[API-users] How to request complete taxonomic classification data for a taxon using GBIF web services?

[Geoff Shuetrim]

Hi Markus,

Thanks for the detailed response on how to work with the checklists.  Just
to clarify, I think the ITIS checklist UUID is
29675850-b60f-11e1-bd72-00145eb45e9a based on information at:

http://www.gbif.org/dataset/29675850-b60f-11e1-bd72-00145eb45e9a

If that is right, then for *Ecsenius bicolor*, I guessed that I should try
to get the taxonomic classification based on the ITIS checklist using:

http://api.gbif.org/v1/species/106963049/related?datasetKey=29675850-b60f-11e1-bd72-00145eb45e9a

but that returns an empty list.

Regards

Geoff Shuetrim



On 18 August 2014 20:06, Markus Döring <mdoering at gbif.org> wrote:

> Hi Geoff,
>
> GBIF keeps track of taxonomies of various quality and extant as "checklist
> datasets" in our Checklist Bank:
> http://www.gbif.org/dataset/search?type=CHECKLIST
>
> Every checklist is free to use any number of ranks it wants to use. NCBI
> for example has a "depth" of about 34 taxa or more I vaguely recall,
> whereas some checklists do not have any classification at all.
> The GBIF backbone taxonomy which we use to organize our occurrence records
> uses the higher taxon terms found in darwin core as ranks plus some
> infraspecific ones:
>
>   kingdom
>   phylum
>   class
>   order
>   family
>   genus
>   subgenus
>   species
>
> To see the different classifications for the same name in various
> checklists we also provide a service that takes the GBIF taxon id:
> http://api.gbif.org/v1/species/2396049/related
>
>
> Please note that a taxon from this response might have more ranks defined
> in its classification as given in this flat view. Only the darwin core
> terms are used for literal name strings, but you might be able to retrieve
> a more complete classification by following up the parent relations using
> the parentKey property. For any given taxon key a full classification is
> shown in our portal here resolving all parentKeys up to the root.
>
> For example the NCBI version of Ecsenius bicolor with 34 levels:
> http://www.gbif.org/species/106963049/classification
>
>
> best,
> Markus
>
>
>
> On 05 Aug 2014, at 05:16, Geoff Shuetrim <geoff at galexy.net> wrote:
>
> > I am new to the GBIF web services but have had some experience using the
> web services exposed by ITIS, WoRMS and the Atlas of Living Australia. I
> have a number of questions that this mailing list may be able to assist
> with.  I will send each question in a separate email to make it easier to
> follow threads in case that becomes important.  If appropriate, please just
> respond by directing me to the relevant web-services documentation (to date
> I have been working from http://www.gbif.org/developer/species and
> http://www.gbif.org/developer/occurrence).
> >
> > My first question is how to request all available taxonomic
> classification data for a taxon using GBIF web services?
> >
> > For example, from Atlas of Living Australia web services, a request for
> that information for the species Ecsenius bicolor yields:
> >
> > kingdom: Animalia
> > phylum: Chordata
> > subphylum: Vertebrata
> > class: Actinopterygii
> > superorder: Acanthopterygii
> > order: Perciformes
> > suborder: Blennioidei
> > family: Blenniidae
> > genus: Ecsenius
> > species: Ecsenius bicolor
> >
> > From ITIS, I get the somewhat more detailed:
> >
> > kingdom:Animalia
> > subkingdom:Bilateria
> > infrakingdom:Deuterostomia
> > phylum:Chordata
> > subphylum:Vertebrata
> > infraphylum:Gnathostomata
> > superclass:Osteichthyes
> > class:Actinopterygii
> > subclass:Neopterygii
> > infraclass:Teleostei
> > superorder:Acanthopterygii
> > order:Perciformes
> > suborder:Blennioidei
> > family:Blenniidae
> > genus:Ecsenius
> > species:Ecsenius bicolor
> >
> > I can currently get the kingdom, phylum, class, order, family, genus and
> species from GBIF but I cannot get ranks like subphylum and superorder etc.
> >
> > I have found an enumeration of taxonomic ranks within GBIF suggesting
> that such ranks are supported:
> > http://gbif.github.io/gbif-api/apidocs/org/gbif/api/vocabulary/Rank.html
> >
> > However, it is not clear to me how to access this information using the
> GBIF web services.
> >
> > Any pointers in the right direction would be very helpful.
> >
> > Many thanks
> >
> > Geoff Shuetrim
> > Gaia Guide Association
> > http://www.gaiaguide.info/
> > _______________________________________________
> > API-users mailing list
> > API-users at lists.gbif.org
> > http://lists.gbif.org/mailman/listinfo/api-users
>
>
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