[Taxacom] How to trace publications based on collections in specific herbaria and/or museums?

Wed Jan 18 12:02:25 CST 2012

The leadership's policy is similar to one we had at a NIH Microscopy lab -
that is that scientists using the facility were supposed to cite the
facility in published papers.
This was so that the NIH could justify the expense of funding a shared
facility.
Unfortunately, there was no system to ensure that this was done, and
although many did cite the facility others did not.

I think that without some outside pressure there is little reason for
facilities to give their specimens unique IDs, and several reasons not to:
    There are the risks of getting it wrong and looking bad
    There are the questions about how this will be paid for and maintained
overtime
    There are the problems of a unclear vision on how this should be done,
with some concern that filling in all the "required" metadata would be
expensive.

However, I was thinking that there might be some easy way to get moving in
this direction without having to change much.
That would be to have information on each specimen in a collection
accessible via a clean URL. (a specimen page)

Wikipedia is down today (http://en.wikipedia.org/wiki/Clean_URL)

In general, a clean URL is stable, and does not incorporate elements
specific to a particular database or framework.

This would give the "specimen page" a URI, which is useful, but different
from a true URI for the specimen itself.

For example here are example of clean URLs:
<http://lod.taxonconcept.org/ses/v6n7p.html>
<http://eol.org/pages/311910/overview>

* < http://data.gbif.org/species/2435099/> (but not stable)

* This are clean, in a sense, but the taxon page is not tied to a specific
integer like 2435099, so they are not useful stable identifiers for a
particular taxon page.

For example, it seems that most of my links to GBIF are now broken.

The URL below is not "clean"  because it incorporates characters than need
to be escaped or they would change if the data was moved to a different
database and web framework:

<
http://mcz-28168.oeb.harvard.edu/mcz/FMPro?-DB=Image.fm&-Lay=web&-Format=images.htm&Species_ID=4871&-Find
>

* I like this site a lot as a model for e-type pages but think it would be
better with cleaner URL's

That would mean that the vocabulary and semantic markup could be decided
later, but at least someone could refer to a specimen via it's specimen
page URL.

Later there might need to be a mapping of IDs for the actual specimen
(since the same specimen might be present in different collections and have
multiple pages)

The result would be a unique page URL for each specimen in a collection,
without having to move to a completely, and somewhat intimidating, fully
semantic representation.

>From this relatively easy step we could work toward something even better.

Respectfully,

- Pete

On Wed, Jan 18, 2012 at 8:36 AM, Roderic Page <r.page at bio.gla.ac.uk> wrote:

> This is one of the "use cases" I had in mind when discussing the potential
> uses for digital identifiers for specimens (see blog post
> http://iphylo.blogspot.com/2012/01/yet-another-reason-why-we-need-specimen.html)
>
> The request to find all papers citing museum material is, in principle,
> reasonable, but the museum has failed to provide the tools to make this
> happen. I'd be tempted to respond to the museum administrators with an
> explanation of why answering their query efficiently would require the
> museum to have digital identifiers for their specimens (in the same way we
> have identifiers for articles).
>
> At the same time, I'd be tempted to make the short trip to GBIF ask why
> they've been so tardy in addressing this issue.
>
> I'm aware that this doesn't help you in the short term. Various ways to
> tackle the problem might be:
>
> 1. Search Google Scholar for the museum name in the year 2011 (if the
> authors use the abbreviation they are likely to explain what it means.
>
> 2. Retrieve a list of all animal and plant names published in 2011, get
> the associated publications and search for the museum's name (much of this
> could be automated once the PDFs are downloaded)
>
> 3. Search GenBank using museum specimen abbreviation codes to find
> sequences (and associated publications) obtained from material from the
> museum.
>
> Regards
>
> Rod
>
>
> On 18 Jan 2012, at 10:32, Ib Friis wrote:
>
> > Dear Taxacom-readers,
> >
> > It is getting more and more necessary for taxonomists to demonstrate
> > that they are useful and used. This does not only apply to the
> > individual scientists, but also to institutions with taxonomic
> > collections, such as museums and herbaria.
> >
> > In an attempt to live up to that increasing demand for documentation,
> > the leadership of the Natural History Museum of Denmark has issued an
> > order to its curatorial staff - The staff members are requested to
> > document which publications from 2011, written entirely by external
> > scientists, that in one way or another are based on material in the
> > collections of the Museum. It is added that "this may be difficult, but
> > very important for the documentation of the use of the collections. Try
> > to get all the scientists that borrow material to inform you about their
> > publications and supplement this information with your own search within
> > reasonable limits."
> >
> > To find publications that are based on collections in the Natural
> > History Museum of Denmark is indeed a difficult task. As curator of the
> > herbarium of vascular plants at the Museum, I know that my particular
> > section of the Museum has 950 outstanding loans to scientists all over
> > the world, including institutions in the developing countries. The loans
> > of herbarium specimens are normally made to institutions, not directly
> > to individual scientists, so even if I wrote to all 950 and asked them
> > if they have published anything on our collections in 2011, I am not
> > sure that the message would reach all.
> >
> > A more practicable solution might be to use digital search for
> > electronic publications that quote the herbarium acronym. However, for
> > the herbaria of the Natural History Museum of Denmark, which is situated
> > in Copenhagen, this acronym is "C". We have normally been rather proud
> > to be an old institution that has a single character as its acronym, but
> > in this case it is rather unfortunate, like it must be for other well
> > known herbaria with acronyms like "A", "B", "E", "F", "G", "H", "J",
> > "K", "L", "M", "N", "O", "P", "Q", "R", "S", "U", "V", "Y" and "Z".
> >
> > In publications, material from our herbarium at "C" is normally referred
> > to in text strings of one of the following forms: "(C)", "(C, ", ", C,"
> > or " C)". But a search in for example Google Scholar or other search
> > engines  result in overflow of thousands and thousands of hits, even
> > when these text strings are combined with other relevant words such as
> > "botany", "plants", etc. - It can be added that this is a specific
> > problem for the botanists - the curators of the zoological and
> > geological collections are lucky that their collections have acronyms
> > with a characteristic sting of four letters.
> >
> > Has any of the Taxacom-readers good ideas about how it might be possible
> > to specifically document answers to the (unfortunately relevant)
> > question about the use of the botanical collections of the Copenhagen
> > Natural History Museum - and of other herbaria with similarly
> > insignificant acronyms?
> >
> > Hoping for a good idea and with best wishes,
> >
> > Ib Friis
> > Professor, dr. scient., curator of vascular plants
> > Natural History Museum of Denmark, Copenhagen
> > ibf at snm.ku.dk
> >
> >
> > _______________________________________________
> >
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> >
> > The Taxacom archive going back to 1992 may be searched with either of
> these methods:
> >
> > (1) by visiting http://taxacom.markmail.org
> >
> > (2) a Google search specified as:  site:
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> >
>
> ---------------------------------------------------------
> Roderic Page
> Professor of Taxonomy
> Institute of Biodiversity, Animal Health and Comparative Medicine
> College of Medical, Veterinary and Life Sciences
> Graham Kerr Building
> University of Glasgow
> Glasgow G12 8QQ, UK
>
> Email: r.page at bio.gla.ac.uk
> Tel: +44 141 330 4778
> Fax: +44 141 330 2792
> AIM: rodpage1962 at aim.com
> Facebook: http://www.facebook.com/profile.php?id=1112517192
> Twitter: http://twitter.com/rdmpage
> Blog: http://iphylo.blogspot.com
> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
>
> _______________________________________________
>
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>
> The Taxacom archive going back to 1992 may be searched with either of
> these methods:
>
> (1) by visiting http://taxacom.markmail.org
>
> (2) a Google search specified as:  site:
> mailman.nhm.ku.edu/pipermail/taxacom  your search terms here
>

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Pete DeVries
Department of Entomology
University of Wisconsin - Madison
445 Russell Laboratories
1630 Linden Drive
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Email: pdevries at wisc.edu
TaxonConcept <http://www.taxonconcept.org/>  &
GeoSpecies<http://about.geospecies.org/> Knowledge
Bases
A Semantic Web, Linked Open Data <http://linkeddata.org/>  Project
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