- API-users - lists.gbif.org

Search for occurrence by identifier
by Roderic D. M. Page 16 Sep '14

16 Sep '14

Am I correct in thinking that it's not currently possible to search for an occurrence by identifier or the occurrenceID fields? For example, if I want to search the recently added Geographically tagged INSDC sequences dataset http://www.gbif.org/dataset/ad43e954-dd79-4986-ae34-9ccdbd8bf568 using the accession number I would need to search on either of these fields. Regards Rod Sent from Acompli

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Using api to get number of download events
by Gallien 16 Sep '14

16 Sep '14

Hi guys, Is it possible to retrieve datasets activity like the number of download events with the API ? (as provided in GBIF portal under "Activity" tab). If not, is there another way to get this piece of information from your site ? Thanks, Gallien Labeyrie

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explanation for unlikely interpretations?
by Ken-ichi 09 Sep '14

09 Sep '14

When viewing many (most?) of the iNat records on GBIF, I see a yellow box at the top of the page listing some "Interpretation Issues." Some of them I understand, like derived country, since iNat doesn't report the country, just the coordinates, but the following are more opaque: * Recorded date unlikely * Modified date unlikely * Identified date unlikely Here's an example: http://www.gbif.org/occurrence/923925309. As far as I know, all three dates are accurate for that record. Why does GBIF think they're "unlikely"? I suppose this is only tangentially related to the API, so if I should be directing this elsewhere please let me know. -ken-ichi

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Is there a GBIF specific LSID that can be used?
by Geoff Shuetrim 27 Aug '14

27 Aug '14

Working with a range of web services, I have found myself making extensive use of the LSIDs that are specific to each data source. For example, for ITIS, I use the Ecsenius bicolor LSID: *urn:lsid:itis.gov:itis_tsn:636326* For WoRMS, the LSID for Ecsenius bicolor is: *urn:lsid:marinespecies.org:taxname:277652* For Atlas of living Australia the LSID for Ecsenius bicolor is: *urn:lsid:biodiversity.org.au:afd.taxon:99c29e7c-5b04-4e57-8e6b-82aa442a801a* Is there a GBIF LSID that can similarly be used as a unique identifier for a taxon? I have come across the various GBIF unique keys but these are not unique outside of the GBIF environment and within the Gaia Guide systems I am deciding how best to work with these, ensuring their uniqueness, alongside identifiers from other data sources. Thanks again for your assistance. Geoff Shuetrim Gaia Guide Association http://www.gaiaguide.info/

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How to request complete taxonomic classification data for a taxon using GBIF web services?
by Geoff Shuetrim 27 Aug '14

27 Aug '14

I am new to the GBIF web services but have had some experience using the web services exposed by ITIS, WoRMS and the Atlas of Living Australia. I have a number of questions that this mailing list may be able to assist with. I will send each question in a separate email to make it easier to follow threads in case that becomes important. If appropriate, please just respond by directing me to the relevant web-services documentation (to date I have been working from http://www.gbif.org/developer/species and http://www.gbif.org/developer/occurrence) My first question is how to request all available taxonomic classification data for a taxon using GBIF web services? For example, from Atlas of Living Australia web services, a request for that information for the species *Ecsenius bicolor* yields: kingdom: Animalia phylum: Chordata subphylum: Vertebrata class: Actinopterygii superorder: Acanthopterygii order: Perciformes suborder: Blennioidei family: Blenniidae genus: Ecsenius species: Ecsenius bicolor >From ITIS, I get the somewhat more detailed: kingdom:Animalia subkingdom:Bilateria infrakingdom:Deuterostomia phylum:Chordata subphylum:Vertebrata infraphylum:Gnathostomata superclass:Osteichthyes class:Actinopterygii subclass:Neopterygii infraclass:Teleostei superorder:Acanthopterygii order:Perciformes suborder:Blennioidei family:Blenniidae genus:Ecsenius species:Ecsenius bicolor I can currently get the kingdom, phylum, class, order, family, genus and species from GBIF but I cannot get ranks like subphylum and superorder etc. I have found an enumeration of taxonomic ranks within GBIF suggesting that such ranks are supported: http://gbif.github.io/gbif-api/apidocs/org/gbif/api/vocabulary/Rank.html However, it is not clear to me how to access this information using the GBIF web services. Any pointers in the right direction would be very helpful. Many thanks Geoff Shuetrim Gaia Guide Association http://www.gaiaguide.info/

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language parameter of Species API
by Nozomi James Ytow 22 Aug '14

22 Aug '14

Hi, SpeciesAPI document http://www.gbif.org/developer/species specifies language parameter of simple get species, i.e. species/{int}. Language parameter is explained at http://www.gbif.org/developer/species#p_language as "default=en or use HTTP header for this", I tried to specify 'de' in HTTP header as Language request property, but it doesn't work. Instead, http://api.gbif.org/v1/species/5231190?language=de works fine. Do I misunderstand the documentation? I also tried languages are not included in vernacular names list http://api.gbif.org/v1/species/5231190/vernacularNames such as http://api.gbif.org/v1/species/5231190?language=ja or zh or kr... I expected empty field for vernacularName or no record returned, but I got English one. It is misleading implementation that one ignorant of the language specified can misundarstand that the language uses the same word with English. I suggest to return null vernacularName if vernacular name of specified language is unavailable. Cheers, James

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How to query for the IDs of species that have been recorded within a specified geographic region?
by Geoff Shuetrim 18 Aug '14

18 Aug '14

My second question in relation to GBIF web services is whether it is possible to request a list of GBIF IDs (keys) for those species (subspecies/variants/cultivars etc) that have occurence data with coordinates within a geographic region specified as part of the web service query. Specifically, I am hoping to use a WKT polygon and the geometry query parameter as described on the occurrences web services page to define the region. I am also hoping to constrain results using a request parameter that indicates a taxonomic rank that all matching species IDs have (e.g. return the IDs of all species that are in the Lepidoptera order. It would also be great if results could be constrained to require that the occurrences driving the results were between a specified start and end date. Note that for performance reasons on both sides it would be great to retrieve the relatively small number of GBIF IDs rather than the potentially huge numbers of occurrence records for each species. Again, many thanks for any assistance that can be provided. Regards Geoff Shuetrim Gaia Guide Association http://www.gaiaguide.info/

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SpeciesAPI suggest do not return class value
by Nozomi James Ytow 18 Aug '14

18 Aug '14

Hi, http://api.gbif.org/v1/species/suggest?datasetKey=d7dddbf4-2cf0-4f39-9b2a-b… does not return class, i.e. clazz value, unlike as it did in v0.9 era. Is it what intended, or by acceident? Cheers, Jame

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SpeciesAPI image returns HTTP status 404
by Nozomi James Ytow 18 Aug '14

18 Aug '14

Hi, image subfunction example of SpeciesAPI http://api.gbif.org/v1/species/5231190/images returns HTTP status 404. Is it still supported, or changed to other name? Cheers, James

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GBIF API v1.0 live
by Markus Döring 29 Jul '14

29 Jul '14

Dear GBIF API users, sorry for the far too long downtime today, but the good news is that version 1.0 of the API is finally live now! http://api.gbif.org/v1/ You can find the updated documentation here as usual: http://www.gbif.org/developer The previous v0.9 API URL will still be running up to the end of August, serving the exact same content. Hope you enjoy it. with best wishes, your GBIF dev team Version 1.0 changes: ---------------------------- - remove all underscores from URLs and replace them with camelCase (mainly species & metrics API) - dataset.owningOrganizationKey renamed to dataset.publishingOrganizationKey - use of lists instead of simple strings for email, phone, homepage, position and address for contacts, organization and node in the registry - include issue column in dwca download - search facets use country iso 2letter codes - species & dataset suggest returns minimal information now: http://api.gbif-uat.org/v0.9/species/suggest?q=Dracul - remove reverse geocode & mendeley GBIF articles from our API

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