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biolink / biolink-model

Schema and generated objects for biolink data model and upper ontology
https://biolink.github.io/biolink-model/
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Post-translational modifications #1043

Closed cbizon closed 1 year ago

cbizon commented 2 years ago

Is your feature request related to a problem? Please describe. We are interested in adding information on histone post-translational modifications to our graphs. There are various things that we'd like to be able to say like H3S10 phosphorylation controls gene expression and H3S10 phosphorylation is a phosphorylation and maybe... phosphorylations are capable of controlling gene expression

Describe the solution you'd like I'm not entirely sure, but this is a guess: some structure for talking about types of PTMs (phosphorylations, acetylations, etc), and an ability to say that specific PTMs at particular places on some proteins (like H3S10 meaning the Serine 10 on the histone H3) is associated with some process or effect or phenotype.

What working group (or team) did this request originate from? Coming from some spinoff work from Translator at RENCI, but we would be wanting to expose this information in a KP as well.

Note: This is relevant for members of NCATS Translator.

Additional context There's a nice description of all this here: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4099259/pdf/nihms576064.pdf

Tag relevant members for discussion @DnlRKorn @beasleyjonm

cbizon commented 2 years ago

Additionally, I think we will want to be able to make statements about DNA modifications in addition to PTMs.

cbizon commented 2 years ago

Note that RHEA has some terms for particular residues / modifications to those residues as in : https://www.rhea-db.org/rhea/60224

beasleyjonm commented 2 years ago

I made a PR to the biolink model https://github.com/biolink/biolink-model/pull/1102 recently that makes new classes for "epigenomic entity (mixin)", "posttranslational modifications", and "nucleosome modifications".

I think any PTMs or histone variants could fall under one of these classes.

sierra-moxon commented 2 years ago

@beasleyjonm - should we close this issue now that your PR has been merged?

sierra-moxon commented 1 year ago

closing as PR has been merged.