July 2010 - tdwg-content - lists.tdwg.org

Fwd: Taxon Concept dilemma
by Mark Wilden 09 Jul '10

09 Jul '10

On Tue, Jul 6, 2010 at 6:10 AM, Richard Pyle <deepreef(a)bishopmuseum.org> wrote: > This is why the only way we're going to be able to establish > RelationshipAssertions (sensu TCS) is via third-party assertions. In other > words, someone is going to have to assert an opinion over whether the > implied members of Smith's Aus bus would have included the population in > Hawaii, and whether the implied set of Jones' Aus cus would have included > the population in the Marshall Islands. I think that a "someone" is always asserting such an opinion - Smith and Jones included. There is no Platonic ideal of a particular species. Every single classification is a matter of educated opinion. Smith has one opinion and Jones has another opinion. Brown may step in and decide that Smith's opinion is the correct one - but that's just another opinion. Consumers of the classification choose whose opinions are the most useful. A taxon is always related to a taxon-assigner. In this sense, "circumscription" is perhaps not the best way to think about it, because very few assigners actually determine taxa by enumerating organisms. The idea of researchers creating taxa, and third parties adjudicating them to arrive at the "true" classification, is too limited. It's third parties all the way down. ///ark

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TDWG Presentation for biologists
by David Remsen (GBIF) 09 Jul '10

09 Jul '10

Hi, On short notice I have been invited to give a presentation on TDWG and the Sept. meeting to the monthly meeting of the Woods Hole Oceanographic Institution biology department on Monday morning. I have looked at the presentations on the TDWG outreach site but they seem a bit too technical for biologists. MIght anyone have any TDWG materials geared toward non-technical biologists? 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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Re: [tdwg-content] [tdwg-tag] WPS for Names
by Matt Jones 08 Jul '10

08 Jul '10

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(a)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(a)lists.tdwg.org [mailto: > tdwg-tag-bounces(a)lists.tdwg.org] *On Behalf Of *Kevin Richards > *Sent:* 8. heinäkuuta 2010 0:32 > *To:* Tony.Rees(a)csiro.au; tdwg-tag(a)lists.tdwg.org > > *Cc:* tdwg-content(a)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(a)csiro.au [mailto:Tony.Rees@csiro.au] > *Sent:* Wednesday, 7 July 2010 7:06 p.m. > *To:* Kevin Richards; tdwg-tag(a)lists.tdwg.org > *Cc:* tdwg-content(a)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(a)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(a)lists.tdwg.org [mailto: > tdwg-tag-bounces(a)lists.tdwg.org] *On Behalf Of *Kevin Richards > *Sent:* Wednesday, 7 July 2010 11:55 AM > *To:* tdwg-tag(a)lists.tdwg.org > *Cc:* tdwg-content(a)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 > > > > > ------------------------------ > > Please consider the environment before printing this email > Warning: This electronic message together with any attachments is > confidential. If you receive it in error: (i) you must not read, use, > disclose, copy or retain it; (ii) please contact the sender immediately by > reply email and then delete the emails. > The views expressed in this email may not be those of Landcare Research New > Zealand Limited. http://www.landcareresearch.co.nz > > > ------------------------------ > > Please consider the environment before printing this email > Warning: This electronic message together with any attachments is > confidential. If you receive it in error: (i) you must not read, use, > disclose, copy or retain it; (ii) please contact the sender immediately by > reply email and then delete the emails. > The views expressed in this email may not be those of Landcare Research New > Zealand Limited. http://www.landcareresearch.co.nz > > _______________________________________________ > tdwg-tag mailing list > tdwg-tag(a)lists.tdwg.org > http://lists.tdwg.org/mailman/listinfo/tdwg-tag > >

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Re: [tdwg-content] WPS for Names
by Kevin Richards 07 Jul '10

07 Jul '10

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(a)csiro.au [mailto:Tony.Rees@csiro.au] Sent: Wednesday, 7 July 2010 7:06 p.m. To: Kevin Richards; tdwg-tag(a)lists.tdwg.org Cc: tdwg-content(a)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(a)csiro.au<mailto:Tony.Rees@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(a)lists.tdwg.org [mailto:tdwg-tag-bounces@lists.tdwg.org] On Behalf Of Kevin Richards Sent: Wednesday, 7 July 2010 11:55 AM To: tdwg-tag(a)lists.tdwg.org Cc: tdwg-content(a)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:image001.gif@01CB1E7E.666E0530] 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 ________________________________ Please consider the environment before printing this email Warning: This electronic message together with any attachments is confidential. If you receive it in error: (i) you must not read, use, disclose, copy or retain it; (ii) please contact the sender immediately by reply email and then delete the emails. The views expressed in this email may not be those of Landcare Research New Zealand Limited. http://www.landcareresearch.co.nz ________________________________ Please consider the environment before printing this email Warning: This electronic message together with any attachments is confidential. If you receive it in error: (i) you must not read, use, disclose, copy or retain it; (ii) please contact the sender immediately by reply email and then delete the emails. The views expressed in this email may not be those of Landcare Research New Zealand Limited. http://www.landcareresearch.co.nz

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Taxon Concept dilemma
by Kevin Richards 07 Jul '10

07 Jul '10

Hello all, I have an issue that I would like some comment on... We have some data that covers Taxa, Names and Concept relationships. Eg - A Taxon table that contains the nomenclatural details + accepted name + parent name - Concept + relationship tables that contain details about the name + references where the name has been used in a taxonomic sense (ie not nomenclatural information) - this is specifically a link between the Name and a Reference We have fairly permanent Ids for the Taxon Name (nomenclatural) and the Concepts, but I now what to consider the ID to cover the whole Taxon (ie the Nomenclatural data + taxon rank + parent name + accepted name, etc, as "we" understand them). (Probably equivalent to the taxonID in Dwc) The problem is this tends to be much more dynamic data - ie, in this particular case we have aggregated data from a variety of providers and are in continual revision of this data - as we revise the data the details such as the accepted name may change - this troubles me a bit, because this could be seen as fundamentally changing the definition of the object behind the taxonID. However, I suspect this is a common case that people find themselves in - ie revision/tidying of aggregated datasets must be quite common. I would prefer to NOT change the taxonID every time we revise that data (taking the angle that these changes are corrections, so are not changing the object itself). Should it be OK to have an object type like this, that is likely to change, but keep the ID permanent for it - ie accept that some object types are quite dynamic? The only other option is to maintain a hideous version audit trail, that probably hinders the use of the data more than it benefits the end user by providing "stability". Any thoughts? Kevin ________________________________ Please consider the environment before printing this email Warning: This electronic message together with any attachments is confidential. If you receive it in error: (i) you must not read, use, disclose, copy or retain it; (ii) please contact the sender immediately by reply email and then delete the emails. The views expressed in this email may not be those of Landcare Research New Zealand Limited. http://www.landcareresearch.co.nz

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WPS for Names
by Kevin Richards 07 Jul '10

07 Jul '10

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.png@01CB1DDB.86BDF370] 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 ________________________________ Please consider the environment before printing this email Warning: This electronic message together with any attachments is confidential. If you receive it in error: (i) you must not read, use, disclose, copy or retain it; (ii) please contact the sender immediately by reply email and then delete the emails. The views expressed in this email may not be those of Landcare Research New Zealand Limited. http://www.landcareresearch.co.nz

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[tdwg-lit] FW: ZooKeys jubilee issue: New publishing tools to accelerate biodiversity research
by Donat Agosti 02 Jul '10

02 Jul '10

Below the announcement of the launch of Zookeys revamp to become a XML based taxonomic journal. I believe this is not only timely, but it allows to study and discuss the use for marked-up and enhanced literature. As far as I know, taxpub, the underlying DTD is the first NLM publishing and archiving DTD that has been enhanced for a specific domain. Lyubo and we at Plazi are interested to hear your opinions and suggestions. Cheers Donat -----Original Message----- From: Lyubomir Penev [mailto:info@pensoft.net] Sent: Thursday, July 01, 2010 7:44 PM To: Donat Agosti Subject: ZooKeys jubilee issue: New publishing tools to accelerate biodiversity research Dear ZooKeys readers, I have certainly good news to share (apologies to Taxacom subscribers for cross-posting!) On the eve of its two-years birthday (4th of July 2008), ZooKeys published its jubilee issue No 50 (http://pensoftonline.net/zookeys/index.php/journal/issue/view/52) This special edition demonstrates how integrating the traditional part of publication with the research and dissemination processes can deliver dramatic benefits by using semantic tagging and semantic enhancements (http://pensoftonline.net/zookeys/index.php/journal/article/view/538/469) Several novelties are described in the two forum papers and demonstrated in four exemplar papers: The papers are published in four different formats: (1) high-resolution, full-colour print version, to satisfy the current requirements of the ICZN, as well as the readers who prefer hardcopy, and for the purposes of paper archiving; (2) PDF to provide an electronic version identical to the printed one, to be archived in BHL and PubMedCentral; (3) HTML to provide links to external resources and semantic enhancements to published texts for interactive reading, and (4) XML version based on the TaxPub extension to the National Library of Medicines DTD (http://sourceforge.net/projects/taxpub/) to provide archiving document format for PubMedCentral and a machine-readable copy of the contents to facilitate future data mining (e.g., by EOL, GBIF, Plazi and others). An XML-based editorial, publication and dissemination workflow was implemented, which permits acceptance of manuscripts generated either from databases (Scratchpads websites, http://www.sciaroidea.info and http://milichiidae.info and Proctotrupoidea website, http://www.vsyslab.osu.edu) or as standard MS Word file. The XML manuscripts generated by pushing the button from Scratchpads are linked to the online dynamic versions of the same after publication. A dynamic web-page for any taxonomic name mentioned in a publication is being created and explored online through the so-called Pensoft Taxon Profile tool, just by clicking on the name during the reading process. The dynamically generated taxon profile gathers and displays information from several leading biodiversity websites, e.g., GBIF, NCBI (GenBank, PubMed and PubMedCentral), EOL, Barcode of Life, BHL, IUCN, ZooBank, Morphbank, Wikipedia, Wikimedia and others. An example can be a plant species, e.g., the cork oak (Quercus suber): http://pmt.pensoft.eu/resources/articles/external_details.php?query=Quercus+ suber, mentioned in a zoological paper (http://pensoftonline.net/zookeys/index.php/journal/article/view/504/448) The tool offers an option to Create your own taxon profile for any taxonomic name of interest. A number of additional semantic enhancements are used in the HTML versions: (i) internal cross-linking between paper sections, citations, references, tables, figures; (ii) vizualisation of main tag elements within the text (e.g., taxon names, taxon treatments, citations); (iii) mapping of georeferenced localities listed in the whole paper or within separate taxon treatments; (iv) enlarging figures and visualization of literature references by pointing on citations within the text; (v) external linking to GenBank and Barcode of Life accession numbers, Morphbank, online maps, literature references, museum collections, and some more. The partnering organisations are listed in: http://pensoftonline.net/Parnering%20organisations-special%20issue-ZooKeys-5 0.pdf It is anticipated that the workflow will be soon implemented also in the forthcoming PhytoKeys, a partner journal of ZooKeys. Needless to say, the editors and authors involved in the current issue are thrilled by this development and would like to receive comments and criticism for further developing of the proposed workflow. Once again, many thanks to all ZooKeys friends for their valuable support! Lyubomir Lyubomir Penev ZooKeys Editorial Manager Pensoft Publishers Phone +359-888-451668 Fax +359-2-8704282 info(a)pensoft.net ZooKeys ZooKeys 50 (2010) Special Issue Table of Contents http://pensoftonline.net/zookeys/index.php/journal/issue/view/52 Editorial -------- Taxonomy shifts up a gear: New publishing tools to accelerate biodiversity research Lyubomir Penev, David Roberts, Vincent Smith, Donat Agosti, Terry Erwin Forum Paper -------- Semantic tagging of and semantic enhancements to systematics papers: ZooKeys working examples Lyubomir Penev, Donat Agosti, Teodor Georgiev, Terry Catapano, Jeremy Miller, Vladimir Blagoderov, David Roberts, Vincent S. Smith, Irina Brake, Simon Ryrcroft, Ben Scott, Norman F. Johnson, Robert A. Morris, Guido Sautter, Vishwas Chavan, Tim Robertson, David Remsen, Pavel Stoev, Cynthia Parr, Sandra Knapp, W. John Kress, F. Christian Thompson, Terry Erwin Streamlining taxonomic publication: a working example with Scratchpads and ZooKeys Vladimir Blagoderov, Irina Brake, Teodor Georgiev, Lyubomir Penev, David Roberts, Simon Ryrcroft, Ben Scott, Donat Agosti, Terrence Catapano, Vincent S. Smith Research Articles -------- The centipede genus Eupolybothrus Verhoeff, 1907 (Chilopoda: Lithobiomorpha: Lithobiidae) in North Africa, a cybertaxonomic revision, with a key to all species in the genus and the first use of DNA barcoding for the group Pavel Stoev, Nesrine Akkari, Marzio Zapparoli, David Porco, Henrik Enghoff, Gregory D. Edgecombe, Teodor Georgiev, Lyubomir Penev Parisognoriste, a new genus of Lygistorrhinidae (Diptera: Sciaroidea) from the Oise amber with redescription of Palaeognoriste Meunier Vladimir Blagoderov, Heikki Hippa, Andre Nel Stomosis arachnophila sp. n., a new kleptoparasitic species of freeloader flies (Diptera, Milichiidae) Irina Brake, Michael von Tschirnhaus World species of the genus Platyscelio Kieffer (Hymenoptera: Platygastridae) Charuwat Taekul, Norman F. Johnson, Lubomír Masner, Andrew Polaszek, Rajmohana K. -- ZooKeys - Launched to accelerate biodiversity research __________ Information from ESET Smart Security, version of virus signature database 5245 (20100702) __________ The message was checked by ESET Smart Security. http://www.eset.com

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