parcellation scheme ingestion

[tgbugs]

There are a number of brain parcellation schemes that we want to ingest into the ontology. Allen MBA and cocomac have been ingested (though cocomac has not been fully integrated into the ontology), but additional schemes should be ingested as well. For example, Paxinos, Swanson (does his new common mammalian work fit as a parcellation scheme or is it another conceptual level along with BrainInfo, NIFGA, UBERON?, CUMBO?), MNI and other fMRI templates.

UBERON has mappings between a number of these, but we need to bring these terminologies in directly.

Consider the impact on search/autocompletion. Assigning a special category for parcellation scheme concepts in scigraph should allow the webservices to demote them. Not entirely clear what the 'right' way is to redirect to the preferred high level identifier, worth consideration at other levels.

[tgbugs]

check http://neurolex.org/wiki/Brain_parcels as well

[tgbugs]

http://www.nature.com/nature/journal/vaop/ncurrent/full/nature18933.html

[tgbugs]

https://www.nitrc.org/frs/?group_id=1081 for the other waxholm versions to make sure the indexes have not changed.

[tgbugs]

#118 for this issue as well

[tgbugs]

From @cmungall in JIRA. For when we merge the parcellations back from interlex.

A lot of the links on
http://neurolex.org/wiki/Brain_parcels
are red - they point to a blank page - even when the intended page exists.

For example, in the ABA subset:

Uvula (IX) of ABA 2009 Uvula (IX) of ABA 2009 nlx_153062 Uvula (IX) ABA 2009 adult mouse brain parcellation scheme

Also visible here:
http://neurolex.org/wiki/Category:Uvula_%28IX%29_of_ABA_2009

Has an overlaps link to:
http://neurolex.org/wiki/Special:AddData/NIF_Standard/Category:Uvula_%28IX%29

Which is blank.

I believe the actual intention is to link to nlx_anat_20081234:
http://neurolex.org/wiki/Category:Vermic_Lobule_IX

Note that there are ABA mapping in Uberon. E.g.

http://purl.obolibrary.org/obo/UBERON_0004078

Maybe we could coordinate on these?

[tgbugs]

http://help.brain-map.org/display/api/Atlas+Drawings+and+Ontologies

Allen has evolved and we need to ingest more things.

[cmungall]

Last did this 3 years ago:
https://github.com/obophenotype/uberon/tree/master/source-ontologies

It appears there is a new adult human one for glioblastoma

pba, hba, dhba and dmba seems to be unchanged over 3 years

mba seems to have added a bunch of new terms

a few name changes

-name: pallidothalmic pathway
+name: pallidothalamic pathway

-name: medial corticohypothalmic tract
+name: medial corticohypothalamic tract

-name: mammilothalmic tract
+name: mammillothalamic tract

[cmungall]

obophenotype/uberon#1406

[tgbugs]

I have the skeleton for a 'one shot' check on all the Allen ontologies using their API endpoints to bound the problem. This should also prevent the usual copy/paste issues that I've brought on myself with the current system.

[tgbugs]

Marmoset.
Hashikawa atlas nifti files https://doi.org/10.1038/sdata.2018.9
MRI https://doi.org/10.1016/j.neuroimage.2017.12.004 supplemental spreadsheets 1 and 2.
Paxinos.

[tgbugs]

Big brain cortical layers.
https://doi.org/10.1093/cercor/bhy074
https://doi.org/10.1101/580597

[tgbugs]

Crossmap and/or include.
https://github.com/brainglobe/bg-atlasapi

[tgbugs]

paxmon https://github.com/HumanBrainProject/openMINDS_SANDS/issues/185