Roger and Donald, Roger's list gets even worse because there are multiple editions and formats (eg. quartile) for many books/journals. The same information may thus occur on different pages across the different editions. Librarians maintain the publication records at this detailed level - ie. which editions and formats are in the library and where.

I agree with Roger. This area of publication information belongs to the library community. In our Botanicus project we are digitizing 18th and 19th center botanical references. For the higher level coding information we have looked to our library management system and engaged our librarians to supply the correct information. There are existing standards and standards bodies for book/journal codification. We should not reinvent the wheel. I think this says we need to engage some library professionals into biodiversity informatics and TDWG, like we have engaged the geographical information professionals.

Chuck

-----Original Message----- From: Roger Hyam To: TDWG-GUID@LISTSERV.NHM.KU.EDU Sent: 3/24/2006 4:54 AM Subject: Re: [TDWG-GUID] PublicationBank - requirements evaluation

Hi Donald,

This makes perfect sense to me but I'd like to introduce one comment that might muddy the waters or help clear them.

We need an understanding of the granularity of a publication in any such publication bank as I think 'publication' means different things to different people. Looking at a monograph I have in front of me:

A Revision of Rhododendron VI subgenus Pentanthera (Sections Sciadorhodion, Rhodora and Viscidula) W.S. Judd and K.A. Kron (1995) Edinburgh Journal of Botany (ISSN 0960-4286), Volume 52, Number 1, Pages 1-54. On page 15 we have a good description of Rhododendron schlippenbachii (a TaxonConcept as this is not a sp nov or comb nov).

The scope of publication bank could be at several levels:

1. LSID for the Journal/Book

2. LSID for the volume 3. LSID for the part 4. LSID for the article 5. LSID for the actual description on page 15.

I would argue quite strongly that taking it beyond level 1 is moderately pointless as we can have a simple vocabulary of fields that can contain nice integers to uniquely identify a place within a Journal (or book). Taking it beyond 1 is also incredibly difficult. An analogy is the use of postal or zip codes. The postal code refers to a block not a single address and must be qualified by house and flat number (in the UK).

Perhaps PublicationBank should really be BookAndJournalBank but identifying books and journals definitely feels to me like it is outside the scope of TDWG and firmly in the scope of the library community.

I don't want to preempt the outcome of any white paper on the subject but it may be that a simple applicability statement is required on how to cite references electronically using existing numbering systems accompanied by several integer fields (year, volume, part etc). i.e. not relying on titles or author names. The above references is uniquely identified by ISSN:0960-4286:52:1:1-54. It may be accompanied by the text as well of course - for humans!

Just my 2 cents.

Roger

Donald Hobern wrote:

Dear Anna,

Thank you for making the connection between these two groups. I think it would help if I explained (particularly for the TDWG-LIT group) what questions are being addressed by the TDWG-GUID work under the general heading of "PublicationBank".

During the first GUID workshop, we recognized that different classes of information require (for want of a better term) different strengths of GUIDs. It is a great help for us to be able to recognise that two references are to the same piece of data because they use the same GUID to reference it. Let me give some examples.

If I state that my taxon concept includes a specimen with LSID urn:lsid:my.org:specimen:123 and someone else also includes the same LSID in the list of specimens examined as part of their revision, it helps us to make some firm deductions about shared material. It seems reasonable that we will be able to associate identifiers with specimens in a way that ensures that the vast majority of specimens can receive a single identifier, meaning that all references to that identifier refer to that specimen and that all references to that specimen use that identifier. This second part is what I mean when I speak of a strong identifier.

Now consider the situation with taxon names. Many people are going to wish to refer to the same names (or nomenclatural acts). It will clearly be really valuable if we can work towards having a single GUID for each validly published name, so that we can maximize the interconnectedness of our data. If I say that refer to the name with the LSID urn:lsid:my.org:names:xyz and that LSID has data or metadata indicating that it relates to Aus bus Jones, 2004, and you use the LSID urn:lsid:another.org:names.abc to refer to the same Aus bus Jones, 2004, then we are still left with the same string matching problems we have right now with names. It therefore seems sensible to work with the nomenclators as the "preferred" issuers of LSIDs for taxon names (recognising the gaps we have today for zoological names) and to encourage a move to using those identifiers whenever we wish to provide a secure reference to each name. (Of course this implies an urgent need for tools and services to make this easy.)

Turning to taxon concepts, we had a long debate as to whether it was plausible to try to enforce the same degree of preferred issuers for LSIDs for taxon concepts. If I publish the first LSID-enabled revision of a group, I may need to assign LSIDs to refer to many different taxon concepts. Someone else databasing the taxonomy of the group will have a similar task. Unless we manage a central easy-to-search registry for people quickly to find out whether someone has already assigned an LSID to Aus bus Jones, 2004 sensu Smith, 2006, we will never be able to make any assumptions based on the fact that I have used urn:lsid:my.org:concepts:123.1 and you have used urn:lsid:my.org:concepts:abc.001. Even though the two identifiers are different there is still a good chance that they may refer to the same concept (expressed as name-according to-publication). It seems much more reasonable instead to tackle the problem of getting really strong LSIDs for names (through the nomenclators) and doing the same thing for the taxonomic literature (through someone for whom we used the placeholder name "PublicationBank"). Any concept LSID can resolve through its metadata to two LSIDs, one for a name and one for a publication. Comparing concept LSIDs can therefore be based on the comparisons between these two more fundamental objects.

So, from the standpoint of the GUID group, the requirement here is a very specific one. We need to find a way to manage assigning LSIDs to the publications that make up the taxonomic literature, so that we can all have what would amount to a master list of relevant publications.

...

...

From this angle, "all" that is needed is a secure registry into which

the bibliographic data can be stored, cleaned and assigned identifiers. Of course such a resource could also be an excellent place to register the location of online digital versions of each publication. At that point it becomes something even more valuable. On the other hand, considering it this way suggests that it may already naturally be addressed as part of the BHL or a similar effort, and part of what we would like to do is to identify any existing initiatives which may serve as a part or all of what is required for the LSID work.

As I see it, the TDWG-LIT work gives a framework for the exchange of these bibliographic data, but we also need to understand the best way to get the kind of integrated biodiversity bibliography we would like to have.

Does that all make sense?

Best wishes,

Donald

--------------------------------------------------------------- Donald Hobern ( dhobern@gbif.org mailto:dhobern@gbif.org ) Programme Officer for Data Access and Database Interoperability Global Biodiversity Information Facility Secretariat Universitetsparken 15, DK-2100 Copenhagen, Denmark Tel: +45-35321483 Mobile: +45-28751483 Fax: +45-35321480 ---------------------------------------------------------------

_____

From: Taxonomic Databases Working Group GUID Project [ mailto:TDWG-GUID@LISTSERV.NHM.KU.EDU mailto:TDWG-GUID@LISTSERV.NHM.KU.EDU ] On Behalf Of Anna Weitzman Sent: 21 March 2006 20:10 To: TDWG-GUID@LISTSERV.NHM.KU.EDU mailto:TDWG-GUID@LISTSERV.NHM.KU.EDU

Subject: Re: PublicationBank - requirements evaluation

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@lists.tdwg.org mailto:tdwg-lit@lists.tdwg.org ; sign up at http://lists.tdwg.org/mailman/listinfo/tdwg-lit_lists.tdwg.org/general 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/ 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@si.edu mailto:weitzman@si.edu INOTAXA - http://www.sil.si.edu/digitalcollections/bca/status.cfm http://www.sil.si.edu/digitalcollections/bca/status.cfm electronic Biologia Centrali-Americana - http://www.sil.si.edu/digitalcollections/bca/ http://www.sil.si.edu/digitalcollections/bca/

...

...

rhuber@WDC-MARE.ORG mailto:rhuber@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 http://www.pangaea.de/ , www.wdc-mare.org http://www.wdc-mare.org/ Stratigraphy.net - www.stratigraphy.net http://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 mailto:rhuber@@wdc-mare.org , robert.huber@stratigraphy.net mailto:robert.huber@stratigraphy.net

--

-------------------------------------

Roger Hyam

Technical Architect

Taxonomic Databases Working Group

-------------------------------------

http://www.tdwg.org http://www.tdwg.org

roger@tdwg.org mailto:roger@tdwg.org

+44 1578 722782

-------------------------------------