Term issue: "histone" and "modified histone"

[sebastianduesing]

OBI is looking for very broad/general terms for "histone" and "modified histone"; PRO has a robust histone hierarchy, but it appears to lack those classes. Would PRO be willing/able to create those classes? We're happy to help with definitions/axioms if that would be useful. Thanks!

[nataled]

Hi @sebastianduesing,

Thank you for your request. We are indeed willing to have those terms. In fact, we already do have 'histone' (PR:000041244), as well as core histone (PR:000043452) and linker histone (PR:000043453). Note that the above terms are defined without regard to organism, so if you need the organism-specific terms those will have to be created.

Biologically speaking, so far as I know, all histones have at least some processing of the protein chain, but I suspect you're interested specifically in those that modify amino acids? Please confirm.

On the assumption that my suspicion is correct, your term is given below (in OBO format; OBO is currently PRO's native format). Please note that any new terms created will NOT appear in the main PRO release file until the release following the one that is about to go live sometime this/next week (we're already far into the release process). As well, new terms will not be searchable on the PRO web site. That being said, the term will indeed go 'live' immediately upon upload of an 'interim' file (that is, the IRI is both usable and will resolve).

[Term] id: PR:000085778 name: modified histone def: "A histone that contains one or more amino acid modifications." [PRO:DAN] comment: Category=modification. Requested by=OBI. intersection_of: PR:000041244 ! histone intersection_of: has_part MOD:00000 ! protein modification

Please let me know if this definition conforms to your needs. If so, I'll upload and let you know when it is live.

Best regards, Darren

[sebastianduesing]

Hi @nataled,

Thank you for your fast and helpful response! Apologies that I missed the existing 'histone' term in PRO—we went looking for that term on OLS on the OBI dev call yesterday, and it seems we just didn't manage to find it.

Regarding your question about us being interested specifically in those that modify amino acids, I'm going to ask @bpeters42 to weigh in as he has a much better understanding of the biological context than I do. Bjoern, could you confirm that the definition for 'modified histone' that Darren proposed in his comment above looks sufficient?

As for what you said about the term going live upon upload of the interim file and then being added to the main PRO release file in the release following the one you're currently working towards, everything about that sounds great. Thanks again for getting to this so quickly!

Best, Sebastian

[nataled]

My pleasure!

On Tuesday, August 13, 2024, Sebastian Duesing @.***> wrote:

Hi @nataled https://github.com/nataled,

Thank you for your fast and helpful response! Apologies that I missed the existing 'histone' term in PRO—we went looking for that term on OLS on the OBI dev call yesterday, and it seems we just didn't manage to find it.

Regarding your question about us being interested specifically in those that modify amino acids, I'm going to ask @bpeters42 https://github.com/bpeters42 to weigh in as he has a much better understanding of the biological context than I do. Bjoern, could you confirm that the definition for 'modified histone' that Darren proposed in his comment above looks sufficient?

As for what you said about the term going live upon upload of the interim file and then being added to the main PRO release file in the release following the one you're currently working towards, everything about that sounds great. Thanks again for getting to this so quickly!

Best, Sebastian

— Reply to this email directly, view it on GitHub https://github.com/PROconsortium/PRoteinOntology/issues/336#issuecomment-2286639728, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADJB7CWWMZU7ZSOUI2SF3GDZRIW35AVCNFSM6AAAAABMM6WLG2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEOBWGYZTSNZSHA . You are receiving this because you were mentioned.Message ID: @.***>

[bpeters42]

Darren is correct, we are only talking about histones with modified amino acids! Thanks for getting to this so quickly, and it is great that we can use this in a species independent fashion for the generic assay term we want, and identify specific modifications and species using PRO terms for particular experiments being performed - that is pretty much OBO at its best!

[nataled]

Just FYI, I have left for a short break and will return to work on Monday, so that "live" statement will now apply to that day. Other PRO people are off as well. The term is, however, done. I just need to upload a file when I return.

On Tuesday, August 13, 2024, bpeters42 @.***> wrote:

Darren is correct, we are only talking about histones with modified amino acids! Thanks for getting to this so quickly, and it is great that we can use this in a species independent fashion for the generic assay term we want, and identify specific modifications and species using PRO terms for particular experiments being performed - that is pretty much OBO at its best!

— Reply to this email directly, view it on GitHub https://github.com/PROconsortium/PRoteinOntology/issues/336#issuecomment-2286662171, or unsubscribe https://github.com/notifications/unsubscribe-auth/ADJB7CQEBJ3XQLLJZ4MBAJTZRIYKLAVCNFSM6AAAAABMM6WLG2VHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDEOBWGY3DEMJXGE . You are receiving this because you were mentioned.Message ID: @.***>

[sebastianduesing]

Got it, thanks! Hope you have a nice break.

[nataled]

This is now live. http://purl.obolibrary.org/obo/PR_000085778

[sebastianduesing]

Excellent, thanks so much!

[sebastianduesing]

Quick question on this: you mentioned that this term will go out in the release following the one that's currently being prepared. I'm looking to estimate when we can expect this to be in the main PRO release file—how often does PRO do releases?

[nataled]

Alas, we're averaging about once every six months. I'm hoping to get to once every four months, but we're running low on manpower.

[bpeters42]

Darren, would you see an issue with us referencing that ID? https://proconsortium.org/cgi-bin/entry_pro?id=PR_000085778 resolves - but I assume the canonical OBO format of the ID won't until the release is out. We could create an OBI placeholder term, and state that it will be replaced with the PR term above once the release is out?

On Tue, Aug 20, 2024 at 11:54 AM Darren A. Natale @.***> wrote:

Alas, we're averaging about once every six months. I'm hoping to get to once every four months, but we're running low on manpower.

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-- Bjoern Peters Professor La Jolla Institute for Immunology 9420 Athena Circle La Jolla, CA 92037, USA Tel: 858/752-6914 Fax: 858/752-6987 http://www.liai.org/pages/faculty-peters

[nataled]

I don't see an issue with referencing, as it does indeed resolve. And the OBO format stanza is available from the resolving page. I guess you want to have it in your own ontology as an import? If you need it in a downloadable version of OBI, you could do the placeholder method; alternatively, you could make a copy of the stanza (converted to owl as necessary). Whatever works best for you.

Sorry for the timing!

[sebastianduesing]

No worries at all—OBI's release schedule has been pretty similar to that, so we've got no high ground. :) We can work with that. Thanks again for your help!