March 2006 - tdwg-tag - lists.tdwg.org

Sorry TDWG folk
by David Remsen 23 Mar '06

23 Mar '06

Apologies for sending the previous mail to the group. I never realized that one can set a Reply-To to a different address from the posting address and therein lies my undoing. I clicked reply, typed and sent. I'm sure there is a lesson to me somewhere in there. David _______________________________________________ David Remsen uBio Project Manager Marine Biological Laboratory Woods Hole, MA 02543 508-289-7632

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Re: PublicationBank - requirements evaluation
by David Remsen 23 Mar '06

23 Mar '06

Dear Anna: Cathy and I were at the SI yesterday meeting with library folks and we sought you out to no avail. I also tried to find and introduce us to your parents but they also appeared to be out. I am good friends with Tamara Clark, who does illustrations for them so we wanted to take advantage of that small world moment to say hello. We are sorry we missed you. Best wishes Anna, David On Mar 21, 2006, at 2:10 PM, Anna Weitzman wrote: > Dear Robert, > You may not be aware that TDWG has a list devoted to taxonomic > literature standards. It would be great if you (and anyone else > interested) would join in that discussion ( TDWG Literature > standards mailing list tdwg-lit(a)lists.tdwg.org; sign up at http:// > lists.tdwg.org/mailman/listinfo/tdwg-lit_lists.tdwg.org/general ) > and add your expertise. The list has only been active since early > February, and the complete correspondence is in the archives > ( http://lists.tdwg.org/pipermail/tdwg-lit_lists.tdwg.org/ ). > > > > Anna L. Weitzman, Ph.D. > Informatics Branch Chief, National Museum of Natural History > Smithsonian Institution, PO Box 37012 > Natural History Building, Room W-623, MRC 136 > Washington, DC 20013-7012 U.S.A. > > phone: (202) 633-0846 > fax: (202) 786-3180 > email: weitzman(a)si.edu > INOTAXA - http://www.sil.si.edu/digitalcollections/bca/status.cfm > electronic Biologia Centrali-Americana - http://www.sil.si.edu/ > digitalcollections/bca/ > > > >>> rhuber(a)WDC-MARE.ORG 21-Mar-2006 5:06:30 AM >>> > Dear all, > > Below is a short 'survey' which hopefully can help to get an overview > on how bibliographic information currently is stored in your > databases. > If you don't like to fill such forms, any other info on your current > literature db is also welcome, just send it to me by email! > > The list maybe incomplete, if you think important questions are > missing > there just let me and the others know. > > I will try to sumarize the results on the wiki later. > > best regards, Robert > > 1) How is your literature database/module organised? > - [ ]Database structure completely normalized > - [ ]Database structure not/incomplete normalized > > 2) How do you hold your bibliographic information? > - [ ]Complete set of Bib info (Author, Title,Source, Volume, Pages) > - [ ]Incomplete set of Bib info > - [ ]Abbreviations (e.g. Stafleu&Cowan) > - [ ]Bib Info and Abbreviations > > - Specify which bibliographic fields you hold in your db: > --[ ]Author(s) > --[ ]Title > --[ ]Source (Journal/Book) > --[ ]Pages > --[ ]Date(s) > --[ ]Volume > --[ ]Issue > --[ ]Series > --[ ]URL/GUID > --[ ]Source Editors > --[ ]Series Editors > --[ ]Other: > > 3) How do you store author names: > - [ ]Abbreviations (e.g. Brummitt & Powell) > - [ ]Complete Name as String, one author per string > - [ ]Complete Name as String, all authors in one string > - [ ]Last Name, First Name separated > > 4) How do you store journal names/ other sources > - [ ]Complete Name > - [ ]Abbreviation > - [ ]Both > - [ ]If you hold abbreviations acc. to which standard? > > Dr. Robert Huber > WDC-MARE / PANGAEA - www.pangaea.de , www.wdc-mare.org > 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@@wdc-mare.org , robert.huber(a)stratigraphy.net

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[tdwg-tapir] (Fwd) Call for technical author to assist TDWG subgroups
by Renato De Giovanni 22 Mar '06

22 Mar '06

Dear all, The message below has been sent to a number of mailing lists, and it also considers documentation for TAPIR (a formal specification and a guide to develop client software). If there's anyone interested, please feel free to contact me or Markus (or Lee Belbin directly). We should be able to help as much as necessary with this work. Regards, -- Renato ------- Forwarded message follows ------- The Taxonomic Databases Working Group (TDWG: www.tdwg.org) is seeking an experienced (English language) Technical Author to develop a range of documentation to support its standards. The person will liaise with members of TDWG subgroups to design and develop informal documentation such as user-guides, primers, a web site, and assist with formal documentation suites. Applicants should have a university degree or equivalent. Experience with interoperability standards would be required and familiarity with TDWG would be an advantage. The work would be part time, and on a contract basis with the Global Biodiversity Information Facility (www.gbif.org). Approximately 6 months full-time work equivalent would be anticipated over the next 18 months. While the work would be done at the contractor's location, some travel may be involved. Expressions of interest with a brief résumé should be forwarded to: Lee Belbin TDWG Infrastructure Project Manager lee(a)tdwg.org ------- End of forwarded message -------

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[tdwg-tapir] Output models based on RDFS class definitions?
by Roger Hyam 22 Mar '06

22 Mar '06

Hi Guys, This may be crazy idea but I thought it was worth running past you. I have been working on RDFS vocabulary for TCS and this has spun off a bunch of ideas. One is stolen from the prismstandard.org thing of having avowed serializations of RDF data. You can read more here http://biodiv.hyam.net/schemas/TCS_RDF/tcs_rdf_examples.zip if you haven't already. Following on from this I have had the idea of generating Tapir output models from RDFS class definitions. The TaxonName class, for instance, has 23 properties. Most of these are literals. It might be possible to automatically generate a Tapir output model using XSLT from this class definition. This would then give people the ability to query for TaxonName objects that are an avowed XML Schema serialization of RDF over Tapir. The data mapping done by the client could be quite simple because they are only having to retrieve a single object (more or less a table per class if we were building a cache database) which would also make it fast. It would be easy for people to understand and work through a data mapping process to set up a provider and the process could make use of querying a central repository of objects types that is periodically updated. The problem comes with properties that are not literals but resource pointers. An example is TaxonName->authorshipTeam. In RDF this would be a resource that points to a team of people. If we all use GUIDs then the data source could just issue a GUID for the resource identifier and the client could then run another query to get the author team (or do it by resolving an LSID...). This multiple calls process is obviously inefficient. It is effectively getting the client to do their own joins but as the client is going to want to do this over multiple data sources and also it could be prohibitive to allow clients to do any arbitrary joins on a single host machine it might be a price worth paying. The other thing is that it solves the non-relational problem i.e. what if the data source can provide AuthorTeams and TaxonNames but can't permit arbitrary queries between the two (e.g. one is a researcher's Access db and the other the institutions collections management system). Effectively this is a mechanism for formally creating lots of Darwin Core schemas to use.... Does this sound like a crazy idea or not? All the best, Roger -- ------------------------------------- Roger Hyam Technical Architect Taxonomic Databases Working Group ------------------------------------- http://www.tdwg.org roger(a)tdwg.org +44 1578 722782 -------------------------------------

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Re: PublicationBank - requirements evaluation
by Anna Weitzman 21 Mar '06

21 Mar '06

Dear Robert, You may not be aware that TDWG has a list devoted to taxonomic literature standards. It would be great if you (and anyone else interested) would join in that discussion ( TDWG Literature standards mailing list tdwg-lit(a)lists.tdwg.org; sign up at http://lists.tdwg.org/mailman/listinfo/tdwg-lit_lists.tdwg.org/general ) and add your expertise. The list has only been active since early February, and the complete correspondence is in the archives ( http://lists.tdwg.org/pipermail/tdwg-lit_lists.tdwg.org/ ). Anna L. Weitzman, Ph.D. Informatics Branch Chief, National Museum of Natural History Smithsonian Institution, PO Box 37012 Natural History Building, Room W-623, MRC 136 Washington, DC 20013-7012 U.S.A. phone: (202) 633-0846 fax: (202) 786-3180 email: weitzman(a)si.edu INOTAXA - http://www.sil.si.edu/digitalcollections/bca/status.cfm electronic Biologia Centrali-Americana - http://www.sil.si.edu/digitalcollections/bca/ >>> rhuber(a)WDC-MARE.ORG 21-Mar-2006 5:06:30 AM >>> Dear all, Below is a short 'survey' which hopefully can help to get an overview on how bibliographic information currently is stored in your databases. If you don't like to fill such forms, any other info on your current literature db is also welcome, just send it to me by email! The list maybe incomplete, if you think important questions are missing there just let me and the others know. I will try to sumarize the results on the wiki later. best regards, Robert 1) How is your literature database/module organised? - [ ]Database structure completely normalized - [ ]Database structure not/incomplete normalized 2) How do you hold your bibliographic information? - [ ]Complete set of Bib info (Author, Title,Source, Volume, Pages) - [ ]Incomplete set of Bib info - [ ]Abbreviations (e.g. Stafleu&Cowan) - [ ]Bib Info and Abbreviations - Specify which bibliographic fields you hold in your db: --[ ]Author(s) --[ ]Title --[ ]Source (Journal/Book) --[ ]Pages --[ ]Date(s) --[ ]Volume --[ ]Issue --[ ]Series --[ ]URL/GUID --[ ]Source Editors --[ ]Series Editors --[ ]Other: 3) How do you store author names: - [ ]Abbreviations (e.g. Brummitt & Powell) - [ ]Complete Name as String, one author per string - [ ]Complete Name as String, all authors in one string - [ ]Last Name, First Name separated 4) How do you store journal names/ other sources - [ ]Complete Name - [ ]Abbreviation - [ ]Both - [ ]If you hold abbreviations acc. to which standard? Dr. Robert Huber WDC-MARE / PANGAEA - www.pangaea.de , www.wdc-mare.org 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@@wdc-mare.org , robert.huber(a)stratigraphy.net

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Re: PublicationBank - requirements evaluation
by Sally Hinchcliffe 21 Mar '06

21 Mar '06

Robert We have a number of databases which store bibliographic information. I have answered for both the KBD - our bibliographic database (http://www.kew.org/kbd/searchpage.do ) and for IPNI. I will pass this on to others for our checklists > Dear all, > > Below is a short 'survey' which hopefully can help to get an overview > on how bibliographic information currently is stored in your databases. > If you don't like to fill such forms, any other info on your current > literature db is also welcome, just send it to me by email! > > The list maybe incomplete, if you think important questions are missing > there just let me and the others know. > > I will try to sumarize the results on the wiki later. > > best regards, Robert > > 1) How is your literature database/module organised? > - [ ]Database structure completely normalized > - [ ]Database structure not/incomplete normalized > IPNI - incompletely normalised KBD - completely normalsed > 2) How do you hold your bibliographic information? > - [ ]Complete set of Bib info (Author, Title,Source, Volume, Pages) > - [ ]Incomplete set of Bib info > - [ ]Abbreviations (e.g. Stafleu&Cowan) > - [ ]Bib Info and Abbreviations > IPNI - incomplete set of Bib info (abbreviated title, Full title if known, collation information (not completely parsed out into volume etc.) occasionally author if different from the plant name author KBD - complete set of Bib info > - Specify which bibliographic fields you hold in your db: > --[ ]Author(s) > --[ ]Title > --[ ]Source (Journal/Book) > --[ ]Pages > --[ ]Date(s) > --[ ]Volume > --[ ]Issue > --[ ]Series > --[ ]URL/GUID > --[ ]Source Editors > --[ ]Series Editors > --[ ]Other: > IPNI - see above) KBD - all except URL/GUID (may be included for future records) > 3) How do you store author names: > - [ ]Abbreviations (e.g. Brummitt & Powell) > - [ ]Complete Name as String, one author per string > - [ ]Complete Name as String, all authors in one string > - [ ]Last Name, First Name separated > IPNI - Abbreviations, linked (for some records) to full author information KBD - Complete name as string, one author per string > 4) How do you store journal names/ other sources > - [ ]Complete Name > - [ ]Abbreviation > - [ ]Both > - [ ]If you hold abbreviations acc. to which standard? > IPNI - both for some records (using modified BPH where available) KBD - Both for some records - no standard yet for abbreviations HTH Sally > Dr. Robert Huber > WDC-MARE / PANGAEA - www.pangaea.de, www.wdc-mare.org > 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@@wdc-mare.org, robert.huber(a)stratigraphy.net *** Sally Hinchcliffe *** Computer section, Royal Botanic Gardens, Kew *** tel: +44 (0)20 8332 5708 *** S.Hinchcliffe(a)rbgkew.org.uk

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Re: LSID tester - new features
by Lee Belbin 21 Mar '06

21 Mar '06

Neat Rod! Lee Lee Belbin Manager, TDWG Infrastructure Project Email: lee(a)tdwg.org Phone: +61(0)419 374 133 -----Original Message----- From: Taxonomic Databases Working Group GUID Project [mailto:TDWG-GUID@LISTSERV.NHM.KU.EDU] On Behalf Of Roderic Page Sent: Tuesday, 21 March 2006 11:48 AM To: TDWG-GUID(a)LISTSERV.NHM.KU.EDU Subject: LSID tester - new features I've tweaked the LSID tester tool mentioned in a previous posting. The tester now lives at http://linnaeus.zoology.gla.ac.uk/~rpage/lsid/tester, and has the following changes: 1. The RDF metadata can be displayed as a graph in PNG and SVG formats (you can also get the underlying graph file which is AT&T's dot format) 2. An additional test that produces a warning if the HTTP binding for the authority is anything other than a server address (i.e., URLs with paths generate a warning) 3. Some minor cosmetic changes to make it a little less hideous on the eyes if you have the misfortune to use Internet Explorer 6 4. I've added some example LSIDs so users have somewhere to start. Still very crude and loads of limitations/bugs... Users of recent versions of Firefox will be disappointed with the SVG graphs. I suggest installing Adobe's SVG plugin and using this extension (http://rr.latenightpc.com/wp/archives/2005/06/10/firefox-extension- for-turning-built-in-svg-on-and-off/) to turn native SVG support off. Regards Rod ------------------------------------------------------------------------ ---------------------------------------- Professor Roderic D. M. Page Editor, Systematic Biology DEEB, IBLS Graham Kerr Building University of Glasgow Glasgow G12 8QP United Kingdom Phone: +44 141 330 4778 Fax: +44 141 330 2792 email: r.page(a)bio.gla.ac.uk web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html Subscribe to Systematic Biology through the Society of Systematic Biologists Website: http://systematicbiology.org Search for taxon names at http://darwin.zoology.gla.ac.uk/~rpage/portal/ Find out what we know about a species at http://ispecies.org

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PublicationBank - requirements evaluation
by Robert Huber 21 Mar '06

21 Mar '06

Dear all, Below is a short 'survey' which hopefully can help to get an overview on how bibliographic information currently is stored in your databases. If you don't like to fill such forms, any other info on your current literature db is also welcome, just send it to me by email! The list maybe incomplete, if you think important questions are missing there just let me and the others know. I will try to sumarize the results on the wiki later. best regards, Robert 1) How is your literature database/module organised? - [ ]Database structure completely normalized - [ ]Database structure not/incomplete normalized 2) How do you hold your bibliographic information? - [ ]Complete set of Bib info (Author, Title,Source, Volume, Pages) - [ ]Incomplete set of Bib info - [ ]Abbreviations (e.g. Stafleu&Cowan) - [ ]Bib Info and Abbreviations - Specify which bibliographic fields you hold in your db: --[ ]Author(s) --[ ]Title --[ ]Source (Journal/Book) --[ ]Pages --[ ]Date(s) --[ ]Volume --[ ]Issue --[ ]Series --[ ]URL/GUID --[ ]Source Editors --[ ]Series Editors --[ ]Other: 3) How do you store author names: - [ ]Abbreviations (e.g. Brummitt & Powell) - [ ]Complete Name as String, one author per string - [ ]Complete Name as String, all authors in one string - [ ]Last Name, First Name separated 4) How do you store journal names/ other sources - [ ]Complete Name - [ ]Abbreviation - [ ]Both - [ ]If you hold abbreviations acc. to which standard? Dr. Robert Huber WDC-MARE / PANGAEA - www.pangaea.de, www.wdc-mare.org 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@@wdc-mare.org, robert.huber(a)stratigraphy.net

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Re: LSID tester - new features
by Roger Hyam 21 Mar '06

21 Mar '06

Looks great Rod. Really nice stuff. I need to look at the errors and warnings and work out what is going on in detail when I turn back to looking at LSID. Hope to suggest additions/improvements in the near future. Keep the site up as I'll use it for testing - better than Launchpad methinks! All the best, Roger Roderic Page wrote: > I've tweaked the LSID tester tool mentioned in a previous posting. The > tester now lives at > http://linnaeus.zoology.gla.ac.uk/~rpage/lsid/tester, and has the > following changes: > > 1. The RDF metadata can be displayed as a graph in PNG and SVG formats > (you can also get the underlying graph file which is AT&T's dot format) > > 2. An additional test that produces a warning if the HTTP binding for > the authority is anything other than a server address (i.e., URLs with > paths generate a warning) > > 3. Some minor cosmetic changes to make it a little less hideous on the > eyes if you have the misfortune to use Internet Explorer 6 > > 4. I've added some example LSIDs so users have somewhere to start. > > Still very crude and loads of limitations/bugs... > > Users of recent versions of Firefox will be disappointed with the SVG > graphs. I suggest installing Adobe's SVG plugin and using this > extension > (http://rr.latenightpc.com/wp/archives/2005/06/10/firefox-extension- > for-turning-built-in-svg-on-and-off/) to turn native SVG support off. > > Regards > > Rod > > ------------------------------------------------------------------------ > ---------------------------------------- > Professor Roderic D. M. Page > Editor, Systematic Biology > DEEB, IBLS > Graham Kerr Building > University of Glasgow > Glasgow G12 8QP > United Kingdom > > Phone: +44 141 330 4778 > Fax: +44 141 330 2792 > email: r.page(a)bio.gla.ac.uk > web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html > reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html > > Subscribe to Systematic Biology through the Society of Systematic > Biologists Website: http://systematicbiology.org > Search for taxon names at http://darwin.zoology.gla.ac.uk/~rpage/portal/ > Find out what we know about a species at http://ispecies.org > -- ------------------------------------- Roger Hyam Technical Architect Taxonomic Databases Working Group ------------------------------------- http://www.tdwg.org roger(a)tdwg.org +44 1578 722782 -------------------------------------

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LSID tester - new features
by Roderic Page 20 Mar '06

20 Mar '06

I've tweaked the LSID tester tool mentioned in a previous posting. The tester now lives at http://linnaeus.zoology.gla.ac.uk/~rpage/lsid/tester, and has the following changes: 1. The RDF metadata can be displayed as a graph in PNG and SVG formats (you can also get the underlying graph file which is AT&T's dot format) 2. An additional test that produces a warning if the HTTP binding for the authority is anything other than a server address (i.e., URLs with paths generate a warning) 3. Some minor cosmetic changes to make it a little less hideous on the eyes if you have the misfortune to use Internet Explorer 6 4. I've added some example LSIDs so users have somewhere to start. Still very crude and loads of limitations/bugs... Users of recent versions of Firefox will be disappointed with the SVG graphs. I suggest installing Adobe's SVG plugin and using this extension (http://rr.latenightpc.com/wp/archives/2005/06/10/firefox-extension- for-turning-built-in-svg-on-and-off/) to turn native SVG support off. Regards Rod ------------------------------------------------------------------------ ---------------------------------------- Professor Roderic D. M. Page Editor, Systematic Biology DEEB, IBLS Graham Kerr Building University of Glasgow Glasgow G12 8QP United Kingdom Phone: +44 141 330 4778 Fax: +44 141 330 2792 email: r.page(a)bio.gla.ac.uk web: http://taxonomy.zoology.gla.ac.uk/rod/rod.html reprints: http://taxonomy.zoology.gla.ac.uk/rod/pubs.html Subscribe to Systematic Biology through the Society of Systematic Biologists Website: http://systematicbiology.org Search for taxon names at http://darwin.zoology.gla.ac.uk/~rpage/portal/ Find out what we know about a species at http://ispecies.org

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