[API-users] API for batch calling GBIF id -> checklist ID

Matthew Blissett mblissett at gbif.org
Wed Feb 22 12:29:30 CET 2017


Adding to what Markus says:

Many (perhaps most, or even almost all) duplicate IPNI records have been 
linked in IPNI, so 391732-1 is indeed the correct one. This work is more 
recent than the 2009 export to GBIF, so GBIF still has the duplicates.  
The IPNI website displays the links, but unfortunately doesn't show it 
in the RDF format.

You can run 2 million queries against our API, this should not be a 
problem.  When we are crawling large datasets, we average around 500 
requests/second to the species API.  Try using several parallel 
connections, if it's too slow otherwise.



On 22/02/17 12:14, Markus Döring wrote:

> Hi Yan,
> the way you describe is the current way to go.
> IPNI unfortunately has 2 problems you should be aware of. The dataset 
> in GBIF is a somewhat outdated and has not been updated since 2009. We 
> are working with Kew to publish a new version for a long time, but 
> things progress very slowly.
> The other issue is that IPNI really is 3 datasets combined all of 
> which can cover the same name. You should therefore be prepared to 
> find multiple ids for the same name - even on their current website. 
> See http://www.ipni.org/about_the_index.html
> For example Avena sativa gives 3 hits from IK, GCI & APNI: 
> http://www.ipni.org/ipni/simplePlantNameSearch.do?find_wholeName=Avena+sativa&output_format=normal&query_type=by_query&back_page=query_ipni.html
> In the future we would like to add a scientificNameID property to the 
> GBIF backbone taxa and populate that with IPNI, IF or ZooBank ids. But 
> that is not available so far.
> Best,
> Markus
>> On 22 Feb 2017, at 12:03, Yan Wong <yan at pixie.org.uk 
>> <mailto:yan at pixie.org.uk>> wrote:
>> Hi
>> I have a large number of GBIF ids (~ 2 million), for which I wish to 
>> know any existing International Plant Names Index IDs (IPNI s). 
>> What’s the easiest way to do this? I can use the standard API, e.g.
>> http://api.gbif.org/v1/species/2705290/related
>> for 2705290 = Avena sativa, which gives me an output that contains 
>> several IPNIs (in this case, 164949-3, 391732-1, 27200-2, of which 
>> the number 391732-1 seems to be the canonical one, although I can’t 
>> figure out how to identify it as such from the GBIF API output)
>> It will obviously be tedious (and unwarranted) to make 2 million API 
>> calls. What’s the recommended way to do this?
>> Yan
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