Re: [Obo-taxonomy] [Phenoscape] Taxonomic synonyms
Chris Mungall
Hi Peter
Yes, you can assign xrefs to particular usages of synonyms.
An xref can be a URL, e.g. http://www.iucnredlist.org/initiatives/amphibians
, which is fine if you can't locate individual identifiers for each
particular usage.
You could also create your own lightweight mini-database, such as the
one GO uses:
http://www.geneontology.org/cgi-bin/references.cgi
this is really just a flat file:
http://www.geneontology.org/doc/GO.references
(these are used in the provenance of gene annotations, rather than
synonyms, but the principle is the same)
This can serve as a source of "personal communication" style
references. You could have a single entry for the whole GAA
initiative, and some text that says pretty much what you say below; or
you could have individual references for particular usages.
On Nov 2, 2010, at 10:15 AM, peter midford wrote:
> Hi Chris,
> Hilmar asked me to clarify what I'm trying to do with
> this - all I'm trying to do is attribute a source for the GAA
> synonyms (so I can distinguish them from synonyms we get from ITIS
> and other sources we may add in the future). I had assumed that the
> xref mechanism in the synonym tag was the way to do this, but
> assigning attribution to the synonym is the underlying problem.
>
> Thanks,
>
> Peter
>
> On Nov 2, 2010, at 12:38, peter midford wrote:
>
>> Hi Chris,
>> I'm helping David Blackburn rebuild the Amphibia
>> Taxonomy Ontology and I'm hoping you can give me some advice about
>> synonyms. We have taxonomic synonyms from two external sources
>> we'd like to include. The first is ITIS, which we should submit as
>> a database identifier and poses no particular issues. The second
>> source is from the Global Amphibian Assessment, for which I have
>> been unable to locate a database, but would like to capture the
>> synonyms and indicate GAA as the source. Do you have any
>> suggestions on how to proceed with these synonyms?
>>
>> Thanks,
>>
>> Peter
>>
>>
>> _______________________________________________
>> Phenoscape mailing list
>> Pheno...@nescent.org
>> https://lists.nescent.org/mailman/listinfo/phenoscape
>
> Peter E. Midford
> Mesquite Developer
> Peter....@gmail.com
>
>
>
>
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Alan Ruttenberg
>
> Hi Peter
>
> Yes, you can assign xrefs to particular usages of synonyms.
Prompted by this discussion I added an issue for the new obo format spec
http://code.google.com/p/oboformat/issues/detail?id=2
Question: Should xrefs be differentiated so you can specify difference
between citing as source, versus citing in different ways.
-Alan
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