Ontology Web Services

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

1. First get owltools from http://googlecode.com/p/owltools svn.
2. Run "ant jar"
3. 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:

• http://localhost:9999/isClassApplicableForTaxon?PARAMS

Main parameters:

• id (one or more)
• taxid (one or more)

Examples:

Debugging:

• http://localhost:9999/isClassApplicableForTaxon?id=GO:0007400&id=GO:0048658&id=GO:0090127&taxid=NCBITaxon:3702&taxid=NCBITaxon:9606&format=pretty

Using OBO IDs:

• http://localhost:9999/isClassApplicableForTaxon?id=GO:0007400&id=GO:0048658&id=GO:0090127&taxid=NCBITaxon:3702&taxid=NCBITaxon:9606&format=txt&idstyle=obo

JSON output:

TODO

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