Sometimes there are good reasons. For example, objects that appear to be the same thing and therefore would share the same identifier are in fact not the same thing, and therefore should not share the same identifier (e.g., ITIS TSNs vs. Catalog of Fishes identifiers). Or, sometimes obvious identifiers (e.g., DOIs) do not cover the full scope (e.g., all historical literature). ORCIDs for dead people. Etc.
Sometimes there are bad reasons (you know these as well as anyone).
So while were at it, can we just stop wishing for an ideal utopia, and recognize the reality that there are already multiple identifiers for things, and there will likely continue to be multiple identifiers for things for a long time yet to come. Instead of lamenting this reality, we should design our data management systems to accommodate it.
Aloha,
Rich
From: API-users [mailto:api-users-bounces@lists.gbif.org] On Behalf Of Roderic Page Sent: Monday, January 26, 2015 1:05 AM To: Donat Agosti Cc: api-users@lists.gbif.org; info@eu-nomen.eu; wp2@eubon.eu; wp1@eubon.eu Subject: Re: [API-users] API GBIF: search species using GUID (LSID)
And while were 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 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
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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-BONs 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 Tims 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 doesnt actually work (in the sense that it cant be resolved), see e.g. http://darwin.zoology.gla.ac.uk/~rpage/lsid/tester/?q=urn%3Alsid%3Afaunaeur .org%3Ataxname%3A115091 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 http://www.eu-nomen.eu/portal/webservices.php Its 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 http://www.gbif.org/dataset/90d9e8a6-0ce1-472d-b682-3451095dbc5a ).
The URL is:
http://api.gbif.org/v1/species?sourceId=115091&datasetKey=90d9e8a6-0ce1-472 d-b682-3451095dbc5a http://api.gbif.org/v1/species?sourceId=115091&datasetKey=90d9e8a6-0ce1-... -b682-3451095dbc5a
This will give you
{"offset":0,"limit":20,"endOfRecords":true,"results":[{"key":103283278,"nubK ey":1097026,"taxonID":"115091","genus":"Prionus","genusKey":103283278,"datas etKey":"90d9e8a6-0ce1-472d-b682-3451095dbc5a","parentKey":103294043,"parent" :"Prioninae","scientificName":"Prionus Geoffroy, 1762","canonicalName":"Prionus","authorship":"Geoffroy, 1762","nameType":"WELLFORMED","rank":"GENUS","origin":"SOURCE","taxonomicSta tus":"ACCEPTED","nomenclaturalStatus":[],"numDescendants":6,"references":" http://www.faunaeur.org/full_results.php?id=115091 http://www.faunaeur.org/full_results.php?id=115091%22,%22modified%22:%222014... 1:04:19.241+0000","lastInterpreted":"2014-11-03T15:22:26.302+0000","issues": [],"synonym":false}]}
The nubKey field has the value 1097026, which is the identifier for GBIFs classification http://www.gbif.org/species/1097026 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: mailto:Roderic.Page@glasgow.ac.uk Roderic.Page@glasgow.ac.uk Tel: +44 141 330 4778 Skype: rdmpage Facebook: http://www.facebook.com/rdmpage http://www.facebook.com/rdmpage LinkedIn: http://uk.linkedin.com/in/rdmpage http://uk.linkedin.com/in/rdmpage Twitter: http://twitter.com/rdmpage http://twitter.com/rdmpage Blog: http://iphylo.blogspot.com/ http://iphylo.blogspot.com ORCID: http://orcid.org/0000-0002-7101-9767 http://orcid.org/0000-0002-7101-9767
Citations: http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ
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On 26 Jan 2015, at 08:48, Tim Robertson < mailto:trobertson@gbif.org 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 http://lists.gbif.org/mailman/listinfo/api-users
We dont make explicit use of LSIDs on http://gbif.org/ 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=Oen ante http://api.gbif.org/v1/species/match?verbose=false&kingdom=Plantae&n... nte
noting the usageID is 3034893 in the response. Youd 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 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=%3Cyour%20id%20here%3E 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] < mailto:eotuama@gbif.org eotuama@gbif.org> wrote:
Tim,
Best for you to answer Antonio.
Éamonn
From: Antonio García Camacho [ mailto:antonio.garcia.camacho@csic.es 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.