Mercurial > repos > mikel-egana-aranguren > ncbo_services
changeset 19:4cd75b0d77af
get ontology view tool added
| author | Mikel Egaña Aranguren <mikel-egana-aranguren@toolshed.g2.bx.psu.edu> |
|---|---|
| date | Wed, 18 Jan 2012 17:59:05 +0100 |
| parents | 0078fe4c89e3 |
| children | 1910c878378c |
| files | NCBO_services/README NCBO_services/get_ontology_view.jar NCBO_services/get_ontology_view.xml |
| diffstat | 3 files changed, 41 insertions(+), 0 deletions(-) [+] |
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--- a/NCBO_services/README Wed Jan 18 16:04:52 2012 +0100 +++ b/NCBO_services/README Wed Jan 18 17:59:05 2012 +0100 @@ -23,6 +23,7 @@ <section name="NCBO services" id="NCBO_services"> <tool file="NCBO_services/get_ontology.xml"/> <tool file="NCBO_services/extract.xml"/> + <tool file="NCBO_services/get_ontology_view.xml"/> <tool file="NCBO_services/ncbo_annotator.xml"/> <tool file="NCBO_services/ncbo_annotator.xml"/> <tool file="NCBO_services/ncbo_recommender.xml"/>
--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/NCBO_services/get_ontology_view.xml Wed Jan 18 17:59:05 2012 +0100 @@ -0,0 +1,40 @@ +<tool id="get_ontology_view" name="Get a concrete view of an ontology" version="1.0.1"> + <description>Retrieves a view of an ontology using the view id</description> + <command>java -jar ${__tool_data_path__}/shared/jars/get_ontology_view.jar $api_key $ontologyviewid > $output </command> + + <inputs> + <param name="api_key" type="text" size="100" label="BioPortal API key" /> + <param name="ontologyviewid" type="text" size="100" label="Ontology view ID" /> + </inputs> + <outputs> + <data format="text" name="output" /> + </outputs> + <tests> + <test> + <param name="api_key"/> + </test> + </tests> + <help> + +**What it does** + +It retrieves a view from an ontology contained in BioPortal. + +**Parameters** + +* Bioportal API key: to obtain an API key, open an account in http://bioportal.bioontology.org. +* Ontology view ID: it can be obtained from BioPortal, in the Ontology page, on the views section, by looking at the view URL. For example, it is 41014 for the generic Gene Ontology slim. + +**Contact** + +Please send any request or comment to mikel.egana.aranguren@gmail.com. + +**More information** + +http://bioportal.bioontology.org + +http://www.bioontology.org/wiki/index.php/BioPortal_REST_services + + </help> + +</tool>