search

obophenotype / insect_neuroanatomy_ontology

Site for the development of an insect neuroanatomy ontology, starting from the Brain Name Standard.
1 stars 0 forks source link

Extend IBDB API to provide relationships between neuropils #1

Open dosumis opened 8 years ago

dosumis commented 8 years ago
ktedore commented 8 years ago

http://insectbraindb.org/api/v1/brain_region/

How does this look to you? One issue is that the id for neuropil and subregion are not applicable to this list. (ex. http://insectbraindb.org/api/v1/neuropil/:id ) They are separate models and this list simply extends the supercategory list. I could create hyperlinks rather than flattening out the structure... Perhaps I need a URI like http://insectbraindb.org/neuropil/:id or a random string.

dosumis commented 8 years ago

Don't seem to have access.

ktedore commented 8 years ago

should work now.

dosumis commented 8 years ago

Thanks. Hierarchy looks good. Easy enough to script a partonomy from this. Will try to work on it later this week.

Re IDs: as you are already using NIN internally for species-specific terms, perhaps we should just go with INO_nnnnnnnn for the species-generic terms? Are there already pages on your site for the species generic neuropils? If so, what IDs (if any) can be used to resolve them?

ktedore commented 8 years ago

The NIN numbers refer only to neurons entries. The neuropils are all species generic (ex. http://insectbraindb.org/api/v1/supercategory/1/ or http://insectbraindb.org/api/v1/subregion/2/ ) The schematic models point to these generic models and a species, but are only used to build the 2-D diagrams.

dosumis commented 8 years ago

Mapping table generation partly done. Still need to map to FBbt. Plan to do this by pulling BrainName subset and then matching on stripped down abbreviations. Not all will match.

Plan is for @cmungall to use the resulting mapping table to generate terms with Uberon IDs in this ontology: https://github.com/obophenotype/insect-anatomy-ontology

cmungall commented 8 years ago

Should these all be SubClass neuropil? I note that CA in FBbt is a subClassOf neuropil domain

dosumis commented 8 years ago

Should these all be SubClass neuropil? I note that CA in FBbt is a subClassOf neuropil domain

We could have 'synaptic neuropil block', 'SN domain and 'SN subdomain' following FBbt. These approximately correspond to BrainName levels 1, 2 and 3. They are not (yet) in the mapping table.