jamesaoverton
commented
2 years ago Thanks @cthoyt. We discussed this on Slack, and I agree that MRO should look for another term. @rvita?
Closed cthoyt closed 2 years ago
jamesaoverton
commented
2 years ago Thanks @cthoyt. We discussed this on Slack, and I agree that MRO should look for another term. @rvita?
cmungall
commented
2 years ago locus is such a slipper concept
current in REO:
a nucleic acid sequence region that is part of a genome and represents a specified location or region on a chromosome or other genomic element.
What is a specified location? How is this concept any different from sequence_feature in SO?
cmungall
commented
2 years ago it looks like MRO wants a more specific concept: something like a nucleic acid sequence region that is part of a genome that codes for a molecule
or to give it it's other name... gene
cmungall
commented
2 years ago I don't have all the answers to the gene question here, but I note that the MRO species-generic B2M concept is what codes for http://purl.obolibrary.org/obo/PR_000004580
And the human B2M (http://purl.obolibrary.org/obo/MRO_0046253) is what codes for http://purl.obolibrary.org/obo/PR_P61769
for species-specific PRO has templates, here
has_gene_template some B2M (human)
PRO uses this as the gene IRI http://www.genenames.org/cgi-bin/gene_symbol_report?hgnc_id=914
But as noted in other forums this is not an ideal URI for a gene concept
I don't have the answers but at the least PRO and MRO should use the same IRI for the B2M human gene concept, and place it in the same place in a hierarchy
bpeters42
commented
2 years ago Thanks for the response Chris, much appreciated, and I know we talked about this a few times, and apologize for keeping raising the same thing.
B2M is, unfortunately, the least relevant locus for MRO, as it is one of the very few that is not hypervariable - in contrast to e.g. HLA-A. But you are right that we can certainly use: "has_gene_template", as a relation, and we are actively aligning with PRO already, so that makes sense. What is the and range of that relation though, may I say 'gene'? And how do we associate specific nucleic acid sequences with an allele of that gene? Those are questions at the core of what MRO is trying to represent.
I have argued for using 'locus' to overcome at least some of the problems in defining 'gene' (which I think your response implies is still controversial). For what we need in MRO, a locus is a part of a genome, that contains an allelic DNA nucleotide sequence, that may or may not be transcribed, and may or may not encode a protein. I had not actually realized that we were using REO for 'locus', and we should definitely move away from that. The question to you was what you would recommend as the next least crappy option.
I understand you as saying that for 'gene' / 'locus', you don't really have an answer yourself. Would you think it is productive to raise this at the COB level?
bpeters42
commented
2 years ago Sorry @cmungall, let me add a more concrete immediate action that we need your advice on: What would you recommend we replace REO:(genetic locus) with? we can go with 'entity' if there is no better solution.
cmungall
commented
2 years ago Well sequence_feature is less committed than gene, but if you think that 'gene' is too restrictive then I think the SO tracker is the best place to raise this. Even if SO isn't funded just now, some of the major genome databases are engaged with issues on the tracker, and I think it's important for databases that mint IDs for things on the genome to be in alignment on basic terms.
On Fri, Dec 3, 2021 at 2:15 PM bpeters42 @.***> wrote:
Sorry @cmungall https://github.com/cmungall, let me add a more concrete immediate action that we need your advice on: What would you recommend we replace REO:(genetic locus) with? we can go with 'entity' if there is no better solution.
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bpeters42
commented
2 years ago I am embarrassed now, to see that there is an SO:gene.
http://purl.obolibrary.org/obo/SO_0000704
While it has remained unclear to us if that is an information artifact or a material, it is better than anything we have so far, and should take it.
On Sat, Dec 4, 2021 at 3:55 PM Chris Mungall @.***> wrote:
Well sequence_feature is less committed than gene, but if you think that 'gene' is too restrictive then I think the SO tracker is the best place to raise this. Even if SO isn't funded just now, some of the major genome databases are engaged with issues on the tracker, and I think it's important for databases that mint IDs for things on the genome to be in alignment on basic terms.
On Fri, Dec 3, 2021 at 2:15 PM bpeters42 @.***> wrote:
Sorry @cmungall https://github.com/cmungall, let me add a more concrete immediate action that we need your advice on: What would you recommend we replace REO:(genetic locus) with? we can go with 'entity' if there is no better solution.
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jamesaoverton
commented
2 years ago Sorry, I lost track of this. If we drop REO:0000079 'gene locus' in favour of SO:0000704 'gene', where do we put 'gene' in MRO? Options:
cthoyt
commented
2 years ago If you wanted to go down route 3, you could consider that sequence ontology also has a notion of Haplotype (SO_0001024).
jamesaoverton
commented
2 years ago Sorry, I was wrong about 'haplotype': we are already using SO:0001024 'haplotype'.
On our call today we decided to:
bpeters42
commented
2 years ago jamesaoverton
commented
2 years ago @bpeters42 @rvita PR #132 implements this, and I think it's ready to merge.
But first I want to check with you: Will these changes, especially renaming everything from 'gene locus' to 'gene', cause problems for the IEDB finders (probably not) or the LJI tools team (possibly?).
I guess I just want to confirm before merging. If I don't hear from you first, I'll raise this in our Thursday meeting.
bpeters42
commented
2 years ago I think the fastest way to find out is to try it. Is a merged version ready that tools and finders can try out? I would give that to Leidos and tools team (or whatever they normally consume) and see what happens in a test run.
On Tue, Jan 11, 2022 at 11:36 AM James A. Overton @.***> wrote:
@bpeters42 https://github.com/bpeters42 @rvita https://github.com/rvita PR #132 https://github.com/IEDB/MRO/pull/132 implements this, and I think it's ready to merge.
But first I want to check with you: Will these changes, especially renaming everything from 'gene locus' to 'gene', cause problems for the IEDB finders (probably not) or the LJI tools team (possibly?).
I guess I just want to confirm before merging. If I don't hear from you first, I'll raise this in our Thursday meeting.
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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
REO:0000079 (genetic locus) is the only term MRO using the Reagent Ontology (REO), which might be discontinued. It comes external entries in https://github.com/IEDB/MRO/blob/eadecf03c7c60ee56726afe8c042f187b0e3b091/ontology/external.tsv.
~Though it seems to be listed using OBO Library PURLs, there's no evidence in the purl.obolibrary.org config nor on the berkleybop ontology server.~ With the help of James, we were able to figure it out and add it to the Bioregistry in https://github.com/biopragmatics/bioregistry/pull/261/commits/ed2b2cfc48bcc9054de77ab7e8a0e2917298ecbc.
I've sent a message on the OBO Community #prefixes channel (https://obo-communitygroup.slack.com/archives/C023P0Z304T/p1638470839039800) in case anyone wants to chat there about what REO itself is, but this issue is more of a question: is there a more appropriate SO term that can be used instead?