- COL-Users - lists.gbif.org

API examples
by Mauro Cavalcanti 28 Jun '24

28 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 12 Feb '24

12 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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Tombstone pages for deleted IDs
by Markus Döring 18 Aug '23

18 Aug '23

Dear COL users, the COL portal now has tombstone pages for once existing, but now deleted COL identifiers. Here is an example: https://www.catalogueoflife.org/data/taxon/64SCW This shows the basic information as it once existed as well as links to the first and last appearance in ChecklistBank. The API still returns a 404 for these ids, but does include a message and an archived usage instance that can be processed: https://api.checklistbank.org/dataset/3LR/taxon/64SCW Btw this is also true for synonyms being looked up as accepted names / taxa: https://api.catalogueoflife.org/dataset/3LR/taxon/7Q8L8 Best wishes, Markus

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CLB API related data
by MANCINI Raffael 17 Aug '23

17 Aug '23

Dear list, I'm developing a national "datawarehouse"/repository for natural history observation/occurrence data integrating several sources including GBIF and iNaturalist. For this purpose I'm generating lists of names and taxa related to the different ingested observation sources. In order to offer unified taxon search and filter functionality, I need equivalence mappings between ID-namespaces of different checklists (GBIF, CoL, internal, ornitho.lu, etc). I noticed that the CLB API offers the call `/dataset/{key}/nameusage/{id}/related` which for key=3LR and datasetKey=139831 [iNat] returns a correspondence. Where does the data for this mapping come from? Examining both the CoL and iNat checklists NameRelation.tsv (from the CoLDP downloads) didn't give a match. Is this data imported into CLB though a different checklist or is it supplemented though some more hidden datasource? The ID-namespace translation does not seem to be universally implemented and seems somehow tied to the dataset (translation from iNat to CoL didn't seem to work), is this correct? Do you plan on supporting my use-case more explicitly in the future? I would prefer not to use the CLB API and instead import the relevant checklists into our postgresql database in order to allow for an efficient and flexible operation. Thanks for the great work that went into CLB and related projects! 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 Test Environment to be reset on 16th January
by Markus Döring 12 Jan '23

12 Jan '23

Dear ChecklistBank users, we will reset the test environment of ChecklistBank next Monday, 16th January. This removes all data, but all datasets registered in GBIF will reappear quickly. If you need to preserve any data please download it before as we do not keep any backups. Users with editor rights will remain editors and can create new datasets, but will not be linked to any existing (GBIF) datasets. With thanks, Markus https://www.dev.checklistbank.org/

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New monthly edition April 2021 live
by Markus Döring 24 Mar '22

24 Mar '22

Dear COL users, we are happy to announce that we have finally started again to publish monthly releases of the Catalogue of Life. The latest early April 2021 edition is not public on the main portal and available in the API. As this is the first time we have reissued our new identifiers, we have also taken some time to write a small post about stable identifiers in COL which I hope is informative and worth a read: https://www.catalogueoflife.org/2021/04/14/stable-ids Best wishes, Markus & the entire COL team +++ 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

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Catalogue of Life - call for proposals to prepare documentation
by Chantal Huijbers 01 Mar '22

01 Mar '22

Dear all, We would like to notify you that the Catalogue of Life has published two calls for proposals to prepare documentation on 1) the COL API, and 2) the COLDP format. We have some funding available for people who are familiar with the API and/or COLDP to write up documentation focused on examples and user guidelines. We anticipate that these will be relatively short projects, which should be completed within the next 6 months. For more information about the calls and how to submit a proposal, please visit our website: Call for API documentation <https://www.catalogueoflife.org/2022/03/01/documentation-call-API> Call for COLDP documentation <https://www.catalogueoflife.org/2022/03/01/documentation-call-COLDP> Regards, Chantal Huijbers COL Secretariat

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