Re: [API-users] Is there any NEO4J or graph-based driver for this API ?
Dear Juan,
Unfortunately we have no tool for creating these kind of SQL like queries to the portal. I am sure you are aware that the filters in the occurrence search pages can be applied in combination in numerous ways. The API can go even further in this regard[1], but it not well suited for retrieving occurrence records since there is a 200.000 records ceiling making it unfit for species exceeding this number.
There is going be updates to the pygbif package[2] in the near future that will enable you to launch user downloads programmatically where a whole list of different species can be used as a query parameter as well as adding polygons.[3]
In the meantime, Mauro’s suggestion is excellent. If you can narrow your search down until it returns a manageable download (say less than 100 million records), importing this into a database should be doable. From there, you can refine using SQL queries.
Best, Jan K. Legind, GBIF Data manager
[1] http://www.gbif.org/developer/occurrence#search [2] https://github.com/sckott/pygbif [3] https://github.com/jlegind/GBIF-downloads
From: API-users [mailto:api-users-bounces@lists.gbif.org] On Behalf Of Mauro Cavalcanti Sent: 30. maj 2016 14:06 To: Juan M. Escamilla Molgora Cc: api-users@lists.gbif.org Subject: Re: [API-users] Is there any NEO4J or graph-based driver for this API ?
Hi, One solution I have successfully adopted for this is to download the records (either "manually" via browser or, yet better, using a Python script using the fine pygbif library), storing them into a MySQL or SQLite database and then perform the relational queries. I can provide examples if you are interested. Best regards,
2016-05-30 8:59 GMT-03:00 Juan M. Escamilla Molgora <j.escamillamolgora@lancaster.ac.ukmailto:j.escamillamolgora@lancaster.ac.uk>: Hola,
Is there any API for making relational queries like taxonomy, location or timestamp?
Thank you and best wishes
Juan _______________________________________________ API-users mailing list API-users@lists.gbif.orgmailto:API-users@lists.gbif.org http://lists.gbif.org/mailman/listinfo/api-users
-- Dr. Mauro J. Cavalcanti E-mail: maurobio@gmail.commailto:maurobio@gmail.com Web: http://sites.google.com/site/maurobio
Hi all,
Python-dwca-reader[1] may also help to extract data from the download when populating the database
[1] http://python-dwca-reader.readthedocs.io/en/latest/
Best,
Nicolas
Le 30/05/16 14:48, Jan Legind a écrit :
Dear Juan,
Unfortunately we have no tool for creating these kind of SQL like queries to the portal. I am sure you are aware that the filters in the occurrence search pages can be applied in combination in numerous ways. The API can go even further in this regard[1], but it not well suited for retrieving occurrence records since there is a 200.000 records ceiling making it unfit for species exceeding this number.
There is going be updates to the pygbif package[2] in the near future that will enable you to launch user downloads programmatically where a whole list of different species can be used as a query parameter as well as adding polygons.[3]
In the meantime, Mauro’s suggestion is excellent. If you can narrow your search down until it returns a manageable download (say less than 100 million records), importing this into a database should be doable. From there, you can refine using SQL queries.
Best,
Jan K. Legind, GBIF Data manager
[1] http://www.gbif.org/developer/occurrence#search
[2] https://github.com/sckott/pygbif
[3] https://github.com/jlegind/GBIF-downloads
*From:*API-users [mailto:api-users-bounces@lists.gbif.org] *On Behalf Of *Mauro Cavalcanti *Sent:* 30. maj 2016 14:06 *To:* Juan M. Escamilla Molgora *Cc:* api-users@lists.gbif.org *Subject:* Re: [API-users] Is there any NEO4J or graph-based driver for this API ?
Hi,
One solution I have successfully adopted for this is to download the records (either "manually" via browser or, yet better, using a Python script using the fine pygbif library), storing them into a MySQL or SQLite database and then perform the relational queries. I can provide examples if you are interested.
Best regards,
2016-05-30 8:59 GMT-03:00 Juan M. Escamilla Molgora <j.escamillamolgora@lancaster.ac.uk mailto:j.escamillamolgora@lancaster.ac.uk>:
Hola,
Is there any API for making relational queries like taxonomy, location or timestamp?
Thank you and best wishes
Juan _______________________________________________ API-users mailing list API-users@lists.gbif.org mailto:API-users@lists.gbif.org http://lists.gbif.org/mailman/listinfo/api-users
--
Dr. Mauro J. Cavalcanti E-mail: maurobio@gmail.com mailto:maurobio@gmail.com Web: http://sites.google.com/site/maurobio
API-users mailing list API-users@lists.gbif.org http://lists.gbif.org/mailman/listinfo/api-users
Nicolas,
That's also a good option, although a little bit less easier to use than pygbif.
Another option is rgbif (https://github.com/ropensci/rgbif), a R package which has much of the same functionality of pygbif.
Best regards,
2016-05-30 14:15 GMT-03:00 Nicolas Noé n.noe@biodiversity.be:
Hi all,
Python-dwca-reader[1] may also help to extract data from the download when populating the database
[1] http://python-dwca-reader.readthedocs.io/en/latest/
Best,
Nicolas
Le 30/05/16 14:48, Jan Legind a écrit :
Dear Juan,
Unfortunately we have no tool for creating these kind of SQL like queries to the portal. I am sure you are aware that the filters in the occurrence search pages can be applied in combination in numerous ways. The API can go even further in this regard[1], but it not well suited for retrieving occurrence records since there is a 200.000 records ceiling making it unfit for species exceeding this number.
There is going be updates to the pygbif package[2] in the near future that will enable you to launch user downloads programmatically where a whole list of different species can be used as a query parameter as well as adding polygons.[3]
In the meantime, Mauro’s suggestion is excellent. If you can narrow your search down until it returns a manageable download (say less than 100 million records), importing this into a database should be doable. From there, you can refine using SQL queries.
Best,
Jan K. Legind, GBIF Data manager
[1] http://www.gbif.org/developer/occurrence#search
[2] https://github.com/sckott/pygbif
[3] https://github.com/jlegind/GBIF-downloads
*From:* API-users [mailto:api-users-bounces@lists.gbif.org api-users-bounces@lists.gbif.org] *On Behalf Of *Mauro Cavalcanti *Sent:* 30. maj 2016 14:06 *To:* Juan M. Escamilla Molgora *Cc:* api-users@lists.gbif.org *Subject:* Re: [API-users] Is there any NEO4J or graph-based driver for this API ?
Hi,
One solution I have successfully adopted for this is to download the records (either "manually" via browser or, yet better, using a Python script using the fine pygbif library), storing them into a MySQL or SQLite database and then perform the relational queries. I can provide examples if you are interested.
Best regards,
2016-05-30 8:59 GMT-03:00 Juan M. Escamilla Molgora < j.escamillamolgora@lancaster.ac.uk>:
Hola,
Is there any API for making relational queries like taxonomy, location or timestamp?
Thank you and best wishes
Juan _______________________________________________ API-users mailing list API-users@lists.gbif.org http://lists.gbif.org/mailman/listinfo/api-users
--
Dr. Mauro J. Cavalcanti E-mail: maurobio@gmail.com Web: http://sites.google.com/site/maurobio
API-users mailing listAPI-users@lists.gbif.orghttp://lists.gbif.org/mailman/listinfo/api-users
API-users mailing list API-users@lists.gbif.org http://lists.gbif.org/mailman/listinfo/api-users
participants (3)
-
Jan Legind -
Mauro Cavalcanti -
Nicolas Noé