Hi Jorn, For viruses specifically, this may be of interest as a complementary option. Through the EVORA project and in collaboration with ICTV, we recently developed a public API providing programmatic access to ICTV taxonomy. One of the objectives was precisely to make historical taxonomy easier to work with: the resource exposes the different ICTV releases and links taxon representations across releases, allowing historical names to be related to their later or current classifications. The API is now referenced directly by ICTV: https://ictv.global/help/evora-api <https://ictv.global/help/evora-api> Documentation and helper libraries are available here: https://evora-project.github.io/ictv-ontology/helpers/ <https://evora-project.github.io/ictv-ontology/helpers/> and there is also a small demonstration interface: https://ictvapi.evora-project.eu/ <https://ictvapi.evora-project.eu/> Of course, this would only address the virus part of your dataset and would not provide a mapping from legacy Catalogue of Life identifiers themselves, but it may be useful where those identifiers correspond to ICTV taxa. Best, Philippe On 23/10/2026 16:28, Jorn Bruggeman via COL-Users wrote:
Ce mail provient de l'extérieur, restons vigilants
Hi Markus,
Revisiting this 5-year-old thread... For a long time, the old webservice athttp://www.catalogueoflife.org/annual-checklist/2019/webservice has kept working, but now it looks definitively retired - I am getting error code 410, "the annual checklist webservice is retired". Is that expected? I recall "We will keep all historic annual checklist versions running on the old software stack"... (cited from below)
If that old web service is not available anymore through any means: Is there currently any other API that would allow me to look up old identifiers? Specifically, I'd like to map (fragments of) taxon names to legacy 2019 annual checklist ids, and to map legacy 2019 annual checklist ids to full taxonomic classifications (that include the legacy ids for higher taxonomic ranks). Perhaps via the /dataset/{key}/legacy API on eitherwww.checklistbank.org or api.catalogueoflife.org? The reason we need it is that we still have a large, expensive-to-generate dataset that links taxon-specific data to 2019 annual checklist ids.
If API access is not an option for this purpose, I could revisit the simple mapping file of old to new identifiers you described previously (see below), if that has been updated to include all higher taxonomic rank ids. However, thehttps://download.catalogueoflife.org/col/legacy_id_map.tsv.gz link no longer works. Is this file still available elsewhere?
Best,
Jorn
-----Original Message----- From: COL-Users<col-users-bounces@lists.gbif.org> On Behalf Of Markus Döring Sent: 17 March 2021 18:11 To: Catalogue of Life user announcements and discussion<col-users@lists.gbif.org> Subject: Re: [COL-Users] API Introduction
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@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@lists.gbif.org> On Behalf Of Markus Döring Sent: 17 March 2021 14:22 To: Catalogue of Life user announcements and discussion <col-users@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/i d/12dca9c49741815f82400bb7bff50553
legacy ID redirected to latest version in new portal https://www.catalogueoflife.org/col/details/species/id/12dca9c49741815 f82400bb7bff50553
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/12dca9c49741815f82400bb7b..."
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@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@lists.gbif.org> On Behalf Of Markus Döring Sent: 17 March 2021 12:31 To:col-users@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 underhttp://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&r a 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 fromhttps://api.catalogueoflife.org/col/webservice like this: https://api.catalogueoflife.org/col/webservice?name=Abies%20alba&form a 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@gbif.org http://www.gbif.org
_______________________________________________ COL-Users mailing list COL-Users@lists.gbif.org https://lists.gbif.org/mailman/listinfo/col-users
COL-Users mailing list COL-Users@lists.gbif.org https://lists.gbif.org/mailman/listinfo/col-users
_______________________________________________ COL-Users mailing list COL-Users@lists.gbif.org https://lists.gbif.org/mailman/listinfo/col-users
COL-Users mailing list COL-Users@lists.gbif.org https://lists.gbif.org/mailman/listinfo/col-users
_______________________________________________ COL-Users mailing list --col-users@lists.gbif.org To unsubscribe send an email tocol-users-leave@lists.gbif.org