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The Ontology for Biomedical Investigations
http://obi-ontology.org
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NTR: Capture Hi-C #1251

Closed bonitalam closed 3 years ago

bonitalam commented 3 years ago

Hello, ENCODE would like to request a NTR for a new type of assay we will be supporting.

editor preferred term: Capture Hi-C alternate terms: cHi-C textual definition: Capture Hi-C is a type of Hi-C assay in which a selection step is performed on ligated fragments in order to enrich for ligation products containing specific regions of interest. definition source for the textual definition: https://pubmed.ncbi.nlm.nih.gov/29979818/ logical definition: subclass of Hi-C assay (OBI:0002440)

jamesaoverton commented 3 years ago

Discussed on 2021-01-25: This looks good. We'd like to add an example from the cited PubMed paper: "PMID:29979818 Chromosome conformation capture (3C), coupled with next-generation sequencing (Hi-C), provides a means for deciphering not only the principles underlying genome folding and architecture, but more broadly, the role 3D chromatin structure plays in gene regulation and the replication and repair of DNA."

@bonitalam You've submitted a number of excellent term requests. We really appreciate this! We're often slow in responding to them, because OBI does not have any direct funding. Would you, or someone from your team, be interested in joining the weekly OBI calls, and contributing terms directly to OBI?

jamesaoverton commented 3 years ago

Sorry, didn't mean to close.

bonitalam commented 3 years ago

@jamesaoverton sure, I could potentially join the calls if I have no scheduling conflicts with existing calls. I'd be happy to contribute terms directly. Are the calls weekly Monday at 9am PST?

jamesaoverton commented 3 years ago

Yes, that's the right time. The call details are at the bottom of this page: http://obi-ontology.org/

Most OBI terms are specified in tables in src/ontology/templates/. To add your term to OBI I just added a row to src/ontology/templates/assays.tsv and made a Pull Request: #1287. If you can add your own terms to the templates, then it saves our volunteers precious time, and help to get your terms in faster.

Our README has more detail. I've been running a public office hour every Monday before the OBI call, where you can ask technical questions. And if neither of those is helpful, we could arrange a call between you and an OBI developer.

Thanks again for your valuable contributions to OBI!

bonitalam commented 3 years ago

Thanks for the information @jamesaoverton. I will take a look at the links and plan to join next week's call.