Clarification - RE: Summary of discussion

[Vincent, Leszek]

Hi Michael (& colleagues)

Thanks for airing your growing clarity on this matter & for reinterpreting earlier comments on this between Pankaj & myself. 

Yes, I was referring to the name info. within a (sensu....) statement. I was puzzling over your earlier reply to me which mentioned using the NCBI taxon ID# wondering how this would go down with readers of the ontology info. who don't usually have the ability to translate an ID# into a taxon name (unlike the rest of us ;-) ). 

Yes, I do think this is extremely important info. to be included in our ontologies and the international format for citing this information has been in use for decades & is published in the International Code of Botanical Nomenclature (ICBN) & the International Code for Zoological Nomenclature (ICZN) etc. - while I know my systematics background does bias my view on the need to incorporate this info. That aside, I think we will do  ourselves harm if we don't provide this hard/basic info. From my perspective the growing global sensitivity to biodiversity issues necessitates that our ontology products reflect the synthesis of excellent science, which explicitly includes adequate inclusion of nomenclatural info. - comprising species name (= genus name & specific epithet), authority; cultivar etc. reference where appropriate; NCBI taxon ID# (where appropriate/available). I think the inclusion of this simple info. could enhance the credibility of our products - for it will further indicate something of the solid foundation (of referencing) on which our ontology info. is based.

Regards,
- Leszek
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P. Leszek D. Vincent Ph.D., FLS
Plant Science Unit, Dept. of Agronomy, 209 Curtis Hall,
University of Missouri-Columbia, Columbia, MO 65211-7020, USA.
Ph: (573) 884-3716 (Agronomy); Fax:(573) 884-7850;
Ph/Fax (Home): (573) 441-1228; 
Email: Leszek at missouri.edu
Plant Systematist on the Maize Mapping Project - NSF award 9872655 -
(http://www.maizemap.org/ and  http://www.agron.missouri.edu/)
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> -----Original Message-----
> From: Michael Ashburner [mailto:ma11 at gen.cam.ac.uk]
> Sent: Tuesday, May 21, 2002 11:46 AM
> To: pj37 at cornell.edu; Vincent, Leszek
> Cc: curator at acoma.Stanford.EDU; ware at cshl.org; Coe, Edward H.;
> gramene at brie.cshl.org; lreiser at acoma.Stanford.EDU; lstein at cshl.org;
> maryp at teosinte.agron.missouri.edu; r.bruskiewich at cgiar.org;
> rhee at acoma.Stanford.EDU; smundodi at acoma.Stanford.EDU; 
> srm4 at cornell.edu;
> tberardi at acoma.Stanford.EDU; V.ULAT at cgiar.org; ma11 at gen.cam.ac.uk;
> sprig-cvo_dev at bioinformatics.org
> Subject: Re: Clarification - RE: Summary of discussion
> 
> 
> 
> I think I mis understood on the taxon names.
> I was refering to annotation files, eg. in this go file
> of SWISS-PROT annotations the identity of the species is indicated by
> its taxon id in the final column:
> SP	O00115	DRN2_HUMAN		GO:0003677	
> PUBMED:9714827	TAS		F	
> Deoxyribonuclease II precursor	IPI00010348	protein	
> taxon:9606
> 
> 
> I think you mean the name after a (sensu ....).  If so, I 
> would agree that
> the taxonomic name should be used. Indeed (and I may suggest 
> this to GO)
> that this should be in the form:
> 
> sensu <Genus species cultivar etc> <authority>; taxon:<taxon_id_int>
> 
> 
> Michael
>