August 2014 - API-users - lists.gbif.org

GBIF API deploy, 12th June
by Markus Döring 20 Nov '14

20 Nov '14

Dear GBIF API users, A new API will be deployed later today. Please expect a short downtime in the central European afternoon, we try to keep it minimal. This is a minor updated and all URLs in the new version will remain the same, keeping v0.9. New features included are improved data processing, multimedia support for occurrences and new occurrence search filters based on media type and processing issues. Please also see http://gbif.blogspot.de/2014/05/multimedia-in-gbif.html If you notice problems or need help with the API feel invited to post questions in this list. with thanks, GBIF dev team -- Markus Döring Software Developer Global Biodiversity Information Facility (GBIF) mdoering(a)gbif.org http://www.gbif.org

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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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