search

cidgoh / geem

Genomic Epidemiology Entity Mart
Creative Commons Attribution 4.0 International
3 stars 1 forks source link

Allow term lookup to query a particular ontology #11

Open Public-Health-Bioinformatics opened 6 years ago

Public-Health-Bioinformatics commented 6 years ago

Currently the "user interface feature'=lookup" annotation on a 'categorical specification tree' input list searches the OBOFoundry ontology given by the term prefix (e.g. NCIT_C28554 = NCIT ontology ) using Embl-EBI's OLS. Enhance this annotation functionality to have option of including a particular ontology to search, e.g. "user interface feature'=lookup:GENEPIO". This allows an application ontology to take over hierarchy subclass items (and be selective about them) beyond what original ontology allows.

Public-Health-Bioinformatics commented 6 years ago

This is implemented now, via "user interface feature'=lookup:http://purl.obofoundry.org/obo/genepio,..." parameter.

However a remaining GenEpiO GEO information problem has been identified that the selection lists for province/territory/state/region have mostly NCIT codes at top level for these individual terms, but they don't have GAZETTEER underlying items, but rather just NCIT ones. Some provision for searching GenEpiO as well as GAZETTEER would be good, and excluding NCIT search.