Hierarchal vs Non-Hierarchal Interfaces to Biological Taxonomy

#11

Quote:

Can you parse this tree (from one of Celko's examples)?:
(Albert(Bert,Chuck(Donna,Eddie,Fred)))

See related thread which also included Gilbert in the hierarchy:
http://groups.google.com/group/comp....6437465d80ec6?

#12

Neo wrote:

Quote:

What is the main difference between the two?

Linnean is morphological. Caldistic follows evolutionary
lines. Species that co-evolved morphologically similar
features can be close in the Linnean taxonomy but distant
in the clastistic; and vice-versa.

Quote:

Thanks, I had breifly visited this site earlier, but dismissed it as
the trees diagrams are graphical instead of textual, thus preventing me
from easily gathering the data

Yeah, that's why I said to "start looking" there. I don't
know of any db-friendly data available, but I guessed that
by following links, you should be able to find one
eventually.

Quote:

But if this the definitive site on bio
taxonomy, I could go ahead and type in the major ones.

Looks like you found another site that better suited
your needs?

Larry Coon
University of California

#13

Quote:

http://tolweb.org/tree/ I could go ahead and type in the major ones.

Looks like you found another site that better suited your needs?

No, not for biological taxanomy. And in fact, others have also
recommend the same site, so it appears to be the definitive one.

#14

Quote:

HOT! HOT! gene wagon. Go here: http://www.geneontology.org/
and download the ontology ...

Ok, I have imported the slim version of the Gene Ontology. It's
structure is essentially identical to the regular Gene Ontology however
it only contains the more common gene products (called terms) making it
much smaller. See current dbd implementation at
www.dbfordummies.com/example/ex705.asp Anybody out there an actual GO
user?

#15

Quote:

I'd start looking at the Tree of Life Project: http://tolweb.org/tree/

Your suggestion paid off! The entire taxanomy is available at
http://tolweb.org/tree/home.pages/downloadtree.html in the form of a
+5Mb XML file.

By the way, do you have a suggestion for a cladistic-type taxonomy?

#16

Quote:

Tree of Life Project: http://tolweb.org/tree/

Ok, I have imported the Tree Of Life XML file which contains approx
36,000 entries. Each entry only has the scientific name and position in
the evolutionary hierarchy. May be able to request the XML file include
more info (ie common names) since it is funded by National Science
Foundation. To find man's position in the hierarchy, submit query
"(verifyRel (. 'Life 'on 'Earth) evolvedTo Homo)". Tree automatically
expands to display him approx 70 levels deep from the root! For more
details, see www.dbfordummies.com/example/ex710.asp

#17

Neo wrote:

Quote:

Your suggestion paid off! The entire taxanomy is available at
http://tolweb.org/tree/home.pages/downloadtree.html in the form of a
+5Mb XML file.

Cool.

Quote:

By the way, do you have a suggestion for a cladistic-type taxonomy?

That one IS clasistic. Linnean is the older taxonomy
of Kingdom-Phylum-Class-Order-Family-Genus-Species.

Larry Coon
University of California

The NBA Salary Cap FAQ:
http://members.cox.net/lmcoon/salarycap.htm

#18

Bob Badour wrote:

Quote:

Which common bird is it that has three cohorts A, B and C where A and B
can interbreed, B and C can interbreed but A and C cannot? Is it the robin?

There's lots of species like that -- it's called a ring
species. I think it's the salamander where every subspecies
but two can interbreed.

An interesting question is when you have subspecies A, B & C,
where A & C cannot interbreed, and B goes extinct, do you now
have two distinct species?

Larry Coon
University of California

#19

Larry Coon wrote:

Quote:

Bob Badour wrote:

Which common bird is it that has three cohorts A, B and C where A and B
can interbreed, B and C can interbreed but A and C cannot? Is it the robin?

There's lots of species like that -- it's called a ring
species. I think it's the salamander where every subspecies
but two can interbreed.

An interesting question is when you have subspecies A, B & C,
where A & C cannot interbreed, and B goes extinct, do you now
have two distinct species?

Which opens the floor to: "How many species did you have before B went
extinct?"

Does anyone consider the horse and the donkey the same species?

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Hierarchal vs Non-Hierarchal Interfaces to Biological Taxonomy

comp.databases comp.databases

Re: Hierarchal vs Non-Hierarchal Interfaces to Biological Taxonomy - 12-16-2006 , 11:55 AM

Re: Hierarchal vs Non-Hierarchal Interfaces to Biological Taxonomy - 12-16-2006 , 01:16 PM

Re: Hierarchal vs Non-Hierarchal Interfaces to Biological Taxonomy - 12-16-2006 , 02:15 PM

Re: Hierarchal vs Non-Hierarchal Interfaces to Biological Taxonomy - 12-19-2006 , 07:11 PM

Re: Hierarchal vs Non-Hierarchal Interfaces to Biological Taxonomy - 12-19-2006 , 09:20 PM

Re: Hierarchal vs Non-Hierarchal Interfaces to Biological Taxonomy - 12-21-2006 , 12:58 AM

Re: Hierarchal vs Non-Hierarchal Interfaces to Biological Taxonomy - 12-22-2006 , 02:47 PM

Re: Hierarchal vs Non-Hierarchal Interfaces to Biological Taxonomy - 12-22-2006 , 02:49 PM

Re: Hierarchal vs Non-Hierarchal Interfaces to Biological Taxonomy - 12-22-2006 , 03:17 PM