[Taxacom] Finding your species in Mendeley

Paul Kirk p.kirk at cabi.org
Tue Dec 6 03:45:54 CST 2011


:-)

The pages linked in IF DO have the (validating) description for new taxa ...

Yes, all the other stuff would be great, but if mycologists cannot do the taxonomy (i.e. decribe the missing species) because they lack the relevant literature where are we with all the fancy stuff you (and I) want.

We are all doing our bit to pull it all together ... e.g. I'm working on 31,000+ article level references to all the pre 20th century mycological (systematics) literature but they don't have DOIs or PubMed ID's - the BHL CiteBank is the place this is heading, not Mendeley.

In haste, you know why ... :-)

Paul

From: Roderic Page [mailto:r.page at bio.gla.ac.uk]
Sent: 06 December 2011 09:38
To: taxacom
Cc: Paul Kirk
Subject: Re: [Taxacom] Finding your species in Mendeley

Dear Paul,

On 6 Dec 2011, at 09:11, Paul Kirk wrote:


Building lists of names and linking them to the literature is the function of nomenclators ... sounds like wheel re-inventing to me :-)

If nomenclators could tell me what I want then I wouldn't be doing this. I want name + bibliographic identifier, not name plus some cryptic citation where the same journal may be written 10 different ways and the citation contains cryptic clues about different dates, or separate articles are joined together because they had the same title, etc.



'We' (mycology and botany) are well served by IF and IPNI but the zoologists ... some work is needed in the domain

Yes, plants & fungi are perhaps better served, but IPNI doesn't link to literature, just "microcitations". IF has lots of names linked to a scanned image of the page that has the name, which is great, but it's not just about people being able to read the description.

I want to get the underlying  text, I want to extract names, localities, ecological interations (e.g., phrases like "x n. sp. a parasite of y"). Furthermore I want to discover related facts. If I have a bibliographic identifier such as a DOI or PubMed id I can retrieve DNA sequences, citations, etc. And the reverse becomes true. A database of phylogenies, say, may include papers that publish new names. We can link this information together, so we can tell the user "here is name x, and there is a phylogeny for the taxon with that name here".

For me it is all about the links -- but I think you knew that ;)

Regards

Rod


In haste, building lists of names and linking them to the literature ... it's what I do - some of the time :-)

Paul

-----Original Message-----
From: taxacom-bounces at mailman.nhm.ku.edu<mailto:taxacom-bounces at mailman.nhm.ku.edu> [mailto:taxacom-bounces at mailman.nhm.ku.edu] On Behalf Of Roderic Page
Sent: 06 December 2011 08:55
To: taxacom
Subject: Re: [Taxacom] Finding your species in Mendeley

Dear Geoff,

On 5 Dec 2011, at 23:40, Geoff Read wrote:


Rod mentioned WoRMS earlier. Just to point out that in WoRMS,
www.marinespecies.org<http://www.marinespecies.org>, one can already get the list of marine species
authored by anyone by a taxon search using the Authority option. For
example 'd'Orbigny' yields links to 412 marine species names
(d'Orbigny is unlikely to be setting up a Mendeley account any time
soon, so this is handy). Name disambiguation is possible at least by
taxon group, and by date of publication (eg., easy to find that
d'Orbigny published at least
179 species in the 1830s, from which a further 106 recombinations exist).

Yes, using Mendeley requires that the author be alive and online! My goal here is to explore various ways of engaging people with what is in many ways a tedious task, building lists of names and linking them to the primary literature. One reason I like Mendeley is that it is technically easy to make it possible for people to discover "their" content in one database simply because they've created an account on Mendeley and added their own publications. In other words, they've done something for one reason and can get added value for minimal effort.



WoRMS has a way to go with achieving literature mapping and the
important facility to quickly open the original publication, supplying
the link for which for new entries may be viewed as optional by some
editors (not me), but it has a good literature list with mostly full
rather than micro citations. There may already be an automatic link to
the BHL mentions of the older species.

My sense is that most of the literature in WoRMS is "secondary", in the sense that it comprises checklists, etc., which are used as sources for names, and an authority for usage of the name. I'm taking with Ward Appeltans about adding links to the primary literature from http://iphylo.org/~rpage/itaxon .

Regards

Rod





Geoff

On Tue, December 6, 2011 5:28 am, Roderic Page wrote:
Following on from my earlier message about Mendeley (and thanks to
those who responded) here's a blog post explaining why I asked the
question, and how you can use your Mendeley account to find species
you've described in my taxonomic name -> literature mapping project:

http://iphylo.blogspot.com/2011/12/these-are-my-species-finding-taxon
omic.html



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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<mailto:r.page at bio.gla.ac.uk>
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Fax: +44 141 330 2792
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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<mailto:r.page at bio.gla.ac.uk>
Tel: +44 141 330 4778
Fax: +44 141 330 2792
AIM: rodpage1962 at aim.com<mailto: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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