Closed maxneal closed 6 years ago
Actually, I think it might be a good idea to provide short descriptions for all of our ontologies. The remaining ones are: CMO, OPB, PATO, SBO, and SNOMED.
I added descriptions to the reference ontologies which show up in the reference term search dialog.
A few suggestions:
And here are hints for the remaining ontologies:
OPB: physical properties and dependencies PATO: phenotypes and traits not represented as properties in the OPB SBO: physical dependencies not in the OPB SNOMED: clinical-domain physical properties not in the OPB
I don't think we need to preserve the CMO in our list. SNOMED probably covers the bases we need. Plus I'm not convinced the CMO subclasses things in a way that jibes with the OPB view.
I've made the suggested formatting changes and added the descriptions.
The background behind the combobox and hints is now SG blue. Can you revert back to gray? Also, the alignment of the hint looks good except for when I first open the dialog. WHen I go through and select the different ontologies, the alignment clicks in. Also, could you increase the space between the hint and the components below a teeny bit more? And use all lower-case characters after "For annotating..." Thanks!
Check out the newest commit.
The only very minor thing I see is that the GUI elements below the hint shift around a little each time a different ontology is selected in the combobox. If we can fix this before the 3.0 release date, great. If not, I'm OK rolling with it as-is. I'll make this a 3.1 issue for now.
This is all looking good now.
In the current draft of the PHN paper we state the following scope for our reference ontologies.
Foundational Model of Anatomy (FMA): Macromolecular to organism-level anatomy Mouse Adult Gross Anatomy (MA): Rodent-specific anatomy Cell Type Ontology (CL): Non-mammalian cell types Gene Ontology:cellular component (GO-cc): Macromolecular structures not represented in the FMA Protein Ontology (PR): Proteins Chemical Entities of Biological Interest (ChEBI): Atoms and small molecules Ontology for Biomedical Investigations (OBI): Laboratory materials
We want to indicate the scope when the the user selects a reference ontology from a drop-down list, as in ReferenceClassFinderPanel