Wikidata

Wikidata:Property proposal/Open Biomedical Ontologies ID

< Wikidata:Property proposal

Sequence Ontology ID edit

Originally proposed at Wikidata:Property proposal/Natural science

   Not done
DescriptionID in Sequence Ontology
Data typeExternal identifier
Template parameter|1= in en:Template:SO
Domainseveral?
Allowed valuesnumber
ExampleCoronavirus frameshifting stimulation element (Q5172252) → 0000233
SourceOpen Biological and Biomedical Ontology Foundry Ontologies (Q4117183)
Formatter URLhttp://www.sequenceontology.org/miso/current_release/term/SO:$1
Robot and gadget jobsYes
Motivation

(Add your motivation for this property here.) GZWDer (talk) 08:29, 17 January 2017 (UTC)[reply]

Discussion

  Weak oppose The formatter URL and example point to a Sequence types and features ontology (Q7452458) identifier, which is just one of the many ontologies within the OBO Foundry. Is this property proposal meant to be specifically for sequence ontology IDs or any biomedical ontology URI? If the former, the ID should contain the prefix/namespace/scheme "SO:" (CURIE). If the latter, we have exact match (P2888) which is meant for holding URIs for equivalent identifiers in other ontologies. Gstupp (talk) 22:42, 23 January 2017 (UTC)[reply]

  Oppose I agree with Gstupp. Each ontology should have its own property, as we already have for e.g. Gene Ontology ID (P686), ChEBI ID (P683), Disease Ontology ID (P699), UBERON ID (P1554), which are all from the OBO space of ontologies. Sebotic (talk) 00:48, 24 January 2017 (UTC)[reply]

  Oppose The way the proposal is written does not correspond with it's label. @GZWDer did you want to propose just the SO ID maybe? Emitraka (talk) 14:35, 24 January 2017 (UTC)[reply]

@Gstupp, Sebotic, Emitraka: What I want to propose is ID in Sequence Ontology, corresponding to en:Template:SO. I didn't know Sequence Ontology is only a part of Open Biomedical Ontologies. If there's already a property for this I'm going to withdraw the request. I have updated the proposal.--GZWDer (talk) 15:35, 24 January 2017 (UTC)[reply]
@GZWDer: I think it would be great to have links to sequence ontology in wikidata! However, two things. 1) The ID needs to have the namespace "SO:" as part of the ID, and 2) Your example is linking Coronavirus frameshifting stimulation element (Q5172252) with the sequence ontology item for "mature_transcript", which is not correct. I think what you mean (and I'm not a geneticist...) is that Coronavirus frameshifting stimulation element (Q5172252) is subclass of (P279) of Mature messenger RNA (Q6792003), where Mature messenger RNA (Q6792003) has the SO ID: SO:0000233. So the example should be that Mature messenger RNA (Q6792003) → SO:0000233 Gstupp (talk) 17:59, 25 January 2017 (UTC)[reply]
@GZWDer: if you implement all the changes suggested by Gstupp above, I am all for the proposal. The SO terms will be very useful for multiple projects. Emitraka (talk) 16:01, 26 January 2017 (UTC)[reply]
I agree with Emitraka. I would also welcome that property! --Andrawaag (talk) 16:06, 26 January 2017 (UTC)[reply]
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