[tdwg-tag] WPS for Names

Tony.Rees at csiro.au Tony.Rees at csiro.au
Wed Jul 7 09:06:18 CEST 2010

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<mailto: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):

[cid:image002.gif at 01CB1DF6.B77E7730]

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 ...


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