How to request complete taxonomic classification data for a taxon using GBIF web services?
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/
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@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@lists.gbif.org http://lists.gbif.org/mailman/listinfo/api-users
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-11...
but that returns an empty list.
Regards
Geoff Shuetrim
On 18 August 2014 20:06, Markus Döring mdoering@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@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@lists.gbif.org http://lists.gbif.org/mailman/listinfo/api-users
participants (2)
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Geoff Shuetrim -
Markus Döring