[API-users] API GBIF: search species using GUID (LSID)
Kohlbecker, Andreas
a.kohlbecker at BGBM.org
Mon Jan 26 12:14:17 CET 2015
I would like to add some more thoughts on this issue.
Not all checklists which are integrated into PESI provide a LSIDs. To be precise: ERMS, Fauna Europaea und the Index Fungorum provide an LSID and the
Euro+Med Plantbase does not, it provides a GUID instead. But in any case the method described by Roderic should be feasible to map the search results returned by the EU BON taxonomic backbone for PESI to the GBIF species record.
The GUID of the Euro+Med Plantbase taxa can be extracted from the EU BON taxonomic backbone responses by parsing the url field of the source information for the respective taxon response, e.g.:
response": [
{
"taxon":
{
"taxonName":
{
"fullName": "Lapsana communis L.",
"canonicalName": "Lapsana communis",
"atomisedName": null,
"authorship": "L.",
"rank": "Species",
"nomenclaturalReference": null
},
"accordingTo": "Greuter, W. (2006-2009): Compositae (pro parte majore). – In: Greuter, W. & Raab-Straube, E. von (ed.): Compositae. Euro+Med Plantbase - the information resource for Euro-Mediterranean plant diversity. Lapsana communis L.",
"url": "http://www.eu-nomen.eu/portal/taxon.php?GUID=1287B582-C995-4DB6-9481-A93E7E1C99B8",
"taxonomicStatus": "accepted",
"sources":
[
{
"url": "http://ww2.bgbm.org/euroPlusMed/PTaxonDetail.asp?UUID=1287B582-C995-4DB6-9481-A93E7E1C99B8",
"datasetID": null,
"datasetName": null,
"name": null,
"title": "Greuter, W. (2006-2009): Compositae (pro parte majore). – In: Greuter, W. & Raab-Straube, E. von (ed.): Compositae. Euro+Med Plantbase - the information resource for Euro-Mediterranean plant diversity. Lapsana communis L."
}
],
....
The EU BON taxonomic backbone provides a federated search on more checklists than only PESI. Also CoL and WoRMS are covered so far and more are to be added (EUNIS, Natura 2000). In case of Natura 2000 it is problematic to do the mapping to GBIF species, since Natura 2000 is not listed a checklist in the proper sense. The Natura 2000 Species data is not covering any classification it consists mainly of species names and the Natura 2000 species ID, so it is rather a name list than a source for taxonomic information. I guess it is not listed in GBIF due to the lack of taxonomic information.
regards
Andreas
On Monday 26 January 2015 11:13:02 Roderic Page wrote:
> 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
>
> _______________________________________________
> API-users mailing list
> API-users at lists.gbif.org
> http://lists.gbif.org/mailman/listinfo/api-users
>
>
>
More information about the API-users
mailing list