February 2008 - tdwg-content

[tdwg-tnc] Testing TCS and some ideas on GUIDs and ontologies: ranking synomymies
by Robert Huber 28 Feb '08

28 Feb '08

Dear all, I just have finished a TCS XML demo page at: http://taxonconcept.stratigraphy.net/taxon_tcs?taxid=793 which is a TCS representation of synonym list (concepts) data on the taxon 'Subbotina patagonica' published by Berggren & Norris (1997) and Pearson et al. (2006), see a html output here: http://taxonconcept.stratigraphy.net/taxon_details?taxid=793 The XML valdates against the schema, but of course, what I have implemented is a 'interpretation' of the standard, e.g. I have now summarized the two synonymies to one DataSet, and I am not sure if this granularity makes sense. So I would like to ask you to check if the output looks reasonable. I was really happy to see how good TCS fits to my data and after I have seen the first results I realized how good this fits to an experiment I was trying some months ago: I tried to apply the Google PageRank algorithm to synonymies and as a first attempt I calculated what I called TaxonRank. I have provided some more info on this here: http://stratigraphynet.blogspot.com/2008/01/how-taxonrank-works.html (+ my geoinformatics community prepared a special volume on ontologies etc and I have also submitted a paper to Computers&Geosciences which will be published soon). After seeing the TCS XML output and reading many RDF and ontology related mailing list contributions I wonder if anybody has ever thought about doing something like this before? My tests are on synonymy list (concepts) only, but I think similar approaches could lead to interesting results also if applied to e.g. genetics. And..wouldn't be ranking based on such ontologies a killer application for GUIDs? apologies for cross posting.. Robert -- Dr. Robert Huber, WDC-MARE / PANGAEA - www.pangaea.de Stratigraphy.net - www.stratigraphy.net _____________________________________________ MARUM - Institute for Marine Environmental Sciences (location) University Bremen Leobener Strasse POP 330 440 28359 Bremen Phone ++49 421 218-65593, Fax ++49 421 218-65505 e-mail rhuber(a)wdc-mare.org

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[tdwg-lit] plazi.org: new repository for taxonomic descriptions
by Donat Agosti 26 Feb '08

26 Feb '08

This is a live application based on TDWG standards and those under discussion (eg Taxonx for literature). It is making use of LSIDs. PLAZI.ORG - THE DIGITAL REPOSITORY FOR SPECIES DESCRIPTIONS. Knowledge of the actual number of species on planet Earth is one of the last frontiers in science. It is not known exactly how many species have been identified and described, much less the number of as yet undescribed species. However, the species we do know are documented in well over hundred million pages of printed scientific books and journals. This knowledge is hidden in libraries, and no single library holds all this knowledge. The species descriptions are very rich in data, essentially a quality controlled summary of what is known at any specific time about a particular species. In best cases, this information includes a detailed morphological description, drawings and images, a summary on behavior and ecology and a detailed list of all the specimens studied. In more recent publications, links to DNA sequences or video documentation among other forms of data may be provided. Recently e-publications have become available, but many of these are copyrighted and thus not generally available open to the public for perusal or use. Nor are they easily machine-searchable for discovery and re-use of contents. Recently, the Biodiversity Heritage Library as a large scale operation to digitize this biodiversity literature has been launched. Currently, it includes major US and UK natural history libraries, with the ultimate goal of including the entire global literature. All publications will be openly accessible to the public, unless they are copyrighted -- thus most of the recent publications are still out of reach. The BHL thus falls short of optimizing the potential uses of these publications. Tagging the boundaries of a species description and identifying the species dealt with, supports discovery and retrieval of data not possible through Google. Mark-up of species descriptions permits queries, such as which are the "red ant in London", a very common form of query. Under some national copyright legislation like the Swiss, descriptions can not be copyrighted because they are through historical constraints (there are tens of millions of descriptions) and peer review standardized and listing factual, in most cases morphological data describing species, and thus they can all be made readily accessible. Plazi.org is a new Web based service that offers access to descriptions of species and an archive to store the publications as marked up documents. GoldenGate, a dedicated editor has been developed to mark up the publications supporting the extraction of descriptions, based on a TaxonX, an XML schema modeling the logic content of these publications. The Plazi Search and Retrieval Server, building on this systematic mark-up of texts, allows powerful search functions to find species descriptions, or even simple mention of species, permitting users to answer questions like: Which species occur together? Plazi.org includes already more than 3,700 description of 3,000 taxa with a goal of archiving all the forthcoming new descriptions and, contingent upon additional funding, all the descriptions of the known 12,278 ant species listed in the Hymenoptera Name Server/ antbase.org, enhanced with globally unique species numbers (LSIDs: Life Science Identifiers). While ants provide the original test case, the service is not restricted to ants but is potentially open to all groups, from Bacteria to Plants, and will support most major languages. All descriptions are machine readable and thus can be picked up for mash-ups or individual Websites. Plazi.org is run and developed by Donat Agosti, Terry Catapano, Christiana Klingenberg and Guido Sautter, its development is supported by Grants from the US National Science Foundation (to the American Museum of Natural History), the German Deutsche Forschungsgemeinschaft (to University of Karlsruhe) and the Global Biodiveristy Facility (GBIF; to Plazi.org and Zootaxa), and is collaborating with the Hymenoptera Name Server at Ohio State University (Norm Johnson), Zoobank (Richard Pyle), University of Massachusetts (Robert Morris), antweb.org (Brian Fisher) and Zootaxa (Zhi-Qiang Zhang). Plazi.org has been released to the public at the EDIT "IPR and the web: challenges for taxonomy" meeting in London, Feb. 20, 2008 (http://www.editwebrevisions.info/content/ipr-and-web) Related Links: First descriptions of the first ant described (Linnaeus, 1758) http://plazi.org:8080/GgSRS/search?searchMode=displayDocument&idQuery=79860… recent publications with fine grained mark-up allowing extraction of specimen data and plotting automatically maps http://plazi.org:8080/GgSRS/search?searchMode=displayDocument&idQuery=4CED5… Description in Russian:(please set encoding=utf-8 in your browser. http://plazi.org:8080/GgSRS/search?searchMode=displayDocument&idQuery=AE3F8… Description in Chinese http://plazi.org:8080/GgSRS/search?searchMode=displayDocument&idQuery=5F64B… Fish http://plazi.org:8080/GgSRS/search?searchMode=displayDocument&idQuery=30E2A… Bacterium http://plazi.org:8080/GgSRS/search?searchMode=displayDocument&idQuery=A4EA4… Plant http://plazi.org:8080/GgSRS/search?searchMode=displayDocument&idQuery=59DE9… Fungi http://plazi.org:8080/GgSRS/search?searchMode=displayDocument&idQuery=C9BDF… Donat -- Dr. Donat Agosti Research Associate, American Museum of Natural History and Smithsonian Institution Email: agosti(a)amnh.org Web: http://antbase.org CV: http://research.amnh.org/entomology/social_insects/agosticv_2003.html Dalmaziquai 45 3005 Bern Switzerland +41-31-351 7152 -- Dr. Donat Agosti Research Associate, American Museum of Natural History and Smithsonian Institution Email: agosti(a)amnh.org Web: http://antbase.org CV: http://research.amnh.org/entomology/social_insects/agosticv_2003.html Dalmaziquai 45 3005 Bern Switzerland +41-31-351 7152

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[tdwg-tnc] Re: [tdwg-guid] taxon concepts in dublin core
by Hannu Saarenmaa 13 Feb '08

13 Feb '08

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