On 26 Jan 2015, at 11:24, Francisco Antonio García Camacho <antonio.garcia.camacho@csic.es> wrote:

Thank you Tim and Roderic for your responses.
Roderic's suggested approach seems promising, but it would help us to resolve anymals LSIDs only.
In any case, we will need to know how the mapping between PESI and GBIF names is done.

We can also search using the scientific names only, but this could lead the users to some misleadings. That is the reason we want to use existing GUIDs to search for biodiversity data in the EU BON data portal.

With regards,
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@csic.es
www.ebd.csic.es

El 26/01/2015 a las 12:04, Roderic Page escribió:

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@glasgow.ac.uk
Tel:  +44 141 330 4778
Skype:  rdmpage
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LinkedIn:  http://uk.linkedin.com/in/rdmpage
Twitter:  http://twitter.com/rdmpage
Blog:  http://iphylo.blogspot.com
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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@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@lists.gbif.org] On Behalf Of Roderic Page
Sent: Monday, January 26, 2015 11:13 AM
To: Tim Robertson; Antonio García Camacho; info@eu-nomen.eu
Cc: api-users@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%3Afaunaeur.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=90d9e8a6-0ce1-472d-b682-3451095dbc5a

 

This will give you

 

{"offset":0,"limit":20,"endOfRecords":true,"results":[{"key":103283278,"nubKey":1097026,"taxonID":"115091","genus":"Prionus","genusKey":103283278,"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","taxonomicStatus":"ACCEPTED","nomenclaturalStatus":[],"numDescendants":6,"references":"http://www.faunaeur.org/full_results.php?id=115091","modified":"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@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 08:48, Tim Robertson <trobertson@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.  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=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> 

 

 

I hope this helps,

Tim

 

 

 

On 26 Jan 2015, at 09:35, Éamonn Ó Tuama [GBIF] <eotuama@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@csic.es
www.ebd.csic.es

 

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