- tdwg-content - lists.tdwg.org

[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

1 0

[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

1 0

[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

1 0

[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

1 1

[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

1 0

[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

1 0

[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/ ------------------------

5 7

[tdwg-tnc] RE: LSIDs and taxon concepts
by Benjamin Clark 08 Oct '07

08 Oct '07

Dear All, I thought I would chip in and say that the two CATE websites are resolving LSIDs for taxon concepts, and returning metadata typed according to http://rs.tdwg.org/ontology/voc/TaxonConcept. Their urls are http://www.cate-araceae.org which is a web-revision of the Araceae (Arums and relatives) and http://www.cate-sphingidae.org which is a web-revision of the Sphingidae (Hawkmoths). In each case, we're returing the concept sensu the web-revision, rather than a paper publication, which means that it is the name as used by the editorial boards of the websites and published on the pages of the website. It is the intention to extend this group through the addition of an open peer-review process (see http://www.cate-project.org). At the moment, we're only returning taxon concepts, name strings, a link to the taxon page on the website, and taxonomic relationships to other taxon concepts (child taxa and synonyms). The Araceae site also returns IPNI lsids where we've been able to match the name to a name in IPNI. We'd like to do the same for the sphingids if an authority for sphingid names becomes available. We've got lots of descriptive information as well, and I expect that we'll use the SPM to make that available eventually. Cheers, Ben

2 1

[tdwg-lit] Lit meeting at TDWG 2007: getting to the Faculty of Science on Sunday 16 September
by Weitzman, Anna 10 Sep '07

10 Sep '07

Hi all, Three things (again): 1. The literature charter has now been approved and the LIT group is now an official Interest Group of TDWG. See http://www.tdwg.org/activities/literature/ for links to the charter , Wiki (currently inactive; hosted by Bob Morris at UMass Boston), and mailing list. 2. As a reminder, we are having a meeting of those interested and available of the Literature interest group meeting on Sunday, 16 September 2007 from 2:30-5:00 pm in Bratislava. The meeting will be held at the Faculty of Science. There is a map at the bottom of the list on: http://www.tdwg.org/conference2007/housingtravel/maps/ <http://www.tdwg.org/conference2007/housingtravel/maps/> There is also a document attached to this message with some ideas (not cleaned up from our Slovakian colleagues English!) for travel to the Faculty of Science. In addition, our host, Eduard has provided the following: * from Suza hotel: - follow green line on map - "downhill" along Korabinskeho street (steeply down among gardens), cross bridge over highway and turn to left, then follow indicators of the conference along Ilkovicova street (there are many new houses compared to Google Earth or Google Maps); total distance about 1.5 km - or you can use trolleybus (lines 203 or 207) and tram (line no. 1, 5 or 9 towards Karlova Ves) - leave tram at 4th stop after tunnel (stop Botanical Garden) - walk uphill to faculty (follow indicators) * from Ibis hotel - use tram line no. 1, 5 or 9 towards Karlova Ves - leave tram at 4th stop after tunnel (stop Botanical Garden) - walk uphill to faculty (follow indicators) * from Hotel no 16 - walk to faculty or to the closest tram or trolleybus stop For people staying at the SUZA or Hotel No. 16 I think walking would be best, although it's a bit of a trek from the latter. 3. Finally, I have heard from only a few of you about the possibility of attending a meeting in November. Given that most of those I have heard from are from North America, I am going to look at holding it someplace over here, as I think that will be cheapest. If you have not responded and are interested, please let me know as soon as possible, so I can include you and the costs to get you to the meeting in my proposal! I look forward to seeing as many of you as possible soon! Cheers, 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

1 0

[tdwg-tnc] looking for volunteers for a spot of user testing at TDWG, Bratislava
by Graham, Martin 06 Sep '07

06 Sep '07

Hi, anyone interested in helping us test a couple of interfaces for interacting with multiple taxonomic classifications based on TCS concept data? --> http://www.dcs.napier.ac.uk/~marting/ProjectWiki/index.php?n=Main.Usabil ityTesting (with 'tdwg' as the password for editing the page) Once I discover 'where' in the complex I'll be based I'll add that info to the page also... Thanks, Martin Graham Napier University This message is intended for the addressee(s) only and should not be read, copied or disclosed to anyone else outwith the University without the permission of the sender. It is your responsibility to ensure that this message and any attachments are scanned for viruses or other defects. Napier University does not accept liability for any loss or damage which may result from this email or any attachment, or for errors or omissions arising after it was sent. Email is not a secure medium. Email entering the University's system is subject to routine monitoring and filtering by the University.

1 0