New neuroanatomy terms

[twhetzel]

New terms requested by Russ Poldrack listed here (left side of spreadsheet, columns A-G (Atlas of Origin)): https://docs.google.com/spreadsheets/d/16_e_n1wuthBfCtH5UTFbz9fO-K70heq0W8eMt_J_Q9E Check the Notes column for some information on my rudimentary searches to see if the term already exists.

[cmungall]

Note to self: Harvard-Oxford Atlas electronic source: http://neuro.imm.dtu.dk/wiki/Category:Brain_regions_in_Harvard-Oxford_Atlas

[cmungall]

This is largely done, with the exception of some highly specific terms that are particular to a single parcelation scheme. We could add these to Uberon, but this hasn't been our policy so far (with an exception for Brodmann as this is so widely used).

What I would recommend here is that terms like the Mars (2011) parietal lobule subdivisions a-e are maintained in a separate repo in OWL, with the relevant uberon classes (e.g.IPL) imported. We could then package up the new NIF-Gross Anatomy as being the union of the uberon brain subset plus these highly specific submodules.

Another possibility is to have the policy that these parcels live only in neurolex. Again, it should be possible to make the new NIFGA be the union of the uberon brain subset plus the OWL translation of these parcels. This would seem to fit in what has been with some parcelations so far.

What I really want to avoid in having both nlx and uberon IDs for these specific parcels

[mellybelly]

I agree that we should have a primary upper level parcellation scheme in uberon and the others in accessory files. Ideally you could choose any given parcellation scheme as a module, that would include the relevant upper level uberon terms. And yes, please no conflicting nlx and uberon IDs for same thing :-).

[twhetzel]

Yes, this plan sounds fine. Although I'm not sure referring to a "new NIFGA" is clear vs. calling this a NIF specific module of Uberon.

What have you done so far with the NIF parcels to avoid having both nlx and uberon IDs? I gather we'll also need more details from Maryann and Mihai as to their plans with neurolex.

[cmungall]

@twhetzel - ok, let's not call it the "new NIFGA" (although it may serve the same purpose - i.e. an OWL resource of brain regions). We could call it a NIF specific module, or even just the nervous system module (which could be further partitioned by species).

Regarding your 2nd question, I have not yet incorporated any specific parcels from nlx, with the exception of those that were already in nifga. These can be included as leaves in the composite ontology. See https://github.com/obophenotype/uberon/wiki/Integration-with-neuroanatomical-atlases

[gouttegd]

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