Thanks Markus, That updated mapping file is ideal for my purposes. It covers 4488 of my 4551 legacy identifiers. The remaining unmatched 63 ids look already like "true" COL2019 ids (e.g. 55068532=Daphnia) - they are higher ranks that I originally extracted from species' "classification" returned by the legacy webservice. I'm not sure why these were not in the legacy hash format. Also, several of those do not appear in the checklistbank.org version of COL2019, as far as I can tell (e.g. https://api.checklistbank.org/dataset/2354/taxon/55068532). In any case, it is only a minor concern as it affects so few nodes. I have also tried the Docker image of COL2019, which works great as a drop-in replacement while I move to the checklistbank.org API. One thing I noted was that the Docker version of the webservice returns URLs that refer to "col" rather than "annual-checklist/2019", which for good reasons does not work with the new redirects. It there a way (environment variable?) to make the Docker image return URLs that include the full version, so they work with your new redirects? Finally, I am trying to match some of my records for extinct species (e.g. 4238ebda1467894e1c5f1ececd209eda = 42094487 = Tyrannosaurus rex), but these do not seem available in the checklistbank.org version of COL2019 (e.g. https://api.checklistbank.org/dataset/2354/taxon/42094487). Is that expected? Best, Jorn -----Original Message----- From: Markus Döring <mdoering@gbif.org> Sent: 23 October 2026 22:16 To: Catalogue of Life user announcements and discussion <col-users@lists.gbif.org>; Jorn Bruggeman <jorn@bolding-bruggeman.com> Subject: Re: [COL-Users] API Introduction Hello Jorn, I managed to setup the redirects for the 2019 hash ids as well. So pages like this now take you to the checklistbank copy: https://www.catalogueoflife.org/annual-checklist/2019/details/species/id/6a3... It even works for synonyms:https://www.catalogueoflife.org/annual-checklist/2019/details/species/id/6a3... And the browse tree urls for higher taxa:https://www.catalogueoflife.org/annual-checklist/2019/browse/tree/id/5ede24b... Every COL release now also generates a mapping file from AC 2019 to that release. For the latest COL26.10 XR it is already available: https://download.checklistbank.org/col/monthly/2026-10-16_xr_col19-idmap.tsv... I haven't checked it much. I would be glad if you could do a quick review. Thanks, Markus
On 23. Oct 2026, at 20:11, Markus Döring <mdoering@gbif.org> wrote:
Hi Jorn,
I found the table with the hash IDs and will produce a new mapping of the 2019 hashes to the record IDs of 2019 in CLB. More on that later. That will allow me also to setup proper redirecting of all the 2019 URLs. I will then also create a script that generates a mapping of the ac2019 hashes to the latest COL XR so anyone can map their legacy COL identifiers to the new ones. All these files will live in the COL download site: https://download.checklistbank.org/col/
If you actually want the legacy webservices, you can always run them yourself in a docker environment. I have prepared docker images that you can quickly spin up with any of the annual mysql dumps from https://download.checklistbank.org/col/annual/ Read more here and feel free to ask if something is unclear: https://github.com/CatalogueOfLife/archives/blob/master/col-archives/R EADME.md The 2019 webservices exist since 2010, from 2007-2009 there was just a /webservice/search.php endpoint.
Best, Markus
On 23. Oct 2026, at 17:03, Markus Döring <mdoering@gbif.org> wrote:
Hello Jorn,
you have probably read in the news that serious security vulnerabilities were discovered in PHP and many major sites had to be shut down. So did we, as we run the old COL software on a very outdated PHP/MySQL stack more than a decade old.
I have transferred all data to the new checklistbank.org system and setup redirects for most of the website, e.g. http://www.catalogueoflife.org/annual-checklist/2011/details/species/ id/6590516 or https://www.catalogueoflife.org/annual-checklist/2019/search/all/key/ Abies+alba/match/1 But the webservices themselves were not replaceable. Also the releases from 2015-2019 used some hashing instead of the real record ids, which also made it impossible to redirect ID based URLs. You can find more details here: https://github.com/CatalogueOfLife/deploy/issues/21
Specifically the 2019 release is available here in CLB: https://www.checklistbank.org/dataset/2354/classification
But as I said above it uses the real database record identifiers, not the hashes that the PHP portal created. I will see what I can do to come up with a mapping - I'll come back to it later. Meanwhile there still is the initial mapping file from our first release in the new system here: https://download.checklistbank.org/col/legacy_id_map.zip But that is a bit outdated, so please give me some time to prepare an update.
Also the migrated AC data has not been reviewed yet and I anticipate some smaller mistakes that still need to be corrected, we are working on that still.
Best, Markus
On 23. Oct 2026, at 16:28, Jorn Bruggeman via COL-Users <col-users@lists.gbif.org> wrote:
Hi Markus,
Revisiting this 5-year-old thread... For a long time, the old webservice at http://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 either www.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, the https://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/specie s/i d/12dca9c49741815f82400bb7bff50553
legacy ID redirected to latest version in new portal https://www.catalogueoflife.org/col/details/species/id/12dca9c49741 815 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?n ame = 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 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=Abie s&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 from https://api.catalogueoflife.org/col/webservice like this: https://api.catalogueoflife.org/col/webservice?name=Abies%20alba&f orm 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
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