[API-users] Using GBIF api for a global insect family website

Wed Jun 14 07:16:48 CEST 2017

Bastiaan, you should definitely check out EOL, but just to be clear:

Your question about name validation stemmed from the thought that the new gallery view of the GBIF occurrence search (i.e. https://demo.gbif.org/occurrence/gallery?taxon_key=6920) was somehow harvesting unverified Flickr images, correct? That is not the case.

In fact, you can identify the source of all the datasets that contribute to the search result by filtering for Media type = images and viewing the dataset tab (https://demo.gbif.org/occurrence/datasets?media_type=StillImage&taxon_key=6920), .

Hope this helps.

Kyle

From: API-users <api-users-bounces at lists.gbif.org<mailto:api-users-bounces at lists.gbif.org>> on behalf of Cyndy Parr <csparr at gmail.com<mailto:csparr at gmail.com>>
Date: Wednesday, 14 June 2017 at 03.32
To: Markus Döring <mdoering at gbif.org<mailto:mdoering at gbif.org>>
Cc: "api-users at lists.gbif.org<mailto:api-users at lists.gbif.org>" <api-users at lists.gbif.org<mailto:api-users at lists.gbif.org>>, Bastiaan Wakkie <bwakkie at syrphidae.com<mailto:bwakkie at syrphidae.com>>
Subject: Re: [API-users] Using GBIF api for a global insect family website

Bastiaan,

I suggest you look into the EOL API, as there should be a way to filter for only images have confirmed identifications. Not sure how much there is for Syrphidae, but there might be a way to combine info from GBIF and EOL to achieve your goals.

http://eol.org/api

Cyndy

On Tue, Jun 13, 2017 at 3:49 AM, Markus Döring <mdoering at gbif.org<mailto:mdoering at gbif.org>> wrote:
Hi Bastiaan,
there is no flickr connection in the new portal, at least not directly. All images are explicitly provided links by the occurrence publishers.
They might point to flickr if they happen to host the images there, but the vast majority does not.

Markus

> On 12. Jun 2017, at 22:03, Bastiaan Wakkie <bwakkie at syrphidae.com<mailto:bwakkie at syrphidae.com>> wrote:
>
> Hi Markus,
>
> Thanks for your answer. No problem, I will get my taxonomy from diptera.org<http://diptera.org> the original source zoobank is using and as I understood gbif is using via zoobank (?). Yes I can imagine it would provide great complications assembling all different sources into one db :)
>
> I really like the flickr connection in the new portal but how do you check the validity of names given to the media in flickr? I can imagine there could be a lot of mistakes, does gbif offer any correction back to the flickr media made by 'authorized persons/professionals/taxonomists'? How would the correction flow go? Via the source you used or could this be done via gbif?
>
> thanks again!
>
> Bastiaan
>
>
>
> On 06/12/2017 10:00 AM, Markus Döring wrote:
>> Hi Bastiaan,
>> the GBIF Backbone only has the major Linnean ranks, i.e. a genus is attached to the family directly and there is no subfamily, tribe or subgenus. As we assemble the taxonomy by code from lots of different sources this would yield a very inconsistent taxonomy otherwise.
>> Best,
>> Markus
>>> On 11. Jun 2017, at 10:13, Bastiaan Wakkie <bwakkie at syrphidae.com<mailto:bwakkie at syrphidae.com> <mailto:bwakkie at syrphidae.com<mailto:bwakkie at syrphidae.com>>> wrote:
>>>
>>> Hi Markus,
>>>
>>> Thank you for the information!
>>> I got the backbone and was fiddling around. Is SUBFAMILY, TRIBUS AND GUBGENUS etc. left out on purpose? I presumed actually this was in de db so created a recursive sql:
>>>
>>> WITH RECURSIVE fulltree(id,parent_key,is_synonym,level,rank,scientific_name,path) AS (
>>>   SELECT id, parent_key, is_synonym, 1 as level,rank, scientific_name, scientific_name||'' as path from backbone where parent_key = 6920
>>> UNION
>>>   SELECT b.id<http://b.id>, b.parent_key, b.is_synonym, ft.level+1 as level,b.rank, b.scientific_name, ft.path||' / '||b.scientific_name as path
>>>   from backbone b, fulltree ft where b.parent_key = ft.id<http://ft.id>
>>> )
>>> SELECT * from fulltree order by path
>>>
>>> But as GENUS falls directly under FAMILY I received just an alphabetic list. Am I doing something wrong here? I might just miss the db concept... or is there a more detailed db which includes more ranks between Family and Genus/Specie?
>>>
>>> kind regards,
>>>
>>> Bastiaan
>>>
>>> On 05/31/2017 01:44 PM, Markus Döring wrote:
>>>> Hi Bastiaan,
>>>> the GBIF page for Syrphidae is
>>>> http://www.gbif.org/species/6920
>>>> or here in a preview of our upcoming new portal:
>>>> https://demo.gbif.org/species/6920
>>>> GBIF does not provide a software to setup your website, but you can surely use our API to build your own Syrphidae portal.
>>>> The GBIF portals above both exclusively use our own API, so all the information is openly accessible to you:
>>>> http://www.gbif.org/developer/species
>>>> If you need help with the API please let us know what you try to achieve.
>>>> This call for example lists all accepted genera in that family:
>>>> http://api.gbif.org/v1/species/search?datasetKey=d7dddbf4-2cf0-4f39-9b2a-bb099caae36c&higherTaxonKey=6920&rank=GENUS&status=accepted&q=
>>>> This lists children of the genus imosyrphus Bigot, 1882:
>>>> http://api.gbif.org/v1/species/1534459/children
>>>> ... or the family wth 10 records per page and an offset of 20:
>>>> http://api.gbif.org/v1/species/6920/children?limit=10&offset=20
>>>> The images you see on our upcoming portal are occurrence images which you can retrieve with such a call knowing the gbif taxon key (Syrphidae in this case):
>>>> http://api.gbif.org/v1/occurrence/search?mediaType=stillImage&taxonKey=6920
>>>> Hope this helps and gives inspirations.
>>>> You can also download the entire backbone if you want to:
>>>> http://rs.gbif.org/datasets/backbone/readme.html
>>>> We try to update it 3-4 times a year.
>>>> Best,
>>>> Markus
>>>> --
>>>> Markus Döring
>>>> Software Developer
>>>> Global Biodiversity Information Facility (GBIF)
>>>> mdoering at gbif.org<mailto:mdoering at gbif.org> <mailto:mdoering at gbif.org<mailto:mdoering at gbif.org>><mailto:mdoering at gbif.org<mailto:mdoering at gbif.org>>
>>>> http://www.gbif.org <http://www.gbif.org/>
>>>>> On 28. May 2017, at 20:03, Bastiaan Wakkie <bwakkie at syrphidae.com<mailto:bwakkie at syrphidae.com> <mailto:bwakkie at syrphidae.com<mailto:bwakkie at syrphidae.com>><mailto:bwakkie at syrphidae.com<mailto:bwakkie at syrphidae.com>>> wrote:
>>>>>
>>>>> Dear all,
>>>>>
>>>>>
>>>>> From 1999 onwards I have created and maintained a insect family website about Syrphidae (http://www.syrphidae.com <http://www.syrphidae.com/>)
>>>>>
>>>>> Main goal is a centralised meeting point for Syrpidologists around the world. My plan is to use the gbif backbone in the future but have no idea where to start.
>>>>>
>>>>> Basically I used national checklists to update the data in the pastbut never reached the whole world (Europe and Africa where partly done). What is the best option for me? I know in the past there was the gibf-npt which was very suitable for my case but was discontinued.
>>>>>
>>>>> Are there examples I can reusefor my purpose? Would it be best to use only api calls all over my website ot receive speciedata and occurences?
>>>>>
>>>>>
>>>>> kind regards,
>>>>>
>>>>>
>>>>> Bastiaan Wakkie
>>>>> _______________________________________________
>>>>> API-users mailing list
>>>>> API-users at lists.gbif.org<mailto:API-users at lists.gbif.org> <mailto:API-users at lists.gbif.org<mailto:API-users at lists.gbif.org>><mailto:API-users at lists.gbif.org<mailto:API-users at lists.gbif.org>>
>>>>> https://lists.gbif.org/mailman/listinfo/api-users
>>>
>>> --
>>> Digital signature:https://wakkie.org/FA3DED4C.asc
>>> fingerprint: 376B 6035 CD31 6437 A0FD  3165 C255 CD3D FA3D ED4C
>
> --
> Digital signature: https://wakkie.org/FA3DED4C.asc
> fingerprint: 376B 6035 CD31 6437 A0FD  3165 C255 CD3D FA3D ED4C

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