Catalogue of Life Repackaged and Sorted hash://sha256/35efd8089b3f86d6789ca75be70630e0e328f2c91b43c2636ecdc49f210b97bb hash://md5/c39e3cbe35f0ae86acf3e77baeb01bfb

# Introduction The Catalogue of Life [@Banki_2023] is "\[...\] is an assembly ofexpert-based global species checklists with the aim to build acomprehensive catalogue of all known species of organisms on Earth.\[...\]" This data publication contains a verifiable copy of the Catalogue ofLife as well as a reverse sorted version of the NameUsage.tsv table. Theaims of this publication are to: 1. provide a signed citation [@Elliott_2023] for a copy of Catalogue of Life2. prepare Catalogue of Life to be included in the Nomer Corpus of Taxonomic Resources [@Poelen_2023a].3. pre-process the Catalogue of Life to facilitate optimized indexing and offline taxonomic name alignments using tools like Nomer [@Poelen_2023b]. Overall, the publications aims to facilitate taxonomic name alignmentusing the wealth of information provided by the Catalogue of Life tohelp enable fast, reproduceable, offline-enabled alignment of namelistswith taxonomic resources of known provenance (or origin). An example of an application facilitated by this publication is theTaxonomic Name Alignment tool as provided throughhttps://github.com/globalbioticinteractions/name-alignment-template.This template repository implements an automated workflow using GitHubAction to align scientific names in csv/tsv files and darwin corearchive with common taxonomic name lists like Catalogue of Life, NCBITaxonomy, Integrated Taxonomic Information System (ITIS), and GBIFBackbone taxonomy. ## Methods To capture and process the Catalogue of Life, the following steps weretaken: 1. track and archive a copy of Catalogue of Life2. reverse sort NameUsage.tsv3. assign an alias to the processed resources Steps 1-3 are captured and documented using Preston, a biodiversity datatracker. Preston not only helps to documents the steps, but alsoincludes the digital resources that were used and produced. ### Track and Archive To track and archive a copy of Catalogue of Life, the following commandwas issued: preston track https://download.catalogueoflife.org/col/latest_coldp.zip With this, a copy ofhttps://download.catalogueoflife.org/col/latest_coldp.zip is downloadedand their sha256 checksum (or hash) is calculated. Also, the downloadprocess is captured machine-readable rdf/nquads statement. The content id (or sha256 hash) of the copy included in this publicationcan be found using: preston alias \ --anchor hash://sha256/35efd8089b3f86d6789ca75be70630e0e328f2c91b43c2636ecdc49f210b97bb \ --remote https://zenodo.org/deposit/18705780/files \ https://download.catalogueoflife.org/col/latest_coldp.zip \ | head -n1 and is <https://download.catalogueoflife.org/col/latest_coldp.zip> <http://purl.org/pav/hasVersion> <hash://sha256/ced8f3b1eb2ee451df4290e2c6135f08fdd4d5da0c697463b9091c75be809ea7> <urn:uuid:284325aa-c0b3-4ba3-9759-0bd5c388a0df> . meaning that`hash://sha256/ced8f3b1eb2ee451df4290e2c6135f08fdd4d5da0c697463b9091c75be809ea7`is the content id (or sha256 hash) of the content produced by`https://download.catalogueoflife.org/col/latest_coldp.zip` at the timethis publication was compiled. ### Reverse Sort NameUsage.tsv The second step was to pre-process (or transform) part of the trackedCatalogue of Life data package and reverse sort their content. We usethe following bash script to do this processing: (sed -u 1q; LC_ALL=C sort -r) | gzip The script first prints the header (i.e., `sed -u 1q`), then reversesorts the following content (i.e., `LC_ALL=C sort -r`). Finally, theoutput is compressed using gzip. This script is part of this data publication, and can be retrieved via: preston cat \ --remote https://zenodo.org/record/18705780/files/ \ hash://sha256/03292e3e40a04c565c83debd26ed521516f158a29c011b57a96d1c720c40b6cd To help make it easier to reference the script, an alias was createdusing preston alias \ urn:example:reverse-sort.sh \ hash://sha256/03292e3e40a04c565c83debd26ed521516f158a29c011b57a96d1c720c40b6cd ~~ Following the authoring of the reverse sort script, and documenting their alias (i.e. 'urn:example:reverse-sort.sh`), we applied the script to the acquired copy of the Catalogue of Life using: preston cat\--remote https://zenodo.org/record/18705780/files/\'zip:hash://sha256/ced8f3b1eb2ee451df4290e2c6135f08fdd4d5da0c697463b9091c75be809ea7!/NameUsage.tsv'\\| preston bash\--anchorhash://sha256/35efd8089b3f86d6789ca75be70630e0e328f2c91b43c2636ecdc49f210b97bb\--remote https://zenodo.org/record/18705780/files/\-c urn:example:reverse-sort.sh \~\~\~ The result of this process was the content identified by sha256 hash hash://sha256/1008433bfa5fe7fb059a720eddfe995e18b3e0e8f25ac0c990f1477c177d18cc as documented in line 22 of the associated preston processing log in preston cat\ --remote https://zenodo.org/record/18705780/files/\ 'line:hash://sha256/8ba35deafc847f0d5d69d357241a431b7fd9b6f2735189575b2b7168d523caa9!/L22' ### Assign An Alias to Processed Resources The alias 'col:NameUsage.tsv.gz' was defined to help make it easier topoint to the result using: preston alias\ col:NameUsage.tsv.gz\ hash://sha256/1008433bfa5fe7fb059a720eddfe995e18b3e0e8f25ac0c990f1477c177d18cc With this, the following command was executed to list the first threelines of the produced resource: preston cat \ --anchor hash://sha256/35efd8089b3f86d6789ca75be70630e0e328f2c91b43c2636ecdc49f210b97bb \ --remote https://zenodo.org/record/18705780/files/ \ col:NameUsage.tsv.gz \ | gunzip \ | head -n3 Where `preston cat ...` prints the produced resource, `gunzip`uncompresses the result, and the first three lines are selected using`head -n3`. The result of the operation is shown below: col:ID col:alternativeID col:nameAlternativeID col:sourceID col:parentID col:basionymID col:status col:scientificName col:authorship col:rank col:notho col:originalSpelling col:uninomial col:genericName col:infragenericEpithet col:specificEpithet col:infraspecificEpithet col:cultivarEpithet col:combinationAuthorship col:combinationAuthorshipID col:combinationExAuthorship col:combinationExAuthorshipID col:combinationAuthorshipYear col:basionymAuthorship col:basionymAuthorshipID col:basionymExAuthorship col:basionymExAuthorshipID col:basionymAuthorshipYear col:namePhrase col:nameReferenceID col:publishedInYear col:publishedInPage col:publishedInPageLink col:gender col:genderAgreement col:etymology col:code col:nameStatus col:accordingToID col:accordingToPage col:accordingToPageLink col:referenceID col:scrutinizer col:scrutinizerID col:scrutinizerDate col:extinct col:temporalRangeStart col:temporalRangeEnd col:environment col:species col:section col:subgenus col:genus col:subtribe col:tribe col:subfamily col:family col:superfamily col:suborder col:order col:subclass col:class col:subphylum col:phylum col:kingdom col:ordinal col:branchLength col:link col:nameRemarks col:remarks col:modified col:modifiedBy clb:merged _UATf344c37VElrQ7H85p0 KZX8B accepted Mystacocarida Pennak & Zinn, 1943 class Mystacocarida Boxshall, Geoff 2015-05-05 marine Crustacea Arthropoda Animalia https://www.marinespecies.org/aphia.php?p=taxdetails&id=1079 false ZZZZ 1026 ZZZY synonym Cryptoripersia arizonensis Ferris, 1919 species Cryptoripersia arizonensis Ferris 1919 zoological 19d717dc-f553-4b71-adfc-7e420620aa50,9fe5b735-fcc8-4d9a-a00d-e0b62dbadecf,c17ead8c-57dd-46fd-b80d-6932443f3479,e14aa0cd-5eb3-4c10-87ec-d44cbfe837d3,c59aec86-4224-43a9-9958-f32a2459cfdc,35906e7a-4d3a-4f42-8b19-315dee356805,67a93281-7ff1-49cb-b8f6-a88c609a7e86,4af3819f-f1fd-4b27-b484-c69e0a73e2be,6b1fb685-e0d9-4423-a00f-499494115f50 false # Results As described in our methods, this publication derived the resource withalias col:NameUsage.tsv.gz and content id`hash://sha256/90cfb4edc5f7fa2b55e8bdd9b26d26aec135d1bc9dd11df77df46f732475d3fa`. This resource contains a reverse-sorted copy of the NameUsage.tsvprovided in the Catalogue of Life data package retrieved fromhttps://download.catalogueoflife.org/col/latest_coldp.zip with contentidentifier`hash://sha256/ced8f3b1eb2ee451df4290e2c6135f08fdd4d5da0c697463b9091c75be809ea7`. The following tools were used to process the Catalogue of Life resource: tool name preston bash gzip sed head sort # Discussion This publication is intended to facilitate re-use of the Catalogue ofLife data package in taxonomic name alignment workflows. While theprimary goal was to generate a resource for use in Nomer v0.6.2[@Poelen_2023b], other usage can be imagined such as: 1. Lots of Copies Keeps Stuff Safe (LOCKSS [@Maniatis_2005]): keep an identical copy of Catalogue of Life data package outside of the Catalogue of Life infrastructure.2. demonstrating how data transformation processes can be documented using Preston3. making a streamable copy of a reverse-sorted copy of Catalogue of Life available via https://zenodo.org/record/18705780/files/90cfb4edc5f7fa2b55e8bdd9b26d26aec135d1bc9dd11df77df46f732475d3fa for use in workflows like looking up the first record that contain *Enhydra lutris* (Sea otter): <!-- --> curl -L 'https://zenodo.org/record/18705780/files/90cfb4edc5f7fa2b55e8bdd9b26d26aec135d1bc9dd11df77df46f732475d3fa'\ | gunzip\ | grep "Enhydra lutris"\ | head -n1 # Acknowledgements This work stands on the shoulders of contributors to open sourcesoftware and openly accessible datasets. Thank you!