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

[Jonathan R. <ja...@cr...>]

2011/3/31 Peter Midford <pet...@gm...>:
> Richard,
>                How do you deal with differences in usage between authorities (e.g., the respective bodies for Botany and Zoology)?
>
> Specifying a sort order field suggests that inserting intermediate level rank terms causes field values to change, which is I suppose is OK for a database, but would at the very least would raise versioning issues for an ontology (less for OWL than OBO 1.2 I expect).  Work arounds like using floats for rank orders seem rather non-ontological.  Perhaps some sort of lattice that accommodates alternate orderings would suffice for this.  I agree with Kevin and Jonathan that using rank assignments and ordering to validate taxonomic ordering is a valid use case, though I'm not sure how compelling I find it.

Peter,

This is not at all what I was saying. I take as a given that you've
chosen the right design; I just don't understand what the design is.
If I did I would be able to answer the non-rhetorical questions about
correct use of the ontology that I posed.

If the answer is that there's no way to say anything incorrect using
these terms, no way that a database using these terms can contain a
mistake, then I'm not sure what it's good for. But I don't think this
is what you mean to imply, and I'm pretty sure that what you've done
is good for something.

As another example, suppose you published an article that said
"Peter's Taxon 12345 has rank Phylum", and then I published another
article that said "Peter's Taxon 12345 has rank Genus".  And I cite
you and say that by "Peter's Taxon 12345" I mean whatever it is that
you mean by the phrase (same taxon concept). Are there any
circumstances under which my rank statement might be incorrect?  (I
understand that we might be talking about a very nondiverse phylum,
but suppose we're not; or re-run this example where I say "Peter's
Taxon 12345 is not a Phylum".)

Jonathan