[COL-Users] API Introduction

Wed Mar 17 13:00:02 UTC 2021

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 <https://www.catalogueoflife.org/annual-checklist/2019/webservice?name=Picea%20abies%20abies&format=json> &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 <http://api.catalogueoflife.org/dataset/3LR/nameusage/search?q=Abies&rank=SPECIES&status=ACCEPTED> &rank=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 <http://api.catalogueoflife.org/dataset/3LR/tree/P> 

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 <https://api.catalogueoflife.org/col/webservice?name=Abies%20alba&format=json&response=full>  like this:

https://api.catalogueoflife.org/col/webservice?name=Abies%20alba <https://api.catalogueoflife.org/col/webservice?name=Abies%20alba&format=json&response=full> &format=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 <mailto:mdoering at gbif.org> 

http://www.gbif.org <http://www.gbif.org/> 

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