[API-users] API GBIF: search species using GUID (LSID)

Richard Pyle deepreef at bishopmuseum.org
Tue Jan 27 11:22:39 CET 2015


Sometimes there are good reasons. For example, objects that appear to be the
same thing and therefore would share the same identifier are in fact not the
same thing, and therefore should not share the same identifier (e.g., ITIS
TSNs vs. Catalog of Fishes identifiers). Or, sometimes obvious identifiers
(e.g., DOIs) do not cover the full scope (e.g., all historical literature).
ORCIDs for dead people. Etc.

 

Sometimes there are bad reasons (you know these as well as anyone).

 

So
 while we’re at it, can we just stop wishing for an ideal utopia, and
recognize the reality that there are already multiple identifiers for
things, and there will likely continue to be multiple identifiers for things
for a long time yet to come. Instead of lamenting this reality, we should
design our data management systems to accommodate it.

 

Aloha,

Rich

 

 

From: API-users [mailto:api-users-bounces at lists.gbif.org] On Behalf Of
Roderic Page
Sent: Monday, January 26, 2015 1:05 AM
To: Donat Agosti
Cc: api-users at lists.gbif.org; info at eu-nomen.eu; wp2 at eubon.eu; wp1 at eubon.eu
Subject: Re: [API-users] API GBIF: search species using GUID (LSID)

 

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
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
<http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ>
&user=4Z5WABAAAAAJ

ResearchGate https://www.researchgate.net/profile/Roderic_Page

 

On 26 Jan 2015, at 10:36, Donat Agosti <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
Cc: 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/~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>
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>
http://www.gbif.org/dataset/90d9e8a6-0ce1-472d-b682-3451095dbc5a ).

 

The URL is:

 

 
<http://api.gbif.org/v1/species?sourceId=115091&datasetKey=90d9e8a6-0ce1-472
d-b682-3451095dbc5a>
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,"nubK
ey":1097026,"taxonID":"115091","genus":"Prionus","genusKey":103283278,"datas
etKey":"90d9e8a6-0ce1-472d-b682-3451095dbc5a","parentKey":103294043,"parent"
:"Prioninae","scientificName":"Prionus Geoffroy,
1762","canonicalName":"Prionus","authorship":"Geoffroy,
1762","nameType":"WELLFORMED","rank":"GENUS","origin":"SOURCE","taxonomicSta
tus":"ACCEPTED","nomenclaturalStatus":[],"numDescendants":6,"references":"
<http://www.faunaeur.org/full_results.php?id=115091>
http://www.faunaeur.org/full_results.php?id=115091","modified":"2014-06-14T2
1:04:19.241+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>
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:   <mailto:Roderic.Page at glasgow.ac.uk> Roderic.Page at glasgow.ac.uk
Tel:  +44 141 330 4778
Skype:  rdmpage
Facebook:   <http://www.facebook.com/rdmpage>
http://www.facebook.com/rdmpage
LinkedIn:   <http://uk.linkedin.com/in/rdmpage>
http://uk.linkedin.com/in/rdmpage
Twitter:   <http://twitter.com/rdmpage> http://twitter.com/rdmpage
Blog:   <http://iphylo.blogspot.com/> http://iphylo.blogspot.com
ORCID:   <http://orcid.org/0000-0002-7101-9767>
http://orcid.org/0000-0002-7101-9767

Citations:   <http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ>
http://scholar.google.co.uk/citations?hl=en&user=4Z5WABAAAAAJ

ResearchGate  <https://www.researchgate.net/profile/Roderic_Page>
https://www.researchgate.net/profile/Roderic_Page

 

On 26 Jan 2015, at 08:48, Tim Robertson < <mailto:trobertson at gbif.org>
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>
http://lists.gbif.org/mailman/listinfo/api-users

 

We don’t make explicit use of LSIDs on  <http://gbif.org/> 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=Oen
ante>
http://api.gbif.org/v1/species/match?verbose=false&kingdom=Plantae&name=Oena
nte

 

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>
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=%3Cyour%20id%20here%3E>
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] < <mailto:eotuama at gbif.org>
eotuama at gbif.org> wrote:






Tim,

Best for you to answer Antonio.

Éamonn

 

From: Antonio García Camacho [ <mailto:antonio.garcia.camacho at csic.es>
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
 <mailto:antonio.garcia.camacho at csic.es> antonio.garcia.camacho at csic.es
 <http://www.ebd.csic.es/> www.ebd.csic.es

 

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