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Thanks for all of the responses to my original question. They have
given me much food for thought. I will throw out several comments that
have come to mind as a result.<br>
<br>
1. With regards to what Dean and Tony have said about the kind of
"linkage" that taxonomists want: <br>
<blockquote
cite="mid:C2994967ABB5D54BB013821E4ABA60E10355D9F729@exvic-mbx03.nexus.csiro.au"
type="cite">
<pre wrap="">
My hypothesis is that taxonomists (and taxonomy) "want" linkage like this:
taxon name ==> correct authority information ==> correct
bibliographic metadata ==> actual original publication (full-text)
</pre>
</blockquote>
Although a linkage to a full text version of the publication would be
nice, it's not really what I wanted/needed when I posed the original
question. As a non-taxonomist, I've absorbed the point which has been
made repeatedly that in an Identification which simply provides a taxon
name is inadequate and that we should be specifying a taxon name usage
(i.e. name sensu publication, or name sec. publication). So I'm more
interested in a globally unique and reusable identifiers for names,
publications, and their intersections as TNUs. As such, I don't care
that much whether there is a linkage to a pdf of the publication as
long as I can refer to the TNU by a GUID and somebody else knows
exactly what taxon usage I'm talking about. I don't have a high degree
of confidence in using text strings like "Andropogon virginicus L. sec.
Radford et al. (1968)" as identifiers for TNUs because all it takes is
one missing period, no parentheses, or an extra space and then I have a
different string from somebody else. If the GUID is going to be a URI,
then I'd really like it to be dereferenceable to RDF. In the event
that the Linked Data world comes together, that gets me out of the
business of thrashing with all of the taxonomy stuff that I'm not
interested in doing myself. I believe that this is exactly one of the
points that Pete was trying to make. <br>
<br>
>From this standpoint, what Paul illustrated in his example of
<a class="moz-txt-link-freetext" href="http://biodiversity.org.au/apni.taxon/118883">http://biodiversity.org.au/apni.taxon/118883</a> is exactly what I had in
mind: a URI for the taxon/TNU/concept with RDF links to the URI for the
name and the URI for the publication. The "fundamental problem"
(recognized by Pete with his asterisk) is that most of these URIs don't
yet exist and it would be counterproductive for a bunch of different
people to start "minting" them on their own. I certainly don't have
the interest or ability to do it and I doubt that Paul has time to
create them all for the rest of us on the planet at biodiversity.org.au
. This should be large scale/community effort. I was disappointed to
see that although <a class="moz-txt-link-freetext" href="http://citebank.org">http://citebank.org</a> seems to be positioning itself as
such a large-scale effort, I can't see any evidence that it is planning
to create "Linked Data-ready" URIs that are subject to content
negotiation (or did I just miss it?). I think that is probably a
mistake. Making a GUID that could be used in the LOD world doesn't
force anybody to subscribe to the LOD model, but making a GUID that is
not suitable for LOD will cause those who are interested in Linked Data
to look elsewhere.<br>
<br>
2. On the subject of DOIs, I discovered what Paul mentioned in his
post: there doesn't seem to be any easy way to search for a DOI or to
know if a DOI exists for a publication. Another problem is who would
pay for the DOIs that would need to be created for all of the obscure,
out of print publications that would need to be put into the system? (I
believe that there is some per-item cost for DOIs, right?) Generic
HTTP URIs seem like an easier solution. <br>
<br>
3. Another issue which I think should be mentioned in the context of
this discussion is that I don't think that it is a good idea to blur
the distinction between a URL pointing to an information resource (such
as a pdf or jpg file) and a URI that is serving as a GUID. If an
information resource URL were considered a GUID, then I believe that it
would be bad practice to ever change even a single byte of the
particular file to which that URL is pointing. It would also be
difficult to achieve content negotiation (i.e. to provide either a
human-readable representation or a machine-readable RDF file when
requested) if a specific file format is specified in the URL. So even
if there were a PDF available for a publication online, the URL of that
PDF shouldn't be used as a GUID. It would be better to represent the
publication as a non-information resource and use a seeAlso link to the
pdf representation. I think what I've said here has bearing on Dean's
message (directly below). In particular I think that the statement<br>
<pre wrap="">"a GUID for the curated, corrected bibliographic metadata as something distinct from a GUID for the actual publication."
</pre>
makes an artificial distinction between a publication and its
metadata. I think the correct approach is to consider that the GUID
represents the publication as a conceptual entity (i.e. non-information
resource) which has properties that can be described by the
bibilographic metadata, and which can have a representation as a pdf,
jpg image, etc. With that approach, the GUID can be an unchanging
identifier for the publication while the metadata and representations
associated with it can be free to be corrected, updated, or improved. <br>
<br>
Steve<br>
<blockquote
cite="mid:C2994967ABB5D54BB013821E4ABA60E10355D9F729@exvic-mbx03.nexus.csiro.au"
type="cite">
<pre wrap="">
________________________________________
From: <a class="moz-txt-link-abbreviated" href="mailto:tdwg-content-bounces@lists.tdwg.org">tdwg-content-bounces@lists.tdwg.org</a> [<a class="moz-txt-link-abbreviated" href="mailto:tdwg-content-bounces@lists.tdwg.org">tdwg-content-bounces@lists.tdwg.org</a>] On Behalf Of Dean Pentcheff [<a class="moz-txt-link-abbreviated" href="mailto:pentcheff@gmail.com">pentcheff@gmail.com</a>]
Sent: Wednesday, 5 January 2011 10:02 AM
To: <a class="moz-txt-link-abbreviated" href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a>
Cc: Chris Freeland
Subject: Re: [tdwg-content] GUIDs for publications (usages and names)
A wrinkle on this is that the authority information (name and year)
are not the same thing as the actual original publication. Nor is the
bibliographic metadata for a publication the same thing as the
publication.
My hypothesis is that taxonomists (and taxonomy) "want" linkage like this:
taxon name ==> correct authority information ==> correct
bibliographic metadata ==> actual original publication (full-text)
In the general case, you can't determine the authority date by
inspection of the actual original publication. You often need external
information regarding publication mechanics. (Yes, I know that the
date printed on the publication is the correct date of publication for
most papers, but anyone who's dealt with taxonomic literature knows
that there are many, many exceptions to that.)
I'm not sure that they actually want:
taxon name ==> actual original publication (full-text)
Which is why I start thinking about a GUID for the curated, corrected
bibliographic metadata as something distinct from a GUID for the
actual publication.
-Dean
--
Dean Pentcheff
<a class="moz-txt-link-abbreviated" href="mailto:pentcheff@gmail.com">pentcheff@gmail.com</a>
<a class="moz-txt-link-abbreviated" href="mailto:dpentche@nhm.org">dpentche@nhm.org</a>
On Tue, Jan 4, 2011 at 1:01 PM, Peter DeVries <a class="moz-txt-link-rfc2396E" href="mailto:pete.devries@gmail.com"><pete.devries@gmail.com></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Hi Chris,
You are missing one of the main benefits of Linked Data.
Users do not want to curate their own bibliographic databases and related
RDF, they want to simply link to a globally unique, resolvable identifier
for that citation.
For example: Felis concolor Linnaeus 1771
Linnaeus 1771 <= What specific publication is this?
"Felis concolor" hasOriginalDescription
<a class="moz-txt-link-rfc2396E" href="http://www.biodiversitylibrary.org/citation/234123412"><http://www.biodiversitylibrary.org/citation/234123412></a>
If the BHL exposed semantic web URI's for each publication, then content
experts could search the BHL, find it, and then link to it with a simple
resolvable URI.
The alternative is that Steve, et al., will create their own identifiers for
specific publications, code their own local bibliographic databases.
In essence, each group or individual then continues to duplicate the efforts
of others.
Right now, I have duplicated your functionality in my species concepts.
Ideally, I would have done this:
<SpeciesConcept> hasOriginalDescription
<a class="moz-txt-link-rfc2396E" href="http://www.biodiversitylibrary.org/citation/234123412"><http://www.biodiversitylibrary.org/citation/234123412></a>
<SpeciesConcept>
hasRevisionalDescription <a class="moz-txt-link-rfc2396E" href="http://www.biodiversitylibrary.org/citation/234124356"><http://www.biodiversitylibrary.org/citation/234124356></a>
Not only are my concepts then linked to your citations, any other data sets
that link to your citations are findable.
For instance, who else has data sets that link to this citation?
To see how this works on the live LOD cloud check out. <a class="moz-txt-link-freetext" href="http://bit.ly/fChHwJ">http://bit.ly/fChHwJ</a>
Browse through the related Linked Data Sets - in particular the has close
match links.
- Pete
On Tue, Jan 4, 2011 at 2:31 PM, Chris Freeland <a class="moz-txt-link-rfc2396E" href="mailto:Chris.Freeland@mobot.org"><Chris.Freeland@mobot.org></a>
wrote:
</pre>
<blockquote type="cite">
<pre wrap="">Ooops, to clarify my very last example, we actually would support "Pallas
1767" if properly parsed:
<a class="moz-txt-link-freetext" href="http://www.biodiversitylibrary.org/openurl?aulast=Pallas&date=1767&format=xml">http://www.biodiversitylibrary.org/openurl?aulast=Pallas&date=1767&format=xml</a>
What we don't yet support & need to is linking at article citation level.
That's where our newly (quietly) launched CiteBank <a class="moz-txt-link-freetext" href="http://citebank.org">http://citebank.org</a> comes
in, and what we're hoping to receive funding to expand.
Chris
________________________________
From: <a class="moz-txt-link-abbreviated" href="mailto:tdwg-content-bounces@lists.tdwg.org">tdwg-content-bounces@lists.tdwg.org</a>
[<a class="moz-txt-link-freetext" href="mailto:tdwg-content-bounces@lists.tdwg.org">mailto:tdwg-content-bounces@lists.tdwg.org</a>] On Behalf Of Chris Freeland
Sent: Tuesday, January 04, 2011 1:57 PM
To: Peter DeVries; Steve Baskauf
Cc: <a class="moz-txt-link-abbreviated" href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a>
Subject: Re: [tdwg-content] GUIDs for publications (usages and names)
Steve, Pete, et al.,
BHL has an OpenURL resolver that can accept a variety of input criteria &
return matching records with responses in JSON (with or without callback),
XML, HTML, or a direct link. Documentation is here:
<a class="moz-txt-link-freetext" href="http://www.biodiversitylibrary.org/openurlhelp.aspx">http://www.biodiversitylibrary.org/openurlhelp.aspx</a>
And linked from our broader documentation here:
<a class="moz-txt-link-freetext" href="http://biodivlib.wikispaces.com/Developer+Tools+and+API">http://biodivlib.wikispaces.com/Developer+Tools+and+API</a>
Here's an example, referenced in the documentation, for querying on a
monograph/book:
<a class="moz-txt-link-freetext" href="http://www.biodiversitylibrary.org/openurl?genre=book&title=Manual+of+North+American+Diptera&aufirst=Samuel+Wendell&aulast=Williston&publisher=New+Haven+:J.T.+Hathaway,&date=1908&spage=16&format=xml">http://www.biodiversitylibrary.org/openurl?genre=book&title=Manual+of+North+American+Diptera&aufirst=Samuel+Wendell&aulast=Williston&publisher=New+Haven+:J.T.+Hathaway,&date=1908&spage=16&format=xml</a>
You can also query based on common abbreviations, like Sp. Pl.:
<a class="moz-txt-link-freetext" href="http://www.biodiversitylibrary.org/openurl?stitle=Sp.%20Pl.&date=1753&format=xml">http://www.biodiversitylibrary.org/openurl?stitle=Sp.%20Pl.&date=1753&format=xml</a>
MOBOT's Tropicos uses the OpenURL resolver to link to protologues, as in
this example:
<a class="moz-txt-link-freetext" href="http://www.tropicos.org/Name/2735114">http://www.tropicos.org/Name/2735114</a>
With Tropicos we have an authority record for each journal or monographic
title. We match Tropicos' TitleID to BHL's TitleID & use that as a more
direct link to the appropriate reference, but still send collation & other
info to get to the appropriate page, as in this link:
<a class="moz-txt-link-freetext" href="http://www.biodiversitylibrary.org/openurl?pid=title:626&volume=5&issue=&spage=244&date=1830">http://www.biodiversitylibrary.org/openurl?pid=title:626&volume=5&issue=&spage=244&date=1830</a>
I know that this is insufficient for zoology & other natural sciences
beyond botany, where we need to be able to support citations like "Pallas
1767", which may or may not be preparsed into appropriate fields. A known
problem, for sure, and one that we're eager to address, pending funding from
NSF.
Chris
Chris Freeland | Director, Center for Biodiversity Informatics | Missouri
Botanical Garden
4344 Shaw Blvd. | St. Louis, Missouri 63110 | 314.577.9548
________________________________
From: <a class="moz-txt-link-abbreviated" href="mailto:tdwg-content-bounces@lists.tdwg.org">tdwg-content-bounces@lists.tdwg.org</a>
[<a class="moz-txt-link-freetext" href="mailto:tdwg-content-bounces@lists.tdwg.org">mailto:tdwg-content-bounces@lists.tdwg.org</a>] On Behalf Of Peter DeVries
Sent: Tuesday, January 04, 2011 1:33 PM
To: Steve Baskauf
Cc: <a class="moz-txt-link-abbreviated" href="mailto:tdwg-content@lists.tdwg.org">tdwg-content@lists.tdwg.org</a>
Subject: Re: [tdwg-content] GUIDs for publications (usages and names)
Hi Steve,
I have been lobbying the BHL for this for some time. Most recently in this
blog post.
<a class="moz-txt-link-freetext" href="http://www.taxonconcept.org/taxonconcept-blog/2010/8/5/why-linked-open-data-makes-sense-for-biodiversity-informatic.html">http://www.taxonconcept.org/taxonconcept-blog/2010/8/5/why-linked-open-data-makes-sense-for-biodiversity-informatic.html</a>
What I have realized is that, for many works that are out of copyright,
Google books has already scanned and converted them to PDF.
You can use these, even extract the relevant PDF pages as long as you keep
the Google watermark.
This is what I have done for the Cougar.
<a class="moz-txt-link-freetext" href="http://lod.taxonconcept.org/ses/v6n7p.html">http://lod.taxonconcept.org/ses/v6n7p.html</a>
For more recent works you may be able to link to the article PDF. As in
this spider example.
<a class="moz-txt-link-freetext" href="http://lod.taxonconcept.org/ses/2mqjL.html">http://lod.taxonconcept.org/ses/2mqjL.html</a>
We also need a URI for to uniquely identify authors and in the absence of
a better solution, I have been using, and in some cases creating, entries in
Wikipedia which currently has over 5,000 taxonomic author profiles.
This results in usable RDF via DBpedia. As you can see in the RDF in this
example.
<a class="moz-txt-link-freetext" href="http://lod.taxonconcept.org/ses/v6n7p.rdf">http://lod.taxonconcept.org/ses/v6n7p.rdf</a>
And in the Knowledge Base
<<a class="moz-txt-link-freetext" href="http://lsd.taxonconcept.org/describe/?url=http%3A%2F%2Flod.taxonconcept.org%2Fses%2Fv6n7p%23OriginalDescription">http://lsd.taxonconcept.org/describe/?url=http%3A%2F%2Flod.taxonconcept.org%2Fses%2Fv6n7p%23OriginalDescription</a>
</pre>
<pre wrap="">That said, I have also been experimenting with this.
<a class="moz-txt-link-freetext" href="http://lod.taxonconcept.org/people/sci_people_1700.rdf">http://lod.taxonconcept.org/people/sci_people_1700.rdf</a>
About: Carl Linnaeus <a class="moz-txt-link-freetext" href="http://bit.ly/gLgElf">http://bit.ly/gLgElf</a>
- Pete
On Mon, Jan 3, 2011 at 7:47 PM, Steve Baskauf
<a class="moz-txt-link-rfc2396E" href="mailto:steve.baskauf@vanderbilt.edu"><steve.baskauf@vanderbilt.edu></a> wrote:
</pre>
<blockquote type="cite">
<pre wrap="">I was reviewing some of the previous posts on taxon name usages in an
attempt to understand them better. I have learned that the Global Names
Index is an attempt to catalog taxon names and that it is possible to
generate a URI that points to a name there. Is there a parallel effort
to do the same thing for literature references? In other words, if I
want to describe the TNU:
Andropogon virginicus L. sec. Radford et al. (1968)
I think I could find a URI GUID for the name Andropogon virginicus .
But is there some place where I could find a unique identifier, or
better a URL, or best a URI providing RDF/XML for Linnaeus 1753 (the
author and publication for the name) and for Radford et al.1968 (the
author and publication that expresses the usage I'm intending).
I suppose that this question has previously been answered in the in the
many posts on taxon names, concepts, etc. However, since usually my
brain goes numb and my eyes glaze over in those threads, I probably
missed it.
Steve
--
Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences
postal mail address:
VU Station B 351634
Nashville, TN 37235-1634, U.S.A.
delivery address:
2125 Stevenson Center
1161 21st Ave., S.
Nashville, TN 37235
office: 2128 Stevenson Center
phone: (615) 343-4582, fax: (615) 343-6707
<a class="moz-txt-link-freetext" href="http://bioimages.vanderbilt.edu">http://bioimages.vanderbilt.edu</a>
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</pre>
</blockquote>
<pre wrap="">
--
---------------------------------------------------------------
Pete DeVries
Department of Entomology
University of Wisconsin - Madison
445 Russell Laboratories
1630 Linden Drive
Madison, WI 53706
TaxonConcept Knowledge Base / GeoSpecies Knowledge Base
About the GeoSpecies Knowledge Base
------------------------------------------------------------
</pre>
</blockquote>
<pre wrap="">
--
---------------------------------------------------------------
Pete DeVries
Department of Entomology
University of Wisconsin - Madison
445 Russell Laboratories
1630 Linden Drive
Madison, WI 53706
TaxonConcept Knowledge Base / GeoSpecies Knowledge Base
About the GeoSpecies Knowledge Base
------------------------------------------------------------
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</pre>
</blockquote>
<pre wrap=""><!---->_______________________________________________
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.
</pre>
</blockquote>
<br>
<pre class="moz-signature" cols="72">--
Steven J. Baskauf, Ph.D., Senior Lecturer
Vanderbilt University Dept. of Biological Sciences
postal mail address:
VU Station B 351634
Nashville, TN 37235-1634, U.S.A.
delivery address:
2125 Stevenson Center
1161 21st Ave., S.
Nashville, TN 37235
office: 2128 Stevenson Center
phone: (615) 343-4582, fax: (615) 343-6707
<a class="moz-txt-link-freetext" href="http://bioimages.vanderbilt.edu">http://bioimages.vanderbilt.edu</a>
</pre>
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