[Obo-taxonomy] Fwd: [Obo-discuss] taxonomy ranks ontology?

[Peter Midford]

Begin forwarded message:

From: "Adam M. Goldstein" <z_californianus-dat...@shiftingbalance.org>

Date: April 2, 2011 21:40:56 EDT

To: obo-d...@lists.sourceforge.net

Cc: Hilmar Lapp <hl...@nescent.org>, Jonathan Rees <j...@creativecommons.org>, Kevin Richards <Rich...@landcareresearch.co.nz>

Subject: Re: [Obo-discuss] [Obo-taxonomy] taxonomy ranks ontology?

Reply-To: obo-d...@lists.sourceforge.net

On Apr 2, 2011, at 8:53 PM, Peter Midford wrote:

My thoughts concern issues addressed by Peter at various places in his comments below.

The reason we haven't added more semantics to rank terms is both because we haven't had a phenoscape use case that requires it (we really only use them for display purposes at present), but also because providing a set of names allows those who need the additional semantics to build  ontologies that reflect the taxonomic thinking of their particular domain authority (zoology, botany, bacteriology, etc.).  There's enough incongruence among the authorities that trying to capture it all in a single ontology would, I expect, require at least a workshop to capture all the issues, apart from the engineering effort to make a consistent ontology that behaved properly across authorities.  It's even messier than that, as there is a term in TAXRANK that seems specific to Drosophilists.  But I'm sure this incongruence isn't news to you.  Since we didn't have a strong use case, I didn't give much consideration to half-way measures such as asserting ordering relations among the standard Linnaean ranks.

Note that has_rank is defined (as an annotation property / OBO metadata tag) in TTO, not TAXRANK.  This allows the property linking taxa and ranks to be defined as needed in a particular taxonomic ontology.  I expect Phenoscape will be experimenting again with individual-based taxonomies in near future as part of transitioning to OWL and allow a reconsideration of our linking property.

I think TAXRANK can provide a common baseline vocabulary for projects whether or not they see the need to define rank ordering relations.  If enough projects decide to build ontologies that order ranks and there is a desire to attempt to integrate across authorities, I expect the Phenotype ontology RCN to welcome proposals for a integration workshop when the time comes.

I think that connecting across authorities will, in many cases, be impossible. Different authorities work with different species concepts, and so I would think in many cases there will be differences in the extension of taxon names, and, even if they are the same, the reasons why their extensions will be the same will differ, so there is not really a link between the authorities.

The same applies, I would think, to the nature and ordering of the hierarchy. My understanding is that on some forms of cladism, for instance, species are the only biologically real taxon.

I am sure my suggestion that linking is not a reasonable goal as a general solution will not be welcomed by those who aim for maximum interoperability, but I think in this case the linking would be a software artifact.

I realize that this is a purely academic concern at this point, but I have been thinking about it because I am starting to create a database of terms structured around my evolutionary process ontology, and I don't quite know how to handle taxonomic categories.

The best working proposal I have come up with is to create a property (metadata property?) for the authority used by the people that collected the data to begin with and then (with a little help from a web services programmer) link to the uBio system, which lists variant names and sources for taxon names.

I appreciate everyone's time and attention. I am not a subscriber to the OBO-taxonomy list so maybe someone who is could forward this to that list.

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Adam M. Goldstein PhD, MSLIS
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Peter E. Midford

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