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PLOS Thesaurus concept tree in BioPortal

Support for SKOS vocabularies in BioPortal

BioPortal is a web-based portal for accessing and sharing ontologies. The application accepts ontology submissions in OWL and OBO format, and SKOS vocabularies that contain particular constructs.

This wiki page documents the minimum set of SKOS constructs that must be present in a SKOS vocabulary for BioPortal to accept and handle the submission properly.

Required SKOS constructs


Concepts are the fundamental elements of SKOS vocabularies and are asserted using the skos:Concept class, e.g.:

 <> rdf:type skos:Concept

SKOS vocabularies submitted to BIoPortal must contain one or more concept assertions. See the W3C's SKOS System Primer and SKOS Reference for SKOS concept documentation and examples:

skos:ConceptScheme & skos:hasTopConcept

For every ontology entry in BioPortal, the application provides a tabbed interface with various views of the ontology data, e.g., a "Classes" tab with a tree structure to graphically depict the hierarchical collection of ontology classes.

In the case of SKOS vocabularies, BioPortal determines which concepts to display as roots in the concept tree by querying vocabulary content for occurrences of skos:hasTopConcept property assertions. Top concepts are the most general concepts contained in SKOS concept schemes (an aggregation of one or more SKOS concepts).

The following example, taken from the SKOS System Primer, shows how to define a concept scheme and link it to the most general concepts it contains:

@prefix skos: <> .
@prefix rdf: <> .
@prefix ex: <> .

ex:animalThesaurus rdf:type skos:ConceptScheme;
  skos:hasTopConcept ex:mammals;
  skos:hasTopConcept ex:fish.

SKOS vocabularies submitted to BioPortal must contain a minimum of one concept scheme and top concept assertion. See the the SKOS System Primer and SKOS Reference for more documentation of concept schemes and top concepts: