[Taxacom] Linking animal names to primary literature

Stephen Thorpe stephen_thorpe at yahoo.co.nz
Fri Dec 2 23:28:45 CST 2011


>As I see it we need three things:

1. a list of names
2. a list of publications
3. a list of links between publications and names

http://iphylo.org/~rpage/itaxon is an example of (3). We are awash in (1). Mendeley is one place we could build (2).<
 
I suggest that what we want is an integrated and continually updated "tree of life", linking to all relevant literature in a modular fashion (i.e., by taxon, by author, by journal, etc.) 
 
Wikispecies is one place where we could build this, and is currently further ahead and more reliable (at least in pages I have edited) than any other place ...
 
Stephen


________________________________
From: Roderic Page <r.page at bio.gla.ac.uk>
To: taxacom <taxacom at mailman.nhm.ku.edu> 
Sent: Saturday, 3 December 2011 6:08 PM
Subject: Re: [Taxacom] Linking animal names to primary literature

Dear Tony,

On 2 Dec 2011, at 22:45, <Tony.Rees at csiro.au> <Tony.Rees at csiro.au> wrote:

> Hi Rod,
> 
> I'm interested to see what you have done and as ever, it is very nicely executed. A couple of comments (well, 3 but I cannot count):
> 
> (1) This needs eventually to mesh somehow with equivalent work elsewhere, as reflected in recent posts - do you see any possibilities of this and if so, how?

I'm looking at two things. In the immediate future I want to provide regularly updated downloads of the mapping so anyone can grab it and make use of it. For example, I've given a copy of the mapping for names in the WoRMS database to Ward Appeltans for him to explore whether the literature links would be useful for that database. And I want to add the mapping I made for the Australian Faunal Directory database so Atlas of Living Australia could grab that if they wished.

Longer term I'd like to house this mapping somewhere more permanent. Without any sense of irony, EOL strikes me as one obvious possibility.


> 
> (2) Also needs to mesh with equivalent coordination activities in the "global names" space, as this is the flip side of this particular coin

I guess I'm not holding my breath regarding "global names". The space is messy and confusing, and lacks a focus driven by tools people actually need. 

> 
> (3) How does this overlap (or not) with your previous posts on the possible benefits of assembling the "bibliography of life" using Mendeley?

As I see it we need three things:

1. a list of names
2. a list of publications
3. a list of links between publications and names

http://iphylo.org/~rpage/itaxon is an example of (3). We are awash in (1). Mendeley is one place we could build (2). 

I've been harvesting 1000's of references from various sources and uploading them to Mendeley, in some several cases whole journal runs have been added. I use these to help map citations to identifiers (for example, I use approximate string matching to compare a citation in a taxonomic database with one in my Mendeley database).

So, I see Mendeley as an obvious place to assemble a list of all taxonomic publications, partly because we can do this without actually thinking about it too much. If people join for the PDF storage, automatic formatting of bibliographies, social networking, iPhone & iPad support they will get benefits, and incidentally contribute papers that may be taxonomic.

I plan to make the links to Mendeley more explicit in future versions of this site. For example, taxonomic databases (such as ION, where the original data comes from) often loose bibliographic details (e.g., full titles, pagination, non-English characters). These can be included in an external bibliographic database like Mendeley, which gives us a way to clean up the original citations.

Regards

Rod


> 
> Cheers,
> 
> Tony Rees - Hobart
> 
>> 
>>> Dear All;,
>>> 
>>> As part of my mantra about linking information together I've started to
>>> build a database linking taxonomic names to primary literature (animals
>>> only at this point). The goal is to (a) discover how easy/difficult this
>>> is, and (b) provide a resource that might be useful.
>>> 
>>> You can view current progress at: http://iphylo.org/~rpage/itaxon/
>>> 
>>> For some background see
>>> http://iphylo.blogspot.com/2011/11/mapping-names-to-literature-closing-in.html
>>> 
>>> The aim is to link names to the primary literature that published that
>>> name using, for example, DOIs, Handles, ISBNs, or other identifiers. Where
>>> the reference is freely available (e.g., in BHL, the French archive
>>> Gallica,or in a journal that makes PDFs freely available) the reference is
>>> displayed.
>>> 
>>> The interface is a bit crude, but I'd welcome suggestions
>>> feedback/suggestions.
>>> 
>>> Regards
>>> 
>>> Rod
>>> 
>>> 
>>> 
>>> ---------------------------------------------------------
>>> 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
>>> 
>>> _______________________________________________

---------------------------------------------------------
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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