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New neuroanatomy terms #630

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twhetzel opened this Issue Dec 19, 2014 · 5 comments

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twhetzel commented Dec 19, 2014

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.

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cmungall commented Dec 19, 2014

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

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This release encompasses multiple imrpovements in the representation
of the nervous system. Many wikipedia-sourced definitions have been
replaced with definitions from neurolex ([632](#632)). We have defined and
implemented a design pattern for cranial and spinal nerves, ganglia
and nuclei ([634](#634)). We made improvements to the mapping to Allen
ontologies. Additionally, we now use the numeric identifiers for all
Allen classes, rather than acronyms. Please note that the "ABA" prefix
has been superseded by "MBA" (mouse brain atlas), to be consistent
with the others (HBA, PBA, DMBA, DHBA). New terms were added from the
HarvardOxford Cortical atlas based on work by Russ Poldrack and Trish
Whetzel ([630](#630)).

This release also ensures that every class from NIF_GrossAnatomy (but
not its successor, neurolex) is represented in Uberon. Note that not
all classes will be in the bridge file. Many of the region-part-of-X
classes are present in Uberon as obsolete classes.

cmungall added a commit that referenced this issue Jan 8, 2015

@cmungall cmungall changed the title New terms New neuroanatomy terms Jan 11, 2015

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cmungall commented Jan 11, 2015

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

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mellybelly commented Jan 11, 2015

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 :-).

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twhetzel commented Jan 11, 2015

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.

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cmungall commented Jan 28, 2015

@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

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