions regarding vcard
http://vitro.mannlib.cornell.edu/filegraph/tbox/contact.owlOntology assertions regarding OBO classes
http://vitro.mannlib.cornell.edu/filegraph/tbox/data-properties.owlOntology assertions regarding data properties
http://vitro.mannlib.cornell.edu/filegraph/tbox/dataDomains.rdfOntology assertions regarding data domains
http://vitro.mannlib.cornell.edu/filegraph/tbox/dataset.owlOntology assertions to define Dataset class
http://vitro.mannlib.cornell.edu/filegraph/tbox/date-time.owlOntology assertions to define DateTimeInterval class
http://vitro.mannlib.cornell.edu/filegraph/tbox/dateTimeValuePrecision.owlOntology assertions to define DateTimeValuePrecision classes
http://vitro.mannlib.cornell.edu/filegraph/tbox/documentStatus.owlOntology assertions regarding document status
http://vitro.mannlib.cornell.edu/filegraph/tbox/education.owlOntology assertions regarding educational processes, roles, and classes
http://vitro.mannlib.cornell.edu/filegraph/tbox/event.owlOntology assertioons regarding event processes, roles, and classes
http://vitro.mannlib.cornell.edu/filegraph/tbox/geo-political.owlOntology assertions required by geopolitical data
http://vitro.mannlib.cornell.edu/filegraph/tbox/grant.owlOntology assertions regarding grants, roles, and classes
http://vitro.mannlib.cornell.edu/filegraph/tbox/linkSuppression.n3?
http://vitro.mannlib.cornell.edu/filegraph/tbox/location.owlOntology assertions regarding location classes
http://vitro.mannlib.cornell.edu/filegraph/tbox/object-properties.owlOntology assertions to define object properties
http://vitro.mannlib.cornell.edu/filegraph/tbox/object-properties2.owlOntology assertions to define BFO properties
http://vitro.mannlib.cornell.edu/filegraph/tbox/object-properties3.owlOntology assertions to define more object properties
http://vitro.mannlib.cornell.edu/filegraph/tbox/objectDomains.rdfOntology assertions to define object domains
http://vitro.mannlib.cornell.edu/filegraph/tbox/objectRanges.rdfOntology assertions to define object ranges
http://vitro.mannlib.cornell.edu/filegraph/tbox/ontologies.owl?
http://vitro.mannlib.cornell.edu/filegraph/tbox/orcid-interface.n3Ontology assertions for ORCiD and confirmed ORCiD
http://vitro.mannlib.cornell.edu/filegraph/tbox/other.owlOntological definitions of object properties
http://vitro.mannlib.cornell.edu/filegraph/tbox/outreach.owlOntological definitions of BFO object properties
http://vitro.mannlib.cornell.edu/filegraph/tbox/personTypes.n3Ontology assertions to define types of people
http://vitro.mannlib.cornell.edu/filegraph/tbox/process.owlOntology assertions to define miscelleaneous processes
http://vitro.mannlib.cornell.edu/filegraph/tbox/publication.owlOntology assertions to define publication types and related roles
http://vitro.mannlib.cornell.edu/filegraph/tbox/relationship.owlOntology assertions to define relationships, including positions
http://vitro.mannlib.cornell.edu/filegraph/tbox/relationshipAxioms.n3Ontology axioms regarding restrictions on relationships
http://vitro.mannlib.cornell.edu/filegraph/tbox/research-resource-iao.owlOntology assertions to define elements of IAO needed for research resources
http://vitro.mannlib.cornell.edu/filegraph/tbox/research-resource.owlOntology assertions to define ERO research resources
http://vitro.mannlib.cornell.edu/filegraph/tbox/research.owlOntology assertions to define clinical trials
http://vitro.mannlib.cornell.edu/filegraph/tbox/role.owlOntology assertions to define miscellaneous roles
http://vitro.mannlib.cornell.edu/filegraph/tbox/sameAs.n3Ontology assertions defining sameAs
http://vitro.mannlib.cornell.edu/filegraph/tbox/skos-vivo.owlOntology assertions to define various classes as subtypes of skos:Concept
http://vitro.mannlib.cornell.edu/filegraph/tbox/teaching.owlOntology assertions for Course and TeacherRole
http://vitro.mannlib.cornell.edu/filegraph/tbox/vitro-0.7.owlOntology assertions for the Vitro application, internal
http://vitro.mannlib.cornell.edu/filegraph/tbox/vitroPublic.owlOntology assertions for the Vitro application, public. Defines files and file types


Notes

  1. Graphs named "default" are built and managed by the Vitro application.  Graphs names "filegraph" are loaded from files when VIVO starts.  Graphs named "filegraph/abox" are data.  Graphs named "filegraph/tbox" are ontology.
  2. filegraph graphs are named with the name of the file they were loaded from.
  3. filegraph files may be in several formats.  You will see graphs loaded from files with type n3, owl and rdf.
  4. The content in some of the filegraphs may repeat content found in other filegraphs.  This does not impact the application.
  5. Data you load by placing a file in filegraph/abox will appear as a result of the graph listing query above.  See grid.n3 below for an example.  grid.n3 is not distributed with VIVO.

 

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