[Taxacom] BioNames

Tony.Rees at csiro.au Tony.Rees at csiro.au
Sun Jun 2 02:15:30 CDT 2013


Dear Rod, all,

The problem Chris Thompson spotted with Cepa is symptomatic of the large-ish (60k+) generic names homonyms issue. In fact there is more than 1 "Cepa" in botany (Cepa P. Miller, 1754, Cepa O. Kuntze, 1891, see Index Nominum Genericorum, both apparently in Amaryllidaceae and non-current) and also 2 instances in zoology (Cepa Humphries, 1797 in Mollusca, Cepa Thompson & Vockeroth, 2007 in Diptera) so just linking species of "Cepa" under any one of these is going to be problematical. My take on this is that if you are sourcing names from ION then you want the associated higher taxonomy too to be sure which instance you then link to name instances in other data sources (plus you want the higher taxonomy there too, if you do not have the genus authorship). In fact ION has the higher taxonomy incorrect for Cepa Humphries, 1797 anyway, listing this as Diptera as well as Cepa Thompson & Vockeroth, 2007, which made me a bit suspicious hence worth checking out further. Sure enough if you go here 

http://books.google.com.au/books?hl=en&lr=&id=2BU5AQAAMAAJ&oi=fnd&pg=PA6&dq=cepa#v=onepage&q=cepa&f=false

you discover that Cepa Humphries is a mollusc, treated therein as a synonym of Anomia. (Since the name has not otherwise been mentioned for 100 years maybe it can be treated as a nomen oblitum so that Chris does not have to rename his Cepa again - it has already been renamed once...).

GRIN taxonomy (for higher plants) tells us that Cepa P. Miller is a synonym of Allium, while Index Nominum Genericorum tells us that Cepa O. Kuntze is a synonym of Proiphys Herbert 1821 (but does not say if the latter is a current name), although helpfully, GRIN does. Then The Plant List (which does not disambiguate homonymous genus names in Botany or give authorities for them at this time) has 24 botanical species names under "Cepa" not in ION (for that reason), with their current status, while ION has all(?) 3 dipteran species - easy, isn't it?

Of course if all this information were assembled in one place and also made freely available (hint to certain data compilers who slap copyright/no re-use over everything they place on the web) then your task would be a lot simpler. If/when the Global Names project delivers all this I at least will be very happy (hint to Rich Pyle et al). However the homonyms will not go away so your application building process will need to take appropriate precautions to prevent the sort of incorrect associations Chris has spotted.

Just something to keep you on your toes this Sunday morning (Sunday evening here...). I'm sure you knew this would not be easy...

Cheers - Tony

Tony Rees
Manager, Divisional Data Centre,
CSIRO Marine and Atmospheric Research,
GPO Box 1538,
Hobart, Tasmania 7001, Australia
Ph: 0362 325318 (Int: +61 362 325318)
Fax: 0362 325000 (Int: +61 362 325000)
e-mail: Tony.Rees at csiro.au
Manager, OBIS Australia regional node, http://www.obis.org.au/
Biodiversity informatics research activities: http://www.cmar.csiro.au/datacentre/biodiversity.htm
Personal info: http://www.fishbase.org/collaborators/collaboratorsummary.cfm?id=1566
LinkedIn profile: http://www.linkedin.com/pub/tony-rees/18/770/36


> -----Original Message-----
> From: taxacom-bounces at mailman.nhm.ku.edu [mailto:taxacom-
> bounces at mailman.nhm.ku.edu] On Behalf Of Roderic Page
> Sent: Sunday, 2 June 2013 12:21 AM
> To: Chris Thompson
> Cc: TAXACOM; TPape at snm.ku.dk
> Subject: Re: [Taxacom] BioNames
> 
> 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





More information about the Taxacom mailing list