GEEM Ontology Import

The general approach for setting up GEEM display of application ontology content is diagrammed below. For GEEM to work, an application ontology must be annotated according to GEEM requirements, as documented in the GEEM Wiki "Curation" pages.

To generate a JSON data structure that GEEM can search and browse, run the scripts/jsonimo.py python script on the command line:

> jsonimo.py [path to ontology input OWL file or URL to online ontology file, both require rdf/xml format] -o [path to output folder]

If the input ontology file has import files, the script assumes they are located in an "imports/" folder in the ontology main file folder. The GEEM portal or the GEEM form renderer only needs this file to display the related web forms and specification formats.

[Add instructions to import the json specification into the GEEM database here].

Currently, if inappropriate relations between entities exist, circular loops might be possible in rendering form elements. A recursive depth limit of 20 descendant form elements has been instituted (in OntologyForm.js) for the form rendering. A loop that exceeds this amount is exited, and is reported in the browser's javascript console as an "AWOL loop".