PublicationBank, Policy/Best Practice

Mon Feb 27 12:48:00 CET 2006

There are current "official" TDWG standards for author names, publications,
etc.  See http://www.tdwg.org/standrds.html.  Although these content
standards are primarily botanical, they do stand as the current TDWG
standards until repealed or amended.

In the 80s and 90s, particularly when TDWG was more botanical, TDWG tended
to address data content standards.  Data exchange structures have taken the
forefront in the last several years, leaving data content dormant.

Now GUIDs may be bringing an old TDWG issue back into view. To envision a
standard repository of common data values for publications and authors is to
return to the TDWG discussions and goals of the 1980s, only now encompassing
all organisms and not just botany.  In the early times we had folks, like
Brummitt and Powell, willing to invest years of time to compiling such data
sources.  Who would take on a similar data content compilation task for
zoology, bacteriology, etc in order to make the TDWG data standards
complete?  Is the desire to have one master standardized list of all
biological authors, publications, journals?  And even more importantly, who
would keep it up to date?

I think Remsen is describing his author list as a start on an "all-biology
author" list, but Sally points out the peril in that given the original
source of the botanical authors being at IPNI.  And we haven't even gotten
started.  Certainly since many authors published in multiple organismal
groups and many publications are also multiple organismal, without synthesis
of the author and publication lists some duplication of GUIDs will
inevitably occur.  But, maybe the amount of this duplication falls outside
what Richard Pyle called "90% of the value 90% of the time" (a quote I
really like) and should just be accepted.

Chuck

-----Original Message-----
From: Sally Hinchcliffe [mailto:S.Hinchcliffe at KEW.ORG]
Sent: Monday, February 27, 2006 10:50 AM
To: TDWG-GUID at LISTSERV.NHM.KU.EDU
Subject: Re: [TDWG-GUID] PublicationBank, Policy/Best Practice

Hi - regarding author names, I'm a little worried about duplication
of effort  here
for botanical authors (plus fungal authors and other authors of algae
and groups not included in the scope of IPNI proper) the authors
served by IPNI cover the original Brummitt & Powell authors plus
Harvard's Authors and it continues to be kept up to date and added to
on a daily basis. The 'Brummitt & Powell' form is the TDWG standard
for citing botanical authors.

I hope uBio aren't reinventing the wheel here ... we can certainly do
more at IPNI to publicise this & to make web services and so on
available but I would hate to think this data is being compiled and
kept up to date in more than one place.
See
http://www.ipni.org/ipni/authorsearch?request_type=search&output_forma
t=query&ret_defaults=on for the authors in IPNI

For publications we too, like many other databases that use
publications and references, have a publications table that more or
less covers electronically what BPH and Taxonomic Literature do on
paper. This was compiled originally by Harvard. and is available at
http://www.ipni.org/ipni/publicationsearch?request_type=search&output_
format=query&ret_defaults=on

I'd love for us to be tapping into some centrally available
'publication bank' that we could use in IPNI instead of our own
internal lists & if this is web servicable would hopefully be looking
to integrating it in via that rather than keeping copies of our own
data.

Sally

> Dear Dr. Huber:  We are interested in being part of the conversation
> on PublicationBank.
>
> One area we are interested in is the resolution of abbreviated and
> lexical forms of citations and I would think this would have to be a
> component of a more fundamental publicationBank resolution system.
> Issues of integrating citations have arisen in the digital conversion
> of taxonomic catalogs.  We have successfully completed Nomenclator
> Zoologicus and are now working on Index Animalium.   Resolving
> citations is a priority because it can identify high-impact
> candidates for future digital conversion, link different cited forms
> to a common source, and provide a foundation for referencing
> bibliographic components of taxonomic circumscriptions.   Between the
> two sources we have over 800,000 citations references as a starting
> point.  I know this issue is also of interest with our library
> colleagues at the Smithsonian.
>
> We have a similar issue with author names annotating taxon names and
> have an web service in place for resolving them.  At the moment this
> is populated primarily with botanical authors but as we post-process
> Sherborne and Neave we will likely be adding many thousands of
> zoological authors.
>
> http://uio.mbl.edu/authors/info.php
>
> Regards,
> David Remsen
>
> On Feb 27, 2006, at 6:23 AM, Robert Huber wrote:
>
> > Dear all,
> >
> > To my earlier email on PublicationBank I got no resonse, so I
> > assume no
> > earlier
> > attempts or discussion on this topic have been started yet?
> >
> > A pragmatic starting point for PublicationBank (PB)would be to use the
> > literature
> > entries of the existing LSID authorities databases to initially
> > populate PB
> > with
> > GUIDs.
> > To get the appropriate GUIDs we ideally would have access to
> > services from
> > the publishers, databases such as PubMed or the DOI foundation
> > (crossref).
> >
> > I called these services Bibliographic Query Resolver and just
> > started to
> > search
> > the web for potential candidates. Results are here:
> >
> > http://wiki.gbif.org/guidwiki/wikka.php?
> > wakka=BibliographicQueryResolver
> >
> >
> > Bibliographic Query Resolver
> > Accepts bibliographic meta-data and returns the corresponding GUID
> > (e.g.
> > DOI, LSID)
> >
> >     * CrossRef offers a variety of possibilities to resolve DOIs. More
> > information can be found at CrossRefs query spec pages. The DOI link
> > directly redirects to the online document (subscription dependent) or
> > abstract.
> >     * PudMed offers a 'Batch Citation Matcher' to retrieve a PMID
> > which can
> > be completed as LSID?
> >
> >
> >
> >
> > best regards,
> > Robert
> >
> > 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 at stratigraphy.net
>
>

*** Sally Hinchcliffe
*** Computer section, Royal Botanic Gardens, Kew
*** tel: +44 (0)20 8332 5708
*** S.Hinchcliffe at rbgkew.org.uk

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<TITLE>RE: [TDWG-GUID] PublicationBank, Policy/Best Practice</TITLE>
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<P><FONT SIZE=3D2>There are current &quot;official&quot; TDWG standards =
for author names, publications, etc.&nbsp; See <A =
HREF=3D"http://www.tdwg.org/standrds.html" =
TARGET=3D"_blank">http://www.tdwg.org/standrds.html</A>.&nbsp; Although =
these content standards are primarily botanical, they do stand as the =
current TDWG standards until repealed or amended.&nbsp; </FONT></P>

<P><FONT SIZE=3D2>In the 80s and 90s, particularly when TDWG was more =
botanical, TDWG tended to address data content standards.&nbsp; Data =
exchange structures have taken the forefront in the last several years, =
leaving data content dormant.</FONT></P>

Now GUIDs may be bringing an old TDWG issue back into =
view. To envision a standard repository of common data values for =
publications and authors is to return to the TDWG discussions and goals =
of the 1980s, only now encompassing all organisms and not just =
botany.&nbsp; In the early times we had folks, like Brummitt and =
Powell, willing to invest years of time to compiling such data =
sources.&nbsp; Who would take on a similar data content compilation =
task for zoology, bacteriology, etc in order to make the TDWG data =
standards complete?&nbsp; Is the desire to have one master standardized =
list of all biological authors, publications, journals?&nbsp; And even =
more importantly, who would keep it up to date?

<P><FONT SIZE=3D2>I think Remsen is describing his author list as a =
start on an &quot;all-biology author&quot; list, but Sally points out =
the peril in that given the original source of the botanical authors =
being at IPNI.&nbsp; And we haven't even gotten started.&nbsp; =
Certainly since many authors published in multiple organismal groups =
and many publications are also multiple organismal, without synthesis =
of the author and publication lists some duplication of GUIDs will =
inevitably occur.&nbsp; But, maybe the amount of this duplication falls =
outside what Richard Pyle called &quot;90% of the value 90% of the =
time&quot; (a quote I really like) and should just be =
accepted.</FONT></P>

<P><FONT SIZE=3D2>Chuck</FONT>
</P>
<BR>

<P><FONT SIZE=3D2>-----Original Message-----</FONT>
<BR><FONT SIZE=3D2>From: Sally Hinchcliffe [<A =
HREF=3D"mailto:S.Hinchcliffe at KEW.ORG">mailto:S.Hinchcliffe at KEW.ORG</A>] =
</FONT>
<BR><FONT SIZE=3D2>Sent: Monday, February 27, 2006 10:50 AM</FONT>
<BR><FONT SIZE=3D2>To: TDWG-GUID at LISTSERV.NHM.KU.EDU</FONT>
<BR><FONT SIZE=3D2>Subject: Re: [TDWG-GUID] PublicationBank, =
Policy/Best Practice</FONT>
</P>

Hi - regarding author names, I'm a little worried =
about duplication
 of effort&nbsp; here
 for botanical authors (plus fungal authors and other =
authors of algae
 and groups not included in the scope of IPNI proper) =
the authors
 served by IPNI cover the original Brummitt &amp; =
Powell authors plus
 Harvard's Authors and it continues to be kept up to =
date and added to
 on a daily basis. The 'Brummitt &amp; Powell' form =
is the TDWG standard
 for citing botanical authors.

I hope uBio aren't reinventing the wheel here ... we =
can certainly do
 more at IPNI to publicise this &amp; to make web =
services and so on
 available but I would hate to think this data is =
being compiled and
 kept up to date in more than one place.
 See
 <A =
HREF=3D"http://www.ipni.org/ipni/authorsearch?request_type=3Dsearch&outp=
ut_forma" =
TARGET=3D"_blank">http://www.ipni.org/ipni/authorsearch?request_type=3Ds=
earch&output_forma</A>
 t=3Dquery&amp;ret_defaults=3Don for the authors in =
IPNI

For publications we too, like many other databases =
that use
 publications and references, have a publications =
table that more or
 less covers electronically what BPH and Taxonomic =
Literature do on
 paper. This was compiled originally by Harvard. and =
is available at
 <A =
HREF=3D"http://www.ipni.org/ipni/publicationsearch?request_type=3Dsearch=
&output_" =
TARGET=3D"_blank">http://www.ipni.org/ipni/publicationsearch?request_typ=
e=3Dsearch&output_</A>
 format=3Dquery&amp;ret_defaults=3Don

<P><FONT SIZE=3D2>I'd love for us to be tapping into some centrally =
available</FONT>
<BR><FONT SIZE=3D2>'publication bank' that we could use in IPNI instead =
of our own</FONT>
<BR><FONT SIZE=3D2>internal lists &amp; if this is web servicable would =
hopefully be looking</FONT>
<BR><FONT SIZE=3D2>to integrating it in via that rather than keeping =
copies of our own</FONT>
<BR><FONT SIZE=3D2>data.</FONT>
</P>

<P><FONT SIZE=3D2>Sally</FONT>
</P>
<BR>

&gt; Dear Dr. Huber:&nbsp; We are interested in being =
part of the conversation
 &gt; on PublicationBank.
 &gt;
 &gt; One area we are interested in is the resolution =
of abbreviated and
 &gt; lexical forms of citations and I would think =
this would have to be a
 &gt; component of a more fundamental publicationBank =
resolution system.
 &gt; Issues of integrating citations have arisen in =
the digital conversion
 &gt; of taxonomic catalogs.&nbsp; We have =
successfully completed Nomenclator
 &gt; Zoologicus and are now working on Index =
Animalium.&nbsp;&nbsp; Resolving
 &gt; citations is a priority because it can identify =
high-impact
 &gt; candidates for future digital conversion, link =
different cited forms
 &gt; to a common source, and provide a foundation =
for referencing
 &gt; bibliographic components of taxonomic =
circumscriptions.&nbsp;&nbsp; Between the
 &gt; two sources we have over 800,000 citations =
references as a starting
 &gt; point.&nbsp; I know this issue is also of =
interest with our library
 &gt; colleagues at the Smithsonian.
 &gt;
 &gt; We have a similar issue with author names =
annotating taxon names and
 &gt; have an web service in place for resolving =
them.&nbsp; At the moment this
 &gt; is populated primarily with botanical authors =
but as we post-process
 &gt; Sherborne and Neave we will likely be adding =
many thousands of
 &gt; zoological authors.
 &gt;
 &gt; <A HREF=3D"http://uio.mbl.edu/authors/info.php" =
TARGET=3D"_blank">http://uio.mbl.edu/authors/info.php</A>
 &gt;
 &gt; Regards,
 &gt; David Remsen
 &gt;
 &gt; On Feb 27, 2006, at 6:23 AM, Robert Huber =
wrote:
 &gt;
 &gt; &gt; Dear all,
 &gt; &gt;
 &gt; &gt; To my earlier email on PublicationBank I =
got no resonse, so I
 &gt; &gt; assume no
 &gt; &gt; earlier
 &gt; &gt; attempts or discussion on this topic have =
been started yet?
 &gt; &gt;
 &gt; &gt; A pragmatic starting point for =
PublicationBank (PB)would be to use the
 &gt; &gt; literature
 &gt; &gt; entries of the existing LSID authorities =
databases to initially
 &gt; &gt; populate PB
 &gt; &gt; with
 &gt; &gt; GUIDs.
 &gt; &gt; To get the appropriate GUIDs we ideally =
would have access to
 &gt; &gt; services from
 &gt; &gt; the publishers, databases such as PubMed =
or the DOI foundation
 &gt; &gt; (crossref).
 &gt; &gt;
 &gt; &gt; I called these services Bibliographic =
Query Resolver and just
 &gt; &gt; started to
 &gt; &gt; search
 &gt; &gt; the web for potential candidates. Results =
are here:
 &gt; &gt;
 &gt; &gt; <A =
HREF=3D"http://wiki.gbif.org/guidwiki/wikka.php" =
TARGET=3D"_blank">http://wiki.gbif.org/guidwiki/wikka.php</A>?
 &gt; &gt; wakka=3DBibliographicQueryResolver
 &gt; &gt;
 &gt; &gt;
 &gt; &gt; Bibliographic Query Resolver
 &gt; &gt; Accepts bibliographic meta-data and =
returns the corresponding GUID
 &gt; &gt; (e.g.
 &gt; &gt; DOI, LSID)
 &gt; &gt;
 &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp; * CrossRef offers =
a variety of possibilities to resolve DOIs. More
 &gt; &gt; information can be found at CrossRefs =
query spec pages. The DOI link
 &gt; &gt; directly redirects to the online document =
(subscription dependent) or
 &gt; &gt; abstract.
 &gt; &gt;&nbsp;&nbsp;&nbsp;&nbsp; * PudMed offers a =
'Batch Citation Matcher' to retrieve a PMID
 &gt; &gt; which can
 &gt; &gt; be completed as LSID?
 &gt; &gt;
 &gt; &gt;
 &gt; &gt;
 &gt; &gt;
 &gt; &gt; best regards,
 &gt; &gt; Robert
 &gt; &gt;
 &gt; &gt; Dr. Robert Huber
 &gt; &gt; WDC-MARE / PANGAEA - www.pangaea.de, =
www.wdc-mare.org
 &gt; &gt; Stratigraphy.net - =
www.stratigraphy.net
 &gt; &gt; =
_____________________________________________
 &gt; &gt; MARUM - Institute for Marine Environmental =
Sciences (location)
 &gt; &gt; University Bremen
 &gt; &gt; Leobener Strasse
 &gt; &gt; POP 330 440
 &gt; &gt; 28359 Bremen
 &gt; &gt; Phone ++49 421 218-65593, Fax ++49 421 =
218-65505
 &gt; &gt; e-mail rhuber@@wdc-mare.org, =
robert.huber at stratigraphy.net
 &gt;
 &gt;

<P><FONT SIZE=3D2>*** Sally Hinchcliffe</FONT>
<BR><FONT SIZE=3D2>*** Computer section, Royal Botanic Gardens, =
Kew</FONT>
<BR><FONT SIZE=3D2>*** tel: +44 (0)20 8332 5708</FONT>
<BR><FONT SIZE=3D2>*** S.Hinchcliffe at rbgkew.org.uk</FONT>
</P>

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