Add prefix CHR

[caufieldjh]

Prefix

chr

Name

Chromosome Ontology

Homepage

https://github.com/monarch-initiative/monochrom

Source Code Repository

https://github.com/monarch-initiative/monochrom

Description

The Chromosome Ontology, Chromo (abbreviation CHR), is an automatically derived ontology of chromosomes and chromosome parts.

License

BSD-3

Publications

No response

Example Local Unique Identifier

chr:10090-chr10qC

Regular Expression Pattern for Local Unique Identifier

No response

URI Format String

No response

Wikidata Property

No response

Contributor Name

Harry Caufield

Contributor GitHub

caufieldjh

Contributor ORCiD

0000-0001-5705-7831

Contributor Email

[email protected]

Contact Name

Chris Mungall

Contact ORCiD

No response

Contact GitHub

No response

Contact Email

[email protected]

Additional Comments

No response

[cthoyt]

@caufieldjh thanks for the submission! A few comments:

1. can you please provide a regular expression pattern for this?
2. how stable do you think this ontology's identifiers are going to be?
3. Is the data really licensed using this software license? Can you clarify?
4. Is chromo also a synonym for this ontology?

[cthoyt]

RE #1212 @matentzn here's an example of an ontology developed using OBO tools, so the OWL file has auto-generated URIs like http://purl.obolibrary.org/obo/CHR_10090-chr1. Following previous ontology submissions, I still think the right thing to do is to add this as the URI format in this Bioregistry submission.

[caufieldjh]

1. can you please provide a regular expression pattern for this?

It's going to have to be something like \d+-chr.+ since IDs contain the actual chromosomal location, like 9606-chrXq27.3-q28 and isn't limited to human chromosomes

2. how stable do you think this ontology's identifiers are going to be?

I expect the local IDs to be stable but the PURLs may change - relevant to #1212 above.

3. Is the data really licensed using this software license? Can you clarify?

That's more of a placeholder because the repo doesn't contain an explicit license (and it should!).
I expect this will use a CC-BY-4.0 as that's what other Monarch-developed ontologies use

4. Is chromo also a synonym for this ontology?

It isn't referred to as chromo anywhere other than the README, as far as I can tell

[matentzn]

My two $:

1. not chromo, no.

I expect the local IDs to be stable but the PURLs may change - relevant to #1212 above.

I think @cmungall fully expects this to be submitted to OBO and in fact, he has asked as a dozen times to do it and no one ever did.. It is totally in scope though.

Agree with rest of Harry's comments, I guess we could try to figure out the regex for chromosomal locations but maybe \d+-chr[a-zA-Z0-9.-]+ cutz it.

[cmungall]

Regexes: C elegans: I mess with your system D melanogaster: hold my beer D miranda: errm…

…

On Wed, Nov 20, 2024 at 8:23 PM Nico Matentzoglu ***@***.***> wrote: My two $: 1. not chromo, no. I expect the local IDs to be stable but the PURLs may change - relevant to #1212 <#1212> above. I think @cmungall <https://github.com/cmungall> fully expects this to be submitted to OBO and in fact, he has asked as a dozen times to do it and no one ever did.. It is totally in scope though. Agree with rest of Harry's comments, I guess we *could* try to figure out the regex for chromosomal locations but maybe \d+-chr[a-zA-Z0-9.-]+ cutz it. — Reply to this email directly, view it on GitHub <#1265 (comment)>, or unsubscribe <https://github.com/notifications/unsubscribe-auth/AAAMMOJVV7G7MDSIWC3IXUD2BTVUDAVCNFSM6AAAAABSE4LF3GVHI2DSMVQWIX3LMV43OSLTON2WKQ3PNVWWK3TUHMZDIOBZGQ3TKOJQGE> . You are receiving this because you were mentioned.Message ID: ***@***.***>

[cthoyt]

Would be nice at least to have an explanation of what strings like chrXq27.3-q28 are, and have examples of different variations