Hi David,
I took a look at the page http://code.google.com/p/taxon-name-processing/wiki/TdwgSession2009
which has an agenda and some documentation prepared in advance of the workshop
you mention, but no summary of the discussion or action items. Does such exist
somewhere else, and/or could it be added to that page perhaps?
Cheers - Tony
From:
tdwg-tag-bounces@lists.tdwg.org [mailto:tdwg-tag-bounces@lists.tdwg.org] On Behalf Of David Remsen (GBIF)
Sent: Friday, 9 July 2010 6:27 AM
To: tdwg-content@lists.tdwg.org
Mailing List
Cc: Technical Architecture Group
mailing list
Subject: Re: [tdwg-tag] [tdwg-content]
WPS for Names
You may recall that at the name processing meeting at TDWG last year
there were many presentations on name recognition, discovery, and
matching (terms we distinguished at a 2009 workshop and documented at http://code.google.com/p/taxon-name-processing/)
and one outcome was the need to polish and operationalise some of these
services. At GBIF, we undertook the following:
Supported the refinement of uBio's TaxonFinder , a
name-recognition service. This upgrade uncoupled the service from client
functions that were hard-coded into the original, abstracted ubio
name-service lookups from the service, and conforms to an API that
returns found names as dwc:scientificName
Our version is here (http://code.google.com/p/taxon-name-processing/wiki/NameFindingAPI)
and is near ready for release.
Markus has experimented with a Lucene-based name-matching algorithm
which has a lot of promise but needs more dedicated time to be operational but
it conforms to the same API.
We also supported the port of TaxaMatch to PHP and I have been
discussing some refinements of this with Mike Giddens to get this service port
into a more simplified and localised web application that basically allows a
user to provide one or more name indexes that serve as target lexicons.
These could be derived via simple lists or database links. I'd like to
see the response conform to the same or extended output format as the name
finding API. What we really want are simple solutions that do small
things well.
Best,
David Remsen
----------------------------------------------------------------------------
David Remsen, Senior
Programme Officer
Electronic Catalog of
Names of Known Organisms
Global Biodiversity
Information Facility Secretariat
Universitetsparken
15, DK-2100
Tel:
+45-35321472 Fax: +45-35321480
Mobile +45 28751472
Skype: dremsen
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On Jul 7, 2010, at 7:15 PM, Matt Jones wrote:
Kevin,
Also of relevance would be the work that iPlant is sponsoring on a
Taxonomic Name Resolution Service (TNRS) -- see:
https://pods.iplantcollaborative.org/wiki/display/iptol/TNRS+Workshop
for background on a recent workshop for this activity. I'm sure they'd
be interested in collaborating. I think Brian Enquist would have a good
idea of progress on the project and would be able to provide more details.
Matt
On Wed, Jul 7, 2010 at 1:49 PM, Evgeniy Meyke <evgeniy@earthcape.com> wrote:
Hi Kevin, Tony, and all
As one of the very likely consumers of
such a service I’ll be following this with great interest.
A quick question at this point. Is
anything like this planned for GNA (www.globalnames.org)? or GBIF?
Evgeniy
From: tdwg-tag-bounces@lists.tdwg.org [mailto:tdwg-tag-bounces@lists.tdwg.org]
On Behalf Of
Sent: 8. heinäkuuta 2010 0:32
To: Tony.Rees@csiro.au; tdwg-tag@lists.tdwg.org
Subject: Re: [tdwg-tag] WPS for Names
Thanks Tony. I would be interested
in any collaboration we can do in this area (assuming I find 5 minutes to work
on it :-))
There seems to be several approaches to
name matching/integration – one working with the name strings, and one working
with more structured data. It would be good to clarify and perhaps
standardise these approaches. (the second approach is discussed in a
recent paper of mine).
It does indeed become a slippery slope,
and this is one of the reasons I am keen to promote some sort of
infrastructure/configurability of a matching system, so that end users can
configure a matching algorithm/workflow to suit their particular data.
Kevin
From: Tony.Rees@csiro.au
[mailto:Tony.Rees@csiro.au]
Sent: Wednesday, 7 July 2010 7:06
p.m.
To:
Cc: tdwg-content@lists.tdwg.org
Subject: RE: WPS for Names
Dear all (actually: I’m not sure who are the recipients currently
on tdwg-tag, maybe I will now find out!!)
As some on this list may be aware, this is an area that has been of
interest to me for quite some time (for example see: http://taxacom.markmail.org/message/ywq7ijiaeks7heiv
), so happy to see what can be done in this space.
Currently my algorithm is web accessible and tests designated genus
names against genus names held, and genus+species combinations against both
genus only, and genus+species combinations as held in my “IRMNG” reference
database (search entry point is at http://www.cmar.csiro.au/datacentre/irmng/
if interested). I am also planning to implement a degree of cross-rank matching
shortly, e.g. if a subgenus is supplied, test this as a possible genus against
genus+species combinations (as this often turns out to be the reason for a
direct mismatch in practice), same with infraspecies vs. subspecies (my current
interface does not yet handle infraspecies, and just detect then “parks”
apparent subgenera, but the intention is to handle these as testable components
in due course).
Maybe I will set up the above options and let you know as available
for testing. Also I may look for genus+species concatenated (think
Homosapiens), genus+subgenus+species with missing brackets around subgenus, and
maybe other things, as per my somewhat extensive exposure to otherwise
non-resolved namestrings floating around in OBIS/GBIF data provider space. Of
course it is a slippery slope; other examples are family in genus field and
vice versa, or common name similar; genus and species reversed; truncated names
not flagged as such; abbreviated genera (which I already handle as exact, but
not fuzzy matches at this time, at least as “H. sapiens” etc.); more..
Any comments on the above welcome,
Regards - Tony
Tony Rees
Manager, Divisional Data Centre,
CSIRO Marine and Atmospheric Research,
GPO
Ph: 0362 325318 (Int: +61 362 325318)
Fax: 0362 325000 (Int: +61 362 325000)
e-mail: Tony.Rees@csiro.au
Manager, OBIS
Biodiversity informatics research activities: http://www.cmar.csiro.au/datacentre/biodiversity.htm
Personal info: http://www.fishbase.org/collaborators/collaboratorsummary.cfm?id=1566
From: tdwg-tag-bounces@lists.tdwg.org [mailto:tdwg-tag-bounces@lists.tdwg.org]
On Behalf Of
Sent: Wednesday, 7 July 2010 11:55
AM
To: tdwg-tag@lists.tdwg.org
Cc: tdwg-content@lists.tdwg.org
Subject: [tdwg-tag] WPS for Names
I have
been pondering taxon name matching type services lately…
I
wonder if the OGC WPS (Web Processing Service) would make a good platform for
integrating the various name matching algorithms that are being worked on
lately.
I was
imagining something like a web interface where you can go to and view a list of
the available algorithms and select different algorithms in different orders to
get the best set of match results your own list of name strings/data.
If
everyone set up their algorithms as a WPS then this interface would call each
WPS in the appropriate order until then end of the configured workflow path.
UI
something like (in diagram):
Where
the bottom part is configurable by the user. Each box being a
representation of a WPS service for doing the match.
Any
thoughts?
Perhaps
something that could be discussed at TDWG?
One
issue would be how to define/specify the list of names to match against – then
when you pass the processing of a match routine how would it access the names
list to match?? Perhaps it could all be based on one server and people
could submit algorithm/WPS services to it?
Hmmmm,
will keep dreaming …
Kevin
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