vocamp follow-up: request for discussion of upper level concepts in CDAO, PhyloWS, etc

[Arlin Stoltzfus]

Dear all--

I've been threatening for a long time to tackle the issue of what
sorts of things are trees, clades, OTUs and so on, and how do they
relate to each other. The CDAO team has not yet worked out these
issues.

This is not an abstract exercise without implications. Its relevant
for basic issues like, when a user asks for a "clade" in PhyloWS, do
we return a subtree (on the grounds that a clade is a part of a tree),
or a collection of nodes (on the grounds that a clade is a collection
of TU things)?

The VoCamp last month made these issues more poignant, and so on the
train ride back from Montpellier to Paris, I scribbled many pages of
notes, which I recently put on the wiki here:

http://www.evoio.org/wiki/UpperOntology

Feel free to edit this page. If you don't have edit permissions, sign
up for an account at NESCent.

This is a rough sketch. It does not get to the point of making
specific recommendations in CDAO yet. However, its a start. As a
next step, I'm inviting comments and discussion on this. If there is
enough interest, we could have a teleconference about it.

Arlin
-------
Arlin Stoltzfus (stol...@umbi.umd.edu)
Fellow, CARB; Adj. Assoc. Prof., UMBI; Research Biologist, NIST
CARB, 9600 Gudelsky Drive, Rockville, MD
tel: 240 314 6208; web: www.molevol.org