[API-users] API GBIF: search species using GUID (LSID)
Bart Vanhoorne
bart.vanhoorne at vliz.be
Mon Jan 26 13:01:42 CET 2015
Agree, I just wanted to explain the PESI workflow.
So your described method seems to be the way forward for EU-BON.
Bart
From: Roderic Page [mailto:Roderic.Page at glasgow.ac.uk]
Sent: Monday, January 26, 2015 12:59
To: Bart Vanhoorne
Cc: Donat Agosti; wp1 at eubon.eu; wp2 at eubon.eu; api-users at lists.gbif.org; Tim Robertson; Antonio García Camacho; info at eu-nomen.eu
Subject: Re: [API-users] API GBIF: search species using GUID (LSID)
Hi Bart,
I guess I´d regard Fauna Europaea, WoRMS, etc. as already too many identifiers, but I digress ;)
The URL you create is nice, but it is for a web page, and furthermore it is for the old GBIF portal. I think the original goal was to programmatically get the GBIF id in order to access GBIF data, via the GBIF API, using a EU-BON-derived identifier.
Regards
Rod
---------------------------------------------------------
Roderic Page
Professor of Taxonomy
Institute of Biodiversity, Animal Health and Comparative Medicine
College of Medical, Veterinary and Life Sciences
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University of Glasgow
Glasgow G12 8QQ, UK
Email: Roderic.Page at glasgow.ac.uk
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On 26 Jan 2015, at 11:49, Bart Vanhoorne <bart.vanhoorne at vliz.be> wrote:
Rod,
Creating new identifiers is exactly what PESI has NOT done!
It has re-used the identifiers from it´s source databases: Fauna Europaea, ERMS/WoRMS & Index Fungorum.
I think the same is true for EU-BON´s taxonomic backbone as they uses PESI.
So maybe we should reformulate the question and ask why GBIF is adding to the identifier soup... :)
Anyway, about the initial question: PESI vs GBIF identifiers.
We have used the short version what you describe: we don´t even need to call the GBIF API to generate the links:
Same example for Prionus Geoffroy, 1762:
http://www.eu-nomen.eu/portal/taxon.php?GUID=urn:lsid:faunaeur.org:taxname:115091
http://data.gbif.org/species/ + [Fauna Europaea species identifier=115091] + /resource/ [GBIF dataset id for FE=13560]
=>
http://data.gbif.org/species/115091/resource/13560
And there is the GBIF link, without calling any API.
Regards,
Bart Vanhoorne
WoRMS Data Management Team
PESI DMT Team
From: Roderic Page [mailto:Roderic.Page at glasgow.ac.uk]
Sent: Monday, January 26, 2015 12:05
To: Donat Agosti
Cc: wp1 at eubon.eu; wp2 at eubon.eu; api-users at lists.gbif.org; Tim Robertson; Antonio García Camacho; info at eu-nomen.eu
Subject: Re: [API-users] API GBIF: search species using GUID (LSID)
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
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> 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
Cc: 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%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 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 08:48, Tim Robertson <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. 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 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
www.ebd.csic.es
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