[tdwg-tag] WPS for Names

Matt Jones jones at nceas.ucsb.edu
Thu Jul 8 01:15:05 CEST 2010


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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