- API-users - lists.gbif.org

Re: [API-users] [gbif/gbif-api] Any place where api's response structures are explanained? (#41)
by Markus Döring 24 Feb '19

24 Feb '19

Hi Javier, you are right, we are lacking a documentation on our API models on our site. The best and probably only place you can find something to read is the java documentation which is here: https://github.com/gbif/gbif-api/tree/master/src/main/java/org/gbif/api/mod… For example the checklist dataset metrics you have mentioned is this: https://github.com/gbif/gbif-api/blob/master/src/main/java/org/gbif/api/mod… ... but it lacks documentation for the properties you were mentioning. "nub" is an alias for "backbone" in GBIF. Hence nubMatchingCount is the count of name usages that can be matched to the GBIF backbone, i.e. do have a corresponding name in the backbone. Similar colMatchingCount is the number of usages that can be matched to the Catalogue of Life. The xxxCoveragePct properties are the same just expressed as percentages compared to the total of the dataset. Hope that helps a little. If you have any further questions please use our API mailing list which I have copied in here to get help. Regards, Markus > On 22. Feb 2019, at 18:17, Javier Seixas <notifications(a)github.com> wrote: > > Hello! > > I'm looking for GBIF API's responses documentation. If this is not the place to ask, please, address me to the correct one. > > I'm currently working with the GBIF API, and I don't understand some of the responses. For example, when asking for dataset metrics GET /v1/dataset/d7dddbf4-2cf0-4f39-9b2a-bb099caae36c/metrics I get that response: > > { > > "key": 210029 > , > > "datasetKey": "d7dddbf4-2cf0-4f39-9b2a-bb099caae36c" > , > > "usagesCount": 5858142 > , > > "synonymsCount": 2361744 > , > > "distinctNamesCount": 5844412 > , > > "nubMatchingCount": 3805144 > , > > "colMatchingCount": 2845782 > , > > "nubCoveragePct": 64 > , > > "colCoveragePct": 48 > , > > "countByConstituent" > : , > > "countByKingdom" > : { > > "ANIMALIA": 1529953 > , > > "PLANTAE": 523372 > , > > "FUNGI": 201853 > , > > "CHROMISTA": 15357 > , > > "BACTERIA": 10847 > , > > "PROTOZOA": 7063 > , > > "INCERTAE_SEDIS": 787 > , > > "ARCHAEA": 439 > , > > "VIRUSES": 119 > > }, > > ... > > } > > What is the meaning of properties such as nubMatchingCount, colMatchingCount, nubCoveragePct, etc?? In the website I can see the API documentation for making request, not explaining responses though. > > I will appreciate any help Thanks! > > — > You are receiving this because you are subscribed to this thread. > Reply to this email directly, view it on GitHub, or mute the thread. >

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Getting number of records for a given scientific name
by Mauro Cavalcanti 31 Jan '19

31 Jan '19

Dear ALL, Is there a way to retrieve the number of georeferenced records for a given scientific name using a GBIF API call? I tried something like " http://api.gbif.org/v1/occurrence/count?ScientificName=Vicia+faba" but it of course didn't work. I realize this is a rather silly question, but most of the time I only access the GBIF API using Python (via pygibf) or R (via rgbif), and therefore I'm not used to direct calls to the API (what a shame!). Thanks in advance for any assistance you can provide? Best regards, -- Dr. Mauro J. Cavalcanti E-mail: maurobio(a)gmail.com Web: http://sites.google.com/site/maurobio "Life is complex. It consists of real and imaginary parts."

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Occurrence Inventories
by Adriaan van Os 31 Jan '19

31 Jan '19

Occurrence Inventories <https://www.gbif.org/developer/occurrence> support only a few properties: basisOfRecord, year, datasets, countries and publishingCountry. I suggest to add /occurrence/counts/monthOfYear /occurrence/counts/dayOfYear These would be useful for creating fligh-period charts. Regards, Adriaan van Os

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Strange line on the base-map
by Adriaan van Os 12 Jan '19

12 Jan '19

At zoom level 7, I get a strange line on the base-map here: <https://tile.gbif.org/3575/omt/7/61/92@4x.png?style=gbif-middle> This happens with three browsers I tried and also with curl. Regards, Adriaan van Os

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Clipping occurrence data to a country
by Adriaan van Os 12 Jan '19

12 Jan '19

I noticed that e.g. "&country=NL" limits occurrence data even within the specified country. That is, for that country, I get less occurrence data than without the "&country=NL" Is this caused by wrong data, by data with the wrong (or no) country identifier attached ? Anyway, I now seek another solution, which is to clip the occurrence data to the specified country on the map. However, how do I get map data tiles with country borders ? I use EPSG:3575. Regards, Adriaan van Os

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Species key change
by Adriaan van Os 22 Dec '18

22 Dec '18

I noticed that a whole range of GBIF keys have changed, e.g. for Aglais io Argynnis pandora Argynnis paphia Melitaea athalia etc. This is really horrifying. Changing keys is about the worst one can do to a database, apart from throwing it away. Regards, Adriaan van Os

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Occurrence download API throwing 406 errors
by Scott Chamberlain 05 Dec '18

05 Dec '18

Hi, The occurrence download API has been throwing 406 errors for some users https://github.com/ropensci/rgbif/issues/333 I concur that it happens for me as well. Has anything changed in the backend for the downloads route? Best, Scott

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Job opening at the GBIF Secretariat
by Federico Mendez 22 Nov '18

22 Nov '18

Hi everyone (again!), Please ignore my previous message, I wrongly mentioned that the position will be locally recruited when in reality it can be INTERNATIONALLY recruited. Complete details here: https://www.gbif.org/news/6BlODHu4xi06EEQIe66Qee/job-opportunity-for-softwa… Please feel free to share this position with your own networks and contacts. Thanks, Federico Mendez Universitetsparken 15 2100 Copenhagen Denmark Phone: +45-35332951 Skype: fede.mendez e-mail: fmendez(a)gbif.org<mailto:fmendez@gbif.org> www.gbif.org<http://www.gbif.org/>

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Job opening at the GBIF Secretariat
by Federico Mendez 22 Nov '18

22 Nov '18

Hi everyone, A quick announcement, the GBIF Secretariat is currently seeking applications for a Software Developer, see complete details here: https://www.gbif.org/news/6BlODHu4xi06EEQIe66Qee/job-opportunity-for-softwa… Deadline for applications is Saturday, 15th December 2018. Please be aware that the successful candidate will be locally recruited (no-relocation involved), according to the GBIF Staff Rules Please feel free to share this position with your own networks and contacts. Thanks, Federico Mendez Universitetsparken 15 2100 Copenhagen Denmark Phone: +45-35332951 Skype: fede.mendez e-mail: fmendez(a)gbif.org<mailto:fmendez@gbif.org> www.gbif.org<http://www.gbif.org/>

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Asynchronous download DwCA format no publishingOrgKey
by Eli Agbayani 17 Aug '18

17 Aug '18

Dear GBIF, Is there a reason why the Asynchronous download DwCA format doesn't have publishingOrgKey while the CSV format has it. We want to use the DwCA format because of the multimedia addition but realized the publishingOrgKey was missing. Hopefully publishingOrgKey will be included in the DwCA format so we don't need to download both formats. Thanks, Eli

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