[API-users] API GBIF: search species using GUID (LSID)

Mon Jan 26 13:37:03 CET 2015

Dear Rod,

i completely and utterly agree.... 
Best
Dirk

On 26 Jan 2015 at 11:04, Roderic Page wrote:

> And while we´re at it, will someone please explain why every
> biodiversity informatics project seems to feel that it is essential
> that it produces its own identifiers, independently of whatever has
> gone before. Simply contributing to the identifier soup is not
> helpful.
> 
> 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 at glasgow.ac.uk<mailto:Roderic.Page at 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
> 
> 
> On 26 Jan 2015, at 10:36, Donat Agosti
> <agosti at amnh.org<mailto:agosti at amnh.org>> wrote:
> 
> Dear Anton and colleagues
> 
> Might it be possible to pick this issue regarding the taxonomic
> backbone  up, since this concerns EU-BON? I think this is an important
> issue to assure that GBIF/EU-BON´s names are mapped.
> 
> Cheers
> Donat
> 
> 
> From: API-users [mailto:api-users-bounces at lists.gbif.org] On Behalf Of
> Roderic Page Sent: Monday, January 26, 2015 11:13 AM To: Tim
> Robertson; Antonio García Camacho;
> info at eu-nomen.eu<mailto:info at eu-nomen.eu> Cc:
> api-users at lists.gbif.org<mailto:api-users at lists.gbif.org> Subject: Re:
> [API-users] API GBIF: search species using GUID (LSID)
> 
> Just to follow up on Tim´s response, as far as I can tell from the EU
> BON taxonomic backbone, the LSID referred to is provided by PESI
> (e.g., urn:lsid:faunaeur.org:taxname:115091) and - like many LSIDs -
> sadly doesn´t actually work (in the sense that it can´t be resolved),
> see e.g.
> http://darwin.zoology.gla.ac.uk/~rpage/lsid/tester/?q=urn%3Alsid%3Afau
> naeur.org%3Ataxname%3A115091
> 
> The PESI web site links names to GBIF, so PESI has a mapping between
> their LSIDs and GBIF. One way to go from a PESI LSID to GBIF would be
> if PESI provided that mapping in their web services
> http://www.eu-nomen.eu/portal/webservices.php It´s not clear to me
> that they do this.
> 
> Alternatively, Fauna Europaea has been indexed by GBIF (more than
> once!), so you could use the GBIF API like this:
> 
> 1. Given a LSID like urn:lsid:faunaeur.org:taxname:115091, trim off
> the "urn:lsid:faunaeur.org:taxname:" to leave "115091"
> 
> 2. Call the GBIF API with 115091 as the sourceId key, and datasetKey
> as 90d9e8a6-0ce1-472d-b682-3451095dbc5a (this is the Fauna Europaea
> dataset that seems to match the PESI ids
> http://www.gbif.org/dataset/90d9e8a6-0ce1-472d-b682-3451095dbc5a ).
> 
> The URL is:
> 
> http://api.gbif.org/v1/species?sourceId=115091&datasetKey=90d9e8a6-0ce
> 1-472d-b682-3451095dbc5a
> 
> This will give you
> 
> {"offset":0,"limit":20,"endOfRecords":true,"results":[{"key":103283278
> ,"nubKey":1097026,"taxonID":"115091","genus":"Prionus","genusKey":1032
> 83278,"datasetKey":"90d9e8a6-0ce1-472d-b682-3451095dbc5a","parentKey":
> 103294043,"parent":"Prioninae","scientificName":"Prionus Geoffroy,
> 1762","canonicalName":"Prionus","authorship":"Geoffroy,
> 1762","nameType":"WELLFORMED","rank":"GENUS","origin":"SOURCE","taxono
> micStatus":"ACCEPTED","nomenclaturalStatus":[],"numDescendants":6,"ref
> erences":"http://www.faunaeur.org/full_results.php?id=115091","modifie
> d":"2014-06-14T21:04:19.241+0000","lastInterpreted":"2014-11-03T15:22:
> 26.302+0000","issues":[],"synonym":false}]}
> 
> The "nubKey" field has the value 1097026, which is the identifier for
> GBIF´s classification http://www.gbif.org/species/1097026  You can use
> 1097026  as the key in a query to get the distribution using the GBIF
> API.
> 
> 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 at glasgow.ac.uk<mailto:Roderic.Page at 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<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
> 
> On 26 Jan 2015, at 08:48, Tim Robertson
> <trobertson at gbif.org<mailto:trobertson at gbif.org>> wrote:
> 
> 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<http://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&n
>   ame=Oenante
> 
> 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><http://api.gbif.org/v1/species?sourceId=%3Cyour%20id%20here%3E
>   >
> 
> 
> I hope this helps,
> Tim
> 
> 
> 
> On 26 Jan 2015, at 09:35, Éamonn Ó Tuama [GBIF]
> <eotuama at gbif.org<mailto:eotuama at gbif.org>> wrote:
> 
> 
> Tim,
> Best for you to answer Antonio.
> Éamonn
> 
> From: Antonio García Camacho [mailto:antonio.garcia.camacho at 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 at csic.es<mailto:antonio.garcia.camacho at csic.es>
> www.ebd.csic.es<http://www.ebd.csic.es/>
> 
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