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Addresses #2103 Edit 'pain receptor cell' #2104

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@ghost ghost commented Aug 16, 2023

Addresses #2103 Edit 'pain receptor cell'

@ghost ghost added the synonym label Aug 16, 2023
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@ghost ghost requested a review from shawntanzk August 16, 2023 13:28
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not 100% sure about the use of seeAlso, but will trust you know what you are doing.
Dont particularly like the use of freedictionary.com (not sure about archival policy and all) but I get that use of nocireceptor is rare in literature. Generally looks alright.

@ghost ghost merged commit ef7bc7b into master Aug 16, 2023
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@ghost ghost deleted the 2103-Edit-pain_receptor_cell branch August 16, 2023 13:41
@ghost ghost restored the 2103-Edit-pain_receptor_cell branch August 16, 2023 13:46
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ghost commented Aug 16, 2023

not 100% sure about the use of seeAlso, but will trust you know what you are doing.
Dont particularly like the use of freedictionary.com (not sure about archival policy and all) but I get that use of nocireceptor is rare in literature. Generally looks alright.

Updated reply.

Thanks for the prompt review.
The idea is that since the MeSH references don't appear to be in the OBO registry format (the references are TreeNumbers and not Unique IDs), 'see Also' was safer than database_cross_reference. The prefix does not create a hyperlink in Protégé with TreeNumbers like the Unique numbers do. Can adjust if advised.

If you have a preferred dbxref for nocireceptor, kindly advise.

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the references are TreeNumbers and not Unique IDs

ah makes sense. one possibility is to use IDs in mesh (eg mesh:D009619 - https://meshb.nlm.nih.gov/record/ui?ui=D009619). This prefix is registered in bioregistry so thats an extra nice thing

The prefix does not create a hyperlink in Protégé

Prefix in protege only creates hyperlink if we go in and add it, see protegeproject/protege#1049 for example

If you have a preferred dbxref for nocireceptor, kindly advise.

The only one I got is not great too. ScienceDirect shows a bit of a dictionary that has it (https://www.sciencedirect.com/topics/immunology-and-microbiology/pain-receptor#:~:text=Nociceptors%20(nocireceptors%2C%20pain%20receptors),in%20response%20to%20certain%20stimuli.)

This is the book https://www.sciencedirect.com/science/article/abs/pii/B9780123849311000143 but I cant download it to verify so dont like that too.

@ghost ghost deleted a comment from dosumis Aug 17, 2023
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ghost commented Aug 17, 2023

Confirmed with @anitacaron and @cmungall that there is an effort to replace MeSH Tree Numbers with MeSH Unique IDs.

#2105 removes the Tree Numbers, retains the Unique ID, and adds datatype anyURI to URL references, which was missed in this PR.

A separate issue will be made to replace MeSH Tree Numbers with Unique IDs across the ontology.
Update: found previous efforts in #1557/#1558.

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nociceptor appears in both uberon and CL as different terms (CL edits)
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