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obophenotype / uberon

An ontology of gross anatomy covering metazoa. Works in concert with https://github.com/obophenotype/cell-ontology
http://obophenotype.github.io/uberon/
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NTR: brain regions #2832

Open paulacalipho opened 1 year ago

paulacalipho commented 1 year ago

Term: left fronto parietal region Related synonym: left fronto parietal lobe https://orcid.org/0000-0002-0819-0473 Related synonym: left fronto-parietal lobe PMID:7556648 Definition: Regional part of brain encompassing the left frontal and parietal lobes of the brain hemisphere. https://orcid.org/0000-0002-0819-0473 SubClass Of: 'regional part of brain' UBERON:0002616 and ('part of' some ‘left cerebral hemisphere’ UBERON:0002812) Term also mentioned in: PMID:3703146, PMID:27003199, PMID:30797641, PMID:3976447 (frontal parietal left), PMID:33251771 (left fronto-parietal lobe)

Term: right fronto parietal region Related synonym: right fronto parietal lobe https://orcid.org/0000-0002-0819-0473 Related synonym: right frontal parietal lobe PMID:29678709 Related synonym: right frontal-parietal lobe PMID:22568892 Related synonym: right fronto-parietal lobe PMID:34234736 Definition: Regional part of brain encompassing the right frontal and parietal lobes of the brain hemisphere. https://orcid.org/0000-0002-0819-0473 SubClass Of: 'regional part of brain' UBERON:0002616 and ('part of' some ‘right cerebral hemisphere’ UBERON:0002813) Term also mentioned in: PMID:34736485 (right fronto-parietal lobe), PMID:30169667 (right fronto-parietal lobe), PMID:2448680 (right frontoparietal)

Term: left occipital parietal region Exact synonym: left occipital-parietal region PMID:17215478 Exact synonym: left occipital/parietal region PMID:22078521 Exact synonym: left occipital parietal region PMID:26027887 Exact synonym: left occipito-parietal region PMID:27303466 Related synonym: left occipital parietal lobe https://orcid.org/0000-0002-0819-0473 Related synonym: left parietal and occipital lobes PMID:30383697 Related synonym: left parietal-occipital lobe PMID:22799762 Related synonym: left parieto-occipital lobe PMID:27028405 Definition: Regional part of brain encompassing the left occipital and parietal lobes of the brain hemisphere. https://orcid.org/0000-0002-0819-0473 SubClass Of: 'regional part of brain' UBERON:0002616 and ('part of' some ‘left cerebral hemisphere’ UBERON:0002812) Term also mentioned in: PMID:23506194 (left parietal-occipital lobe), PMID:36462980 (left parieto-occipital lobe), PMID:36542021 (left parieto-occipital lobe), PMID:36198519 (left parieto-occipital lobe), PMID:36451532 (left parieto-occipital lobe), PMID:36090026 (left parieto-occipital lobe), PMID:26300758 (occipital-parietal, left), PMID:35257944 (left occipital-parietal region), PMID:36561241 (left occipital/parietal region). [Mapping to other ontologies: Left parietal and occipital lobes, CS C1267724]

Term: right occipital parietal region Exact synonym: right occipital-parietal region PMID:35257944 Exact synonym: right occipital parietal region PMID:31053785 Related synonym: right occipital parietal lobe https://orcid.org/0000-0002-0819-0473 Related synonym: right parieto-occipital lobe https://orcid.org/0000-0002-0819-0473 Definition: Regional part of brain encompassing the right occipital and parietal lobes of the brain hemisphere. https://orcid.org/0000-0002-0819-0473 SubClass Of: 'regional part of brain' UBERON:0002616 and ('part of' some ‘right cerebral hemisphere’ UBERON:0002813) Term also mentioned in: PMID:22711620 (right occipital parietal region) [Mapping to other ontologies: Right parietal and occipital lobes CS C1267723]

Term: temporo occipital region Related synonym: temporo occipital lobe https://orcid.org/0000-0002-0819-0473 Related synonym: temporo-occipital lobe https://orcid.org/0000-0002-0819-0473 Definition: Regional part of brain encompassing the temporal and occipital lobes of the brain hemisphere. https://orcid.org/0000-0002-0819-0473 SubClass Of: 'regional part of brain' UBERON:0002616 and ('part of' some ‘cerebral hemisphere’ UBERON_0001869)

Term: left temporo occipital region Related synonym: left temporo occipital lobe https://orcid.org/0000-0002-0819-0473 Related synonym: left temporo-occipital lobe PMID:24366606 Related synonym: occipitotemporal lobe PMID:36093544 Definition: Regional part of brain encompassing the left temporal and occipital lobes of the brain hemisphere. https://orcid.org/0000-0002-0819-0473 SubClass Of: 'regional part of brain' UBERON:0002616 and ('part of' some ‘left cerebral hemisphere’ UBERON:0002812) Term also mentioned in: PMID: 33452388 (left temporo-occipital lobe), PMID:29077534 (occipitotemporal lobe), PMID:14983026 (occipitotemporal lobe)

Term: right temporo occipital region Related synonym: right temporo occipital lobe https://orcid.org/0000-0002-0819-0473 Related synonym: right temporo-occipital lobe PMID:34595871 Definition: Regional part of brain encompassing the right temporal and occipital lobes of the brain hemisphere. https://orcid.org/0000-0002-0819-0473 SubClass Of: 'regional part of brain' UBERON:0002616 and ('part of' some ‘right cerebral hemisphere’ UBERON:0002813) Term (right temporo-occipital lobe) also mentioned in: PMID:24299901, PMID:31036340, PMID:15883270, PMID:36626518, PMID:27250577, PMID:21219302, PMID:31068568

Term: temporo parietal region Exact synonym: temporo-parietal region https://orcid.org/0000-0002-0819-0473 Exact synonym: parieto-temporal region https://orcid.org/0000-0002-0819-0473 Exact synonym: parieto temporal region https://orcid.org/0000-0002-0819-0473 Related synonym: temporo-parietal lobe https://orcid.org/0000-0002-0819-0473 Related synonym: parieto-temporal lobe https://orcid.org/0000-0002-0819-0473 Definition: Regional part of brain encompassing the temporal and parietal lobes of the brain hemisphere. https://orcid.org/0000-0002-0819-0473 SubClass Of: 'regional part of brain' UBERON:0002616 and ('part of' some ‘cerebral hemisphere’ UBERON_0001869)

Term: left temporo parietal region Related synonym: left temporo parietal lobe https://orcid.org/0000-0002-0819-0473 Related synonym: left temporal-parietal lobe PMID:34858900 Related synonym: left temporo-parietal lobe PMID:9652669 Broad synonym: left temporo-parietal PMID:8154317 Definition: Regional part of brain encompassing the left temporal and parietal lobes of the brain hemisphere. https://orcid.org/0000-0002-0819-0473 SubClass Of: 'regional part of brain' UBERON:0002616 and ('part of' some ‘left cerebral hemisphere’ UBERON:0002812) Term also mentioned in: PMID:31903645 (left temporal-parietal lobe), PMID:28711476 (left temporo-parietal lobe), PMID:27324529 (left temporo-parietal lobe), PMID:21453038 (left temporo-parietal lobe)

Term: right temporo parietal region Exact synonym: right temporo-parietal region PMID:21112225 Related synonym: right temporo parietal lobe https://orcid.org/0000-0002-0819-0473 Related synonym: right temporoparietal lobe PMID:35795795 Related synonym: right temporo-parietal lobe PMID:33251771 Definition: Regional part of brain encompassing the right temporal and parietal lobes of the brain hemisphere. https://orcid.org/0000-0002-0819-0473 SubClass Of: 'regional part of brain' UBERON:0002616 and ('part of' some ‘right cerebral hemisphere’ UBERON:0002813) Term (right temporo-parietal lobe) also mentioned in: PMID:21112225, PMID:30797641, PMID:33787635, PMID:35331158

Term: right parasagittal parietal region Exact synonym: right parasagittal parietal region PMID:23835274 Definition: Regional part of brain encompassing the right parasagittal parietal region of the brain hemisphere. https://orcid.org/0000-0002-0819-0473 SubClass Of: 'regional part of brain' UBERON:0002616 and ('part of' some ‘right cerebral hemisphere’ UBERON:0002813)

Term: right periatrial region of the brain Exact synonym: right peri-atrial region PMID:25304435 Exact synonym: right periatrial region PMID:27028405 Definition: - SubClass Of: 'regional part of brain' UBERON:0002616 and ('part of' some ‘right cerebral hemisphere’ UBERON:0002813) Term also mentioned in: PMID:28834867 (right peri-atrial region), PMID:11498414 (right periatrial region), PMID:36340223 (right periatrial region), PMID:36324946 (right periatrial region), PMID:23859284 (right periatrial region), PMID:30937235 (right periatrial region), PMID:31133966 (right periatrial region), PMID:12748099 (right periatrial region), PMID:18417739 (right periatrial region) Note: check if occipitotemporal periventricular white matter in the right hemisphere is synonym of right periatrial (PMID:26744442) https://orcid.org/0000-0002-0819-0473

Term: medial temporal region Related synonym: medial temporal lobe PMID:28428747 Definition: Regional part of brain encompassing the hippocampus, amygdala and parahippocampal regions. This region is crucial for episodic and spatial memory (PMID:28428747) SubClass Of: 'regional part of brain' UBERON:0002616 and ('part of' some ‘temporal lobe’ UBERON:0001871) Mapping to other ontologies: BTO:0004477

Term: left temporo-medial region Exact synonym: left temporal-medial region PMID:28144495 Exact synonym: left temporal medial region PMID:28144495 Definition: Regional part of brain encompassing the left medial temporal lobe of the brain hemisphere. https://orcid.org/0000-0002-0819-0473 SubClass Of: 'regional part of brain' UBERON:0002616 and ('part of' some 'medial temporal lobe' UBERON:0001871)

Term: right frontal parietal occipital cortex Exact synonym: right frontal parieto-occipital cortex PMID:35372056 Definition: The right frontal, parietal, and occipital cortex of the brain hemisphere. https://orcid.org/0000-0002-0819-0473 SubClass Of: ‘cortex of cerebral lobe' UBERON:0016529 and ('part of' some ‘right cerebral hemisphere’ UBERON:0002813) Term (right frontal parieto-occipital cortex) also mentioned in: PMID:34045642, PMID:33375627, PMID:27003178

Term: left prefrontal cortex Broad synonym: left prefrontal lobe PMID:35964192 Definition: The left prefrontal cortex of the brain. https://orcid.org/0000-0002-0819-0473 SubClass Of: ‘prefrontal cortex' UBERON:0000451 and ('part of' some ‘left cerebral hemisphere’ UBERON:0002812) Term (left prefrontal lobe) also mentioned in: PMID:35556171, PMID:34483857 Mapping to other ontologies: Left prefrontal cortex FMA:242627

Term: right fronto temporo parietal region Exact synonym: right fronto-temporo-parietal region https://orcid.org/0000-0002-0819-0473 Related synonym: right fronto-temporo-parietal lobe PMID:28428747 Definition: Regional part of brain encompassing the right frontal, temporal and parietal lobes of the brain. https://orcid.org/0000-0002-0819-0473 SubClass Of: 'regional part of brain' UBERON:0002616 and ('part of' some ‘right cerebral hemisphere’ UBERON:0002813)

Term: fronto temporal region Exact synonym: fronto-temporal region https://orcid.org/0000-0002-0819-0473 Related synonym: fronto temporal lobe https://orcid.org/0000-0002-0819-0473 Definition: Regional part of brain encompassing the frontal and temporal lobes of the brain hemisphere. https://orcid.org/0000-0002-0819-0473 SubClass Of: 'regional part of brain' UBERON:0002616 and ('part of' some ‘cerebral hemisphere’ UBERON_0001869)

Term: left fronto temporal region Exact synonym: left fronto-temporal region https://orcid.org/0000-0002-0819-0473 Related synonym: left fronto-temporal lobe https://orcid.org/0000-0002-0819-0473 Definition: Regional part of brain encompassing the left frontal and temporal lobes of the brain hemisphere. https://orcid.org/0000-0002-0819-0473 SubClass Of: 'regional part of brain' UBERON:0002616 and ('part of' some ‘left cerebral hemisphere’ UBERON:0002812)

Term: right fronto temporal region Related synonym: right fronto temporal lobe https://orcid.org/0000-0002-0819-0473 Exact synonym: right fronto-emporal region https://orcid.org/0000-0002-0819-0473 Definition: Regional part of brain encompassing the right frontal and temporal lobes of the brain hemisphere. https://orcid.org/0000-0002-0819-0473 SubClass Of: 'regional part of brain' UBERON:0002616 and ('part of' some ‘right cerebral hemisphere’ UBERON:0002813)

Term: temporo insular region Exact synonym: temporo-insular region https://orcid.org/0000-0002-0819-0473 Related synonym: temporo-insular lobe https://orcid.org/0000-0002-0819-0473 Definition: Regional part of brain encompassing the temporal lobe and insula of the brain hemisphere. https://orcid.org/0000-0002-0819-0473 SubClass Of: 'regional part of brain' UBERON:0002616 and ('part of' some ‘cerebral hemisphere’ UBERON_0001869)

Term: occipito-medial region Definition: The medial part of the occipital lobe. https://orcid.org/0000-0002-0819-0473 SubClass Of: 'regional part of brain' UBERON:0002616 and ('part of' some ‘occipital lobe’ UBERON_0002021)

ghost commented 1 year ago

@patrick-lloyd-ray, would you mind scanning these potential new terms and providing feedback on whether they would be appropriate classes in Uberon?

Some of the terms seem to represent brain regions instead of actual lobes ("right parasagittal parietal lobe") even though they may be referred to as lobes in literature. If these are appropriate to add to Uberon, do you have thoughts on the proposed modelling?

patrick-lloyd-ray commented 1 year ago

@bvarner-ebi You're right in that these classes labeled lobes are regions, not lobes. But, I think it would be helpful for UBERON to capture usage, so listing these as synonyms is fine if UBERON wants to add them.

As far as whether UBERON should add these terms, that's a decision for @cmungall and/or @dosumis. These regions cut across well defined structures and that raises some questions regarding design that should be coordinated going forward.

IMO, I think that brain anatomy is complex in that there are many equally meaningful/important/useful parcellations (even in a single species). On one hand, it would be great to have all of these represented UBERON. On the other hand, it would be a ton of work.

paulacalipho commented 1 year ago

Dear @patrick-lloyd-ray and @bvarner-ebi thanks for your feedback. I updated the NTR with the following:

I let you decide the relevance of these terms in UBERON. Thanks, Paula

ghost commented 1 year ago

Thanks for the feedback, @patrick-lloyd-ray. Thanks for the modifications, @paulacalipho.

@cmungall, @dosumis: appreciate your feedback on whether all these terms should be added as new classes.

github-actions[bot] commented 5 months ago

This issue has not seen any activity in the past 6 months; it will be closed automatically one year from now if no action is taken.

paulacalipho commented 1 month ago

Hi @cmungall do you think theses term are in the scope of UBERON?

cmungall commented 3 weeks ago

IMO, I think that brain anatomy is complex in that there are many equally meaningful/important/useful parcellations (even in a single species).

Definitely - but Uberon already has many alternate parcelations

On one hand, it would be great to have all of these represented UBERON. On the other hand, it would be a ton of work

My main concern is the L/R ones, while it seems easy to add these keeping relationships consistent is hard, especially as new L/R requests come in. However, we really have to solve this by getting the patterns down..