December 2016 - API-users - lists.gbif.org

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

5 11

Downloading large numbers of datasets
by Coggins, Clint 08 Dec '16

08 Dec '16

Hi Matt, Thanks so much for your help. I was able to successfully get the file from your link. I did notice there was not "Content-Length" header in the original download response. Maybe that has something to do with the wget trouble. > Subject: Re: [API-users] Downloading large numbers of datasets > Message-ID: <14c80817-da32-23c4-e1ee-eded21481079(a)gbif.org> > Content-Type: text/plain; charset="windows-1252"; Format="flowed" > > Hi Clint, > > You're first to report a problem, though trying to download the file > (64-bit Linux, wget) within the GBIF network also failed for me. > > I've copied it with a different method to here: > http://download.gbif.org/2016/12/0039949-160910150852091.zip -- on a > plain Apache server, so wget's "--continue" option should work if necessary. > > The MD5 checksum is e976523c9e6c7ec0cd9d3cb30030020b and the size is > exactly 43,184,530,448 bytes. > > If downloading that doesn't work, I could split the file into chunks. > We'll also look into why the download failed [1]. > > Cheers, > > Matt Blissett > > [1] http://dev.gbif.org/issues/browse/POR-3199 > > > On 07/12/2016 14.53, Coggins, Clint wrote: >> I'm trying to download all the occurrence data with COUNTRY=US >> >> http://www.gbif.org/occurrence/search?COUNTRY=US >> >> I've requested a download file, which is here >> http://www.gbif.org/occurrence/download/0039949-160910150852091 >> >> However, I've been having a lot of trouble getting the download to >> complete since it is so large(43.2GB). I've tried various browsers and >> also wget on both Linux and Mac. It typically fails with a network >> error in the browser. wget displayed strange behavior in that it >> claimed the download was successful after downloading 4.1GB. This was >> on 64 bit linux with ext4, so I don't think there was a filesystem >> limitation. >> >> Any ideas on how to download this data? Does it make sense to write a >> script to use the API to request the datasets one by one to split it up? >> >> Thanks for any help >> >> -- >> Clint Coggins

1 0

Downloading large numbers of datasets
by Coggins, Clint 07 Dec '16

07 Dec '16

I'm trying to download all the occurrence data with COUNTRY=US http://www.gbif.org/occurrence/search?COUNTRY=US I've requested a download file, which is here http://www.gbif.org/occurrence/download/0039949-160910150852091 However, I've been having a lot of trouble getting the download to complete since it is so large(43.2GB). I've tried various browsers and also wget on both Linux and Mac. It typically fails with a network error in the browser. wget displayed strange behavior in that it claimed the download was successful after downloading 4.1GB. This was on 64 bit linux with ext4, so I don't think there was a filesystem limitation. Any ideas on how to download this data? Does it make sense to write a script to use the API to request the datasets one by one to split it up? Thanks for any help -- Clint Coggins

2 1

Types call not working
by Roderic Page 05 Dec '16

05 Dec '16

Not sure if I’ve reported this before. The call to getting type specimens for a species consistently fails. For example, http://www.gbif.org/species/7424919 has a holotype specimen, but the API call http://api.gbif.org/v1/species/7424919/typeSpecimens returns no records. 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(a)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 ResearchGate https://www.researchgate.net/profile/Roderic_Page

2 2