Dear Rod, i completely and utterly agree.... Best Dirk
On 26 Jan 2015 at 11:04, Roderic Page wrote: > 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<mailto: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<mailto: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 Garc?a Camacho; > info at eu-nomen.eu<mailto:info at eu-nomen.eu> Cc: > api-users at lists.gbif.org<mailto: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%3Afau > naeur.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=90d9e8a6-0ce > 1-472d-b682-3451095dbc5a > > This will give you > > {"offset":0,"limit":20,"endOfRecords":true,"results":[{"key":103283278 > ,"nubKey":1097026,"taxonID":"115091","genus":"Prionus","genusKey":1032 > 83278,"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","taxono > micStatus":"ACCEPTED","nomenclaturalStatus":[],"numDescendants":6,"ref > erences":"http://www.faunaeur.org/full_results.php?id=115091","modifie > d":"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<mailto: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<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<mailto: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<http://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&n > ame=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><http://api.gbif.org/v1/species?sourceId=%3Cyour%20id%20here%3E > > > > > I hope this helps, > Tim > > > > On 26 Jan 2015, at 09:35, ?amonn ? Tuama [GBIF] > <eotuama at gbif.org<mailto:eotuama at gbif.org>> wrote: > > > Tim, > Best for you to answer Antonio. > ?amonn > > From: Antonio Garc?a Camacho [mailto:antonio.garcia.camacho at csic.es] > Sent: 26 January 2015 01:42 To: ?amonn ? Tuama Subject: API GBIF: > search species using GUID (LSID) > > Dear ?amonn, > 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 Garc?a Camacho > Estacion Biologica de Do?ana (CSIC) > Americo Vespucio s/n Isla de la Cartuja > 41092 Sevilla, Espa?a > Tel. +34 954232340 / Fax. +34 954621125 > antonio.garcia.camacho at csic.es<mailto:antonio.garcia.camacho at csic.es> > www.ebd.csic.es<http://www.ebd.csic.es/> > > _______________________________________________ > API-users mailing list > API-users at lists.gbif.org<mailto:API-users at lists.gbif.org> > http://lists.gbif.org/mailman/listinfo/api-users > >
