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Add peripheral and central retina terms #52

Closed zperova closed 3 years ago

zperova commented 4 years ago

For new term requests, please provide the following information:

Preferred term label

peripheral retina

central retina

Synonyms

Textual definition

Peripheral retina - region of retina that extends from central retina to ora serrata. Peripheral retina is dominated by rods and also has less ganglion cells and is not as thick as central retina. It is responsible for peripheral and night vision. Link: https://webvision.med.utah.edu/book/part-i-foundations/simple-anatomy-of-the-retina/

Central retina - region of retina around the fovea that extends approximately for 6 mm. Central retina is considerably thick due to increased density of photoreceptors, particularly cones and their associated bipolar and ganglion cells. Link: https://webvision.med.utah.edu/book/part-i-foundations/simple-anatomy-of-the-retina/

Suggested parent term

retina - UBERON:0000966 https://ontology.staging.data.humancellatlas.org/ontologies/hcao/terms?iri=http%3A%2F%2Fpurl.obolibrary.org%2Fobo%2FUBERON_0000966

Use case

Currently there is no way to indicate the difference between central and peripheral retina while these parts of retina have different structure and function.

Attribution

If you would like a nanoattribution, please indicate your ORCID id

zoependlington commented 4 years ago

Hi @zperova, is this term good for peripheral retina? If so I can import this into HCAO.

I'll have to request the central retina term from UBERON.

zperova commented 4 years ago

@zoependlington Could the description be updated?

zoependlington commented 4 years ago

@zperova I'll create a ticket and as UBERON to update to the above :-)

zoependlington commented 4 years ago

@zperova Just an update (I haven't forgotten about this ticket, promise!): The new term and the updated definition are done, just waiting for a new release of UBERON and then they will be pulled into HCAO.

zperova commented 4 years ago

thanks @zoependlington

zoependlington commented 4 years ago

@zperova Just an update, I'm still waiting for an UBERON release with these changes/additional term to pull into HCAO. Unfortunately the last release was in November (that I can see on OLS anyway) and so there has been no update since. I'll keep an eye on it and as soon as I can, I'll pull them into HCAO.

zperova commented 4 years ago

thanks for the update @zoependlington !

dosumis commented 4 years ago

The last Uberon release was about a month ago, so should now be available

image

paolaroncaglia commented 4 years ago

Summary: the term that's still needed for this ticket (UBERON:8000004 central retina) wasn't imported in the HCAO release dated 2020-10-26. Pinning this ticket for discussion with @zoependlington at our next meeting. Update 5/11/20: we'll discuss with @dosumis .

paolaroncaglia commented 3 years ago

Update: Zoe and David modified the HCAO pipeline to overcome issues like this one. Zoe and I will meet late-next week and will see that UBERON:8000004 central retina gets imported in the HCAO release scheduled for then.

paolaroncaglia commented 3 years ago

@zperova The term UBERON:8000004 central retina is now in the HCAO release. It will be visible in public OLS in a day or so. Thanks, Paola