[COL-Users] API Introduction

Wed Mar 17 18:11:02 UTC 2021

Thanks for reminding us. We'll improve the mapping soon.
We will also update that mapping file with new monthly releases, as we might add taxa in the latest edition compared to the 2019 version which had some names treated in non global sources that have been temporarily been removed.

Markus

> On 17. Mar 2021, at 18:03, Jorn Bruggeman <jorn at bolding-bruggeman.com> wrote:
> 
> Thanks Markus!
> 
> I can see the mapping between legacy and new identifiers could be useful for my purpose. However, it seems to cover species only, not higher taxonomic ranks. I would need both. Does something similar exist for those higher ranks?
> 
> Glad to hear the webservices for historic annual checklists will keep running for the foreseeable future.
> 
> Best,
> 
> Jorn
> 
> -----Original Message-----
> From: COL-Users <col-users-bounces at lists.gbif.org> On Behalf Of Markus Döring
> Sent: 17 March 2021 14:22
> To: Catalogue of Life user announcements and discussion <col-users at lists.gbif.org>
> Subject: Re: [COL-Users] API Introduction
> 
> Hi Jorn,
> 
> we unfortunately do not have the old IDs directly embedded in the taxon data. But there are ways to deal with the problem:
> 
> We provide a simple mapping file of old to new identifiers that you can use to locally update your data:
> https://download.catalogueoflife.org/col/legacy_id_map.tsv.gz
> 
> 
> The legacy API and portal is setup to redirect old IDs to their counterpart in the new applications
> 
> Abies alba examples:
> 
> COL 2019 legacy portal:
> http://www.catalogueoflife.org/annual-checklist/2019/details/species/id/12dca9c49741815f82400bb7bff50553
> 
> legacy ID redirected to latest version in new portal
> https://www.catalogueoflife.org/col/details/species/id/12dca9c49741815f82400bb7bff50553
> 
> legacy ID redirected to latest version in new API, Accept header required:
> curl -L -H "Accept: application/json" "https://api.catalogueoflife.org/dataset/3LR/legacy/12dca9c49741815f82400bb7bff50553" 
> 
> 
> If you use the new search and other features old IDs are not directly supported.
> We will keep all historic annual checklist versions running on the old software stack. But all new releases will only be available via the new API which also includes the ported legacy API, but not the old IDs (apart from above's redirects).
> 
> 
> Best,
> Markus
> 
> 
> 
>> On 17. Mar 2021, at 14:00, Jorn Bruggeman <jorn at bolding-bruggeman.com> wrote:
>> 
>> Dear Markus,
>> 
>> Thanks for this information, it is very welcome.
>> 
>> One quick question: I develop an application that depends on the old-style taxon identifiers (e.g., c526234e655cec65618f58161d24932a), as it uses its own dataset that cross-references these. It currently uses the 2019 annual checklist webservice:
>> 
>> https://www.catalogueoflife.org/annual-checklist/2019/webservice?name=
>> Picea%20abies%20abies&format=json
>> 
>> I would be happy to migrate to the new webservice API, but that would only possible if I can still query taxonomic classifications by old-style taxon id, as well as search for old-style taxon ids by taxon name. Is that possible? I do not immediately see an attribute with the old identifier in the sample queries you provided.
>> 
>> And should migration to the new API not be possible for me: could you give an indication how long the 2019 annual checklist webservice is expected to remain available?
>> 
>> Best,
>> 
>> Jorn
>> 
>> From: COL-Users <col-users-bounces at lists.gbif.org> On Behalf Of Markus 
>> Döring
>> Sent: 17 March 2021 12:31
>> To: col-users at lists.gbif.org
>> Subject: [COL-Users] API Introduction
>> 
>> Dear all,
>> 
>> as you all know at the end of last year the Catalogue of Life has moved to a whole new infrastructure and now offers a new and richer API.
>> As I had a few similar requests vie email lately I thought it would be good to give you a quick introduction to get started, while we are still working on better documentation.
>> 
>> 
>> The basic concept has changed in the sense that the API does not only 
>> expose the Catalogue of Life (COL), but all of ChecklistBank (CLB) 
>> which hosts a large number of taxonomic or nomenclatural datasets 
>> including the sources that we use to assemble the COL. You can read 
>> here more about it: https://www.catalogueoflife.org/about/colpipeline
>> 
>> The base URL of the API uses Swagger to exposes a rudimentary 
>> documentation of all the available REST resources and allows you to 
>> test it with real data: https://api.catalogueoflife.org
>> 
>> In order to access the latest version of COL you need to use the 
>> datasetKey=3LR (note that the swagger generated API docs do not allow 
>> strings, please use the currents release key 2242 for testing or 
>> curl). Pretty much all calls of interest to you should be scoped under 
>> http://api.catalogueoflife.org/dataset/3LR
>> 
>> In order to search for a name you could be doing this:
>> http://api.catalogueoflife.org/dataset/3LR/nameusage/search?q=Abies&ra
>> nk=SPECIES&status=ACCEPTED
>> 
>> To get taxon details for a given taxonID this does most of it:
>> Basics: http://api.catalogueoflife.org/dataset/2242/taxon/5QQJ9
>> Full Infos: 
>> http://api.catalogueoflife.org/dataset/2242/taxon/5QQJ9/info
>> 
>> To browse the tree you can use the Tree API which in its basic form works like this:
>> Root taxa: http://api.catalogueoflife.org/dataset/3LR/tree
>> Plant Children: 
>> http://api.catalogueoflife.org/dataset/3LR/tree/P/children
>> 
>> 
>> We now also offer reusable React UI components that you can embed in 
>> your own site or application to browse the tree, search and present 
>> species pages: https://github.com/CatalogueOfLife/portal-components
>> 
>> 
>> We have also migrated the previous "legacy" API which you can access with the latest data from https://api.catalogueoflife.org/col/webservice like this:
>> https://api.catalogueoflife.org/col/webservice?name=Abies%20alba&forma
>> t=json&response=full
>> 
>> There are a few small differences how we treat references compared to the previous version, otherwise it should work just as before.
>> We do consider this a legacy API and would like to encourage everyone using it still to migrate to our new API above.
>> 
>> 
>> Please don't hesitate to ask any questions on this list if you want to know more on how to use our API.
>> 
>> 
>> With best wishes,
>> Markus
>> 
>> 
>> 
>> +++ COL RESOURCES +++
>> 
>> COL Website:
>> http://www.catalogueoflife.org/
>> 
>> COL ChecklistBank:
>> http://data.catalogueoflife.org/
>> 
>> COL ChecklistBank API:
>> http://api.catalogueoflife.org/
>> 
>> COL latest release in API:
>> http://api.catalogueoflife.org/dataset/3LR
>> 
>> 
>> 
>> --
>> Markus Döring
>> Lead Developer Catalogue of Life
>> Global Biodiversity Information Facility (GBIF) mdoering at gbif.org 
>> http://www.gbif.org
>> 
>> _______________________________________________
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>> COL-Users at lists.gbif.org
>> https://lists.gbif.org/mailman/listinfo/col-users
> 
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