- API-users - lists.gbif.org

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

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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

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Backbone data as SQL
by Köhler Christian 21 Nov '16

21 Nov '16

Hi, we are developing an application to curate taxonomic and morphological data for scientists. At the moment we are evaluating different taxonomic backbones to be used within our application. The GIBF taxonomic backbone seems to be an good choice in regards to quality, number of entries and acceptance. Due to the nature of our application, a web service to browse the taxonomy will not fulfil our requirements. A local copy of the GIBF data as SQL would be an ideal solution. I looked for this data publicly available to no avail. "Harvesting" the GBIF rest api seems not a good option. Are there plans to provide current taxonomic backbone data in the future? Maybe the data is already available, but I failed to find it yet. Regards Chris -- Christian Köhler Tel.: 0228 9122-434 Zoologisches Forschungsmuseum Alexander Koenig Leibniz-Institut für Biodiversität der Tiere Adenauerallee 160, 53113 Bonn, Germany www.zfmk.de Stiftung des öffentlichen Rechts Direktor: Prof. J. Wolfgang Wägele Sitz: Bonn -- Zoologisches Forschungsmuseum Alexander Koenig - Leibniz-Institut für Biodiversität der Tiere - Adenauerallee 160, 53113 Bonn, Germany www.zfmk.de Stiftung des öffentlichen Rechts; Direktor: Prof. J. Wolfgang Wägele Sitz: Bonn

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Demo site updated with species pages
by Morten Høfft 11 Nov '16

11 Nov '16

Hi everyone As you know by now, we are developing a new site. Yesterday we released a new version to http://demo.gbif.org The most notably changes in this version is: Species pages http://demo.gbif.org/species/5230740 http://demo.gbif.org/species/5786064 Integration with IUCN and CITES Dataset pages have had another iteration http://demo.gbif.org/dataset/e635240a-3cb1-4d26-ab87-57d8c7afdfdb Option to explore taxonomy on both checklist datasets and occurrence datasets And last, but not least - new maps. You will notice that it shows hexagons. More styles and projections are coming up. This is all still work in development, but should give you an idea of where we are heading. Hope you like it - Morten Høfft

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Early access to a new GBIF.org site
by Tim Robertson 02 Nov '16

02 Nov '16

Hi all, Sent to the GBIF API users and EU BON lists for information - sorry if you receive this more than once I'm happy to let you all know that we recently opened access to a very early version of work which is underway on a new GBIF.org site. It has limited functionality today, but we've tackled the most challenging issue which is cross content search. We're also working on making a consistent search experience across the various content types GBIF deal with. Some examples: - Gallery of images associated occurrences in a search result: http://demo.gbif.org/occurrence/gallery?taxon_key=5190137 - Cross content search: http://demo.gbif.org/search?q=argentina - Improved faceted search of occurrences: http://demo.gbif.org/occurrence/search?month=5&taxon_key=3026341 - Consistent search of species: http://demo.gbif.org/species/search?q=flabellina - Revision to the general news details visuals: http://demo.gbif.org/data-use/newsroom/uses/2015-feuda-et-al - Revised occurrence detail pages: http://demo.gbif.org/occurrence/1233599085 - Work in progress on dataset detail pages: http://demo.gbif.org/dataset/7bd65a7a-f762-11e1-a439-00145eb45e9a - A homepage which is yet-to-be designed, but with a simple search: http://demo.gbif.org The menu structure is provisional now, as is the majority of the styling (much of which needs revision) but I hope this helps give a sense of the direction. We aim to have this near completion by the end of 2016. There are several pages that have begun but are not ready yet, including the species detail page, and the country / participant pages. There will also be a revision to maps to include (just demos with example styling here): http://api.gbif-uat.org/v2/map/demo1.html (pixel maps) http://api.gbif-uat.org/v2/map/demo2.html (hexagon binning) http://api.gbif-uat.org/v2/map/demo6.html (CartoCSS styling example) http://tinyurl.com/gbif-arctic-html (arctic projection - we support WGS84 (EPSG:4326), Arctic (3575), Antarctic (3031) and Mercator (3857) http://s3-eu-west-1.amazonaws.com/gbif-demo/animalia-time.html (year resolution data on the maps instead of decade) http://api.gbif-uat.org/v2/map/debug (diagnostic view, which shows the vector tile format, for browser side rendering) All of this work in the mapping API is to set GBIF up to implement the species trends for all species (currently demo'ed for Lepidoptera only): http://demo.gbif.org/generic/tools/species-population [Maps are the only /v2 API change, and we'll shortly document the changes and will also continue to support /v1 maps in the API. v2 maps have all basisOfRecord, multiple projections, year resolution, and hexagon binning and will be available as PNGs and as Mapbox Vector Tile format] Once those developments are included in a forthcoming release we'll enable the feedback functions and then iterate over the developments releasing regularly with updates. The work is on GitHub [1], and primarily developed in Node with AngluarJS using the GBIF APIs. We will be deploying all of this on HTTPS and are exploring HTTP2 now to increase performance. Many thanks, Tim [1] https://github.com/gbif/portal16

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Error in /dataset route
by Scott Chamberlain 30 Oct '16

30 Oct '16

Hi, Found that in pygbif test suite, this request http://api.gbif.org/v1/dataset gives Invalid metadata xml document All other tests are passing. Best, Scott

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MULTIPOLYGON support appears to be gone?
by Scott Chamberlain 05 Oct '16

05 Oct '16

Hi all, It appears that MULTIPOLYGON is rejected again now. E.g., http://api.gbif-uat.org/v1/occurrence/search?GEOMETRY=MULTIPOLYGON(((30%202… gives Invalid simple WKT: MULTIPOLYGON(((30 20, 45 40, 10 40, 30 20)),((15 5, 40 10, 10 20, 5 10, 15 5 And same for api.gbif.org base URL. Did support for MULTIPOLYGON get reverted? Thanks! Scott Chamberlain

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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 01 Sep '16

01 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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