September 2016 - API-users

Re: [API-users] Is there any NEO4J or graph-based driver for this API ?
by Collins, Matthew 15 Feb '17

15 Feb '17

Jorrit pointed out this thread to us at iDigBio. Downloading and importing data into a relational database will work great, especially if as Jan said you can cut the data size down to a reasonable amount. Another approach we've been working on in a collaboration called GUODA [1] is to build an Apache Spark environment with pre-formatted data frames with common data sets in them for researchers to use. This approach would offer a remote service where you could write arbitrary Spark code, probably in Jupyter notebooks, to iterate over data. Spark does a lot of cool stuff including GraphX which might be of interest. This is definitely pre-alpha at this point and if anyone is interested, I'd like to hear your thoughts. I'll also be at SPNHC talking about this. One thing we've found in working on this is that importing data into a structured data format isn't always easy. If you only want a few columns, it'll be fine. But getting the data typing, format standardization, and column name syntax of the whole width of an iDigBio record right requires some code. I looked to see if EcoData Retriever [2] had a GBIF data source and they have an eBird one that perhaps you might find useful as a starting point if you wanted to try to use someone else's code to download and import data. For other data structures like BHL, we're kind of making stuff up since we're packaging a relational structure and not something nearly as flat as GBIF and DWC stuff. [1] http://guoda.bio/ [2] http://www.ecodataretriever.org/ Matthew Collins Technical Operations Manager Advanced Computing and Information Systems Lab, ECE University of Florida 352-392-5414<callto:352-392-5414> ________________________________ From: jorrit poelen <jhpoelen(a)xs4all.nl> Sent: Monday, May 30, 2016 11:16 AM To: Collins, Matthew; Thompson, Alexander M; Hammock, Jennifer Subject: Fwd: [API-users] Is there any NEO4J or graph-based driver for this API ? Hey y’all: Interesting request below on the GBIF mailing list - sounds like a perfect fit for the GUODA use cases. Would it be too early to jump onto this thread and share our efforts/vision? thx, -jorrit Begin forwarded message: From: Jan Legind <jlegind(a)gbif.org<mailto:jlegind@gbif.org>> Subject: Re: [API-users] Is there any NEO4J or graph-based driver for this API ? Date: May 30, 2016 at 5:48:51 AM PDT To: Mauro Cavalcanti <maurobio(a)gmail.com<mailto:maurobio@gmail.com>>, "Juan M. Escamilla Molgora" <j.escamillamolgora(a)lancaster.ac.uk<mailto:j.escamillamolgora@lancaster.ac.uk>> Cc: "api-users(a)lists.gbif.org<mailto:api-users@lists.gbif.org>" <api-users(a)lists.gbif.org<mailto:api-users@lists.gbif.org>> 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(a)lists.gbif.org<mailto: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(a)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(a)lists.gbif.org<mailto:API-users@lists.gbif.org> http://lists.gbif.org/mailman/listinfo/api-users -- Dr. Mauro J. Cavalcanti E-mail: maurobio(a)gmail.com<mailto:maurobio@gmail.com> Web: http://sites.google.com/site/maurobio _______________________________________________ API-users mailing list API-users(a)lists.gbif.org<mailto:API-users@lists.gbif.org> http://lists.gbif.org/mailman/listinfo/api-users

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Seeking feedback for upcoming changes to the occurrence API
by Christian Gendreau 16 Sep '16

16 Sep '16

Dear API users, The GBIF informatics team is seeking feedback and opinions from users of the GBIF API regarding upcoming changes the occurrence API. We created an issue on the gbif-api GitHub project to facilitate the process: -What and how to return Occurrence eventDate? https://github.com/gbif/gbif-api/issues/4 We also created the following issue to document the current definition of the "eventDate" returned by the API: -Definition of eventDate returned by the API https://github.com/gbif/gbif-api/issues/3 Best regards, The GBIF Informatics team

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Reporting bugs/etc with GBIF API?
by Scott Chamberlain 02 Sep '16

02 Sep '16

Hi! I just looked over issues I've opened in the GBIF JIRA instance. I noticed that none of the 4 received any comments or action as far as I could tell. Is there a better place to raise issues with the GBIF API? This mailing list? Twitter? A Github repo? Thanks!, Scott

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Changes in GBIF.org and API
by Tim Robertson 01 Sep '16

01 Sep '16

Hi folks, I am very happy to let you know that a new release of GBIF.org went online at lunchtime today with the following enhancements: Occurrence search (http://www.gbif.org/occurrence/search) * New locality based filters: * locality, province/state and water body * These are not interpreted terms, but allow search based on what publishers state * http://www.gbif.org/occurrence/search?STATE_PROVINCE=California * http://www.gbif.org/occurrence/search?WATER_BODY=AMAZONAS+BASIN%2C+RIO+JURUA * A new organismID filter * http://www.gbif.org/occurrence/search?ORGANISM_ID=100 * Publishing protocol filter * http://www.gbif.org/occurrence/search?PROTOCOL=TAPIR * License filter and facet: * http://www.gbif.org/occurrence/search?license=CC_BY_4_0 * The occurrence API supports all the filters mentioned above with the addition of also allowing search by publishing organisation Occurrence downloads: * The rights.txt file: has been changed to list all the licenses of datasets included in that download. * DwC-A based downloads and the Datacite metada (DOIs) use the most restrictive license of the datasets included in the download defaulting to CC-BY. * The CSV downloads contain a new column 'License'. The Dataset search page now supports faceted navigation by license: http://www.gbif.org/dataset/search?license=CC_BY_4_0 In the release, we have temporarily broken the "repatriation" filter which is being re-enabled now, and will be online again tomorrow. Sorry about this partial outage of that search term. Many thanks, Tim

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