- tdwg-content - lists.tdwg.org

[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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[tdwg-lit] Position announcement: Senior Programmer Analyst at Missouri Botanical Garden
by Chris Freeland 04 Jan '08

04 Jan '08

Apologies for cross posts. The Missouri Botanical Garden (MOBOT), located in St. Louis, MO, is seeking to hire a Senior Programmer Analyst to work on several large biodiversity informatics projects, including the Biodiversity Heritage Library (BHL) online at www.biodiversitylibrary.org. Primary responsibilities for this position include leading the development effort for MOBOT's LAMP-based applications, complementing the existing .Net team. Up first on the development schedule is the instantiation of Fedora (www.fedora-commons.org) at MOBOT as a repository layer in our multi-platform, SOA-based infrastructure, then refactoring applications and building new ones to utilize Fedora. Future projects include enhancement of the BHL GUI and development of tools for managing digital library content. Qualifications include a BS in Computer Science or related field, 5 years experience developing enterprise-level applications, and 2 years experience leading a development team. Experience managing data and applications in an open source environment (LAMP and its variants) required. Experience managing biodiversity and/or library datasets preferred, but not required. To apply online, please visit: http://www.mobot.org/jobs/mbgjobs.asp#H005 ******************************* Chris Freeland Manager, Bioinformatics Missouri Botanical Garden chris.freeland(a)mobot.org (314) 577-9548

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[tdwg-lit] Biodiversity Heritage Library Name Services v.1.0 released
by Chris Freeland 06 Dec '07

06 Dec '07

*Apologies for cross-posts* The Biodiversity Heritage Library (BHL) has released its first suite of Name Services into production. Using these services application providers can retrieve "discovered bibliographies" for a given taxonomic name showing where that name occurs throughout the entire corpus of natural history literature available through BHL. To view an example response, go to: http://www.biodiversitylibrary.org/services/name/NameService.asmx?op=Nam eGetDetail Enter 6663950 in nameBankID: box and hit Invoke. Full documentation of the services, including examples, can be found at: http://docs.google.com/Doc?id=dgvjvvkz_1x5qbm3 These services complement the human-readable interface to "discovered bibliographies" currently deployed at http://www.biodiversitylibrary.org/NameSearch.aspx. See http://www.biodiversitylibrary.org/name/Tapirus_bairdi for an example bibliography for Baird's Tapir. How it works Each digitized page image in BHL has an accompanying OCR text file. As users navigate to a page, the uncorrected OCR file is sent to uBio's TaxonFinder, which identifies text strings that match the characteristics of Latin binomials. Those potential name strings are then compared to the 10.7 million+ names in uBio's NameBank, and the results, both matched and unmatched, are stored in the BHL database. BHL also has automated processes to reindex pages at regular intervals since NameBank is a growing repository. What we've found As of 20 Nov 2007 more than 6.8 million potential name strings have been identified throughout the BHL corpus, with more than 3.8 million matched to a corresponding NameBank identifier. There are more than 431,000 unique names within that 3.8 million set. Of those, more than 156,000 are known by a single occurrence. These results will be evaluated more thoroughly in the coming months to determine potential errors such as false positives and how to refine the TaxonFinder algorithm to reduce them. Caveat: These results are generated from uncorrected OCR, which range in quality from pretty good (contemporary publications, such as modern issues of Rhodora) to downright terrible (18th century Latin texts, such as Species Plantarum). Again, further evaluation is required to determine the full scope of this problem. Metadata in response The metadata currently returned from the services is not yet explicitly mapped to Dublin Core, MODS, or other schemata but will be in subsequent revisions. This current response is the most verbose offering possible, encompassing every piece of information we have to share about the digitized page and the book from which it was scanned. For this first release we wanted to expose all metadata possible then work to map to other schema according to community wants and needs. Where we're headed This service, and the metadata it serves, will be incorporated into the Encyclopedia of Life by its launch next year. Discussions are already underway with other data providers to demonstrate how these services can be used. To see a simple example of how the human-readable interface can be used from external sites, check out the 'External Links' at the bottom of the Wikipedia article for Mimosa pudica L., the sensitive plant: http://en.wikipedia.org/wiki/Mimosa_pudica Up next: Development of an OpenURL parser that will allow service providers to submit requests for citations and retrieve page images or resolve to appropriate pages in the BHL portal. Any and all comments welcome! E-mail directly to me, or leave them on the BHL blog at http://biodiversitylibrary.blogspot.com. Chris Freeland Technical Director, Biodiversity Heritage Library Application Development Manager, Missouri Botanical Garden

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[tdwg-lit] Biodiversity Heritage Library Name Services v.1.0 released
by Chris Freeland 05 Dec '07

05 Dec '07

*Apologies for cross-posts* The Biodiversity Heritage Library (BHL) has released its first suite of Name Services into production. Using these services application providers can retrieve "discovered bibliographies" for a given taxonomic name showing where that name occurs throughout the entire corpus of natural history literature available through BHL. To view an example response, go to: http://www.biodiversitylibrary.org/services/name/NameService.asmx?op=Nam eGetDetail Enter 6663950 in nameBankID: box and hit Invoke. Full documentation of the services, including examples, can be found at: http://docs.google.com/Doc?id=dgvjvvkz_1x5qbm3 These services complement the human-readable interface to "discovered bibliographies" currently deployed at http://www.biodiversitylibrary.org/NameSearch.aspx. See http://www.biodiversitylibrary.org/name/Tapirus_bairdi for an example bibliography for Baird's Tapir. How it works Each digitized page image in BHL has an accompanying OCR text file. As users navigate to a page, the uncorrected OCR file is sent to uBio's TaxonFinder, which identifies text strings that match the characteristics of Latin binomials. Those potential name strings are then compared to the 10.7 million+ names in uBio's NameBank, and the results, both matched and unmatched, are stored in the BHL database. BHL also has automated processes to reindex pages at regular intervals since NameBank is a growing repository. What we've found As of 20 Nov 2007 more than 6.8 million potential name strings have been identified throughout the BHL corpus, with more than 3.8 million matched to a corresponding NameBank identifier. There are more than 431,000 unique names within that 3.8 million set. Of those, more than 156,000 are known by a single occurrence. These results will be evaluated more thoroughly in the coming months to determine potential errors such as false positives and how to refine the TaxonFinder algorithm to reduce them. Caveat: These results are generated from uncorrected OCR, which range in quality from pretty good (contemporary publications, such as modern issues of Rhodora) to downright terrible (18th century Latin texts, such as Species Plantarum). Again, further evaluation is required to determine the full scope of this problem. Metadata in response The metadata currently returned from the services is not yet explicitly mapped to Dublin Core, MODS, or other schemata but will be in subsequent revisions. This current response is the most verbose offering possible, encompassing every piece of information we have to share about the digitized page and the book from which it was scanned. For this first release we wanted to expose all metadata possible then work to map to other schema according to community wants and needs. Where we're headed This service, and the metadata it serves, will be incorporated into the Encyclopedia of Life by its launch next year. Discussions are already underway with other data providers to demonstrate how these services can be used. To see a simple example of how the human-readable interface can be used from external sites, check out the 'External Links' at the bottom of the Wikipedia article for Mimosa pudica L., the sensitive plant: http://en.wikipedia.org/wiki/Mimosa_pudica Up next: Development of an OpenURL parser that will allow service providers to submit requests for citations and retrieve page images or resolve to appropriate pages in the BHL portal. Any and all comments welcome! E-mail directly to me, or leave them on the BHL blog at http://biodiversitylibrary.blogspot.com. Chris Freeland Technical Director, Biodiversity Heritage Library Application Development Manager, Missouri Botanical Garden

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[tdwg-lit] Literature Interest Group Meeting Agenda & Information
by Weitzman, Anna 13 Nov '07

13 Nov '07

Dear all, As most of you know, there is a meeting next week (14-16 November) of our group to draft some first standards and discuss other issues and the future of the group. The meeting will be in St Louis, Missouri (USA) AND worldwide via video/phone/desktop conference. The agenda for the meeting is attached (for those who got the previous version, please note that the schedule for discussing, though not the content, has changed). If you (or a colleague) have any thought of attending the meeting in any form (AND PLEASE do so if you can for even part(s) of it), please let me know immediately with full details of how you intend to participate, so I can ensure that everything is prepared. *More importantly*, if you intend to attend by video (thank goodness for cheap PC video), see the attached document prepared by Arturo Ariño for the video conference facilities and testing. *MOST IMPORTANTLY*, please contact Arturo ASAP to test your connection, speed, and video facilities. Background documentation is (1) listed in the agenda and (2) will soon be posted to the Literature Interest Group Wiki (http://wiki.tdwg.org/twiki/bin/view/Literature/WebHome) I am in the process of working on the Wiki, but check there Friday for all the documents that I have and frequently for those expected to be posted by others (hint, hint to the others who promised). Thanks again and best regards to you all, Anna Anna L. Weitzman, PhD Botanical and Biodiversity Informatics Research National Museum of Natural History Smithsonian Institution office: 202.633.0846 mobile: 202.415.4684 weitzman(a)si.edu

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[tdwg-img] abstract objects and digital representations: metadata
by Bob Morris 07 Nov '07

07 Nov '07

In connection with a discussion on the tdwg-tag mailing list, I am roughly agreeing with a proposal Rich Pyle makes to the effect of having separate LSIDs for digital representations (e.g. media files) of non-digital objects (e.g. a scene in the world). Because it is easy to see the distinctions for media files, I've carried that discussion to the Image Wiki at the page http://wiki.tdwg.org/twiki/bin/view/Image/ImageOrImageFile I hope you will join the discussion there. You can also subscribe to mail or RSS notification of changes to that Wiki at http://wiki.tdwg.org/twiki/bin/view/Image/WebNotify Bob -- Robert A. Morris Professor of Computer Science UMASS-Boston http://www.cs.umb.edu/~ram phone (+1)617 287 6466

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[tdwg-lit] November Lit Interest Group meeting
by Weitzman, Anna 10 Oct '07

10 Oct '07

Dear all, As was discussed previously (on the list and in Bratislava) we plan to have a meeting 14-16 November. At this time, I am working on a budget for a meeting in St Louis. I am also looking at options for including those who cannot make it to St Louis (due to time constraints) for electronic conferencing. * Skype can handle up to nine connections in a conference call, and only handle 2 in a video conference. * I have access to a Webex account that will allow for shared desktops (that can be moved around among various people--either control of the mouse on a remote screen, or the desktop being used). * VRVS (http://www.vrvs.org/) appears to be another option for video/phone conferencing and desktop sharing. If you are interested in participating remotely, take a look at the quick tour at the top of the page and see if you will be able to use this. Please let me know ASAP if (a) you want to participate electronically and if you think VRVS will work for you. Arturo Ariño will be testing the VRVS shortly. As a fallback, I suggest we go with Webex & Skype (we may be able to patch some people from a Skype conference into the Webex conference so those who are overseas can avoid the call charges--I will test this). Remember, the meeting will take place during the day in US Central Standard Time (UTC/GMT -6 hours), so if you want to participate electronically, you will need to be prepared for our hours (or overlapping with some as best you can). At the current time, there are only a few people who have expressed firm interest in attending the conference in person: * Anna Weitzman * Chris Lyal * Terry Catapano * Donat Agosti * Chris Freeland * Chuck Miller If your name is not on that list, and you would like to attend, please let me know ASAP, so I can include your costs in the budget. Conversely, if you are on the list and will not be able to attend, please also let me know. I need to finalize the budget for this within a week, so please let me know if and how you want to be included ASAP! Thanks & best regards, Anna Anna L. Weitzman, PhD Botanical and Biodiversity Informatics Research National Museum of Natural History Smithsonian Institution office: 202.633.0846 mobile: 202.415.4684 weitzman(a)si.edu

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[tdwg-tnc] LSIDs and taxon concepts
by Paul Allen 09 Oct '07

09 Oct '07

Hi all, I'm new to this list and hope that the following are appropriate questions. In Bratislava, I wasn't keeping detailed enough notes on projects and their current and future plans wrt TCS. What sites are currently publishing TCS-formatted data or will be within the year? I know that zoobank.org will be publishing TCS data in the near future. Is GBIF? ITIS? Species2000? What sites are publishing real "taxon concept" data (in TCS format or not)? Conversely, what sites are simply publishing "nominal taxon concepts" as opposed to detailed authoritative taxon concepts? Is this the kind of thing for which we should generate a survey to send to sites (i.e. their plans for publishing TCS) or distrubute to TDWG members? Thanks, Paul ------------------------ Paul Allen, Assistant Director Information Science pea1(a)cornell.edu Cornell Lab of Ornithology (800) 843-BIRD 159 Sapsucker Woods Road (607) 254-2480 (direct) Ithaca, NY 14850 (607) 254-2415 (fax) http://www.birds.cornell.edu/ http://bna.birds.cornell.edu/ http://www.ebird.org/ http://bird.atlasing.org/ ------------------------

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