Thanks, Chuck. I agree that this is the
best approach and that our goal should simply be to find the right communities
with whom to align this activity.
Best wishes,
Donald
---------------------------------------------------------------
Donald Hobern (dhobern@gbif.org)
Programme Officer for Data Access and Database Interoperability
Global Biodiversity Information Facility Secretariat
Universitetsparken 15, DK-2100
Tel: +45-35321483
---------------------------------------------------------------
From:
Sent: 24 March 2006 16:43
To: TDWG-GUID@LISTSERV.NHM.KU.EDU
Subject: Re: PublicationBank -
requirements evaluation
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)
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
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
Tel: +45-35321483
---------------------------------------------------------------
_____
From:
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,
Smithsonian Institution,
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
Leobener Strasse
POP 330 440
28359
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
-------------------------------------