Re: [API-users] API GBIF: search species using GUID (LSID)
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. 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...
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>
I hope this helps, Tim
On 26 Jan 2015, at 09:35, Éamonn Ó Tuama [GBIF] eotuama@gbif.org wrote:
Tim, Best for you to answer Antonio. Éamonn
From: Antonio García Camacho [mailto:antonio.garcia.camacho@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@csic.es www.ebd.csic.es
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....
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-...
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%22,%22modified%22:%222014...
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@glasgow.ac.ukmailto:Roderic.Page@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 08:48, Tim Robertson <trobertson@gbif.orgmailto:trobertson@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.orghttp://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...
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@gbif.orgmailto:eotuama@gbif.org> wrote:
Tim, Best for you to answer Antonio. Éamonn
From: Antonio García Camacho [mailto:antonio.garcia.camacho@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@csic.esmailto:antonio.garcia.camacho@csic.es www.ebd.csic.eshttp://www.ebd.csic.es/
_______________________________________________ API-users mailing list API-users@lists.gbif.orgmailto:API-users@lists.gbif.org http://lists.gbif.org/mailman/listinfo/api-users
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@lists.gbif.org] On Behalf Of Roderic Page Sent: Monday, January 26, 2015 11:13 AM To: Tim Robertson; Antonio García Camacho; info@eu-nomen.eu Cc: api-users@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....
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-...
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%22,%22modified%22:%222014...
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@glasgow.ac.ukmailto:Roderic.Page@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 08:48, Tim Robertson <trobertson@gbif.orgmailto:trobertson@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.orghttp://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...
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@gbif.orgmailto:eotuama@gbif.org> wrote:
Tim, Best for you to answer Antonio. Éamonn
From: Antonio García Camacho [mailto:antonio.garcia.camacho@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@csic.esmailto:antonio.garcia.camacho@csic.es www.ebd.csic.eshttp://www.ebd.csic.es/
_______________________________________________ API-users mailing list API-users@lists.gbif.orgmailto:API-users@lists.gbif.org http://lists.gbif.org/mailman/listinfo/api-users
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@glasgow.ac.ukmailto:Roderic.Page@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@amnh.orgmailto:agosti@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@lists.gbif.org] On Behalf Of Roderic Page Sent: Monday, January 26, 2015 11:13 AM To: Tim Robertson; Antonio García Camacho; info@eu-nomen.eumailto:info@eu-nomen.eu Cc: api-users@lists.gbif.orgmailto:api-users@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....
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-...
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%22,%22modified%22:%222014...
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@glasgow.ac.ukmailto:Roderic.Page@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.comhttp://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@gbif.orgmailto:trobertson@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.orghttp://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...
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@gbif.orgmailto:eotuama@gbif.org> wrote:
Tim, Best for you to answer Antonio. Éamonn
From: Antonio García Camacho [mailto:antonio.garcia.camacho@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@csic.esmailto:antonio.garcia.camacho@csic.es www.ebd.csic.eshttp://www.ebd.csic.es/
_______________________________________________ API-users mailing list API-users@lists.gbif.orgmailto:API-users@lists.gbif.org http://lists.gbif.org/mailman/listinfo/api-users
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@csic.es mailto:antonio.garcia.camacho@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@glasgow.ac.uk mailto:Roderic.Page@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@amnh.org mailto:agosti@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@lists.gbif.org]*On Behalf Of*Roderic Page *Sent:*Monday, January 26, 2015 11:13 AM *To:*Tim Robertson; Antonio García Camacho; info@eu-nomen.eu mailto:info@eu-nomen.eu *Cc:*api-users@lists.gbif.org mailto:api-users@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.... 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:
- 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-... 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%22,%22modified%22:%222014... 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@glasgow.ac.uk mailto:Roderic.Page@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@gbif.org <mailto:trobertson@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@gbif.org <mailto:eotuama@gbif.org>> wrote: Tim, Best for you to answer Antonio. Éamonn *From:*Antonio García Camacho [mailto:antonio.garcia.camacho@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@csic.es <mailto:antonio.garcia.camacho@csic.es> www.ebd.csic.es <http://www.ebd.csic.es/> _______________________________________________ API-users mailing list API-users@lists.gbif.org <mailto:API-users@lists.gbif.org> http://lists.gbif.org/mailman/listinfo/api-users
Hi Francisco,
In principle the approach will work with any identifier, providing:
(a) The EU BON web service (or whatever the source is) returns identifiers for taxa (they don’t have to be LSIDs)
(b) The provider that supports those identifiers has been indexed by GBIF (and the source indexed by GBIF has those identifiers)
(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).
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@glasgow.ac.ukmailto:Roderic.Page@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 11:24, Francisco Antonio García Camacho <antonio.garcia.camacho@csic.esmailto:antonio.garcia.camacho@csic.es> wrote:
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@csic.esmailto:antonio.garcia.camacho@csic.es www.ebd.csic.eshttp://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@glasgow.ac.ukmailto:Roderic.Page@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.comhttp://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@amnh.orgmailto:agosti@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@lists.gbif.org] On Behalf Of Roderic Page Sent: Monday, January 26, 2015 11:13 AM To: Tim Robertson; Antonio García Camacho; info@eu-nomen.eumailto:info@eu-nomen.eu Cc: api-users@lists.gbif.orgmailto:api-users@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....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-...
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%22,%22modified%22:%222014...
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@glasgow.ac.ukmailto:Roderic.Page@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.comhttp://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@gbif.orgmailto:trobertson@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.orghttp://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...
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@gbif.orgmailto:eotuama@gbif.org> wrote:
Tim, Best for you to answer Antonio. Éamonn
From: Antonio García Camacho [mailto:antonio.garcia.camacho@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@csic.esmailto:antonio.garcia.camacho@csic.es www.ebd.csic.eshttp://www.ebd.csic.es/
_______________________________________________ API-users mailing list API-users@lists.gbif.orgmailto:API-users@lists.gbif.org http://lists.gbif.org/mailman/listinfo/api-users
Rod,
Creating new identifiers is exactly what PESI has NOT done! It has re-used the identifiers from it´s source databases: Fauna Europaea, ERMS/WoRMS & Index Fungorum. I think the same is true for EU-BON´s taxonomic backbone as they uses PESI.
So maybe we should reformulate the question and ask why GBIF is adding to the identifier soup... :)
Anyway, about the initial question: PESI vs GBIF identifiers. We have used the short version what you describe: we don´t even need to call the GBIF API to generate the links: Same example for Prionus Geoffroy, 1762: http://www.eu-nomen.eu/portal/taxon.php?GUID=urn:lsid:faunaeur.org:taxname:1... http://data.gbif.org/species/ + [Fauna Europaea species identifier=115091] + /resource/ [GBIF dataset id for FE=13560] => http://data.gbif.org/species/115091/resource/13560
And there is the GBIF link, without calling any API.
Regards, Bart Vanhoorne WoRMS Data Management Team PESI DMT Team
From: Roderic Page [mailto:Roderic.Page@glasgow.ac.uk] Sent: Monday, January 26, 2015 12:05 To: Donat Agosti Cc: wp1@eubon.eu; wp2@eubon.eu; api-users@lists.gbif.org; Tim Robertson; Antonio García Camacho; info@eu-nomen.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@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@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@lists.gbif.org] On Behalf Of Roderic Page Sent: Monday, January 26, 2015 11:13 AM To: Tim Robertson; Antonio García Camacho; info@eu-nomen.eu Cc: api-users@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....
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-...
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%22,%22modified%22:%222014...
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@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 08:48, Tim Robertson trobertson@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. 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...
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>
I hope this helps, Tim
On 26 Jan 2015, at 09:35, Éamonn Ó Tuama [GBIF] eotuama@gbif.org wrote:
Tim, Best for you to answer Antonio. Éamonn
From: Antonio García Camacho [mailto:antonio.garcia.camacho@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.
Hi Bart,
I guess I’d regard Fauna Europaea, WoRMS, etc. as already too many identifiers, but I digress ;)
The URL you create is nice, but it is for a web page, and furthermore it is for the old GBIF portal. I think the original goal was to programmatically get the GBIF id in order to access GBIF data, via the GBIF API, using a EU-BON-derived identifier.
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@glasgow.ac.ukmailto:Roderic.Page@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 11:49, Bart Vanhoorne <bart.vanhoorne@vliz.bemailto:bart.vanhoorne@vliz.be> wrote:
Rod,
Creating new identifiers is exactly what PESI has NOT done! It has re-used the identifiers from it’s source databases: Fauna Europaea, ERMS/WoRMS & Index Fungorum. I think the same is true for EU-BON’s taxonomic backbone as they uses PESI.
So maybe we should reformulate the question and ask why GBIF is adding to the identifier soup… :)
Anyway, about the initial question: PESI vs GBIF identifiers. We have used the short version what you describe: we don’t even need to call the GBIF API to generate the links: Same example for Prionus Geoffroy, 1762: http://www.eu-nomen.eu/portal/taxon.php?GUID=urn:lsid:faunaeur.org:taxname:1... http://data.gbif.org/species/ + [Fauna Europaea species identifier=115091] + /resource/ [GBIF dataset id for FE=13560] => http://data.gbif.org/species/115091/resource/13560
And there is the GBIF link, without calling any API.
Regards, Bart Vanhoorne WoRMS Data Management Team PESI DMT Team
From: Roderic Page [mailto:Roderic.Page@glasgow.ac.uk] Sent: Monday, January 26, 2015 12:05 To: Donat Agosti Cc: wp1@eubon.eumailto:wp1@eubon.eu; wp2@eubon.eumailto:wp2@eubon.eu; api-users@lists.gbif.orgmailto:api-users@lists.gbif.org; Tim Robertson; Antonio García Camacho; info@eu-nomen.eumailto:info@eu-nomen.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@glasgow.ac.ukmailto:Roderic.Page@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@amnh.orgmailto:agosti@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@lists.gbif.org] On Behalf Of Roderic Page Sent: Monday, January 26, 2015 11:13 AM To: Tim Robertson; Antonio García Camacho; info@eu-nomen.eumailto:info@eu-nomen.eu Cc: api-users@lists.gbif.orgmailto:api-users@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....
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-...
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%22,%22modified%22:%222014...
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@glasgow.ac.ukmailto:Roderic.Page@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.comhttp://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@gbif.orgmailto:trobertson@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.orghttp://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...
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@gbif.orgmailto:eotuama@gbif.org> wrote:
Tim, Best for you to answer Antonio. Éamonn
From: Antonio García Camacho [mailto:antonio.garcia.camacho@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@csic.esmailto:antonio.garcia.camacho@csic.es www.ebd.csic.eshttp://www.ebd.csic.es/
_______________________________________________ API-users mailing list API-users@lists.gbif.orgmailto:API-users@lists.gbif.org http://lists.gbif.org/mailman/listinfo/api-users
Agree, I just wanted to explain the PESI workflow. So your described method seems to be the way forward for EU-BON.
Bart
From: Roderic Page [mailto:Roderic.Page@glasgow.ac.uk] Sent: Monday, January 26, 2015 12:59 To: Bart Vanhoorne Cc: Donat Agosti; wp1@eubon.eu; wp2@eubon.eu; api-users@lists.gbif.org; Tim Robertson; Antonio García Camacho; info@eu-nomen.eu Subject: Re: [API-users] API GBIF: search species using GUID (LSID)
Hi Bart,
I guess I´d regard Fauna Europaea, WoRMS, etc. as already too many identifiers, but I digress ;)
The URL you create is nice, but it is for a web page, and furthermore it is for the old GBIF portal. I think the original goal was to programmatically get the GBIF id in order to access GBIF data, via the GBIF API, using a EU-BON-derived identifier.
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@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 11:49, Bart Vanhoorne bart.vanhoorne@vliz.be wrote:
Rod,
Creating new identifiers is exactly what PESI has NOT done! It has re-used the identifiers from it´s source databases: Fauna Europaea, ERMS/WoRMS & Index Fungorum. I think the same is true for EU-BON´s taxonomic backbone as they uses PESI.
So maybe we should reformulate the question and ask why GBIF is adding to the identifier soup... :)
Anyway, about the initial question: PESI vs GBIF identifiers. We have used the short version what you describe: we don´t even need to call the GBIF API to generate the links: Same example for Prionus Geoffroy, 1762: http://www.eu-nomen.eu/portal/taxon.php?GUID=urn:lsid:faunaeur.org:taxname:1... http://data.gbif.org/species/ + [Fauna Europaea species identifier=115091] + /resource/ [GBIF dataset id for FE=13560] => http://data.gbif.org/species/115091/resource/13560
And there is the GBIF link, without calling any API.
Regards, Bart Vanhoorne WoRMS Data Management Team PESI DMT Team
From: Roderic Page [mailto:Roderic.Page@glasgow.ac.uk] Sent: Monday, January 26, 2015 12:05 To: Donat Agosti Cc: wp1@eubon.eu; wp2@eubon.eu; api-users@lists.gbif.org; Tim Robertson; Antonio García Camacho; info@eu-nomen.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@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@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@lists.gbif.org] On Behalf Of Roderic Page Sent: Monday, January 26, 2015 11:13 AM To: Tim Robertson; Antonio García Camacho; info@eu-nomen.eu Cc: api-users@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....
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-...
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%22,%22modified%22:%222014...
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@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 08:48, Tim Robertson trobertson@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. 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...
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>
I hope this helps, Tim
On 26 Jan 2015, at 09:35, Éamonn Ó Tuama [GBIF] eotuama@gbif.org wrote:
Tim, Best for you to answer Antonio. Éamonn
From: Antonio García Camacho [mailto:antonio.garcia.camacho@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.
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@glasgow.ac.ukmailto:Roderic.Page@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@amnh.orgmailto:agosti@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@lists.gbif.org] On Behalf Of Roderic Page Sent: Monday, January 26, 2015 11:13 AM To: Tim Robertson; Antonio García Camacho; info@eu-nomen.eumailto:info@eu-nomen.eu Cc: api-users@lists.gbif.orgmailto:api-users@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:
- Given a LSID like urn:lsid:faunaeur.org:taxname:115091, trim off
the "urn:lsid:faunaeur.org:taxname:" to leave "115091"
- 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%22,%22modifie 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@glasgow.ac.ukmailto:Roderic.Page@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.comhttp://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@gbif.orgmailto:trobertson@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.orghttp://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, Éamonn Ó Tuama [GBIF] <eotuama@gbif.orgmailto:eotuama@gbif.org> wrote:
Tim, Best for you to answer Antonio. Éamonn
From: Antonio García Camacho [mailto:antonio.garcia.camacho@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@csic.esmailto:antonio.garcia.camacho@csic.es www.ebd.csic.eshttp://www.ebd.csic.es/
API-users mailing list API-users@lists.gbif.orgmailto:API-users@lists.gbif.org http://lists.gbif.org/mailman/listinfo/api-users
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 were 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@lists.gbif.org] On Behalf Of Roderic Page Sent: Monday, January 26, 2015 1:05 AM To: Donat Agosti Cc: api-users@lists.gbif.org; info@eu-nomen.eu; wp2@eubon.eu; wp1@eubon.eu Subject: Re: [API-users] API GBIF: search species using GUID (LSID)
And while were 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@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@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-BONs names are mapped.
Cheers
Donat
From: API-users [mailto:api-users-bounces@lists.gbif.org] On Behalf Of Roderic Page Sent: Monday, January 26, 2015 11:13 AM To: Tim Robertson; Antonio García Camacho; info@eu-nomen.eu Cc: api-users@lists.gbif.org Subject: Re: [API-users] API GBIF: search species using GUID (LSID)
Just to follow up on Tims 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 doesnt actually work (in the sense that it cant 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 Its 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-... -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%22,%22modified%22:%222014... 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 GBIFs 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@glasgow.ac.uk Roderic.Page@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@gbif.org trobertson@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 dont 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&n... nte
noting the usageID is 3034893 in the response. Youd 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@gbif.org eotuama@gbif.org> wrote:
Tim,
Best for you to answer Antonio.
Éamonn
From: Antonio García Camacho [ mailto:antonio.garcia.camacho@csic.es mailto:antonio.garcia.camacho@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.
I would like to add some more thoughts on this issue.
Not all checklists which are integrated into PESI provide a LSIDs. To be precise: ERMS, Fauna Europaea und the Index Fungorum provide an LSID and the Euro+Med Plantbase does not, it provides a GUID instead. But in any case the method described by Roderic should be feasible to map the search results returned by the EU BON taxonomic backbone for PESI to the GBIF species record.
The GUID of the Euro+Med Plantbase taxa can be extracted from the EU BON taxonomic backbone responses by parsing the url field of the source information for the respective taxon response, e.g.:
response": [ { "taxon": { "taxonName": { "fullName": "Lapsana communis L.", "canonicalName": "Lapsana communis", "atomisedName": null, "authorship": "L.", "rank": "Species", "nomenclaturalReference": null }, "accordingTo": "Greuter, W. (2006-2009): Compositae (pro parte majore). – In: Greuter, W. & Raab-Straube, E. von (ed.): Compositae. Euro+Med Plantbase - the information resource for Euro-Mediterranean plant diversity. Lapsana communis L.", "url": "http://www.eu-nomen.eu/portal/taxon.php?GUID=1287B582-C995-4DB6-9481-A93E7E1...", "taxonomicStatus": "accepted", "sources": [
{ "url": "http://ww2.bgbm.org/euroPlusMed/PTaxonDetail.asp?UUID=1287B582-C995-4DB6-948...", "datasetID": null, "datasetName": null, "name": null, "title": "Greuter, W. (2006-2009): Compositae (pro parte majore). – In: Greuter, W. & Raab-Straube, E. von (ed.): Compositae. Euro+Med Plantbase - the information resource for Euro-Mediterranean plant diversity. Lapsana communis L." }
], ....
The EU BON taxonomic backbone provides a federated search on more checklists than only PESI. Also CoL and WoRMS are covered so far and more are to be added (EUNIS, Natura 2000). In case of Natura 2000 it is problematic to do the mapping to GBIF species, since Natura 2000 is not listed a checklist in the proper sense. The Natura 2000 Species data is not covering any classification it consists mainly of species names and the Natura 2000 species ID, so it is rather a name list than a source for taxonomic information. I guess it is not listed in GBIF due to the lack of taxonomic information.
regards Andreas
On Monday 26 January 2015 11:13:02 Roderic Page wrote:
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....
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:
Given a LSID like urn:lsid:faunaeur.org:taxname:115091, trim off the “urn:lsid:faunaeur.org:taxname:” to leave “115091”
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-...
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%22,%22modified%22:%222014...
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@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 08:48, Tim Robertson trobertson@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. 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...
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>
I hope this helps, Tim
On 26 Jan 2015, at 09:35, Éamonn Ó Tuama [GBIF] eotuama@gbif.org wrote:
Tim, Best for you to answer Antonio. Éamonn
From: Antonio García Camacho [mailto:antonio.garcia.camacho@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@csic.es www.ebd.csic.es
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participants (8)
-
Bart Vanhoorne -
Dirk S. Schmeller -
Donat Agosti -
Francisco Antonio García Camacho -
Kohlbecker, Andreas -
Richard Pyle -
Roderic Page -
Tim Robertson