[Taxacom] BioNames

Roderic Page r.page at bio.gla.ac.uk
Sat Jun 1 09:21:06 CDT 2013


Hi Chris,

Thanks for letting me know about these examples. Bunch of issues here, I've documented them here https://github.com/rdmpage/bionames/issues/2 and https://github.com/rdmpage/bionames/issues/3

The problem with Cepa is mostly not my fault (honest). I mapped the names to GBIF, which has the plant genus Cepa in the fly family Syrphidae, and has include a plant species as well. GBIF has a lot of these issues, one reason I built BioNames was to help catch these sorts of errors.

Bill Gate's fly was missed because my mapping between ION names and taxa in GBIF doesn't handle subgeneric names yet (on the todo list), so ION has "Eristalis (Eoseristalis) gatesi" and GBIF has "Eristalis gatesi". Fixed this for this example. EOL images only appear if either GBIF or NCBI taxa have been mapped to EOL, I haven't loaded every taxon in EOL.

My main goal in BioNames is to link names to the primary literature, and provide a way to navigate through those links using large classifications. Obviously there will be errors in this process.But I like the fact that I can search for these flies and get some information (e.g.,  http://bionames.org/taxa/gbif/1541332 ).

Lastly, there are lots of databases, and I could link to lots of them, but that's not the goal. I want something arguably better, the original research (e.g., your papers http://bionames.org/references/2ea0b01944a05be1545cfba2bc9c6efd and http://bionames.org/references/c4cfe67040fcd81143fce4411142e90 ). 

Regards

Rod

On 1 Jun 2013, at 13:59, Chris Thompson wrote:

> Interesting Rod,
> 
> you say that BioNames is a database of ANIMAL (and other ICZN) names ...
> 
> So, my first attempt with one of my favorite fly names generate a plant name.
> 
> Try Cepa Thompson 2007, a small neotropical genus of flower flies. And you get as its author Kuntze 1891 and included the species "cunninghamii Lindl." which are onion of Alliaceae, etc.
> 
> At least Species2000 and IT IS get it right.
> 
> And what also interested me was that the EoL link to its type species, Cepa alex (Thompson 1999)
> http://eol.org/pages/85361/overview was not picked up, etc.
> 
> You did better with Eristalis gatesi, but still the EoL link is not there. So, for the common users, going directly to EoL is the best generic source of overall information.
> 
> And then there is Stephen's comment of:
> What I don't find is the "honourable thing to do", i.e., link to sites with better data than you have got, so the user can actually end up somewhere useful ...
> 
> So, if you had properly used the data from our Systema Dipterorum from which ALL others have taken name information but from various earlier versions, you would have got the best and most recent information on this fly, etc.
> 
> Oh, well ...
> 
> Chris
> 
> from home
> 
> -----Original Message----- From: Roderic Page
> Sent: Saturday, June 01, 2013 4:30 AM
> To: TAXACOM
> Subject: [Taxacom] BioNames
> 
> Dear All,
> 
> I've released "BioNames", a database of animal (and other ICZN) names linked, wherever possible, to either a digital identifier for the publication that described it, or (even better) the full text (from BioStor and other digital archives). I've wrapped this an interface built with Ryan Schrenk (whose elegant work was funded by EOL). BioNames combines data from ION, BHL, CrossRef, Mendeley, GBIF, NCBI, EOL (yes, a veritable acronym soup) to make something I hope people find useful.
> 
> The web site is here: http://bionames.org
> 
> It's basic (this was built to a deadline) but functional (albeit with the usual issues concerning gaps and errors). There's a blog post about it here: http://iphylo.blogspot.co.uk/2013/05/bionames-now-live-report-on-project.html
> 
> If you want some quick links into interesting pages, try:
> 
> http://bionames.org/taxa/gbif/2432946  (make sure you click on the "bibliography tab")
> 
> http://bionames.org/authors/R%20D%20Price
> 
> http://bionames.org/authors/R%20Mesibov
> 
> http://bionames.org/taxa/ncbi/261974
> 
> http://bionames.org/taxa/ncbi/51026
> 
> http://bionames.org/references/21f41b69cf44c2dee6b4c1d3307e428f
> 
> http://bionames.org/taxa/gbif/9491
> 
> 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
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> Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
> Wikipedia: http://en.wikipedia.org/wiki/Roderic_D._M._Page
> Citations: http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
> ORCID id: http://orcid.org/0000-0002-7101-9767
> 
> 
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> Celebrating 26 years of Taxacom in 2013. 
> 

---------------------------------------------------------
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
Skype: rdmpage
Facebook: http://www.facebook.com/rdmpage
Twitter: http://twitter.com/rdmpage
Blog: http://iphylo.blogspot.com
Home page: http://taxonomy.zoology.gla.ac.uk/rod/rod.html
Wikipedia: http://en.wikipedia.org/wiki/Roderic_D._M._Page
Citations: http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
ORCID id: http://orcid.org/0000-0002-7101-9767




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