[API-users] API GBIF: search species using GUID (LSID)
Francisco Antonio García Camacho
antonio.garcia.camacho at csic.es
Mon Jan 26 12:24:25 CET 2015
Thank you Tim and Roderic for your responses.
Roderic's suggested approach seems promising, but it would help us to
resolve anymals LSIDs only.
In any case, we will need to know how the mapping between PESI and GBIF
names is done.
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.
With regards,
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 <mailto:antonio.garcia.camacho at csic.es>
www.ebd.csic.es <http://www.ebd.csic.es/>
El 26/01/2015 a las 12:04, Roderic Page escribió:
> 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
> ResearchGatehttps://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 García 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%3Afaunaeur.org%3Ataxname%3A115091
>> <http://darwin.zoology.gla.ac.uk/%7Erpage/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 <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
>>
>> ResearchGatehttps://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 onGBIF.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&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>
>> <http://api.gbif.org/v1/species?sourceId=%3Cyour%20id%20here%3E>
>> I hope this helps,
>> Tim
>> On 26 Jan 2015, at 09:35, Éamonn Ó Tuama [GBIF] <eotuama at gbif.org
>> <mailto: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
>> <mailto:antonio.garcia.camacho at csic.es>
>> www.ebd.csic.es <http://www.ebd.csic.es/>
>>
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>
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