[tdwg-content] GUIDs for publications (usages and names)

Wed Jan 5 00:55:31 CET 2011

Hi all,

Basically I agree with Dean when he writes:

<snip>
My hypothesis is that taxonomists (and taxonomy) "want" linkage like this:
    taxon name ==> correct authority information ==> correct
bibliographic metadata ==> actual original publication (full-text)
</snip>

However there is probably an intermediate step, too, namely "Brief citation (Nomenclator Style)" or similar, e.g. for the first entry in my IRMNG genera list:

Genus: Aa
Authority: Baker, 1940
Brief citation (from Nomenclator Zoologicus): Bull. Bishop Mus., 165, 107, 108. 
Original Publication: Baker, H. B. (1940). Zonitid snails from Pacific Islands. Part 2. Hawaiian
  genera of Microcystinae. Bull. Bishop Mus., 165: 103-291.
Online link (as available): xxxxx

(The full publication details would ideally be atomised further as required i.e. author, stated publication year, article title, journal titles, etc.)

For a large number of names this type of brief citation is all that is readily available in present bulk data compilations (typically nomenclators for animal and plant names), but ideally can be expanded to a full citation retrospectively and as time / resources are available.

I have not looked at CiteBank as yet but recall hearing that it would accommodate both types. Of course the article details would most likely be more re-useable for many purposes than the brief citation (including individual page ref/s) as the latter will typically apply only to a single name initial publication instance whereas the whole work will contain a lot more and better fit the "enter once, use many times" rationale of giving things identifiers suitable for re-use.

Regards - Tony
________________________________________
From: tdwg-content-bounces at lists.tdwg.org [tdwg-content-bounces at lists.tdwg.org] On Behalf Of Dean Pentcheff [pentcheff at gmail.com]
Sent: Wednesday, 5 January 2011 10:02 AM
To: tdwg-content at lists.tdwg.org
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
pentcheff at gmail.com
dpentche at nhm.org

On Tue, Jan 4, 2011 at 1:01 PM, Peter DeVries <pete.devries at gmail.com> wrote:
> 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
> <http://www.biodiversitylibrary.org/citation/234123412>
> 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
>   <http://www.biodiversitylibrary.org/citation/234123412>
> <SpeciesConcept>
> hasRevisionalDescription <http://www.biodiversitylibrary.org/citation/234124356>
> 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. http://bit.ly/fChHwJ
> 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 <Chris.Freeland at mobot.org>
> wrote:
>>
>> Ooops, to clarify my very last example, we actually would support "Pallas
>> 1767" if properly parsed:
>>
>>
>> http://www.biodiversitylibrary.org/openurl?aulast=Pallas&date=1767&format=xml
>>
>> What we don't yet support & need to is linking at article citation level.
>> That's where our newly (quietly) launched CiteBank http://citebank.org comes
>> in, and what we're hoping to receive funding to expand.
>>
>> Chris
>> ________________________________
>> From: tdwg-content-bounces at lists.tdwg.org
>> [mailto:tdwg-content-bounces at lists.tdwg.org] On Behalf Of Chris Freeland
>> Sent: Tuesday, January 04, 2011 1:57 PM
>> To: Peter DeVries; Steve Baskauf
>> Cc: tdwg-content at lists.tdwg.org
>> 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:
>> http://www.biodiversitylibrary.org/openurlhelp.aspx
>>
>> And linked from our broader documentation here:
>> http://biodivlib.wikispaces.com/Developer+Tools+and+API
>> Here's an example, referenced in the documentation, for querying on a
>> monograph/book:
>>
>> 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
>>
>> You can also query based on common abbreviations, like Sp. Pl.:
>>
>> http://www.biodiversitylibrary.org/openurl?stitle=Sp.%20Pl.&date=1753&format=xml
>>
>> MOBOT's Tropicos uses the OpenURL resolver to link to protologues, as in
>> this example:
>> http://www.tropicos.org/Name/2735114
>>
>> 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:
>>
>> http://www.biodiversitylibrary.org/openurl?pid=title:626&volume=5&issue=&spage=244&date=1830
>>
>> 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: tdwg-content-bounces at lists.tdwg.org
>> [mailto:tdwg-content-bounces at lists.tdwg.org] On Behalf Of Peter DeVries
>> Sent: Tuesday, January 04, 2011 1:33 PM
>> To: Steve Baskauf
>> Cc: tdwg-content at lists.tdwg.org
>> 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.
>>
>> http://www.taxonconcept.org/taxonconcept-blog/2010/8/5/why-linked-open-data-makes-sense-for-biodiversity-informatic.html
>>
>> 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.
>> http://lod.taxonconcept.org/ses/v6n7p.html
>>
>> For more recent works you may be able to link to the article PDF. As in
>> this spider example.
>> http://lod.taxonconcept.org/ses/2mqjL.html
>>
>> 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.
>> http://lod.taxonconcept.org/ses/v6n7p.rdf
>>
>> And in the Knowledge Base
>>
>> <http://lsd.taxonconcept.org/describe/?url=http%3A%2F%2Flod.taxonconcept.org%2Fses%2Fv6n7p%23OriginalDescription
>> >
>> That said, I have also been experimenting with this.
>> http://lod.taxonconcept.org/people/sci_people_1700.rdf
>>
>> About: Carl Linnaeus http://bit.ly/gLgElf
>> - Pete
>> On Mon, Jan 3, 2011 at 7:47 PM, Steve Baskauf
>> <steve.baskauf at vanderbilt.edu> wrote:
>>>
>>> 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
>>> http://bioimages.vanderbilt.edu
>>>
>>> _______________________________________________
>>> tdwg-content mailing list
>>> tdwg-content at lists.tdwg.org
>>> http://lists.tdwg.org/mailman/listinfo/tdwg-content
>>
>>
>>
>> --
>> ---------------------------------------------------------------
>> 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
>> ------------------------------------------------------------
>
>
>
> --
> ---------------------------------------------------------------
> 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
> ------------------------------------------------------------
>
> _______________________________________________
> tdwg-content mailing list
> tdwg-content at lists.tdwg.org
> http://lists.tdwg.org/mailman/listinfo/tdwg-content
>
>
_______________________________________________
tdwg-content mailing list
tdwg-content at lists.tdwg.org
http://lists.tdwg.org/mailman/listinfo/tdwg-content