Posting for Dave Remsen re: MBL project

[Les Kaufman]

Hi, all.

Dave Remsen asked me to post this message for him regarding the MBL
Taxonomic Name Server, since he isn't a member of our list.  He ought to
be and wants to be though.  Somebody tell him how to sign up!

Les

******(from Dave Remsen)******

I noticed that there was a post regarding our project here and I thought
I might qualify a few comments in case there was interest.  The UPI
reporter did a very brief phone interview last week and appears to have
muddled a few facts.  The implication that there are different naming
conventions between different groups for example was a bit unsettling. I
told him he should let me have a read as he was typing (not taping) as
we spoke.

The Taxonomic Name Server we are building and the tool sets which
interact with it have a very simple purpose: to provide a consistent
mechanism to retrieve and qualify taxonomic name and classification
information.  There is a significant need for this from a biological
data development standpoint.  Our laboratory is developing data systems
ranging from contemporary cladistic-based, molecular evolution data to
300 year old voyage manuscripts.  The one common theme among them are
their links to biology and the only thing that links their associated
data to biodiversity is a name.  For better or worse the name is the
only means to give that data an associated context within contemporary
systematics.  Place the name to a contemporary taxonomic concept and
your data has the context.   Fail, and it does not.

The Taxonomic Name Server is intended to qualify names and link them to
one or more relevant taxonomic concepts.  Concepts have relationships
which form classifications.  Classifications also have relations with
one another.  This is simply the reality of systematics and taxonomic
revisions.  We felt we needed to have a data model that followed reality
and the reality is that different folks hold different views.  If there
are five classifications of Cephalopods in the literature then it seems
I need a means to record them and then return them when they are asked for.

The TNS is based on the Unified Medical Language System (UMLS)
metathesaurus, a well-planned and flexible data model made just for this
sort of problem.  It does't decide which classification of term is
preferred.  These are all aspects outside the realm of TNS and addressed
individually by application developers who interact with the name
server.

We are in contact with the large taxonomic aggregators.  Our goal isn't
to duplicate any efforts but rather to facilitate delivering this
information in ways that maximize their value.  A consistent interface
to all name and classification information, a fast public service, a
means to leverage a taxonomists work into any imaginable application are
all goals because we need them.  The response from the library, museum,
and even corporate world (publishers, info aggregators) is quite
astonishing and very clear.  There is a need for taxonomic name and
classification information (we refer to this all as taxonomic metadata)
and I believe that if the demand is met there will be a greatly
increased value for this sort of work

Look no further than JSTOR (www.jstor.org).  Use my example and try to
find articles on our local bluefish, Pomatomus saltator.  This is the
name you will find at FishBase as the current preferred form for this
animal.  You will find exactly one article.  Go to
http://zeus.mbl.edu/public/tns/jstor/index.php and try it again and send
the query again.  JSTOR has 42 articles which match this organism.  Take
your pick of fungi, bacteria, cnidarian, mollusk or mammal.   I have
this JSTOR problem in every data set and document I publish.

If someone can let me know how to join the group I'll try to explain our
intentions.   There are things we want to do and things we do not want
to do.   We wish to make the best use of the resources available to us
to meet what we believe are our legitimate needs and to include and
foster relationships within the taxonomic community upon which we depend.

Thank you, David Remsen



--
Les Kaufman
Biology Department
Boston University
5 Cummington St.
Boston, MA 02215
lesk at bu.edu
617-353-5560 office
617-353-6965 lab
617-353-6340 fax

and

BUMP
7 MBL St.
Woods Hole, MA 02543
508-289-7579 office
508-289-7950 fax