- API-users - lists.gbif.org

How to get the 'right' kingdom nodes
by Martin Wendt 20 Dec '15

20 Dec '15

I try to implement a lazy-loading taxonomy tree (as a demo for a open source javascript tree plugin). See here for an example: http://rawgit.com/mar10/fancytree/master/demo/taxonomy-browser/index.html#k… What JSON API should use to get the top level nodes (i.e. Kingdoms)? Currently I call http://api.gbif.org/v1/species/search?rank=kingdom <http://api.gbif.org/v1/species/search?rank=kingdom> but this returns much more than the ~7 entries I expect (Animalia, Plantae, Fungi, …) I seem to get reasonable results, if I only display nodes with key == nubKey. But the search results retrieved by `species/search?q=homo sapiens` returns multiple hits, and some of them have keys different from nubKey. Those matches seem to be descendants of an `Animals` kingdom that also has nubKey != key. I guess my mental model of the data structure is too naïve: - why are there different ‚Animals‘ kingdoms with different keys but identical nubKey? - does it make sense at all to display a tree (with only one ‚animals‘ node)? - when I restrict the search results to entries that have a kingdom with key == nubKey, what will the user miss? Thanks Martin Wendt

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GBIF down
by Scott Chamberlain 19 Dec '15

19 Dec '15

GBIF assets are all down for me. Is it just me? Best, Scott

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API returns incorrect eventDate
by Roderic Page 01 Dec '15

01 Dec '15

This may be related to http://dev.gbif.org/issues/browse/POR-1508 but it looks like “eventDate” is consistently incorrect in every API call I make, e.g. http://api.gbif.org/v1/occurrence/891423484 returns: “eventDate”:"2002-04-11T22:00:00.000+0000” when the verbatim date is 2002-04-12 The web version of the record http://www.gbif.org/occurrence/891423484 has the correct date, together with a time (12:00:00 AM) that seems to be based on no evidence at all (it’s always puzzled me why GBIF reports spuriously precise date and time strings on the web page). Regards Rod --------------------------------------------------------- Roderic Page Professor of Taxonomy Institute of Biodiversity, Animal Health and Comparative Medicine College of Medical, Veterinary and Life Sciences Graham Kerr Building University of Glasgow Glasgow G12 8QQ, UK Email: Roderic.Page(a)glasgow.ac.uk<mailto:Roderic.Page@glasgow.ac.uk> Tel: +44 141 330 4778 Skype: rdmpage Facebook: http://www.facebook.com/rdmpage LinkedIn: http://uk.linkedin.com/in/rdmpage Twitter: http://twitter.com/rdmpage Blog: http://iphylo.blogspot.com ORCID: http://orcid.org/0000-0002-7101-9767 Citations: http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ ResearchGate https://www.researchgate.net/profile/Roderic_Page

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funny characters in common names / vernaculars for species
by jorrit poelen 24 Nov '15

24 Nov '15

Hey y’all: I am noticing some funny characters (e.g. "WintergrÃ¼n”) for species available here: http://www.gbif.org/species/2882753/vernaculars <http://www.gbif.org/species/2882753/vernaculars> Same is observed using the api: http://api.gbif.org/v1/species/2882753/vernacularNames <http://api.gbif.org/v1/species/2882753/vernacularNames> I am assuming that the actual common name should be something like “Wintergrün”. While I was looking into this, I also noticed that no characterset is specified in http response headers. Please confirm that this is expected behavior. thx, -jorrit

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Download statistics
by Holetschek, Jörg 20 Nov '15

20 Nov '15

Dear all, I'd like to combine the registry API with the occurrence API to create some download statistics for certain institutions. According to the documentation, datasets are not removed from the registry, but get a "deleted" timestamp when removed. Does the same apply to the occurrence download service, so that downloads of removed datasets remain visible? Precisely: Is it possible to get the download activities for a dataset that doesn't exist anymore by using http://api.gbif.org/v1/occurrence/download/dataset/{datasetKey} ? Cheers, Jörg

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numOccurrences always 0 for species
by Peter Desmet 18 Nov '15

18 Nov '15

Hi, In the species/search API, one of the properties of a taxon is "numOccurrences", which I assume is the number of occurrences across GBIF for this taxon. The value seems to be always "0" though. Example: http://api.gbif.org/v1/species/search?datasetKey=d7dddbf4-2cf0-4f39-9b2a-bb… First result: http://www.gbif.org/species/3134959 On that page you can see 47,617 occurrences, 332 infraspecies. The API however gives: numOccurrences: 0 numDescendants: 332 (= correct) Is this a bug? Related: - I know I can find the number of occurrences for a taxon by doing an occurrence search (http://api.gbif.org/v1/occurrence/search?taxonKey=3134959) but that means doing an extra call per taxon. - Why does the species API list far fewer properties per taxon ( http://api.gbif.org/v1/species/3134959) than the species search API? E.g. numOccurrences, descriptions, etc. Cheers, Peter

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Why is the key of organismID a URI?
by Peter Desmet 17 Nov '15

17 Nov '15

Hi, I just noticed in the response of the occurrence search API, that the key for "organismID" is "http://unknown.org/organismID". It is the only key that is returned as a URI. What is the reasoning behind this (datasetID, gbifID, etc. are all normal)? Is this a bug? "dynamicProperties": "{\"device_info_serial\":858}", "georeferenceProtocol": "doi:10.1080/13658810412331280211", *"http://unknown.org/organismID <http://unknown.org/organismID>": "L907004",* "georeferenceVerificationStatus": "unverified", "samplingEffort": "{\"secondsSinceLastOccurrence\":1806}", http://api.gbif.org/v1/occurrence/search?datasetKey=83e20573-f7dd-4852-9159… Cheers, Peter

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org.gbif.api.vocabulary.Rank.INFRAORDER marker
by Nozomi James Ytow 17 Nov '15

17 Nov '15

Hi, INFRAORDER of API Java librarie's vocabulary Rank, i.e. org.gbif.api.vocabulary.Rank.INFRAORDER, doesn't have the marker value, unlike other INFRA- Ranks. Is it what designed? There are API response records having INFRAORDER as its rank which results in null maerker value, unlike other ranks. If it is what intended, why? Regerds, James

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Suggestion to add nomenclaturalCode to NameUsage of checklistbank
by Nozomi James Ytow 17 Nov '15

17 Nov '15

Hi, the subject says all. I suspect that some data in GBIF Checklist Bank are derived from checklits formatted in Dawrin Core, e.g. http://www.gbif.org/dataset/7a9bccd4-32fc-420e-a73b-352b92267571 or http://data.canadensys.net/ipt/resource.do?r=coleoptera-ca-ak the source. DwC data may contain nomenclaturalCode whichi is crucial to explore name usages, especially the same literal is used under different nomenclatural codes. Please consider to add nomenclaturalCode element (or something equivalent) to Species API response if it is available in the soure data. Regerds, James

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Re: [API-users] GBIF API
by Markus Döring 05 Nov '15

05 Nov '15

Hi Mauro, you can get to the next page by increasing the offset: http://api.gbif.org/v1/occurrence/search?basisOfRecord=HUMAN_OBSERVATION&co… <http://api.gbif.org/v1/occurrence/search?basisOfRecord=HUMAN_OBSERVATION&co…> But you should probably be using the asynchroneous downloads if your resultset is 400k. We have a hard limit of 200k records max when using the search service so you will never get hold of them all. http://www.gbif.org/developer/occurrence#search <http://www.gbif.org/developer/occurrence#search> best, Markus > On 04 Nov 2015, at 14:50, ei11063 <ei11063(a)fe.up.pt> wrote: > > Good afternoon. > I am doing a pratical work that involves the use of a GBIF API. My request is something like http://api.gbif.org/v1/occurrence/search?basisOfRecord=HUMAN_OBSERVATION&co…. My question is: how can i get the second page? The total results have 400k results. > > Thanks a lot, > Mauro Costa >

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