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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>
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<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="">
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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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<div class="">On 26 Jan 2015, at 10:36, Donat Agosti <<a 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="">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, 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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<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 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 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 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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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 href="http://darwin.zoology.gla.ac.uk/~rpage/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 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 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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The URL is:<o:p class=""></o:p></div>
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<a 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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This will give you<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 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 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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Regards<o:p class=""></o:p></div>
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Rod<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 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="">
Skype: <span class="apple-tab-span"><span class="Apple-converted-space"> </span></span>rdmpage<br class="">
Facebook: <span class="apple-tab-span"><span class="Apple-converted-space"> </span></span><a href="http://www.facebook.com/rdmpage" style="color: purple; text-decoration: underline;" class="">http://www.facebook.com/rdmpage</a><br class="">
LinkedIn: <span class="apple-tab-span"><span class="Apple-converted-space"> </span></span><a href="http://uk.linkedin.com/in/rdmpage" style="color: purple; text-decoration: underline;" class="">http://uk.linkedin.com/in/rdmpage</a><br class="">
Twitter: <span class="apple-tab-span"><span class="Apple-converted-space"> </span></span><a href="http://twitter.com/rdmpage" style="color: purple; text-decoration: underline;" class="">http://twitter.com/rdmpage</a><br class="">
Blog: <span class="apple-tab-span"><span class="Apple-converted-space"> </span></span><a href="http://iphylo.blogspot.com/" style="color: purple; text-decoration: underline;" class="">http://iphylo.blogspot.com</a><br class="">
ORCID: <span class="apple-tab-span"><span class="Apple-converted-space"> </span></span><a href="http://orcid.org/0000-0002-7101-9767" style="color: purple; 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 href="http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ" style="color: purple; text-decoration: underline;" class="">http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ</a><o:p class=""></o:p></span></div>
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<span style="" class="">ResearchGate<span class="apple-tab-span"><span class="Apple-converted-space"> </span></span><a 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 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 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 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 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 href="http://api.gbif.org/v1/occurrence/search?taxonKey=3034893" style="color: purple; text-decoration: underline;" class="">http://api.gbif.org/v1/occurrence/search?taxonKey=3034893</a><o:p class=""></o:p></div>
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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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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 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 lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Tim,</span><span lang="EN-GB" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Best for you to answer Antonio.</span><span lang="EN-GB" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class="">Éamonn</span><span lang="EN-GB" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-GB" style="font-size: 11pt; font-family: Calibri, sans-serif; color: rgb(31, 73, 125);" class=""> </span><span lang="EN-GB" class=""><o:p class=""></o:p></span></div>
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<b class=""><span style="font-size: 10pt; font-family: Tahoma, 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 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 lang="EN-GB" class=""><o:p class=""></o:p></span></div>
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<span lang="EN-GB" class="">Dear Éamonn,<o:p class=""></o:p></span></div>
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<span lang="EN-GB" class="">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 lang="EN-GB" class="">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 lang="EN-GB" class="">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 lang="EN-GB" class="">Thanks,<o:p class=""></o:p></span></div>
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<span lang="EN-GB" class="">Antonio.<o:p class=""></o:p></span></div>
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<span lang="EN-GB" style="background-color: white; background-position: initial initial; background-repeat: initial initial;" class="">-- </span><span lang="EN-GB" class=""><o:p class=""></o:p></span></div>
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<strong class=""><span lang="EN-GB" class="">Antonio García Camacho</span></strong><span lang="EN-GB" class=""><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" style="color: purple; text-decoration: underline;" class=""><span style="color: purple;" class="">antonio.garcia.camacho@csic.es</span></a><br class="">
<a 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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