February 2016 - API-users - lists.gbif.org

API download using geometry
by Dag Endresen 18 Feb '16

18 Feb '16

Hi all, I am trying to download all occurrences inside the CAFF boundary area following a request from the CAFF focal point in Norway. I have converted the polygon to a Well Known Text object for use with the GBIF API. (The WKT polygon looks fine when I test to open in QGIS). http://www.gbif.org/developer/summary#authentication http://www.gbif.org/developer/occurrence#predicates http://www.gbif.org/developer/occurrence#p_geometry My filter.json file is attached and looks like this (the polygon definition is truncated here at (...) for the purpose as example): { "creator":"dag.endresen", "notification_address": ["dag.endresen(a)gmail.com"], "predicate": { "type":"within", "geometry":"POLYGON((179.285633734761433 50.81429697072722,179.600130309538514 50.798132663162107,180.0 50.825202656741141,-179.985731034706419 50.826168623278733,-179.642658093259286 50.834515997684633,-179.213664117412264 (...) 50.826278190103068,179.014229185979531 50.811745655072343,179.285633734761433 50.81429697072722))" } } Error message: Instantiation of [simple type, class org.gbif.api.model.occurrence.predicate.WithinPredicate] value failed: null (through reference chain: org.gbif.api.model.occurrence.predicate.WithinPredicate["geometry"]) It might possible to download all occurrence data north of 50 degrees (southernmost edge of the CAFF area) - and cut to CAFF area offline. But because this is more than 200 million records, I am very interested to check if it is possible to filter using the CAFF boundary polygon. http://www.gbif.org/occurrence/search?HAS_COORDINATE=true&decimalLatitude=5… Best wishes Dag -- Dag Endresen Node manager for GBIF Norway ORCID: http://orcid.org/0000-0002-2352-5497

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Manuscript on R client (and perhaps Python)
by Scott Chamberlain 10 Feb '16

10 Feb '16

Hi all, Apologies if this is not what you want here, but not sure where else to post this. I'm writing a manuscript on the R client (https://github.com/ropensci/rgbif/ ) I maintain for the GBIF API. I may also include some stuff about the Python client (https://github.com/sckott/pygbif ) as well. If you have any feedback, please do chime in soon, either on the Github repo at https://github.com/sckott/msrgbif, or on our discussion forum at https://discuss.ropensci.org/t/feedback-on-rgbif-manuscript/290 Best, Scott

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Canonical name of subgenus and species under a subgenus
by Nozomi James Ytow 01 Feb '16

01 Feb '16

Hi, A verbatim record of a sugenus http://api.gbif.org/v1/species/100969508/verbatim results in a name usage record http://api.gbif.org/v1/species/100969508 where genus name, instead of subgenus name, treated as the canonical name. I suspect it is issue at the data sorurce, because Ficus (Diconoficus) is the generic part of species name under the subgenus such as Ficus (Diconoficus) gayana but never a subgenus name itself. Looking at species record under the subgenus, however, e.g. http://api.gbif.org/v1/species/100969511/verbatim http://api.gbif.org/v1/species/100969511 gives Ficus gayana as the canonical name. This interpretation, i.e. omitting subgenus part from a canonical name, might be issue of data parsing. Or, is it an extpected client task to check verbatim records also? Regards, James

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