RE: [Obo-discuss] RE: Obo-discuss digest, Vol 1 #127 - 2 msgs

[Mark M. <mm...@sd...>]

At the risk of being a fool, what tools are you all viewing the results
of spire in?

MSIE gives me raw xml, and fire fox and opera give me text streams, but
no relations.



-----Original Message-----
From: obo...@li...
[mailto:obo...@li...] On Behalf Of Parr,
Cynthia
Sent: Monday, March 13, 2006 8:51 AM
To: obo...@li...
Subject: [Obo-discuss] RE: Obo-discuss digest, Vol 1 #127 - 2 msgs

I wanted to alert others that we've also been working with representing
taxonomy (and phylogeny) as ontologies. You can use a utility to see
examples in OWL at http://spire.umbc.edu/ont/ethan.php .
We also have (and may make available soon) the phylogeny of the Tree of
Life website (http://www.tolweb.org) represented in OWL.=20

We are also ignoring rank and common names for now and using nested
subclasses. That should suit our purposes. Our ranks and common names
remain in traditional relational data tables.

Cynthia Parr
http://www.cs.umd.edu/hcil/biodiversity
http://www.leptree.net
http://spire.umbc.edu



|Date: Sun, 12 Mar 2006 21:58:18 -0500
|From: Pankaj Jaiswal <pj...@co...>
|To: obo...@li...
|Subject: Re: [Obo-discuss] Taxonomy Data
|Reply-To: obo...@li...
|
|Hi Chris,
|
|For Gramene's requirements, I did build the taxonomy in OBO format
|(http://www.gramene.org/plant_ontology/#tax). Take a look. Instead of
|creating the classes like
|kingdom/tribe/class/subclass/phylum/order/genus/species/sunspecies/vari
etas
|,
|I simply created the 'subsets' like categories. These subsets were used
|to flag the term suggesting its type in the taxonomy tree. Looks like
|creating a classes for each subsets is a good idea, but this will
|eventually result in a very complex network, which in Gramene we though
|is a bit overkill. If we do want the classes, the major problem I see
is
|for such taxon terms that have no taxonomic qualifier (rank) defined
|(e.g. in my file subsetdef: no rank "no taxonomic rank").
|
|Another problem is on relationships and I was not sure how to address
|this. I simply used the is_a everywhere, but if one looks at it the
|instances of species are considered part_of a given genus parent
whereas
|the current format has is_a. Do you have any suggestions?


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