[tdwg-tag] [tdwg-content] WPS for Names
David Remsen (GBIF)
dremsen at gbif.org
Thu Jul 8 22:26:48 CEST 2010
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 Copenhagen, Denmark
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 at 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 at lists.tdwg.org [mailto:tdwg-tag-bounces at lists.tdwg.org
> ] On Behalf Of Kevin Richards
> Sent: 8. heinäkuuta 2010 0:32
> To: Tony.Rees at csiro.au; tdwg-tag at lists.tdwg.org
>
>
> Cc: tdwg-content at 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 at csiro.au [mailto:Tony.Rees at csiro.au]
> Sent: Wednesday, 7 July 2010 7:06 p.m.
> To: Kevin Richards; tdwg-tag at lists.tdwg.org
> Cc: tdwg-content at 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 Box 1538,
> Hobart, Tasmania 7001, Australia
> Ph: 0362 325318 (Int: +61 362 325318)
> Fax: 0362 325000 (Int: +61 362 325000)
> e-mail: Tony.Rees at csiro.au
> Manager, OBIS Australia regional node, http://www.obis.org.au/
> 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 at lists.tdwg.org [mailto:tdwg-tag-bounces at lists.tdwg.org
> ] On Behalf Of Kevin Richards
> Sent: Wednesday, 7 July 2010 11:55 AM
> To: tdwg-tag at lists.tdwg.org
> Cc: tdwg-content at 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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