Ontology Web Services
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Purpose
Ontology Web Services provide a means of querying and possibly manipulating ontologies.
- logical relationships for and metadata about an ontology class
- ontology visualization
- graph traversal
- reasoning
- Consistency checking
- Finding inferred relationships
Implementation
The majority of Ontology Web Services are provided using OWLTools. See the OWLTools Web Services Documentation.
OWLTools is neutral about whether the input ontology is obo or owl.
Starting a server
- First get owltools from http://googlecode.com/p/owltools svn.
- Run "ant jar"
- Start it up
$ owltools go.obo --start-server -p 9031
Examples
TODO
Visualization
- http://localhost:9031/qviz?id=GO:2001055 positive regulation of mesenchymal cell apoptosis
Taxon Checks
Running the server:
cd go/quality_control/annotation_checks/taxon_checks cvs update owltools ncbi_taxon_slim.obo taxon_go_triggers.obo taxon_union_materialized.obo ../../../ontology/editors/gene_ontology_write.obo --merge-support-ontologies --start-server -p 9999
Running the server from PURLs:
owltools http://purl.obolibrary.org/obo/go/extensions/x-taxon-importer.owl --merge-imports-closure --start-server -p 9999
(startup time of ~2 mins)
Connecting:
Main parameters:
- id (one or more)
- taxid (one or more)
Examples:
Debugging:
Using OBO IDs:
JSON output:
TODO
API Documentation
Authentication
TODO
Clients
TODO
See also
TermGenie is an application for requesting and generating ontology terms. TermGenie Web Services can be considered a subset of Ontology Web Services