November 2015 - API-users - lists.gbif.org

API returns incorrect eventDate
by Roderic Page 30 Nov '15

30 Nov '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 19 Nov '15

19 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 17 Nov '15

17 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 16 Nov '15

16 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 04 Nov '15

04 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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more data with depth value??
by ptrans2004es 02 Nov '15

02 Nov '15

Hello, I work mainly with occurrences from marine species that I programmatically download through GBIF API. Maybe it is just an impression, but it seems to me that there are now clearly more occurrences with depth values than some months ago. I've seen for some species data downloaded 3-4 months ago that I had around 200 occurrences with not-null depth value; and redownloading them now, there is around ten times more occurrences with not-null depth value. I was very surprised! Can this be possible? Maybe there was changes in API or reloaded data in last months that can explain that? (if not, it should be my own problem, but I don't understand, I don't think I modified anything.) Thank you very much. Best regards, E.Gracia

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