- API-users - lists.gbif.org

Changes in the API
by eli eltsufin 05 Feb '15

05 Feb '15

Hi, You have changed the language description to 3 word short description. Because we are entering the final weeks of the competition, is it possible to avoid any more changes. If i haven't notice the change, my app wouldn't work properly. Thanks, Eli

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Re: [API-users] API GBIF: search species using GUID (LSID)
by Tim Robertson 27 Jan '15

27 Jan '15

Hola Antonio Can you please join and use the GBIF API mailing list for questions relating to the API? http://lists.gbif.org/mailman/listinfo/api-users We don’t make explicit use of LSIDs on GBIF.org. I expect what you want to do is lookup the GBIF species key using the species API, and then use that on the occurrence API to get occurrences. E.g. Given the plant genus Oenanthe you can look up the taxon (name usage) information using: http://api.gbif.org/v1/species/match?verbose=false&kingdom=Plantae&name=Oen… noting the usageID is 3034893 in the response. You’d presumably either do this on demand or map this to your own backbone periodically. This can then be used to search for occurrences: http://api.gbif.org/v1/occurrence/search?taxonKey=3034893 Alternatively, if you were to publish your own checklist and have GBIF index it, the taxa would be searchable using your own sourceId: http://api.gbif.org/v1/species?sourceId=<your id here> I hope this helps, Tim On 26 Jan 2015, at 09:35, Éamonn Ó Tuama [GBIF] <eotuama(a)gbif.org> wrote: > Tim, > Best for you to answer Antonio. > Éamonn > > From: Antonio García Camacho [mailto:antonio.garcia.camacho@csic.es] > Sent: 26 January 2015 01:42 > To: Éamonn Ó Tuama > Subject: API GBIF: search species using GUID (LSID) > > Dear Éamonn, > We found some problems using the GBIF API to search for occurrences and datasets. I will explain the use scenario: > Using the EU BON taxonomic backbone we will find out the LSID of a given species. Therefore, we want to use this LSID, a universal identifier actually, to ask for datasets and occurrences to each data provider. Using GBIF occurrence API we can search filtering by scientific name or even by taxonKey, but it seems that we can not filter using the LSID. > Is there a way to filter using species LSIDs or even translating these LSIDs to taxonKeys? > > Thanks, > Antonio. > > > -- > Antonio García Camacho > Estacion Biologica de Doñana (CSIC) > Americo Vespucio s/n Isla de la Cartuja > 41092 Sevilla, España > Tel. +34 954232340 / Fax. +34 954621125 > antonio.garcia.camacho(a)csic.es > www.ebd.csic.es

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GBIF to WoRMS identifiers
by Yan Wong 13 Jan '15

13 Jan '15

Is it possible to use the GBIF API to convert GBIF taxon ids (e.g. 6459778, from http://www.gbif.org/species/6459778) for taxa that have originally been obtained from WoRMS, to their original WoRMS IDs (in this case 431166, see http://www.marinespecies.org/aphia.php?p=taxdetails&id=431166). Yan

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Does typeSpecimens API work?
by Nozomi James Ytow 09 Jan '15

09 Jan '15

Hi, I tried typeSpecimens function of Species API: http://api.gbif.org/v1/species/2435098/typeSpecimens It returned non-empty record in summer, but now I get an empty record. Does it work,? James

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Count of occurrences
by Otsubo, Takayuki 08 Jan '15

08 Jan '15

Hi, I accessed the following page; http://www.gbif.org/dataset/7d981632-c6f6-446d-a987-239704ac0641 This page displays "0 Occurrences" but Darwin Core Archive that is available for download at lower right of this page contains non-zero occurrences. These two counts of occurrences should be same. # API gives count "0". http://api.gbif.org/v1/occurrence/count?datasetKey=7d981632-c6f6-446d-a987-… Other some pages are also in this situation. http://www.gbif.org/dataset/ddce7f9a-3b1b-460f-ba50-99344281fc60 I would appreciate if you determine the cause. Best Regards, Otsubo, T.

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Suggetion on BoundingBox#setGlobalCoverage()
by Nozomi James Ytow 26 Dec '14

26 Dec '14

Hi, org.gbif.api.model.registry.eml.geospatial.BoundingBox#setGlobalCoverage() does not accept boolean but four doubles. Jackson's ObjectMapper is unhappy with that. I suggest to add setGlobalCoverage(boolean) method or to add @JsonIgnoreProperties to ignore. Regards, James

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Re: [API-users] Order By
by Tim Robertson 23 Dec '14

23 Dec '14

Sorry Eli, but no. Occurrences are only returned by the most recent modified record first. Cheers, Tim On 23 Dec 2014, at 12:16, eli eltsufin <elijaelt(a)gmail.com> wrote: > Hi, > > Is it possible to sort the occurrence search query by date and time ? > > Thanks, > Eli

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Usage of endOfRecords
by Nozomi James Ytow 23 Dec '14

23 Dec '14

Hi, I tried http://api.gbif.org/v1/species/search?q=Puma&rank=GENUS&limit=20&offset=0 which returns JSON starting with {"offset":0,"limit":20,"endOfRecords":false,"count":50,"results":[ I expect that there are 50 records to be returend against the query. Howerver, http://api.gbif.org/v1/species/search?q=Puma&rank=GENUS&limit=60&offset=0 returns 50 records as expected, but it says as {"offset":0,"limit":50,"endOfRecords":false,"count":50,"results":[ Shouldn't it be true, if the returned fragment represents end of records? Or, shoud I check not only endOfRecords but also (limit > 0 && (offset + limit) < count) ? -- James

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Re: [API-users] GBIF Challenge
by Tim Robertson 08 Dec '14

08 Dec '14

Hi Eli, Please can you join and post to the api users mailing list [1] for these kind of questions? > 1. I have used "/species" addition and received only 20 results. how do i remove this limit ? > or how can i read the next page ? Please see the documentation on paging http://www.gbif.org/developer/summary#common If you add ?limit=100 you will receive 100 results, and if you add &offset=100 you will receive the second 100 results for example. Please bear in mind that if you request limit=10000000 it will be reduced to a sensible limit, which is state on the response. In most case 20 or 100 will be the optimal page size for performance. > 2. For the Map section, how can i get the Keys for the Taxson, Dataset and Publisher (The ISO keys for countries i found with Google) ? Please see the documentation on the Registry API [2] for dataset (/dataset) and publishing organisation (/oraganization) and Species API [3] for taxa keys. ISO country codes are on many sites such as wikipedia but the authoritative site is https://www.iso.org/obp/ui/#search I hope this helps. Best wishes, Tim [1] http://lists.gbif.org/mailman/listinfo/api-users [2] http://www.gbif.org/developer/registry [3] http://www.gbif.org/developer/species On 05 Dec 2014, at 18:33, eli eltsufin <elijaelt(a)gmail.com> wrote: > Hi, > > Regarding the published API for the Challenge : > > 2. For the Map section, how can i get the Keys for the Taxson, Dataset and Publisher (The ISO keys for countries i found with Google) ? > > For now :-) > > Eli

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GBIF Ebbe Nielsen Challenge
by Kyle Copas [GBIF] 04 Dec '14

04 Dec '14

No disrespect intended to the group, but I neglected to alert the API users list to Tuesday's launch of the re-engineered GBIF Ebbe Nielsen Challenge. If you haven’t seen the announcement through other channels, please do have a look at either the announcement or the Challenge website on ChallengePost. http://www.gbif.org/page/62262 http://gbif.challengepost.com My sincere apologies for this sin of omission! Kyle ===== Kyle Copas Science Writer +45 35 32 14 75 | mobile +45 28 75 14 75 | Skype kylecopas GBIF Secretariat Universitetsparken 15 2100 Copenhagen Ø Denmark http://www.gbif.org <http://www.gbif.org/>

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