[Taxacom] Linking animal names to primary literature

Stephen Thorpe stephen_thorpe at yahoo.co.nz
Sat Dec 3 00:22:15 CST 2011


on the ION website, full bibliographical details are given only for original names proposed after 1976 (or 1977 or thereabouts). The website gives titles only of other "recent publications" in which the name appears. Full bibliographical details are sometimes given for pre-1976 publications, but they are taken from secondary (post-1976) sources, so they are sometimes incorrect if the source cited it wrongly in its references ...
 
Stephen


________________________________
From: Roderic Page <r.page at bio.gla.ac.uk>
To: taxacom <taxacom at mailman.nhm.ku.edu> 
Cc: Stephen Thorpe <stephen_thorpe at yahoo.co.nz> 
Sent: Saturday, 3 December 2011 7:11 PM
Subject: Re: [Taxacom] Linking animal names to primary literature


Dear Stephen, 

I should have been more precise. In the LSID metadata for ION (which is what I use) citations are only given if the name is original. If it's a new combination there's no literature given (although there may be on the web site).

I used ION because of it's scope, and because the literature is reasonably well formatted (although it's still a nightmare to parse, which is one reason why I want identifiers).

Obviously it has gaps, but it serves as a nice place to start. 

Regards

Rod


On 3 Dec 2011, at 05:46, Stephen Thorpe wrote:

>because as it stands most names from ION aren't linked to literature because they are new combinations<
> 
>I'm not sure this is the main reason. ION has "evolved" somewhat since its inception. Originally, it was just indexing post-1977 new names from Zoological Record, but somewhere down the track it started to try to do more. But, it *never*, to my knowledge, indexes a pre-1977 name from the original publication, only from post-1977 publications which mention the name. I may have some of the fine details not quite right, but the important point is that ION can never be anywhere near comprehensive for older names, as it doesn't "go out of its way" to find and index them ...
>
>
>
>________________________________
>From: Roderic Page <r.page at bio.gla.ac.uk>
>To: taxacom <taxacom at mailman.nhm.ku.edu> 
>Cc: Stephen Thorpe <stephen_thorpe at yahoo.co.nz> 
>Sent: Saturday, 3 December 2011 6:35 PM
>Subject: Re: [Taxacom] Linking animal names to primary literature
>
>
>Dear Stephen, 
>
>
>All I want is the link (name -> literature). Whether that's the best link to learn about that name doesn't matter to me in the context of this project. I just want the link.
>
>
>Ultimately yes we want more. For example, I'd really like new combinations to be linked to original names, because as it stands most names from ION aren't linked to literature because they are new combinations. 
>
>
>Yes, taxonomic navigation would be useful, so we can see literature coverage for particular groups (e.g., show me how many frog names have been mapped). I'm working on this.
>
>
>I'll probably add links to other sources as I tidy up the web site. But for now I just want the links.
>
>
>Regards
>
>
>Rod
>
>
>
>
>On 3 Dec 2011, at 05:23, Stephen Thorpe wrote:
>
>yeah, yeah, but I was thinking more along these lines:
>> 
>>Rod, your way of doing things has certain weaknesses, such as lack of taxonomic navigation, and you seem only to be wanting (for now) to link to the original references, which, as I said (and Geoff disagreed with, so I must be correct!), are often of little or no use. These weaknesses of yours are strengths of Wikispecies, so you should look at using bidirectional links to and from Wikispecies for navigation purposes, and for linking to more extensive literature (i.e., not just original descriptions). I am working on creating pages for original combinations which redirect to the current combination, which is probably needed for this to work. If you try to use CoL, or EoL, for this purpose, instead of Wikispecies, well ... you might get fewer blind links (maybe?), but you would run the risk of linking to nonsense in some important groups ...
>> 
>>Stephen
>>
>>
>>
>>________________________________
>>From: Roderic Page <r.page at bio.gla.ac.uk>
>>To: taxacom <taxacom at mailman.nhm.ku.edu> 
>>Cc: Stephen Thorpe <stephen_thorpe at yahoo.co.nz> 
>>Sent: Saturday, 3 December 2011 5:29 PM
>>Subject: Re: [Taxacom] Linking animal names to primary literature
>>
>>
>>Dear Stephen, 
>>
>>
>>No offense taken :)
>>
>>
>>I think there are several ways to arrive at the same goal. In my case, it's automation. I'm one guy with a few computers, so I write code to link stuff together. Another approach is to get a community of people together to create a resource, such as WikiSpecies. That's great, but that's not a skill that I have.
>>
>>
>>Regarding collaboration, I plan to be making the results available as downloads so people can grab the mapping and use it in their own projects. For example, you may well find it useful when populating Wikispecies, and I will be looking at getting some additional mappings out of Wikispecies.
>>
>>
>>In terms of "co-ordination", my sense is that often ends up being a case of marking out territory. I want this mapping for my own projects, no one seems to have it in the form I want (e.g., digital identifiers rather than text strings), I can discuss with others  how one might make the mapping, or I can just go ahead and do it. I'm a believer in "small pieces loosely joined".
>>
>>
>>Regards
>>
>>
>>Rod
>>
>>
>>On 2 Dec 2011, at 23:04, Stephen Thorpe wrote:
>>
>>yes, the problem here, as always, is that everybody (Rod in this case) is touting their own pet project to accomplish this enormous task, without giving fair dues to the other projects (such as Wikispecies, tout, tout!), or making any obvious attempts to coordinate/cooperate with these other initiatives. We should be asking, "what can I do to contribute to the task", and not "hey look, I'm doing it, get it here!"
>>> 
>>>Stephen
>>> 
>>>PS: No offence Rod! :)
>>>
>>>
>>>
>>>________________________________
>>>From: "Tony.Rees at csiro.au" <Tony.Rees at csiro.au>
>>>To: r.page at bio.gla.ac.uk; taxacom at mailman.nhm.ku.edu 
>>>Sent: Saturday, 3 December 2011 11:45 AM
>>>Subject: Re: [Taxacom] Linking animal names to primary literature
>>>
>>>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?
>>>
>>>(2) Also needs to mesh with equivalent coordination activities in the "global names" space, as this is the flip side of this particular coin
>>>
>>>(3) How does this overlap (or not) with your previous posts on the possible benefits of assembling the "bibliography of life" using Mendeley?
>>>
>>>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
>>>>>
>>>>> _______________________________________________
>>>_______________________________________________
>>>
>>>Taxacom Mailing List
>>>Taxacom at mailman.nhm.ku.edu
>>>http://mailman.nhm.ku.edu/mailman/listinfo/taxacom
>>>
>>>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
>>>
>>>
>>>
>>
>>---------------------------------------------------------
>>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
>
>
>
>

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