Topic 3: GUIDs for Taxon Names and Taxon Concepts

Chuck Miller Chuck.Miller at MOBOT.ORG
Fri Nov 4 12:24:00 CET 2005


Rod Page has made some excellent observations today that bear repeating:

"we make a mistake if we equate GUIDs with solving all our problems"

And
"mapping different GUIDs can be tricky, but this is an entirely separate
question. I think there's a huge confusion between GUIDs and some sort of
global taxonomy -- they are not the same thing."

I think it will be a difficult enough task for GBIF/TDWG to standardize and
implement the simplest of GUID approaches.  To do more risks getting the
whole thing bogged down.  Can we limit the first round of this work to the
simpler, easier-to-do solution?

But even then, as Richard pointed out in his very first post, there still
exists ambiguity and debate on what constitutes the object to which the GUID
applies.  At the extreme simplest end of the spectrum, there are many
occurrences of a "name string" that are different and unique but are meant
to be the same - for instance "aus bus" and "aus  bus" (with two spaces) are
strictly different to a computer, but are clearly the same thing to a human.
>>>From that simplistic variation, there are ever more complex variations on
this theme all the way up to "global taxonomy" as Rod calls it.  So,
precisely deciding even the simplest of name "atoms" for which GUIDs will be
standardized and implemented is a significant task.

Chuck



-----Original Message-----
From: Roderic Page [mailto:r.page at BIO.GLA.AC.UK]
Sent: Friday, November 04, 2005 4:22 AM
To: TDWG-GUID at LISTSERV.NHM.KU.EDU
Subject: Re: [TDWG-GUID] Topic 3: GUIDs for Taxon Names and Taxon Concepts

>
>> Assigning GUIDs solely to basionyms strikes me as crazy -- I'd suggest
>> most taxa aren't known by their basionyms. I'd advocate GUIDs for
>> every
>> name string (with the possible exception of orthographic variants,
>> spelling mistakes, etc.).
>
> By "Namestring", do you include author, our just taxonomic
> nomenclatural
> elements?  In either case, why even bother establishing a GUID for
> taxonomic
> names at all?  Why not just use the namestring itself?

Oh come on, you can't be serious ;-) Names aren't unique, GUIDs are.


>
> Moreover, I don't think anyone has suggest that GUIDs be assigned
> "solely"
> to basionyms.

Er, I quote from your earlier post.

 > I completely agree -- but again, what gets a "Name" GUID? (as opposed
to a
 > "usage" GUID or a "concept" GUID)  Only basionyms? (I hope!)  Or also
 > different combinations? (I hope not!) Or also spelling variants? (I
*really*
 > hope not!!)


> The point is, there shouldn't be six different "units" to
> which GUIDs are assigned to represent "taxon names" [basionyms,
> combinations, namestrings, namestrings with authors, concept
> definitions,
> name usage instances, etc.]
>
>> Lastly, "imposing standards" is the wrong way to think about this.
>> Standards win support if they work, and are adopted. I'd suggest this
>> stuff will happen if people make compelling applications that others
>> make use of, not because TDWG decides what should be done.
>
> O.K., my choice of the word "imposing" was bad.  I should have said
> something like "implementing".  The one lesson that the web has taught
> us
> more vividly than decentralization is the power of standards for
> information
> exchange. We could have all invented our own version of DarwinCore for
> exposing specimen records to the internet, and allowed natural
> selection to
> take its course such that only the most useful few versions survived
> -- but
> I don't think that would have been the most effective path to where we
> are
> now (and where we could be soon, once DarwinCore V2 is ratified and
> mapped
> against ABCD elements).

Yes, standards are nice, but in practise there is usually more than one
(like Darwin Core and ABCD), and the winner isn't always decided by
committee. But this is a side issue...

>
>> So, my final question is, what is wrong with having each taxonomic
>> database serve their own GUIDs for their own data (using an agreed
>> format, such as RDF), and where possible GUIDs from different sources
>> are mapped (e.g., a name string in IPNI to one in uBio). Users employ
>> whatever GUID they find useful -- at least we then know what digital
>> object they are referring to.
>
> To me, GUIDs are only valuable and serve the information exchange
> needs of
> our community if they are, to some extent at least, reusable.  I do not
> understand the value of assigning GUIDs to the records in my taxonomic
> database, if I am the only one who will ever use them. I understand the
> practical value of establishing "local" GUIDs to my taxon name records
> independently from other databases, if the long-term goal is to
> eventually
> map my GUIDs to the corresponding "equivalent" GUIDs of other
> databases.

For me the point is that if you have a GUID, I can map to you and add
value to my projects. Without a GUID, it's a pain.

>
> Donald started out this discussion by suggesting that "Taxon Name"
> objects
> might be thought of as fundamentally different from "Taxon Concept"
> objects
> (in an analagous way to how publication objects are fundamentally
> different
> from specimen objects).  If you agree with this, then it would be nice
> if we
> could find a standard line to draw between these two objects, so that
> when
> we later try to cross-walk our respective datasets, we're mapping
> apples to
> apples, and oranges to oranges (rather than apples to bananas and then
> back
> to oranges -- which aptly represents what I'm having to resort to in
> mapping
> my taxonomic data records to ITIS records).

If it hurts don't do it! Put another way, why not make the mapping
purely nomenclatural -- this name string also occurs in ITIS, and don't
make any claims that whatever ITIS means by that name is what you mean.
Alternatively, let users decide what mappings they want to make between
you and ITIS. Expertise is rare and widely distributed. I think you're
making things harder for yourself than the need to be.



>
>> If we think of the scientific literature, many paper have at least two
>> GUIDs (DOI and PubMed), both of which are useful, and which serve
>> different purposes.
>
> What is the value of expanding that to potentially hundreds, or
> thousands of
> GUIDs for each paper -- one GUID from each database that has a table of
> literature records?  Wouldn't our information exchange be much more
> efficient if we all adopted (or at least mapped to) either the DOI or
> the
> PubMed GUID (or both)? If so, why doesn't this same logic apply to
> taxon
> names?

I guess my point was that this is a case where more than one GUID
exists for the "same" thing (a publication), and we manage to cope.
Yes, "one GUID to rule them all" might be nice, but I just don't buy
that it's going to happen any time soon. Just look at the discussion
this topic has generated...

Again, I think we make a mistake if we equate GUIDs with solving all
our problems. Rather, I suggest they give us an infrastructure on which
to build tools for mapping names/concepts/whatever.

Regards

Rod


------------------------------------------------------------------------
----------------------------------------
Professor Roderic D. M. Page
Editor, Systematic Biology
DEEB, IBLS
Graham Kerr Building
University of Glasgow
Glasgow G12 8QP
United Kingdom

Phone:    +44 141 330 4778
Fax:      +44 141 330 2792
email:    r.page at bio.gla.ac.uk
web:      http://taxonomy.zoology.gla.ac.uk/rod/rod.html
reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html

Subscribe to Systematic Biology through the Society of Systematic
Biologists Website:  http://systematicbiology.org
Search for taxon names at http://darwin.zoology.gla.ac.uk/~rpage/portal/
Find out what we know about a species at http://ispecies.org

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<TITLE>RE: [TDWG-GUID] Topic 3: GUIDs for Taxon Names and Taxon =
Concepts</TITLE>
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<BODY>

<P><FONT SIZE=3D2>Rod Page has made some excellent observations today =
that bear repeating:</FONT>
</P>

<P><FONT SIZE=3D2>&quot;we make a mistake if we equate GUIDs with =
solving all our problems&quot;</FONT>
</P>

<P><FONT SIZE=3D2>And</FONT>
<BR><FONT SIZE=3D2>&quot;mapping different GUIDs can be tricky, but =
this is an entirely separate question. I think there's a huge confusion =
between GUIDs and some sort of global taxonomy -- they are not the same =
thing.&quot;</FONT></P>

<P><FONT SIZE=3D2>I think it will be a difficult enough task for =
GBIF/TDWG to standardize and implement the simplest of GUID =
approaches.&nbsp; To do more risks getting the whole thing bogged =
down.&nbsp; Can we limit the first round of this work to the simpler, =
easier-to-do solution?</FONT></P>

<P><FONT SIZE=3D2>But even then, as Richard pointed out in his very =
first post, there still exists ambiguity and debate on what constitutes =
the object to which the GUID applies.&nbsp; At the extreme simplest end =
of the spectrum, there are many occurrences of a &quot;name =
string&quot; that are different and unique but are meant to be the same =
- for instance &quot;aus bus&quot; and &quot;aus&nbsp; bus&quot; (with =
two spaces) are strictly different to a computer, but are clearly the =
same thing to a human.&nbsp; From that simplistic variation, there are =
ever more complex variations on this theme all the way up to =
&quot;global taxonomy&quot; as Rod calls it.&nbsp; So, precisely =
deciding even the simplest of name &quot;atoms&quot; for which GUIDs =
will be standardized and implemented is a significant task.</FONT></P>

<P><FONT SIZE=3D2>Chuck&nbsp;&nbsp; </FONT>
</P>

<P><FONT SIZE=3D2>&nbsp;</FONT>
</P>

<P><FONT SIZE=3D2>-----Original Message-----</FONT>
<BR><FONT SIZE=3D2>From: Roderic Page [<A =
HREF=3D"mailto:r.page at BIO.GLA.AC.UK">mailto:r.page at BIO.GLA.AC.UK</A>] =
</FONT>
<BR><FONT SIZE=3D2>Sent: Friday, November 04, 2005 4:22 AM</FONT>
<BR><FONT SIZE=3D2>To: TDWG-GUID at LISTSERV.NHM.KU.EDU</FONT>
<BR><FONT SIZE=3D2>Subject: Re: [TDWG-GUID] Topic 3: GUIDs for Taxon =
Names and Taxon Concepts</FONT>
</P>

<P><FONT SIZE=3D2>&gt;</FONT>
<BR><FONT SIZE=3D2>&gt;&gt; Assigning GUIDs solely to basionyms strikes =
me as crazy -- I'd suggest</FONT>
<BR><FONT SIZE=3D2>&gt;&gt; most taxa aren't known by their basionyms. =
I'd advocate GUIDs for</FONT>
<BR><FONT SIZE=3D2>&gt;&gt; every</FONT>
<BR><FONT SIZE=3D2>&gt;&gt; name string (with the possible exception of =
orthographic variants,</FONT>
<BR><FONT SIZE=3D2>&gt;&gt; spelling mistakes, etc.).</FONT>
<BR><FONT SIZE=3D2>&gt;</FONT>
<BR><FONT SIZE=3D2>&gt; By &quot;Namestring&quot;, do you include =
author, our just taxonomic</FONT>
<BR><FONT SIZE=3D2>&gt; nomenclatural</FONT>
<BR><FONT SIZE=3D2>&gt; elements?&nbsp; In either case, why even bother =
establishing a GUID for</FONT>
<BR><FONT SIZE=3D2>&gt; taxonomic</FONT>
<BR><FONT SIZE=3D2>&gt; names at all?&nbsp; Why not just use the =
namestring itself?</FONT>
</P>

<P><FONT SIZE=3D2>Oh come on, you can't be serious ;-) Names aren't =
unique, GUIDs are.</FONT>
</P>
<BR>

<P><FONT SIZE=3D2>&gt;</FONT>
<BR><FONT SIZE=3D2>&gt; Moreover, I don't think anyone has suggest that =
GUIDs be assigned</FONT>
<BR><FONT SIZE=3D2>&gt; &quot;solely&quot;</FONT>
<BR><FONT SIZE=3D2>&gt; to basionyms.</FONT>
</P>

<P><FONT SIZE=3D2>Er, I quote from your earlier post.</FONT>
</P>

<P><FONT SIZE=3D2>&nbsp;&gt; I completely agree -- but again, what gets =
a &quot;Name&quot; GUID? (as opposed</FONT>
<BR><FONT SIZE=3D2>to a</FONT>
<BR><FONT SIZE=3D2>&nbsp;&gt; &quot;usage&quot; GUID or a =
&quot;concept&quot; GUID)&nbsp; Only basionyms? (I hope!)&nbsp; Or =
also</FONT>
<BR><FONT SIZE=3D2>&nbsp;&gt; different combinations? (I hope not!) Or =
also spelling variants? (I</FONT>
<BR><FONT SIZE=3D2>*really*</FONT>
<BR><FONT SIZE=3D2>&nbsp;&gt; hope not!!)</FONT>
</P>
<BR>

<P><FONT SIZE=3D2>&gt; The point is, there shouldn't be six different =
&quot;units&quot; to</FONT>
<BR><FONT SIZE=3D2>&gt; which GUIDs are assigned to represent =
&quot;taxon names&quot; [basionyms,</FONT>
<BR><FONT SIZE=3D2>&gt; combinations, namestrings, namestrings with =
authors, concept</FONT>
<BR><FONT SIZE=3D2>&gt; definitions,</FONT>
<BR><FONT SIZE=3D2>&gt; name usage instances, etc.]</FONT>
<BR><FONT SIZE=3D2>&gt;</FONT>
<BR><FONT SIZE=3D2>&gt;&gt; Lastly, &quot;imposing standards&quot; is =
the wrong way to think about this.</FONT>
<BR><FONT SIZE=3D2>&gt;&gt; Standards win support if they work, and are =
adopted. I'd suggest this</FONT>
<BR><FONT SIZE=3D2>&gt;&gt; stuff will happen if people make compelling =
applications that others</FONT>
<BR><FONT SIZE=3D2>&gt;&gt; make use of, not because TDWG decides what =
should be done.</FONT>
<BR><FONT SIZE=3D2>&gt;</FONT>
<BR><FONT SIZE=3D2>&gt; O.K., my choice of the word =
&quot;imposing&quot; was bad.&nbsp; I should have said</FONT>
<BR><FONT SIZE=3D2>&gt; something like &quot;implementing&quot;.&nbsp; =
The one lesson that the web has taught</FONT>
<BR><FONT SIZE=3D2>&gt; us</FONT>
<BR><FONT SIZE=3D2>&gt; more vividly than decentralization is the power =
of standards for</FONT>
<BR><FONT SIZE=3D2>&gt; information</FONT>
<BR><FONT SIZE=3D2>&gt; exchange. We could have all invented our own =
version of DarwinCore for</FONT>
<BR><FONT SIZE=3D2>&gt; exposing specimen records to the internet, and =
allowed natural</FONT>
<BR><FONT SIZE=3D2>&gt; selection to</FONT>
<BR><FONT SIZE=3D2>&gt; take its course such that only the most useful =
few versions survived</FONT>
<BR><FONT SIZE=3D2>&gt; -- but</FONT>
<BR><FONT SIZE=3D2>&gt; I don't think that would have been the most =
effective path to where we</FONT>
<BR><FONT SIZE=3D2>&gt; are</FONT>
<BR><FONT SIZE=3D2>&gt; now (and where we could be soon, once =
DarwinCore V2 is ratified and</FONT>
<BR><FONT SIZE=3D2>&gt; mapped</FONT>
<BR><FONT SIZE=3D2>&gt; against ABCD elements).</FONT>
</P>

<P><FONT SIZE=3D2>Yes, standards are nice, but in practise there is =
usually more than one</FONT>
<BR><FONT SIZE=3D2>(like Darwin Core and ABCD), and the winner isn't =
always decided by</FONT>
<BR><FONT SIZE=3D2>committee. But this is a side issue...</FONT>
</P>

<P><FONT SIZE=3D2>&gt;</FONT>
<BR><FONT SIZE=3D2>&gt;&gt; So, my final question is, what is wrong =
with having each taxonomic</FONT>
<BR><FONT SIZE=3D2>&gt;&gt; database serve their own GUIDs for their =
own data (using an agreed</FONT>
<BR><FONT SIZE=3D2>&gt;&gt; format, such as RDF), and where possible =
GUIDs from different sources</FONT>
<BR><FONT SIZE=3D2>&gt;&gt; are mapped (e.g., a name string in IPNI to =
one in uBio). Users employ</FONT>
<BR><FONT SIZE=3D2>&gt;&gt; whatever GUID they find useful -- at least =
we then know what digital</FONT>
<BR><FONT SIZE=3D2>&gt;&gt; object they are referring to.</FONT>
<BR><FONT SIZE=3D2>&gt;</FONT>
<BR><FONT SIZE=3D2>&gt; To me, GUIDs are only valuable and serve the =
information exchange</FONT>
<BR><FONT SIZE=3D2>&gt; needs of</FONT>
<BR><FONT SIZE=3D2>&gt; our community if they are, to some extent at =
least, reusable.&nbsp; I do not</FONT>
<BR><FONT SIZE=3D2>&gt; understand the value of assigning GUIDs to the =
records in my taxonomic</FONT>
<BR><FONT SIZE=3D2>&gt; database, if I am the only one who will ever =
use them. I understand the</FONT>
<BR><FONT SIZE=3D2>&gt; practical value of establishing =
&quot;local&quot; GUIDs to my taxon name records</FONT>
<BR><FONT SIZE=3D2>&gt; independently from other databases, if the =
long-term goal is to</FONT>
<BR><FONT SIZE=3D2>&gt; eventually</FONT>
<BR><FONT SIZE=3D2>&gt; map my GUIDs to the corresponding =
&quot;equivalent&quot; GUIDs of other</FONT>
<BR><FONT SIZE=3D2>&gt; databases.</FONT>
</P>

<P><FONT SIZE=3D2>For me the point is that if you have a GUID, I can =
map to you and add</FONT>
<BR><FONT SIZE=3D2>value to my projects. Without a GUID, it's a =
pain.</FONT>
</P>

<P><FONT SIZE=3D2>&gt;</FONT>
<BR><FONT SIZE=3D2>&gt; Donald started out this discussion by =
suggesting that &quot;Taxon Name&quot;</FONT>
<BR><FONT SIZE=3D2>&gt; objects</FONT>
<BR><FONT SIZE=3D2>&gt; might be thought of as fundamentally different =
from &quot;Taxon Concept&quot;</FONT>
<BR><FONT SIZE=3D2>&gt; objects</FONT>
<BR><FONT SIZE=3D2>&gt; (in an analagous way to how publication objects =
are fundamentally</FONT>
<BR><FONT SIZE=3D2>&gt; different</FONT>
<BR><FONT SIZE=3D2>&gt; from specimen objects).&nbsp; If you agree with =
this, then it would be nice</FONT>
<BR><FONT SIZE=3D2>&gt; if we</FONT>
<BR><FONT SIZE=3D2>&gt; could find a standard line to draw between =
these two objects, so that</FONT>
<BR><FONT SIZE=3D2>&gt; when</FONT>
<BR><FONT SIZE=3D2>&gt; we later try to cross-walk our respective =
datasets, we're mapping</FONT>
<BR><FONT SIZE=3D2>&gt; apples to</FONT>
<BR><FONT SIZE=3D2>&gt; apples, and oranges to oranges (rather than =
apples to bananas and then</FONT>
<BR><FONT SIZE=3D2>&gt; back</FONT>
<BR><FONT SIZE=3D2>&gt; to oranges -- which aptly represents what I'm =
having to resort to in</FONT>
<BR><FONT SIZE=3D2>&gt; mapping</FONT>
<BR><FONT SIZE=3D2>&gt; my taxonomic data records to ITIS =
records).</FONT>
</P>

<P><FONT SIZE=3D2>If it hurts don't do it! Put another way, why not =
make the mapping</FONT>
<BR><FONT SIZE=3D2>purely nomenclatural -- this name string also occurs =
in ITIS, and don't</FONT>
<BR><FONT SIZE=3D2>make any claims that whatever ITIS means by that =
name is what you mean.</FONT>
<BR><FONT SIZE=3D2>Alternatively, let users decide what mappings they =
want to make between</FONT>
<BR><FONT SIZE=3D2>you and ITIS. Expertise is rare and widely =
distributed. I think you're</FONT>
<BR><FONT SIZE=3D2>making things harder for yourself than the need to =
be.</FONT>
</P>
<BR>
<BR>

<P><FONT SIZE=3D2>&gt;</FONT>
<BR><FONT SIZE=3D2>&gt;&gt; If we think of the scientific literature, =
many paper have at least two</FONT>
<BR><FONT SIZE=3D2>&gt;&gt; GUIDs (DOI and PubMed), both of which are =
useful, and which serve</FONT>
<BR><FONT SIZE=3D2>&gt;&gt; different purposes.</FONT>
<BR><FONT SIZE=3D2>&gt;</FONT>
<BR><FONT SIZE=3D2>&gt; What is the value of expanding that to =
potentially hundreds, or</FONT>
<BR><FONT SIZE=3D2>&gt; thousands of</FONT>
<BR><FONT SIZE=3D2>&gt; GUIDs for each paper -- one GUID from each =
database that has a table of</FONT>
<BR><FONT SIZE=3D2>&gt; literature records?&nbsp; Wouldn't our =
information exchange be much more</FONT>
<BR><FONT SIZE=3D2>&gt; efficient if we all adopted (or at least mapped =
to) either the DOI or</FONT>
<BR><FONT SIZE=3D2>&gt; the</FONT>
<BR><FONT SIZE=3D2>&gt; PubMed GUID (or both)? If so, why doesn't this =
same logic apply to</FONT>
<BR><FONT SIZE=3D2>&gt; taxon</FONT>
<BR><FONT SIZE=3D2>&gt; names?</FONT>
</P>

<P><FONT SIZE=3D2>I guess my point was that this is a case where more =
than one GUID</FONT>
<BR><FONT SIZE=3D2>exists for the &quot;same&quot; thing (a =
publication), and we manage to cope.</FONT>
<BR><FONT SIZE=3D2>Yes, &quot;one GUID to rule them all&quot; might be =
nice, but I just don't buy</FONT>
<BR><FONT SIZE=3D2>that it's going to happen any time soon. Just look =
at the discussion</FONT>
<BR><FONT SIZE=3D2>this topic has generated...</FONT>
</P>

<P><FONT SIZE=3D2>Again, I think we make a mistake if we equate GUIDs =
with solving all</FONT>
<BR><FONT SIZE=3D2>our problems. Rather, I suggest they give us an =
infrastructure on which</FONT>
<BR><FONT SIZE=3D2>to build tools for mapping =
names/concepts/whatever.</FONT>
</P>

<P><FONT SIZE=3D2>Regards</FONT>
</P>

<P><FONT SIZE=3D2>Rod</FONT>
</P>
<BR>

<P><FONT =
SIZE=3D2>---------------------------------------------------------------=
---------</FONT>
<BR><FONT SIZE=3D2>----------------------------------------</FONT>
<BR><FONT SIZE=3D2>Professor Roderic D. M. Page</FONT>
<BR><FONT SIZE=3D2>Editor, Systematic Biology</FONT>
<BR><FONT SIZE=3D2>DEEB, IBLS</FONT>
<BR><FONT SIZE=3D2>Graham Kerr Building</FONT>
<BR><FONT SIZE=3D2>University of Glasgow</FONT>
<BR><FONT SIZE=3D2>Glasgow G12 8QP</FONT>
<BR><FONT SIZE=3D2>United Kingdom</FONT>
</P>

<P><FONT SIZE=3D2>Phone:&nbsp;&nbsp;&nbsp; +44 141 330 4778</FONT>
<BR><FONT SIZE=3D2>Fax:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; +44 141 330 =
2792</FONT>
<BR><FONT SIZE=3D2>email:&nbsp;&nbsp;&nbsp; r.page at bio.gla.ac.uk</FONT>
<BR><FONT SIZE=3D2>web:&nbsp;&nbsp;&nbsp;&nbsp;&nbsp; <A =
HREF=3D"http://taxonomy.zoology.gla.ac.uk/rod/rod.html" =
TARGET=3D"_blank">http://taxonomy.zoology.gla.ac.uk/rod/rod.html</A></FO=
NT>
<BR><FONT SIZE=3D2>reprints: <A =
HREF=3D"http://taxonomy.zoology.gla.ac.uk/rod/pubs.html" =
TARGET=3D"_blank">http://taxonomy.zoology.gla.ac.uk/rod/pubs.html</A></F=
ONT>
</P>

<P><FONT SIZE=3D2>Subscribe to Systematic Biology through the Society =
of Systematic</FONT>
<BR><FONT SIZE=3D2>Biologists Website:&nbsp; <A =
HREF=3D"http://systematicbiology.org" =
TARGET=3D"_blank">http://systematicbiology.org</A></FONT>
<BR><FONT SIZE=3D2>Search for taxon names at <A =
HREF=3D"http://darwin.zoology.gla.ac.uk/~rpage/portal/" =
TARGET=3D"_blank">http://darwin.zoology.gla.ac.uk/~rpage/portal/</A></FO=
NT>
<BR><FONT SIZE=3D2>Find out what we know about a species at <A =
HREF=3D"http://ispecies.org" =
TARGET=3D"_blank">http://ispecies.org</A></FONT>
</P>

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