Wikidata Taxon Items in JSON Lines Format hash://sha256/13ffa9679bae381aa5914d810638fb5a0c75d71f5f7d47f38b3c00d750c88b9c hash://md5/bdcc99bfedfd34abdfdd3802182f225c

<p>Wikidata contains information about taxonomic names, and these taxonomic names are key to integrating biodiversity datasets across different platforms, datasets and institutions.&nbsp;</p> <h2>Content</h2> <table> <tbody> <tr> <td><strong>filename/alias</strong></td> <td><strong>content ids</strong></td> </tr> <tr> <td>wikidata-taxon.json.bz2</td> <td> <p><a href="https://linker.bio/hash://sha256/a7592b72c9013d67d655b6ea5d1f4f67f2057dc5b5ee52578a07f58fea835580">hash://sha256/</a><a href="https://zenodo.org/api/records/13920038/draft/files/701a1382e304a6b1bb38fe828d82f7b8b562c77f918f33097966e38bacf0b2e7/content" target="_blank" rel="noopener noreferrer">701a1382e304a6b1bb38fe828d82f7b8b562c77f918f33097966e38bacf0b2e7</a></p> <p><a href="https://linker.bio/hash://md5/d5bad3553470506f3bde383566a5dea3">hash://md5/d5bad3553470506f3bde383566a5dea3</a></p> </td> </tr> <tr> <td>wikidata-taxa.sh</td> <td> <p><a href="https://linker.bio/hash://sha256/6f4fac44054d54ec3006d091ba702f872b3f4d013628add98fcca08a3b768962">hash://sha256/6f4fac44054d54ec3006d091ba702f872b3f4d013628add98fcca08a3b768962</a></p> <p><a href="https://linker.bio/hash://md5/1d80083d498d61c8b63fbd46d51f7c5c">hash://md5/1d80083d498d61c8b63fbd46d51f7c5c</a></p> </td> </tr> <tr> <td>Q140.json (example)</td> <td> <p><a href="https://linker.bio/hash://md5/44ab0031091fb96caa063e3fe41a85f2">hash://md5/44ab0031091fb96caa063e3fe41a85f2</a></p> </td> </tr> </tbody> </table> <h2>Provenance</h2> <h3>for humans</h3> <p>This dataset contains a subset of Wikidata items referencing the taxonomic name concept https://www.wikidata.org/wiki/Q16521 and is expressed in JSON Lines format.&nbsp;</p> <p>An example of such item is https://wikidata.org/wiki/Q140, an item that describes the taxonomic name associated with&nbsp;<em>Panthera leo</em>, commonly known as Lion (English), Le&oacute;n (Spanish), or 狮子 (Chinese). You can find a "pretty" printed example of Q140 in the file "Q140.json" included in this publication. The first 10 lines of "Q140.json" are shown below:&nbsp;</p> <pre><code>{ "type": "item", "id": "Q140", "labels": { "fr": { "language": "fr", "value": "lion" }, "it": { "language": "it", ...</code></pre> <p>&nbsp;</p> <p>The reason for creating a wikidata subset is because all of wikidata (~85G) didn't fit in Zenodo.&nbsp;</p> <h3>for machines</h3> <p>This dataset was generated using the script below with content id&nbsp;<a href="https://linker.bio/hash://sha256/6f4fac44054d54ec3006d091ba702f872b3f4d013628add98fcca08a3b768962">hash://sha256/6f4fac44054d54ec3006d091ba702f872b3f4d013628add98fcca08a3b768962</a>&nbsp; or <a href="https://linker.bio/hash://md5/1d80083d498d61c8b63fbd46d51f7c5c">hash://md5/1d80083d498d61c8b63fbd46d51f7c5c</a></p> <pre><code> 1 #!/bin/bash 2 # 3 # streams Wikidata taxon items (or items containing https://www.wikidata.org/wiki/Q16521) 4 # from latest data dump in line json (one json object per line) 5 # 6 curl --silent "https://dumps.wikimedia.org/wikidatawiki/entities/latest-all.json.bz2"\ 7 | bunzip2\ 8 | grep -E "Q16521[^0-9]"\ 9 | sed 's/,$//g'\ 10 | bzip2 </code></pre> <p>The script first downloads a recent copy of all wikidata entities in bzip2 compressed format (line 6), decompresses them (line 7), selects only lines containing "Q16521" (line 8), removes any trailing commas (line 9), and recompresses the output. With this, the output contains wikidata items/entities as described earlier.</p> <p>Preston, a biodiversity data tracker, was used to (a) track the script, as well as (b) recording a script execution and (c) tracking the outcome by running :</p> <pre><code>#!/bin/bash # # run the script with id hash://sha256/13ff... # preston bash\ --remote https://linker.bio\ -c "hash://sha256/13ffa9679bae381aa5914d810638fb5a0c75d71f5f7d47f38b3c00d750c88b9c" </code></pre> <p>The recording of this process is identified with hash://sha256/13ffa9679bae381aa5914d810638fb5a0c75d71f5f7d47f38b3c00d750c88b9c and hash://md5/bdcc99bfedfd34abdfdd3802182f225c , and can be reconstructed using&nbsp;</p> <pre><code>preston ls\ --remote https://linker.bio/,https://zenodo.org/records/13920038/files\ --anchor hash://sha256/13ffa9679bae381aa5914d810638fb5a0c75d71f5f7d47f38b3c00d750c88b9c</code></pre> <p>Which is expected to produce:</p> <pre><code>&lt;https://preston.guoda.bio&gt; &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#type&gt; &lt;http://www.w3.org/ns/prov#SoftwareAgent&gt; &lt;urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440&gt; .<br>&lt;https://preston.guoda.bio&gt; &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#type&gt; &lt;http://www.w3.org/ns/prov#Agent&gt; &lt;urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440&gt; .<br>&lt;https://preston.guoda.bio&gt; &lt;http://purl.org/dc/terms/description&gt; "Preston is a software program that finds, archives and provides access to biodiversity datasets."@en &lt;urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440&gt; .<br>&lt;urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440&gt; &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#type&gt; &lt;http://www.w3.org/ns/prov#Activity&gt; &lt;urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440&gt; .<br>&lt;urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440&gt; &lt;http://purl.org/dc/terms/description&gt; "Executes script and captures stdout"@en &lt;urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440&gt; .<br>&lt;urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440&gt; &lt;http://www.w3.org/ns/prov#startedAtTime&gt; "2024-10-10T16:37:36.659Z"^^&lt;http://www.w3.org/2001/XMLSchema#dateTime&gt; &lt;urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440&gt; .<br>&lt;urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440&gt; &lt;http://www.w3.org/ns/prov#wasStartedBy&gt; &lt;https://preston.guoda.bio&gt; &lt;urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440&gt; .<br>&lt;https://doi.org/10.5281/zenodo.1410543&gt; &lt;http://www.w3.org/ns/prov#usedBy&gt; &lt;urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440&gt; &lt;urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440&gt; .<br>&lt;https://doi.org/10.5281/zenodo.1410543&gt; &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#type&gt; &lt;http://purl.org/dc/dcmitype/Software&gt; &lt;urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440&gt; .<br>&lt;https://doi.org/10.5281/zenodo.1410543&gt; &lt;http://purl.org/dc/terms/bibliographicCitation&gt; "Jorrit Poelen, Icaro Alzuru, &amp; Michael Elliott. 2018-2024. Preston: a biodiversity dataset tracker (Version 0.9.9-SNAPSHOT) [Software]. Zenodo. https://doi.org/10.5281/zenodo.1410543"@en &lt;urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440&gt; .<br>&lt;urn:uuid:0659a54f-b713-4f86-a917-5be166a14110&gt; &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#type&gt; &lt;http://www.w3.org/ns/prov#Entity&gt; &lt;urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440&gt; .<br>&lt;urn:uuid:0659a54f-b713-4f86-a917-5be166a14110&gt; &lt;http://purl.org/dc/terms/description&gt; "A biodiversity dataset graph archive."@en &lt;urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440&gt; .<br>&lt;hash://sha256/e76276c283090381fc4b3efe28fc61c28f5bf03db0f3743f7178b999ebccada2&gt; &lt;http://www.w3.org/ns/prov#usedBy&gt; &lt;urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440&gt; &lt;urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440&gt; .<br>&lt;hash://sha256/6f4fac44054d54ec3006d091ba702f872b3f4d013628add98fcca08a3b768962&gt; &lt;http://purl.org/dc/elements/1.1/format&gt; "text/x-shellscript" .<br>&lt;urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440&gt; &lt;http://www.w3.org/ns/prov#used&gt; &lt;hash://sha256/6f4fac44054d54ec3006d091ba702f872b3f4d013628add98fcca08a3b768962&gt; .<br>&lt;urn:uuid:7ecf1c84-0438-4224-8909-0804028cf3f6&gt; &lt;http://www.w3.org/ns/prov#wasGeneratedBy&gt; &lt;urn:uuid:fdc316b0-457d-4d22-85a1-d2ce65c2e440&gt; .<br>&lt;hash://sha256/701a1382e304a6b1bb38fe828d82f7b8b562c77f918f33097966e38bacf0b2e7&gt; &lt;http://www.w3.org/ns/prov#wasGeneratedBy&gt; &lt;urn:uuid:bb57ae4b-1ba1-4188-8e95-3f3f6cdcab6b&gt; &lt;urn:uuid:bb57ae4b-1ba1-4188-8e95-3f3f6cdcab6b&gt; .<br>&lt;hash://sha256/701a1382e304a6b1bb38fe828d82f7b8b562c77f918f33097966e38bacf0b2e7&gt; &lt;http://www.w3.org/ns/prov#qualifiedGeneration&gt; &lt;urn:uuid:bb57ae4b-1ba1-4188-8e95-3f3f6cdcab6b&gt; &lt;urn:uuid:bb57ae4b-1ba1-4188-8e95-3f3f6cdcab6b&gt; .<br>&lt;urn:uuid:bb57ae4b-1ba1-4188-8e95-3f3f6cdcab6b&gt; &lt;http://www.w3.org/ns/prov#generatedAtTime&gt; "2024-10-11T02:08:03.739Z"^^&lt;http://www.w3.org/2001/XMLSchema#dateTime&gt; &lt;urn:uuid:bb57ae4b-1ba1-4188-8e95-3f3f6cdcab6b&gt; .<br>&lt;urn:uuid:bb57ae4b-1ba1-4188-8e95-3f3f6cdcab6b&gt; &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#type&gt; &lt;http://www.w3.org/ns/prov#Generation&gt; &lt;urn:uuid:bb57ae4b-1ba1-4188-8e95-3f3f6cdcab6b&gt; .<br>&lt;urn:uuid:bb57ae4b-1ba1-4188-8e95-3f3f6cdcab6b&gt; &lt;http://www.w3.org/ns/prov#used&gt; &lt;urn:uuid:7ecf1c84-0438-4224-8909-0804028cf3f6&gt; &lt;urn:uuid:bb57ae4b-1ba1-4188-8e95-3f3f6cdcab6b&gt; .<br>&lt;urn:uuid:7ecf1c84-0438-4224-8909-0804028cf3f6&gt; &lt;http://purl.org/pav/hasVersion&gt; &lt;hash://sha256/701a1382e304a6b1bb38fe828d82f7b8b562c77f918f33097966e38bacf0b2e7&gt; &lt;urn:uuid:bb57ae4b-1ba1-4188-8e95-3f3f6cdcab6b&gt; .<br>&lt;https://preston.guoda.bio&gt; &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#type&gt; &lt;http://www.w3.org/ns/prov#SoftwareAgent&gt; &lt;urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758&gt; . &lt;https://preston.guoda.bio&gt; &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#type&gt; &lt;http://www.w3.org/ns/prov#Agent&gt; &lt;urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758&gt; . &lt;https://preston.guoda.bio&gt; &lt;http://purl.org/dc/terms/description&gt; "Preston is a software program that finds, archives and provides access to biodiversity datasets."@en &lt;urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758&gt; . &lt;urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758&gt; &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#type&gt; &lt;http://www.w3.org/ns/prov#Activity&gt; &lt;urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758&gt; . &lt;urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758&gt; &lt;http://purl.org/dc/terms/description&gt; "Executes script and captures stdout"@en &lt;urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758&gt; . &lt;urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758&gt; &lt;http://www.w3.org/ns/prov#startedAtTime&gt; "2024-06-22T10:40:12.016Z"^^&lt;http://www.w3.org/2001/XMLSchema#dateTime&gt; &lt;urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758&gt; . &lt;urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758&gt; &lt;http://www.w3.org/ns/prov#wasStartedBy&gt; &lt;https://preston.guoda.bio&gt; &lt;urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758&gt; . &lt;https://doi.org/10.5281/zenodo.1410543&gt; &lt;http://www.w3.org/ns/prov#usedBy&gt; &lt;urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758&gt; &lt;urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758&gt; . &lt;https://doi.org/10.5281/zenodo.1410543&gt; &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#type&gt; &lt;http://purl.org/dc/dcmitype/Software&gt; &lt;urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758&gt; . &lt;https://doi.org/10.5281/zenodo.1410543&gt; &lt;http://purl.org/dc/terms/bibliographicCitation&gt; "Jorrit Poelen, Icaro Alzuru, &amp; Michael Elliott. 2021. Preston: a biodiversity dataset tracker (Version 0.8.4) [Software]. Zenodo. https://doi.org/10.5281/zenodo.1410543"@en &lt;urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758&gt; . &lt;urn:uuid:0659a54f-b713-4f86-a917-5be166a14110&gt; &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#type&gt; &lt;http://www.w3.org/ns/prov#Entity&gt; &lt;urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758&gt; . &lt;urn:uuid:0659a54f-b713-4f86-a917-5be166a14110&gt; &lt;http://purl.org/dc/terms/description&gt; "A biodiversity dataset graph archive."@en &lt;urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758&gt; . &lt;hash://sha256/6f4fac44054d54ec3006d091ba702f872b3f4d013628add98fcca08a3b768962&gt; &lt;http://purl.org/dc/elements/1.1/format&gt; "text/x-shellscript" . &lt;urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758&gt; &lt;http://www.w3.org/ns/prov#used&gt; &lt;hash://sha256/6f4fac44054d54ec3006d091ba702f872b3f4d013628add98fcca08a3b768962&gt; . &lt;urn:uuid:6fa51a99-a137-4387-90b1-23589d7b60ae&gt; &lt;http://www.w3.org/ns/prov#wasGeneratedBy&gt; &lt;urn:uuid:096ba92f-9d5c-4cb1-9a3d-7a95c5228758&gt; . &lt;hash://sha256/a7592b72c9013d67d655b6ea5d1f4f67f2057dc5b5ee52578a07f58fea835580&gt; &lt;http://www.w3.org/ns/prov#wasGeneratedBy&gt; &lt;urn:uuid:e0d76a06-5241-4dfe-8429-46164190ab0e&gt; &lt;urn:uuid:e0d76a06-5241-4dfe-8429-46164190ab0e&gt; . &lt;hash://sha256/a7592b72c9013d67d655b6ea5d1f4f67f2057dc5b5ee52578a07f58fea835580&gt; &lt;http://www.w3.org/ns/prov#qualifiedGeneration&gt; &lt;urn:uuid:e0d76a06-5241-4dfe-8429-46164190ab0e&gt; &lt;urn:uuid:e0d76a06-5241-4dfe-8429-46164190ab0e&gt; . &lt;urn:uuid:e0d76a06-5241-4dfe-8429-46164190ab0e&gt; &lt;http://www.w3.org/ns/prov#generatedAtTime&gt; "2024-06-22T19:01:55.863Z"^^&lt;http://www.w3.org/2001/XMLSchema#dateTime&gt; &lt;urn:uuid:e0d76a06-5241-4dfe-8429-46164190ab0e&gt; . &lt;urn:uuid:e0d76a06-5241-4dfe-8429-46164190ab0e&gt; &lt;http://www.w3.org/1999/02/22-rdf-syntax-ns#type&gt; &lt;http://www.w3.org/ns/prov#Generation&gt; &lt;urn:uuid:e0d76a06-5241-4dfe-8429-46164190ab0e&gt; . &lt;urn:uuid:e0d76a06-5241-4dfe-8429-46164190ab0e&gt; &lt;http://www.w3.org/ns/prov#used&gt; &lt;urn:uuid:6fa51a99-a137-4387-90b1-23589d7b60ae&gt; &lt;urn:uuid:e0d76a06-5241-4dfe-8429-46164190ab0e&gt; . &lt;urn:uuid:6fa51a99-a137-4387-90b1-23589d7b60ae&gt; &lt;http://purl.org/pav/hasVersion&gt; &lt;hash://sha256/a7592b72c9013d67d655b6ea5d1f4f67f2057dc5b5ee52578a07f58fea835580&gt; &lt;urn:uuid:e0d76a06-5241-4dfe-8429-46164190ab0e&gt; . </code></pre>