- COL-Users - lists.gbif.org

TaxonWorks Together 2025 - Registration open and free! (TWT2025 May 6 - 8)
by Deborah Paul 22 Apr '25

22 Apr '25

Greetings COL Community, RE: TaxonWorks Together 2025 <https://together.taxonworks.org/> - Registration open and free! It's May 6 - 8. ‪This year's #TWT2025 offers topics local-to-planetary and relevant to COL contributors. Please see below a few TWT2025 session themes here to entice you to have a look-see and join us. Please check the agenda for speakers and panelists <https://together.taxonworks.org/> and details and times for each session. * taxonomy * data migration * systematic research tools * field stations and collections * collections track disease * research software engineering * TaxonWorks 101 * AI-informatics * software and services * eDNA * geoSpatial data Most sessions are moderated discussions with opportunities for your input. Hear from people that inspire us, and take part in the on-line conversation that pervades throughout. We welcome everyone and look forward to seeing you there. In anticipation, Debbie, for the SFG and TWT2025 /PS -- *please (please) share with your colleagues and students far and wide, thanks!* PPS -- yes there is cross-posting :-)/ -- - Deborah Paul, Biodiversity Informatics Community Liaison - Species File Group (INHS), University of Illinois -- Natural History Collections and Museomics NHCM Editor-in-Chiefhttps://nhcm.pensoft.net -- Biodiversity Information Standards (TDWG) Past Chair 2021-2022 -- Florida State University Courtesy Appointment -- Species File Group and Eventshttps://speciesfilegroup.org

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Removal of old monthly COL releases
by Markus Döring 15 Apr '25

15 Apr '25

Dear users of the Catalogue of Life, Since we started to use the new checklistbank.org infrastructure COL has released new versions every month since. We have always promised to keep these releases available in ChecklistBank for at least a year, but differently to the Annual Releases, we never planned to keep them forever. Finally we will now start deleting old monthly releases if they have exceeded one year, starting with the oldest releases from 2020-2023. https://www.checklistbank.org/dataset?releasedFrom=3&sortBy=created Both the alias and version of a COL release tells you whether it is a long term supported (LTS) annual release which we will keep forever, or a monthly one. If you need stable links to immutable content, we recommend to use the annual editions of COL. Otherwise identifiers of names in COL are stable and will resolve to the same name in subsequent versions, both monthly and annual. Their status, classification and associated information can change over time though. There will still be the option to download binary archives (coldp & dwca) of all monthly releases of COL once they have been deleted in ChecklistBank: https://download.checklistbank.org/col/ With best wishes, Markus -- Markus Döring GBIF & Catalogue of Life https://www.checklistbank.org https://www.catalogueoflife.org

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COL Februar edition with LPSN
by Markus Döring 15 Feb '25

15 Feb '25

Dear friends, COL has just released it’s monthly February edition, which for the first time includes LPSN as a source for Prokaryotes. With that we also changed the root classification of COL, introducing 3 domains with Eukaryota grouping most of our former kingdoms. https://www.catalogueoflife.org/data/browse Best wishes, Markus [cid:98a61022-3906-4452-b203-63a7a1be4a92@eurprd09.prod.outlook.com]

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Please update React components
by Markus Döring 12 Dec '24

12 Dec '24

Dear all, we have changed the React portal components for ChecklistBank and would ask every user of these to update their dependency. There are some small changes to the Tree API coming up by the end of the week that will potentially break older tree browser components. Instead of a fixed version we recommend to refer to the latest release so the components stay up to date as we do future releases: <script src="https://cdn.jsdelivr.net/gh/CatalogueOfLife/portal-components@latest/umd/co…" ></script> See here for more details on how to use them: https://github.com/CatalogueOfLife/portal-components/blob/master/README.md#… Thanks, Markus PS: All GBIF hosted portal will be updated by us. -- Markus Döring GBIF & Catalogue of Life Tech Lead ChecklistBank m.doering(a)gbif.org https://www.checklistbank.org https://www.catalogueoflife.org

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Fetching citations from CoL
by Mauro Cavalcanti 06 Nov '24

06 Nov '24

Hi, Given a list of referenceIds as shown below: $referenceIds [1] "a74e1990-ef89-4d84-b4da-20a594f53f6c" "196c9fa6-dc61-4053-99bb-3c2f454627e1" [3] "b651fcf9-bae5-46bd-8bd5-3ec8e5268b4a" "0639bf15-c078-466f-9a03-1bdfdae664d8" How can one get the bibliographic citations corresponding to each of these Id's? I scanned the CheckListBank API (https://api.checklistbank.org) but could not found out any entry point for the citations. Thanks in advance for any assistance you can provide. Best regards, -- Dr. Mauro J. Cavalcanti E-mail: maurobio(a)gmail.com GitHub: https://github.com/maurobio ORCID: https://orcid.org/0000-0003-2389-1902 "Life is complex. It consists of real and imaginary parts."

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API examples
by Mauro Cavalcanti 29 Jun '24

29 Jun '24

Dear ALL, Are there any simple examples of the usage of the new Checklist API (as there was for the old API)? Thanks in advance! Best regards, -- Dr. Mauro J. Cavalcanti E-mail: maurobio(a)gmail.com Web: http://sites.google.com/site/maurobio

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Synonyms missing in coldp download of CoL
by MANCINI Raffael 13 Feb '24

13 Feb '24

Dear List, I've been downloading the latest coldp formatted release of COL24.1 and expected to find a synonyms file (NameRelation.tsv afaik) since I requested "synonyms: true". Am I doing things wrong or is this an issue on the side of CLB? For reference, the download I generated: https://www.checklistbank.org/download/6eb72b1f-60c4-431f-8c87-ead613f04945 Best regards! -- Raffael Mancini IT administrator and developer SIDPNat - Data unit Musée National d'Histoire Naturelle Luxembourg T: +352 46 22 40 - 3476 - https://mnhn.lu

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Unstable COL identifiers in latest October release
by Markus Döring 28 Nov '23

28 Nov '23

Dear friends of COL, we have released a new monthly October version recently that contains some bad identifiers: https://doi.org/10.48580/df7lv Some taxa have temporary identifiers in the UUID format, for example Apis mellifera: https://www.catalogueoflife.org/data/taxon/bc15e6bb-fe11-4a8c-ac6f-a1f7d919… The old identifier FN46 has been deleted. Luckily we provide tombstone pages for these so you can still resolve them and find their latest use: https://www.catalogueoflife.org/data/taxon/FN46 We are working hard to find the problem and fix it in the next release where these temporary identifiers will be replaced with their previous versions again. Please do not store the temporary UUIDs as they will expire soon. Once resolved I will inform you all on this list. Meanwhile progress on this problem can be followed on github: https://github.com/CatalogueOfLife/general/issues/100 We are very sorry for the inconvenience, we just realised this today. Regards, Markus -- Markus Döring GBIF & Catalogue of Life Technical lead ChecklistBank.org m.doering(a)gbif.org http://www.checklistbank.org https://www.catalogueoflife.org

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NamesIndex missing translations?
by MANCINI Raffael 15 Sep '23

15 Sep '23

Dear list, I'm using the very handy NamesIndex in order to translate between different taxonomic sources. In the case of CoL and iNaturalist, I found that only roughly half of the entries (from a recent export) have both the CoL ID and iNaturalist ID set. For the entries pertaining to the rank "species" the situation is particularly bad, only roughly 10% (4353 of 41109) of the entries do any real translation. 1. Why does the nidx export contain rows with either of the IDs empty at all? 2. Why are so many of the species in particular not correctly mapped? Is this due to missing authorship in the iNaturalist checklist coupled with a strict matching algorithm? Best regards, -- Raffael Mancini IT administrator and developer Service d'information digital sur le patrimoine naturel (SIDPNAT) Musée National d'Histoire Naturelle Luxembourg T: +352 247 66667 - https://mnhn.lu

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ChecklistBank in read only mode
by Markus Döring 21 Aug '23

21 Aug '23

Dear users, we are upgrading the ChecklistBank database this week and unfortunately have to turn the system into a read only mode for some time. We expect work to be finished by the end of the week. Until then you can use CLB as normal, but all changes to data including newly registered datasets, users, downloads or editorial work will not persist and be discarded. Sorry for the inconvenience, but we hope for a more performant and stable system afterwards. Best wishes, Markus Döring

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