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<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D">Excellent. This sound like a really good start towards what I was envisioning.<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D">Thanks<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D">Kevin<o:p></o:p></span></p>
<p class="MsoNormal"><span style="font-size:11.0pt;font-family:"Calibri","sans-serif";
color:#1F497D"><o:p> </o:p></span></p>
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<p class="MsoNormal"><b><span lang="EN-US" style="font-size:10.0pt;font-family:
"Tahoma","sans-serif"">From:</span></b><span lang="EN-US" style="font-size:10.0pt;
font-family:"Tahoma","sans-serif""> tdwg-content-bounces@lists.tdwg.org [mailto:tdwg-content-bounces@lists.tdwg.org]
<b>On Behalf Of </b>David Remsen (GBIF)<br>
<b>Sent:</b> Friday, 9 July 2010 8:27 a.m.<br>
<b>To:</b> tdwg-content@lists.tdwg.org Mailing List<br>
<b>Cc:</b> Technical Architecture Group mailing list<br>
<b>Subject:</b> Re: [tdwg-content] [tdwg-tag] WPS for Names<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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 <a href="http://code.google.com/p/taxon-name-processing/)">http://code.google.com/p/taxon-name-processing/)</a>
and one outcome was the need to polish and operationalise some of these services. At GBIF, we undertook the following:<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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 <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Our version is here (<a href="http://code.google.com/p/taxon-name-processing/wiki/NameFindingAPI">http://code.google.com/p/taxon-name-processing/wiki/NameFindingAPI</a>) and is near ready for release. <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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.<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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.<o:p></o:p></p>
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<p class="MsoNormal">Best,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">David Remsen<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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color:black">----------------------------------------------------------------------------<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black">David Remsen, Senior Programme Officer<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black">Electronic Catalog of Names of Known Organisms<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black">Global Biodiversity Information Facility Secretariat<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black">Universitetsparken 15, DK-2100 Copenhagen, Denmark<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black">Tel: +45-35321472 Fax: +45-35321480<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black">Mobile +45 28751472<o:p></o:p></span></p>
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<p class="MsoNormal"><span style="font-size:9.0pt;font-family:"Helvetica","sans-serif";
color:black">Skype: dremsen<o:p></o:p></span></p>
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color:black">----------------------------------------------------------------------------<o:p></o:p></span></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">On Jul 7, 2010, at 7:15 PM, Matt Jones wrote:<o:p></o:p></p>
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<p class="MsoNormal">Kevin,<o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">Also of relevance would be the work that iPlant is sponsoring on a Taxonomic Name Resolution Service (TNRS) -- see: <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal"><a href="https://pods.iplantcollaborative.org/wiki/display/iptol/TNRS+Workshop">https://pods.iplantcollaborative.org/wiki/display/iptol/TNRS+Workshop</a> <o:p></o:p></p>
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<p class="MsoNormal"><o:p> </o:p></p>
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<p class="MsoNormal">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.<o:p></o:p></p>
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<p class="MsoNormal" style="margin-bottom:12.0pt">Matt<o:p></o:p></p>
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<p class="MsoNormal">On Wed, Jul 7, 2010 at 1:49 PM, Evgeniy Meyke <<a href="mailto:evgeniy@earthcape.com">evgeniy@earthcape.com</a>> wrote:<o:p></o:p></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="FI" style="color:#1F497D">Hi Kevin, Tony, and all</span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="FI" style="color:#1F497D"> </span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="color:#1F497D">As one of the very likely consumers of such a service I’ll be following this with great interest.</span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"> </span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="color:#1F497D">A quick question at this point. Is anything like this planned for GNA (<a href="http://www.globalnames.org" target="_blank">www.globalnames.org</a>)?
or GBIF? </span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"> </span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="color:#1F497D">Evgeniy</span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-US" style="color:#1F497D"> </span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span lang="EN-US" style="font-size:10.0pt">From:</span></b><span lang="EN-US" style="font-size:10.0pt">
<a href="mailto:tdwg-tag-bounces@lists.tdwg.org" target="_blank">tdwg-tag-bounces@lists.tdwg.org</a> [mailto:<a href="mailto:tdwg-tag-bounces@lists.tdwg.org" target="_blank">tdwg-tag-bounces@lists.tdwg.org</a>]
<b>On Behalf Of </b>Kevin Richards<br>
<b>Sent:</b> 8. heinäkuuta 2010 0:32<br>
<b>To:</b> <a href="mailto:Tony.Rees@csiro.au">Tony.Rees@csiro.au</a>; <a href="mailto:tdwg-tag@lists.tdwg.org" target="_blank">
tdwg-tag@lists.tdwg.org</a></span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="FI"><br>
<b>Cc:</b> <a href="mailto:tdwg-content@lists.tdwg.org" target="_blank">tdwg-content@lists.tdwg.org</a><o:p></o:p></span></p>
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<p class="MsoNormal"><b><span lang="FI">Subject:</span></b><span lang="FI"> Re: [tdwg-tag] WPS for Names<o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="FI"><o:p> </o:p></span></p>
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<p class="MsoNormal"><span lang="FI"> <o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#1F497D">Thanks Tony. I would be interested in any collaboration we can do in this area (assuming I find 5 minutes to work on it :-))</span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#1F497D"> </span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#1F497D">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).
</span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#1F497D"> </span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#1F497D">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.</span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#1F497D"> </span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span style="color:#1F497D">Kevin</span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#1F497D"> </span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"><span style="color:#1F497D"> </span><span lang="FI"><o:p></o:p></span></p>
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<div style="border:none;border-top:solid #B5C4DF 1.0pt;padding:3.0pt 0cm 0cm 0cm">
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span lang="EN-US" style="font-size:10.0pt">From:</span></b><span lang="EN-US" style="font-size:10.0pt">
<a href="mailto:Tony.Rees@csiro.au">Tony.Rees@csiro.au</a> [mailto:<a href="mailto:Tony.Rees@csiro.au" target="_blank">Tony.Rees@csiro.au</a>]
<br>
<b>Sent:</b> Wednesday, 7 July 2010 7:06 p.m.<br>
<b>To:</b> Kevin Richards; <a href="mailto:tdwg-tag@lists.tdwg.org" target="_blank">
tdwg-tag@lists.tdwg.org</a><br>
<b>Cc:</b> <a href="mailto:tdwg-content@lists.tdwg.org" target="_blank">tdwg-content@lists.tdwg.org</a><br>
<b>Subject:</b> RE: WPS for Names</span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"> <span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-AU" style="font-size:10.0pt;color:navy">Dear all (actually: I’m not sure who are the recipients currently on tdwg-tag, maybe I will now find out!!)</span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-AU" style="font-size:10.0pt;color:navy"> </span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-AU" style="font-size:10.0pt;color:navy">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:
<a href="http://taxacom.markmail.org/message/ywq7ijiaeks7heiv" target="_blank">http://taxacom.markmail.org/message/ywq7ijiaeks7heiv</a> ), so happy to see what can be done in this space.</span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-AU" style="font-size:10.0pt;color:navy"> </span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-AU" style="font-size:10.0pt;color:navy">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
<a href="http://www.cmar.csiro.au/datacentre/irmng/" target="_blank">http://www.cmar.csiro.au/datacentre/irmng/</a> 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).</span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-AU" style="font-size:10.0pt;color:navy"> </span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-AU" style="font-size:10.0pt;color:navy">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..</span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-AU" style="font-size:10.0pt;color:navy"> </span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-AU" style="font-size:10.0pt;color:navy">Any comments on the above welcome,</span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-AU" style="font-size:10.0pt;color:navy"> </span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-AU" style="font-size:10.0pt;color:navy">Regards - Tony</span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-AU" style="font-size:10.0pt;color:navy"> </span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><span lang="EN-US" style="font-size:10.0pt;color:navy">Tony Rees<br>
Manager, Divisional Data Centre,<br>
CSIRO Marine and Atmospheric Research,<br>
GPO Box 1538,<br>
Hobart, Tasmania 7001, Australia<br>
Ph: 0362 325318 (Int: +61 362 325318)<br>
Fax: 0362 325000 (Int: +61 362 325000)<br>
e-mail: <a href="mailto:Tony.Rees@csiro.au" target="_blank" title="mailto:Tony.Rees@csiro.au">
Tony.Rees@csiro.au</a><br>
Manager, OBIS Australia regional node, <a href="http://www.obis.org.au/" target="_blank">
http://www.obis.org.au/</a> <br>
Biodiversity informatics research activities: <a href="http://www.cmar.csiro.au/datacentre/biodiversity.htm" target="_blank">
http://www.cmar.csiro.au/datacentre/biodiversity.htm</a><br>
Personal info: <a href="http://www.fishbase.org/collaborators/collaboratorsummary.cfm?id=1566" target="_blank" title="http://www.fishbase.org/collaborators/collaboratorsummary.cfm?id=1566">http://www.fishbase.org/collaborators/collaboratorsummary.cfm?id=1566</a></span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-AU" style="font-size:10.0pt;color:navy"> </span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span lang="EN-US" style="font-size:10.0pt">From:</span></b><span lang="EN-US" style="font-size:10.0pt">
<a href="mailto:tdwg-tag-bounces@lists.tdwg.org" target="_blank">tdwg-tag-bounces@lists.tdwg.org</a> [mailto:<a href="mailto:tdwg-tag-bounces@lists.tdwg.org" target="_blank">tdwg-tag-bounces@lists.tdwg.org</a>]
<b>On Behalf Of </b>Kevin Richards<br>
<b>Sent:</b> Wednesday, 7 July 2010 11:55 AM<br>
<b>To:</b> <a href="mailto:tdwg-tag@lists.tdwg.org" target="_blank">tdwg-tag@lists.tdwg.org</a><br>
<b>Cc:</b> <a href="mailto:tdwg-content@lists.tdwg.org" target="_blank">tdwg-content@lists.tdwg.org</a><br>
<b>Subject:</b> [tdwg-tag] WPS for Names</span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"><span lang="EN-AU"> </span><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">I have been pondering taxon name matching type services lately…<span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"> <span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">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.<span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"> <span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">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.<span lang="FI"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">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.<span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"> <span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">UI something like (in diagram):<span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"> <span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto"><b><span lang="EN-US">Error! Filename not specified.</span></b><span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"> <span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Where the bottom part is configurable by the user. Each box being a representation of a WPS service for doing the match.<span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"> <span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Any thoughts?<span lang="FI"><o:p></o:p></span></p>
<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Perhaps something that could be discussed at TDWG?<span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"> <span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">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?<span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"> <span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Hmmmm, will keep dreaming …<span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"> <span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal" style="mso-margin-top-alt:auto;mso-margin-bottom-alt:auto">Kevin<span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"> <span lang="FI"><o:p></o:p></span></p>
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<p class="MsoNormal"> <span lang="FI"><o:p></o:p></span></p>
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