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Hi Francisco,
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<div class="">In principle the approach will work with any identifier, providing:</div>
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<div class="">(a) The EU BON web service (or whatever the source is) returns identifiers for taxa (they don’t have to be LSIDs)</div>
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</div>
<div class="">(b) The provider that supports those identifiers has been indexed by GBIF (and the source indexed by GBIF has those identifiers)</div>
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<div class="">(c) You can figure out the mapping between the identifier served by the source and identifier as indexed by GBIF (in the example I gave only the integer part of the identifier was indexed, which rather defeats the point of identifiers, sigh).</div>
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<div class="">Regards</div>
<div class=""><br class="">
</div>
<div class="">Rod</div>
<div class=""><br class="">
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---------------------------------------------------------<br class="">
Roderic Page<br class="">
Professor of Taxonomy<br class="">
Institute of Biodiversity, Animal Health and Comparative Medicine<br class="">
College of Medical, Veterinary and Life Sciences<br class="">
Graham Kerr Building<br class="">
University of Glasgow<br class="">
Glasgow G12 8QQ, UK<br class="">
<br class="">
Email: <span class="Apple-tab-span" style="white-space: pre;"> </span><a href="mailto:Roderic.Page@glasgow.ac.uk" class="">Roderic.Page@glasgow.ac.uk</a><br class="">
Tel: <span class="Apple-tab-span" style="white-space: pre;"> </span>+44 141 330 4778<br class="">
Skype: <span class="Apple-tab-span" style="white-space: pre;"> </span>rdmpage<br class="">
Facebook: <span class="Apple-tab-span" style="white-space: pre;"> </span>http://www.facebook.com/rdmpage<br class="">
LinkedIn: <span class="Apple-tab-span" style="white-space: pre;"> </span>http://uk.linkedin.com/in/rdmpage<br class="">
Twitter: <span class="Apple-tab-span" style="white-space: pre;"> </span>http://twitter.com/rdmpage<br class="">
Blog: <span class="Apple-tab-span" style="white-space: pre;"> </span>http://iphylo.blogspot.com<br class="">
ORCID: <span class="Apple-tab-span" style="white-space: pre;"> </span>http://orcid.org/0000-0002-7101-9767</div>
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Citations: <span class="Apple-tab-span" style="white-space: pre;"> </span><a href="http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ" class="">http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ</a></div>
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ResearchGate<span class="Apple-tab-span" style="white-space: pre;"> </span><a href="https://www.researchgate.net/profile/Roderic_Page" class="">https://www.researchgate.net/profile/Roderic_Page</a><br class="">
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<blockquote type="cite" class="">
<div class="">On 26 Jan 2015, at 11:24, Francisco Antonio García Camacho <<a href="mailto:antonio.garcia.camacho@csic.es" class="">antonio.garcia.camacho@csic.es</a>> wrote:</div>
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<div class="moz-cite-prefix">Thank you Tim and Roderic for your responses.<br class="">
Roderic's suggested approach seems promising, but it would help us to resolve anymals LSIDs only.<br class="">
In any case, we will need to know how the mapping between PESI and GBIF names is done.<br class="">
<br class="">
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.<br class="">
<br class="">
With regards,<br class="">
Antonio.<br class="">
<br class="">
<div class="moz-signature">
<div class="moz-signature"><strong class="">Antonio García Camacho</strong><br class="">
Estacion Biologica de Doñana (CSIC)<br class="">
Americo Vespucio s/n Isla de la Cartuja<br class="">
41092 Sevilla, España<br class="">
Tel. +34 954232340 / Fax. +34 954621125<br class="">
<a href="mailto:antonio.garcia.camacho@csic.es" class="">antonio.garcia.camacho@csic.es</a><br class="">
<a href="http://www.ebd.csic.es/" class="">www.ebd.csic.es</a> <br class="">
</div>
</div>
El 26/01/2015 a las 12:04, Roderic Page escribió:<br class="">
</div>
<blockquote cite="mid:D85863D1-3D94-480B-9B16-F5994BE7A3AC@glasgow.ac.uk" type="cite" class="">
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.
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<div class="">Regards</div>
<div class=""><br class="">
</div>
<div class="">Rod</div>
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---------------------------------------------------------<br class="">
Roderic Page<br class="">
Professor of Taxonomy<br class="">
Institute of Biodiversity, Animal Health and Comparative Medicine<br class="">
College of Medical, Veterinary and Life Sciences<br class="">
Graham Kerr Building<br class="">
University of Glasgow<br class="">
Glasgow G12 8QQ, UK<br class="">
<br class="">
Email: <span class="Apple-tab-span" style="white-space: pre;"> </span><a moz-do-not-send="true" href="mailto:Roderic.Page@glasgow.ac.uk" class="">Roderic.Page@glasgow.ac.uk</a><br class="">
Tel: <span class="Apple-tab-span" style="white-space:
pre;">
</span>+44 141 330 4778<br class="">
Skype: <span class="Apple-tab-span" style="white-space: pre;"> </span>rdmpage<br class="">
Facebook: <span class="Apple-tab-span" style="white-space: pre;"> </span><a class="moz-txt-link-freetext" href="http://www.facebook.com/rdmpage">http://www.facebook.com/rdmpage</a><br class="">
LinkedIn: <span class="Apple-tab-span" style="white-space: pre;"> </span><a class="moz-txt-link-freetext" href="http://uk.linkedin.com/in/rdmpage">http://uk.linkedin.com/in/rdmpage</a><br class="">
Twitter: <span class="Apple-tab-span" style="white-space: pre;"> </span><a class="moz-txt-link-freetext" href="http://twitter.com/rdmpage">http://twitter.com/rdmpage</a><br class="">
Blog: <span class="Apple-tab-span" style="white-space:
pre;">
</span><a class="moz-txt-link-freetext" href="http://iphylo.blogspot.com/">http://iphylo.blogspot.com</a><br class="">
ORCID: <span class="Apple-tab-span" style="white-space: pre;"> </span><a class="moz-txt-link-freetext" href="http://orcid.org/0000-0002-7101-9767">http://orcid.org/0000-0002-7101-9767</a></div>
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Citations: <span class="Apple-tab-span" style="white-space: pre;"> </span><a moz-do-not-send="true" href="http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ" class="">http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ</a></div>
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ResearchGate<span class="Apple-tab-span" style="white-space: pre;"> </span><a moz-do-not-send="true" href="https://www.researchgate.net/profile/Roderic_Page" class="">https://www.researchgate.net/profile/Roderic_Page</a><br class="">
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<div class="">On 26 Jan 2015, at 10:36, Donat Agosti <<a moz-do-not-send="true" href="mailto:agosti@amnh.org" class="">agosti@amnh.org</a>> wrote:</div>
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<span style="font-size: 11pt; font-family: Calibri,
sans-serif; color: rgb(31, 73, 125);" class="">Dear Anton and colleagues<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri,
sans-serif; color: rgb(31, 73, 125);" class=""> </span></div>
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<span style="font-size: 11pt; font-family: Calibri,
sans-serif; color: rgb(31, 73, 125);" class="">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.<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri,
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<span style="font-size: 11pt; font-family: Calibri,
sans-serif; color: rgb(31, 73, 125);" class="">Cheers<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri,
sans-serif; color: rgb(31, 73, 125);" class="">Donat<o:p class=""></o:p></span></div>
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<span style="font-size: 11pt; font-family: Calibri,
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<span style="font-size: 11pt; font-family: Calibri,
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<b class=""><span style="font-size: 11pt;
font-family: Calibri, sans-serif;" class="">From:</span></b><span style="font-size: 11pt; font-family: Calibri,
sans-serif;" class=""><span class="Apple-converted-space"> </span>API-users
[<a moz-do-not-send="true" href="mailto:api-users-bounces@lists.gbif.org" class="">mailto:api-users-bounces@lists.gbif.org</a>]<span class="Apple-converted-space"> </span><b class="">On Behalf Of<span class="Apple-converted-space"> </span></b>Roderic Page<br class="">
<b class="">Sent:</b><span class="Apple-converted-space"> </span>Monday, January 26, 2015 11:13 AM<br class="">
<b class="">To:</b><span class="Apple-converted-space"> </span>Tim Robertson; Antonio García Camacho;
<a moz-do-not-send="true" href="mailto:info@eu-nomen.eu" class="">info@eu-nomen.eu</a><br class="">
<b class="">Cc:</b><span class="Apple-converted-space"> </span><a moz-do-not-send="true" href="mailto:api-users@lists.gbif.org" class="">api-users@lists.gbif.org</a><br class="">
<b class="">Subject:</b><span class="Apple-converted-space"> </span>Re: [API-users] API GBIF: search species using GUID (LSID)<o:p class=""></o:p></span></div>
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<o:p class=""> </o:p></div>
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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. <a moz-do-not-send="true" href="http://darwin.zoology.gla.ac.uk/%7Erpage/lsid/tester/?q=urn%3Alsid%3Afaunaeur.org%3Ataxname%3A115091" style="color: purple; text-decoration: underline;" class="">http://darwin.zoology.gla.ac.uk/~rpage/lsid/tester/?q=urn%3Alsid%3Afaunaeur.org%3Ataxname%3A115091</a><o:p class=""></o:p></div>
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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 <a moz-do-not-send="true" href="http://www.eu-nomen.eu/portal/webservices.php" style="color: purple; text-decoration: underline;" class="">http://www.eu-nomen.eu/portal/webservices.php</a> It’s
not clear to me that they do this.<o:p class=""></o:p></div>
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Alternatively, Fauna Europaea has been indexed by GBIF (more than once!), so you could use the GBIF API like this:<o:p class=""></o:p></div>
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1. Given a LSID like urn:lsid:faunaeur.org:taxname:115091, trim off the “urn:lsid:faunaeur.org:taxname:” to leave “115091”<o:p class=""></o:p></div>
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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 <a moz-do-not-send="true" href="http://www.gbif.org/dataset/90d9e8a6-0ce1-472d-b682-3451095dbc5a" style="color: purple; text-decoration: underline;" class="">http://www.gbif.org/dataset/90d9e8a6-0ce1-472d-b682-3451095dbc5a</a> ).<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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The URL is:<o:p class=""></o:p></div>
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<a moz-do-not-send="true" href="http://api.gbif.org/v1/species?sourceId=115091&datasetKey=90d9e8a6-0ce1-472d-b682-3451095dbc5a" style="color: purple; text-decoration: underline;" class="">http://api.gbif.org/v1/species?sourceId=115091&datasetKey=90d9e8a6-0ce1-472d-b682-3451095dbc5a</a><o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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This will give you<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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{"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":"<a moz-do-not-send="true" href="http://www.faunaeur.org/full_results.php?id=115091" style="color: purple; text-decoration: underline;" class="">http://www.faunaeur.org/full_results.php?id=115091</a>","modified":"2014-06-14T21:04:19.241+0000","lastInterpreted":"2014-11-03T15:22:26.302+0000","issues":[],"synonym":false}]}<o:p class=""></o:p></div>
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The “nubKey” field has the value 1097026, which is the identifier for GBIF’s classification <a moz-do-not-send="true" href="http://www.gbif.org/species/1097026" style="color: purple; text-decoration: underline;" class="">http://www.gbif.org/species/1097026</a>
You can use 1097026 as the key in a query to get the distribution using the GBIF API.<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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Regards<o:p class=""></o:p></div>
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Rod<o:p class=""></o:p></div>
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<o:p class=""> </o:p></div>
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<span style="" class="">---------------------------------------------------------<br class="">
Roderic Page<br class="">
Professor of Taxonomy<br class="">
Institute of Biodiversity, Animal Health and Comparative Medicine<br class="">
College of Medical, Veterinary and Life Sciences<br class="">
Graham Kerr Building<br class="">
University of Glasgow<br class="">
Glasgow G12 8QQ, UK<br class="">
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Email: <span class="apple-tab-span"><span class="Apple-converted-space"> </span></span><a moz-do-not-send="true" href="mailto:Roderic.Page@glasgow.ac.uk" style="color: purple;
text-decoration: underline;" class="">Roderic.Page@glasgow.ac.uk</a><br class="">
Tel: <span class="apple-tab-span"><span class="Apple-converted-space"> </span></span>+44 141 330 4778<br class="">
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text-decoration: underline;" class="">http://orcid.org/0000-0002-7101-9767</a><o:p class=""></o:p></span></div>
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<span style="" class="">Citations: <span class="apple-tab-span"><span class="Apple-converted-space"> </span></span><a moz-do-not-send="true" href="http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ" style="color: purple;
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<span style="" class="">ResearchGate<span class="apple-tab-span"><span class="Apple-converted-space"> </span></span><a moz-do-not-send="true" href="https://www.researchgate.net/profile/Roderic_Page" style="color: purple;
text-decoration: underline;" class="">https://www.researchgate.net/profile/Roderic_Page</a><o:p class=""></o:p></span></p>
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On 26 Jan 2015, at 08:48, Tim Robertson <<a moz-do-not-send="true" href="mailto:trobertson@gbif.org" style="color: purple; text-decoration:
underline;" class="">trobertson@gbif.org</a>> wrote:<o:p class=""></o:p></div>
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Hola Antonio<o:p class=""></o:p></div>
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Can you please join and use the GBIF API mailing list for questions relating to the API?<o:p class=""></o:p></div>
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<a moz-do-not-send="true" href="http://lists.gbif.org/mailman/listinfo/api-users" style="color: purple; text-decoration:
underline;" class="">http://lists.gbif.org/mailman/listinfo/api-users</a><o:p class=""></o:p></div>
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We don’t make explicit use of LSIDs on<span class="Apple-converted-space"> </span><a moz-do-not-send="true" href="http://gbif.org/" style="color:
purple; text-decoration: underline;" class="">GBIF.org</a>. 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.<o:p class=""></o:p></div>
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E.g. Given the plant genus<span class="Apple-converted-space"> </span><i class="">Oenanthe </i> you can look up the taxon (name usage) information using:<o:p class=""></o:p></div>
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<a moz-do-not-send="true" href="http://api.gbif.org/v1/species/match?verbose=false&kingdom=Plantae&name=Oenante" style="color: purple; text-decoration:
underline;" class="">http://api.gbif.org/v1/species/match?verbose=false&kingdom=Plantae&name=Oenante</a><o:p class=""></o:p></div>
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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:<o:p class=""></o:p></div>
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<a moz-do-not-send="true" href="http://api.gbif.org/v1/occurrence/search?taxonKey=3034893" style="color: purple; text-decoration:
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Alternatively, if you were to publish your own checklist and have GBIF index it, the taxa would be searchable using your own sourceId:<o:p class=""></o:p></div>
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<a moz-do-not-send="true" href="http://api.gbif.org/v1/species?sourceId=%3Cyour%20id%20here%3E" style="color: purple; text-decoration:
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I hope this helps,<o:p class=""></o:p></div>
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Tim<o:p class=""></o:p></div>
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On 26 Jan 2015, at 09:35, Éamonn Ó Tuama [GBIF] <<a moz-do-not-send="true" href="mailto:eotuama@gbif.org" style="color: purple;
text-decoration: underline;" class="">eotuama@gbif.org</a>> wrote:<o:p class=""></o:p></div>
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<span style="font-size: 11pt;
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<span style="font-size: 11pt;
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Antonio.</span><span class="" lang="EN-GB"><o:p class=""></o:p></span></div>
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<span style="font-size: 11pt;
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<span style="font-size: 11pt;
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<b class=""><span style="font-size: 10pt;
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sans-serif;" class="">From:</span></b><span class="apple-converted-space"><span style="font-size: 10pt; font-family:
Tahoma, sans-serif;" class=""> </span></span><span style="font-size: 10pt;
font-family: Tahoma,
sans-serif;" class="">Antonio
García Camacho [<a moz-do-not-send="true" href="mailto:antonio.garcia.camacho@csic.es" style="color: purple;
text-decoration:
underline;" class=""><span style="color: purple;" class="">mailto:antonio.garcia.camacho@csic.es</span></a>]<span class="apple-converted-space"> </span><br class="">
<b class="">Sent:</b><span class="apple-converted-space"> </span>26 January 2015 01:42<br class="">
<b class="">To:</b><span class="apple-converted-space"> </span>Éamonn Ó Tuama<br class="">
<b class="">Subject:</b><span class="apple-converted-space"> </span>API GBIF: search species using GUID (LSID)</span><span class="" lang="EN-GB"><o:p class=""></o:p></span></div>
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<span class="" lang="EN-GB"> <o:p class=""></o:p></span></div>
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<span class="" lang="EN-GB">Dear Éamonn,<o:p class=""></o:p></span></div>
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<span class="" lang="EN-GB">We found some problems using the GBIF API to search for occurrences and datasets. I will explain the use scenario:<o:p class=""></o:p></span></div>
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<span class="" lang="EN-GB">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.<o:p class=""></o:p></span></div>
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<span class="" lang="EN-GB">Is there a way to filter using species LSIDs or even translating these LSIDs to taxonKeys?<o:p class=""></o:p></span></div>
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<span class="" lang="EN-GB">Thanks,<o:p class=""></o:p></span></div>
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<span class="" lang="EN-GB">Antonio.<o:p class=""></o:p></span></div>
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<span style="background-color:
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background-repeat: initial
initial;" class="" lang="EN-GB">-- </span><span class="" lang="EN-GB"><o:p class=""></o:p></span></div>
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<strong class=""><span class="" lang="EN-GB">Antonio García Camacho</span></strong><span class="" lang="EN-GB"><br class="">
Estacion Biologica de Doñana (CSIC)<br class="">
Americo Vespucio s/n Isla de la Cartuja<br class="">
41092 Sevilla, España<br class="">
Tel. +34 954232340 / Fax. +34 954621125<br class="">
<a moz-do-not-send="true" href="mailto:antonio.garcia.camacho@csic.es" style="color: purple;
text-decoration:
underline;" class=""><span style="color: purple;" class="">antonio.garcia.camacho@csic.es</span></a><br class="">
<a moz-do-not-send="true" href="http://www.ebd.csic.es/" style="color: purple; text-decoration:
underline;" class=""><span style="color: purple;" class="">www.ebd.csic.es</span></a><o:p class=""></o:p></span></div>
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_______________________________________________<br class="">
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