- API-users - lists.gbif.org

Searching GBIF for all synonyms of a taxa
by Hugh Burley 15 Aug '18

15 Aug '18

Hi, My name is Hugh and I'm hoping to download all records for several hundred trees species. I've been speaking to Scott Chamberlain, and I'm trying to determine if *occ_data* can be used to return all records identified as all synonyms for a given taxa, if you search using either the scientific name, or the taxon key? It seems that for some taxa with unresolved synonyms, we could be missing records, depending on which synonym we use, and thus underestimating the range. Ideally we' like to get all records for a taxa in one go, regardless of which synonym we search. However, both different synonyms, and different numbers of records, are returned for these species: ## Create keys palustris.key <- name_backbone(name = 'Quercus palustris', rank = 'species')$usageKey coccinea.key <- name_backbone(name = 'Quercus coccinea', rank = 'species')$ usageKey ## Search data palustris.occ = occ_data(taxonKey = palustris.key, limit = 200000) ## equivalent to gbif( 'Quercus palustris' , download = TRUE) coccinea.occ = occ_data(taxonKey = coccinea.key, limit = 200000) > unique(palustris.occ$data$scientificName) [1] "Quercus palustris Münchh." > unique(coccinea.occ$data$scientificName) [1] "Quercus coccinea Münchh." "Quercus palustris Regel ex A.DC." "Quercus coccinea var. tuberculata Sarg." [4] "Quercus coccinea subsp. microcarpa Torrey" "Quercus coccinea var. coccinea Scott suggested an alternative approach :: x = name_lookup('Quercus palustris') keys = x$data$key out = occ_data(taxonKey = keys, limit = 200000) However, using this approach on another species (e.g. Acacia baileyana) returns names for other organisms (e.g. invertebrates!). So it sounds like using occ_data on the taxon key, then searching all synonyms separately might be the safest approach? Thanks very much, -- Hugh

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Citations
by Stephan Lehmler 15 Aug '18

15 Aug '18

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Multiple taxonKey values with maps API ?
by Scott Chamberlain 14 Aug '18

14 Aug '18

Hello! Are there any plans to allow passing any of the primary parameters (taxonKey, datasetKey, country, publishingOrg, publishingCountry) more than once. e.g. ...?taxonKey=1&taxonKey=2 or comma separated. Perhaps up to some max number? Or is there a good reason not to suppor that? Woud it lead to jobs that run too long on your servers? Thanks! Scott

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How to get all publishers list
by Otsubo, Takayuki 07 Aug '18

07 Aug '18

Hi all. I want to get all GBIF publishers list from API as follows. http://api.gbif.org/v1/organization?limit=10000 However, it does not contain the item below. http://api.gbif.org/v1/organization/c3367060-856b-11d9-8486-b8a03c50a862 The number of publishers is about 1,200, so I think the first URL give all publishers list. But it seems to be wrong. Could you tell me how to get the list? Regards, Takayuki

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Asynchronous download service
by Akshat Pant 20 Jun '18

20 Jun '18

Hi all, I'm trying to use the asynchronous download service to download specific organism occurrences using their taxon keys. But the download status says 'KILLED'. Does anyone know why that might be happening? Thanks, Akshat

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Networks list route only returning one result
by Scott Chamberlain 09 Jun '18

09 Jun '18

HI, http://api.gbif.org/v1/network is only returning 1 result, for OBIS. Is that correct? Best, Scott

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Asynchronous download service
by Akshat Pant 02 Jun '18

02 Jun '18

Hi all, I'm using the asynchronous download service. The download keeps interrupting. The max I've gotten to is 1.2gb of 68gb. I tried changing my network and computer. Any suggestions? Thanks

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Some geometry searches seem to not be working
by Scott Chamberlain 01 Jun '18

01 Jun '18

Hi, Users of rgbif have been reporting problems with geometry parameter in /occurrence route not working sometimes. It does indeed appear to work sometimes, but other times, it appears I think to be using latitude, but ignoring longitude. It's hard to give reproducible examples for command line or so, but here's a query where the longitude values appear to be all over the map, whereas latitude appear to be in the bounds. https://api.gbif.org/v1/occurrence/search?limit=300&offset=0&geometry=POLYG… using hasGeospatialIssue doesn't appear to help so I'm guessing there could be user error on my part or perhaps something going on with geometry WKT usage? Best, Scott

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Re: [API-users] Number of coordinates in "within" predicate
by Reetz, Michael (NLPV) 31 May '18

31 May '18

Dear Jan, thank you very much. I will use coordinates from a generalized version of the national park border for future downloads. This will reduce the length of the string significantly and will still be accurate enough. Best regards Michael Mit freundlichen Grüßen Im Auftrag Michael Reetz ***************************************** Nationalpark-Verwaltung Niedersächsisches Wattenmeer Virchowstr. 1 26382 Wilhelmshaven Tel.: +49 (0) 4421 911 291 Fax.: +49 (0) 441 799 61039 e-mail: michael.reetz(a)nlpv-wattenmeer.niedersachsen.de<mailto:michael.reetz@nlpv-wattenmeer.niedersachsen.de> Web: http://www.<http://www.nationalpark-wattenmeer.niedersachsen.de/>nationalpark-wattenmeer.de Flussgebietsmanagement Übergangs-/Küstengewässer NLWKN * Betriebsstelle Brake / Oldenburg e-mail: michael.reetz(a)nlwkn-ol.niedersachsen.de<mailto:michael.reetz@nlwkn-ol.niedersachsen.de> Web: http://www.nlwkn.de Von: Jan Legind [mailto:jlegind@gbif.org] Gesendet: Mittwoch, 30. Mai 2018 14:23 An: Reetz, Michael (NLPV) <Michael.Reetz(a)nlpv-wattenmeer.niedersachsen.de>; api-users(a)lists.gbif.org Cc: helpdesk <helpdesk(a)gbif.org> Betreff: RE: Number of coordinates in "within" predicate Dear Michael, In case you have not received a reply yet - If you are submitting requests through the GBIF API there is a limit to the size of the string that can be submitted. It would seem that a 1000 coordinate pairs would break the limit. I would recommend downloading data for the general area you are interested in and filter using a GIS application. I have done something similar using a complex polygon in R and I can help you in this regard. Sincerely, Jan K. Legind Data manager, GBIF From: API-users [mailto:api-users-bounces@lists.gbif.org] On Behalf Of Reetz, Michael (NLPV) Sent: 18 May 2018 09:43 To: api-users(a)lists.gbif.org<mailto:api-users@lists.gbif.org> Subject: [API-users] Number of coordinates in "within" predicate Dear all, I'm working on a procedure for data download for the "Lower Saxon Wadden Sea" national park using the API. It works for a smaller region defined by a polygon with 183 coordinate pairs (vertices). For a larger region (more than 1000 coordinate pairs), I receive status 400 and the following response text: 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"]) My question is where the limit for the number of coordinate pairs is. Thanks for help. Kind regards Michael Reetz ***************************************** Nationalpark-Verwaltung Niedersächsisches Wattenmeer Virchowstr. 1 26382 Wilhelmshaven Tel.: +49 (0) 4421 911 291 Fax.: +49 (0) 441 799 61039 e-mail: michael.reetz(a)nlpv-wattenmeer.niedersachsen.de<mailto:michael.reetz@nlpv-wattenmeer.niedersachsen.de> Web: http://www.<http://www.nationalpark-wattenmeer.niedersachsen.de/>nationalpark-wattenmeer.de Flussgebietsmanagement Übergangs-/Küstengewässer NLWKN * Betriebsstelle Brake / Oldenburg e-mail: michael.reetz(a)nlwkn-ol.niedersachsen.de<mailto:michael.reetz@nlwkn-ol.niedersachsen.de> Web: http://www.nlwkn.de

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Number of coordinates in "within" predicate
by Reetz, Michael (NLPV) 31 May '18

31 May '18

Dear all, I'm working on a procedure for data download for the "Lower Saxon Wadden Sea" national park using the API. It works for a smaller region defined by a polygon with 183 coordinate pairs (vertices). For a larger region (more than 1000 coordinate pairs), I receive status 400 and the following response text: 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"]) My question is where the limit for the number of coordinate pairs is. Thanks for help. Kind regards Michael Reetz ***************************************** Nationalpark-Verwaltung Niedersächsisches Wattenmeer Virchowstr. 1 26382 Wilhelmshaven Tel.: +49 (0) 4421 911 291 Fax.: +49 (0) 441 799 61039 e-mail: michael.reetz(a)nlpv-wattenmeer.niedersachsen.de<mailto:michael.reetz@nlpv-wattenmeer.niedersachsen.de> Web: http://www.<http://www.nationalpark-wattenmeer.niedersachsen.de/>nationalpark-wattenmeer.de Flussgebietsmanagement Übergangs-/Küstengewässer NLWKN * Betriebsstelle Brake / Oldenburg e-mail: michael.reetz(a)nlwkn-ol.niedersachsen.de<mailto:michael.reetz@nlwkn-ol.niedersachsen.de> Web: http://www.nlwkn.de

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