September 2021 - COL-Users

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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API Introduction
by Markus Döring 24 Feb '22

24 Feb '22

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&rank=SP… 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=jso…> like this: https://api.catalogueoflife.org/col/webservice?name=Abies%20alba&format=jso… 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(a)gbif.org<mailto:mdoering@gbif.org> http://www.gbif.org<http://www.gbif.org/>

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Question about Catalogue of Life (COL) Data Package file format
by Cheng, Tiejun (NIH/NLM/NCBI) [E] 30 Sep '21

30 Sep '21

Dear COL team, I'm trying to download the ColDP Archive of THE COL CHECKLIST VERSION 2021-09-21 on this page: https://www.catalogueoflife.org/data/download. However, the actual download link https://download.catalogueoflife.org/col/monthly/2021-09-21_coldp.zip is not working and returns 404. I am able to find another data file here: https://download.catalogueoflife.org/col/. The most recent one I believe is https://download.catalogueoflife.org/col/latest_coldp.zip with a timestamp of 2021-08-27 11:00. According to the description of ColDP file format here: https://www.catalogueoflife.org/about/colusage#data-formats. The ZIP archive is supposed to bundle the following delimited text files: * Name<https://github.com/CatalogueOfLife/coldp/blob/master/README.md#name> * NameRelation<https://github.com/CatalogueOfLife/coldp/blob/master/README.md#namerelation> * Taxon<https://github.com/CatalogueOfLife/coldp/blob/master/README.md#taxon> * Synonym<https://github.com/CatalogueOfLife/coldp/blob/master/README.md#synonym> * NameUsage<https://github.com/CatalogueOfLife/coldp/blob/master/README.md#nameusage> * Reference<https://github.com/CatalogueOfLife/coldp/blob/master/README.md#reference> * TypeMaterial<https://github.com/CatalogueOfLife/coldp/blob/master/README.md#typematerial> * Distribution<https://github.com/CatalogueOfLife/coldp/blob/master/README.md#distribution> * VernacularName<https://github.com/CatalogueOfLife/coldp/blob/master/README.md#vernacularna…> * Media<https://github.com/CatalogueOfLife/coldp/blob/master/README.md#media> * SpeciesInteraction<https://github.com/CatalogueOfLife/coldp/blob/master/README.md#speciesinter…> * TaxonConceptRelation<https://github.com/CatalogueOfLife/coldp/blob/master/README.md#taxonconcept…> * SpeciesEstimate<https://github.com/CatalogueOfLife/coldp/blob/master/README.md#speciesestim…> * Treatments<https://github.com/CatalogueOfLife/coldp/blob/master/README.md#treatment> However, In the latest_coldp.zip I downloaded, I got something different. $zipinfo -1 latest_coldp.zip * NameUsage.tsv * NameRelation.tsv * TypeMaterial.tsv * VernacularName.tsv * Distribution.tsv * Media.tsv * SpeciesEstimate.tsv * SpeciesInteraction.tsv * TaxonConceptRelation.tsv * Reference.tsv * reference.json (<- this is new) Some important files are missing. * Name * Taxon * Synomym * Treatments Could you please help understand it? Thanks. Best regards, Tiejun CHENG, Ph.D. --------------------------- National Center for Biotechnology Information (NCBI) National Library of Medicine (NLM) National Institutes of Health (NIH) Bldg. 38A, Rm. 8S816A 8600 Rockville Pike Bethesda, MD 20894 Phone: 301-402-9527 Email: chengt2(a)ncbi.nlm.nih.gov<mailto:chengt2@ncbi.nlm.nih.gov>

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