PublicationBank - requirements evaluation

Fri Mar 24 08:41:55 CET 2006

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 at 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 at LISTSERV.NHM.KU.EDU] On Behalf Of Anna Weitzman
Sent: 21 March 2006 20:10
To: TDWG-GUID at 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 at 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 at si.edu
INOTAXA - http://www.sil.si.edu/digitalcollections/bca/status.cfm
electronic Biologia Centrali-Americana -
http://www.sil.si.edu/digitalcollections/bca/

>>> rhuber at 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 , robert.huber at stratigraphy.net

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margin-right:3.0pt;margin-bottom:.75pt'>

<div class=3DSection1>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Dear =
Anna,<o:p></o:p></span></font></p>

Thank you for making the connection
between these two groups. &nbsp;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 =
&#8220;PublicationBank&#8221;.<o:p></o:p>

During the first GUID workshop, we =
recognized
that different classes of information require (for want of a better =
term)
different strengths of =
GUIDs. &nbsp;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. =
&nbsp;Let me
give some examples.<o:p></o:p>

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. &nbsp;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.&nbsp; This second part is what =
I mean
when I speak of a strong
identifier.<o:p></o:p>

Now consider the situation with =
taxon
names.&nbsp; Many people are going to wish to refer to the same names =
(or
nomenclatural acts). &nbsp;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. &nbsp;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.&nbsp; It therefore seems sensible to work with the =
nomenclators as
the &#8220;preferred&#8221; 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. =
&nbsp;(Of
course this implies an urgent need for tools and services to make this =
easy.)<o:p></o:p>

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.&nbsp; If I publish the first =
LSID-enabled
revision of a group, I may need to assign LSIDs to refer to many =
different
taxon concepts. &nbsp;Someone else databasing the taxonomy of the group =
will
have a similar task. &nbsp;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.
&nbsp;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).
&nbsp;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 &#8220;PublicationBank&#8221;).&nbsp; Any concept LSID =
can
resolve through its metadata to two LSIDs, one for a name and one for a
publication. &nbsp;Comparing concept LSIDs can therefore be based on the
comparisons between these two more fundamental =
objects.<o:p></o:p>

So, from the standpoint of the GUID =
group,
the requirement here is a very specific one. &nbsp;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. &nbsp;From this angle, &#8220;all&#8221; that is =
needed
is a secure registry into which the bibliographic data can be stored, =
cleaned
and assigned identifiers.&nbsp; Of course such a resource could also be =
an
excellent place to register the location of online digital versions of =
each publication.
&nbsp;At that point it becomes something even more valuable.&nbsp; 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.<o:p></o:p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>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.<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Does that all make =
sense?<o:p></o:p></span></font></p>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Best =
wishes,<o:p></o:p></span></font></p>

<div>

<p class=3DMsoNormal><font size=3D2 color=3Dnavy face=3DArial><span =
style=3D'font-size:
10.0pt;font-family:Arial;color:navy'>Donald<br>
&nbsp;<br>
---------------------------------------------------------------<br>
Donald Hobern (<a =
href=3D"mailto:dhobern at gbif.org">dhobern at gbif.org</a>)<br>
Programme Officer for Data Access and Database Interoperability <br>
Global Biodiversity Information Facility Secretariat <br>
Universitetsparken 15, DK-2100 <st1:place w:st=3D"on"><st1:City =
w:st=3D"on">Copenhagen</st1:City>,
 <st1:country-region =
w:st=3D"on">Denmark</st1:country-region></st1:place><br>
Tel: +45-35321483&nbsp;&nbsp; <st1:place w:st=3D"on"><st1:City =
w:st=3D"on">Mobile</st1:City></st1:place>:
+45-28751483&nbsp;&nbsp; Fax: +45-35321480<br>
---------------------------------------------------------------</span></f=
ont><font
size=3D2 face=3DArial><span =
style=3D'font-size:10.0pt;font-family:Arial'><o:p></o:p></span></font></p=
>

</div>

<div>

<div class=3DMsoNormal align=3Dcenter =
style=3D'margin:0cm;margin-bottom:.0001pt;
text-align:center'><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'>

<hr size=3D2 width=3D"100%" align=3Dcenter tabindex=3D-1>

</span></font></div>

<p class=3DMsoNormal style=3D'margin:0cm;margin-bottom:.0001pt'><b><font =
size=3D2
face=3DTahoma><span =
style=3D'font-size:10.0pt;font-family:Tahoma;font-weight:bold'>From:</spa=
n></font></b><font
size=3D2 face=3DTahoma><span =
style=3D'font-size:10.0pt;font-family:Tahoma'> <st1:PersonName
w:st=3D"on">Taxonomic Databases Working Group GUID =
Project</st1:PersonName>
[mailto:TDWG-GUID at LISTSERV.NHM.KU.EDU] <b><span =
style=3D'font-weight:bold'>On
Behalf Of </span></b>Anna Weitzman<br>
<b><span style=3D'font-weight:bold'>Sent:</span></b> 21 March 2006 =
20:10<br>
<b><span style=3D'font-weight:bold'>To:</span></b> =
TDWG-GUID at LISTSERV.NHM.KU.EDU<br>
<b><span style=3D'font-weight:bold'>Subject:</span></b> Re: =
PublicationBank -
requirements evaluation</span></font><o:p></o:p></p>

</div>

<p class=3DMsoNormal><font size=3D3 face=3D"Times New Roman"><span =
style=3D'font-size:
12.0pt'><o:p>&nbsp;</o:p></span></font></p>

<div>

<p class=3DMsoNormal style=3D'margin:0cm;margin-bottom:.0001pt'><font =
size=3D2
face=3D"Microsoft Sans Serif"><span =
style=3D'font-size:10.0pt;font-family:"Microsoft Sans Serif"'>Dear
Robert,<o:p></o:p></span></font></p>

</div>

<div>

<p class=3DMsoNormal style=3D'margin:0cm;margin-bottom:.0001pt'><font =
size=3D2
face=3D"Microsoft Sans Serif"><span =
style=3D'font-size:10.0pt;font-family:"Microsoft Sans Serif"'>You
may not be aware that TDWG has a list devoted to taxonomic literature
standards.&nbsp; It would be great if you (and anyone else interested) =
would
join in that discussion (&nbsp;TDWG Literature standards mailing list <a
href=3D"mailto:tdwg-lit at lists.tdwg.org">tdwg-lit at lists.tdwg.org</a>; =
sign up
at&nbsp;<a
href=3D"http://lists.tdwg.org/mailman/listinfo/tdwg-lit_lists.tdwg.org/ge=
neral">http://lists.tdwg.org/mailman/listinfo/tdwg-lit_lists.tdwg.org/gen=
eral</a>
) and add your expertise.&nbsp; The list has only been active since =
early
February, and the complete correspondence is in the archives (&nbsp;<a
href=3D"http://lists.tdwg.org/pipermail/tdwg-lit_lists.tdwg.org/">http://=
lists.tdwg.org/pipermail/tdwg-lit_lists.tdwg.org/</a>
).<o:p></o:p></span></font></p>

</div>

<div>

<p class=3DMsoNormal style=3D'margin:0cm;margin-bottom:.0001pt'><font =
size=3D2
face=3D"Microsoft Sans Serif"><span =
style=3D'font-size:10.0pt;font-family:"Microsoft Sans =
Serif"'>&nbsp;<o:p></o:p></span></font></p>

</div>

<div>

<p class=3DMsoNormal style=3D'margin:0cm;margin-bottom:.0001pt'><font =
size=3D2
face=3D"Microsoft Sans Serif"><span =
style=3D'font-size:10.0pt;font-family:"Microsoft Sans =
Serif"'>&nbsp;<o:p></o:p></span></font></p>

</div>

<div>

<p class=3DMsoNormal style=3D'margin:0cm;margin-bottom:.0001pt'><font =
size=3D2
face=3D"Microsoft Sans Serif"><span =
style=3D'font-size:10.0pt;font-family:"Microsoft Sans =
Serif"'>&nbsp;<o:p></o:p></span></font></p>

</div>

<div>

<p class=3DMsoNormal style=3D'margin:0cm;margin-bottom:.0001pt'><font =
size=3D2
face=3D"Microsoft Sans Serif"><span =
style=3D'font-size:10.0pt;font-family:"Microsoft Sans Serif"'>Anna
L. Weitzman, Ph.D.<br>
Informatics Branch Chief, <st1:place w:st=3D"on"><st1:PlaceName =
w:st=3D"on">National</st1:PlaceName>
 <st1:PlaceType w:st=3D"on">Museum</st1:PlaceType></st1:place> of =
Natural History<br>
Smithsonian Institution, <st1:address w:st=3D"on"><st1:Street =
w:st=3D"on">PO Box</st1:Street>
 37012</st1:address><br>
<st1:place w:st=3D"on"><st1:PlaceName =
w:st=3D"on">Natural</st1:PlaceName> <st1:PlaceName
 w:st=3D"on">History</st1:PlaceName> <st1:PlaceType =
w:st=3D"on">Building</st1:PlaceType></st1:place>,
Room W-623, MRC 136<br>
<st1:place w:st=3D"on"><st1:City w:st=3D"on">Washington</st1:City>, =
<st1:State
 w:st=3D"on">DC</st1:State> <st1:PostalCode =
w:st=3D"on">20013-7012</st1:PostalCode>&nbsp;
 <st1:country-region =
w:st=3D"on">U.S.A.</st1:country-region></st1:place><br>
&nbsp;<br>
phone:&nbsp; (202) 633-0846<br>
fax:&nbsp; (202) 786-3180<br>
email:&nbsp; <a href=3D"mailto:weitzman at si.edu">weitzman at si.edu</a><br>
INOTAXA - <a =
href=3D"http://www.sil.si.edu/digitalcollections/bca/status.cfm">http://w=
ww.sil.si.edu/digitalcollections/bca/status.cfm</a><br>
electronic Biologia Centrali-Americana - <a
href=3D"http://www.sil.si.edu/digitalcollections/bca/">http://www.sil.si.=
edu/digitalcollections/bca/</a><br>
<br>
<br>
&gt;&gt;&gt; rhuber at WDC-MARE.ORG 21-Mar-2006 5:06:30 AM &gt;&gt;&gt;<br>
Dear all,<br>
<br>
Below is a short 'survey' which hopefully can help to get an =
overview<br>
on how bibliographic information currently is stored in your =
databases.<br>
If you don't like to fill such forms, any other info on your current<br>
literature db is also welcome, just send it to me by email!<br>
<br>
The list maybe incomplete, if you think important questions are =
missing<br>
there just let me and the others know.<br>
<br>
I will try to sumarize the results on the wiki later.<br>
<br>
best regards, Robert<br>
<br>
1) How is your literature database/module organised?<br>
- [ ]Database structure completely normalized<br>
- [ ]Database structure not/incomplete normalized<br>
<br>
2) How do you hold your bibliographic information?<br>
- [ ]Complete set of Bib info (Author, Title,Source, Volume, Pages)<br>
- [ ]Incomplete set of Bib info<br>
- [ ]Abbreviations (e.g. Stafleu&amp;Cowan)<br>
- [ ]Bib Info and Abbreviations<br>
<br>
- Specify which bibliographic fields you hold in your db:<br>
--[ ]Author(s)<br>
--[ ]Title<br>
--[ ]Source (Journal/Book)<br>
--[ ]Pages<br>
--[ ]Date(s)<br>
--[ ]Volume<br>
--[ ]Issue<br>
--[ ]Series<br>
--[ ]URL/GUID<br>
--[ ]Source Editors<br>
--[ ]Series Editors<br>
--[ ]Other:<br>
<br>
3) How do you store author names:<br>
- [ ]Abbreviations (e.g. Brummitt &amp; Powell)<br>
- [ ]Complete Name as String, one author per string<br>
- [ ]Complete Name as String, all authors in one string<br>
- [ ]Last Name, First Name separated<br>
<br>
4) How do you store journal names/ other sources<br>
- [ ]Complete Name<br>
- [ ]Abbreviation<br>
- [ ]Both<br>
- [ ]If you hold abbreviations acc. to which standard?<br>
<br>
Dr. Robert Huber<br>
WDC-MARE / PANGAEA - <u><a =
href=3D"http://www.pangaea.de/">www.pangaea.de</a></u>
, <u><a href=3D"http://www.wdc-mare.org/">www.wdc-mare.org</a></u> <br>
Stratigraphy.net - <u><a =
href=3D"http://www.stratigraphy.net/">www.stratigraphy.net</a></u>
<br>
_____________________________________________<br>
MARUM - Institute for Marine Environmental Sciences (location)<br>
University <st1:State w:st=3D"on"><st1:place =
w:st=3D"on">Bremen</st1:place></st1:State><br>
Leobener Strasse<br>
POP 330 440<br>
28359 <st1:State w:st=3D"on"><st1:place =
w:st=3D"on">Bremen</st1:place></st1:State><br>
Phone ++49 421 218-65593, Fax ++49 421 218-65505<br>
e-mail <u><a =
href=3D"mailto:rhuber@@wdc-mare.org">rhuber@@wdc-mare.org</a></u> , =
<u><a
href=3D"mailto:robert.huber at stratigraphy.net">robert.huber at stratigraphy.n=
et</a></u>
<o:p></o:p></span></font></p>

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