Global Biotic Interactions: Taxon Graph Patches

2018-11-23T00:00:00Z (GMT) by Poelen, Jorrit H.
<p>Global Biotic Interactions: Taxon Graph Patch 20181123-01 </p> <p>Abstract / Introduction </p> <p>On release of Encyclopedia of Life (EOL) v3 in<br> November 2018, an unspecified collection of EOL page ids (aka taxon concept ids)<br> were deprecated and no longer supported. This issue was<br> documented in https://github.com/jhpoelen/eol-globi-data/issues/383 . This<br> issue describes an EOL page https://eol.org/pages/216713 previously associated <br> with Bees (Apis) was no longer available and generated a server error. </p> <p>Methods</p> <p>To prevent pointing to no longer present EOL web pages from GloBI, <br> an automated precedure was implemented to do the following. First, an EOL v3 taxon<br> archive ([1]) was compared against a list of EOL ids on GloBI's Taxon Graph<br> v0.3.8 ([2]) to create a list of EOL ids only present in GloBI's list. Then, all<br> no longer supported EOL ids were marked in taxonMap.tsv.gz and taxonCache.tsv.gz by<br> replacing the prefix "EOL:" to "EOL_V2:". Patch files were then generated using<br> the unix "diff" comment to document the changes between the original<br> taxonMap/taxonCache files. The procedure was captured as a bash script in<br> "create_patch.sh". </p> <p>To apply the patch, run the "patch" program against the original<br> taxonCache/taxonMap files with the .patch files on any linux-y system.</p> <p>Patch files taxonMap.tsv.patch.gz and taxonCache.tsv.patch.gz were <br> created using: create_patch.sh in period 2018-11-21/2018-11-23 .</p> <p>Result/Discussion </p> <p>The resulting patches inform us that 27,087 of 103,638 (~26%)<br> EOL ids present in GloBI Taxon Graph v0.3.8 were no longer included in EOL v3. A<br> simular exercise can be performed to prune dead link pointing into EOL from<br> platforms like Wikidata. </p> <p>References</p> <p>[1] "EOL Dynamic Hierarchy with landmark taxa",<br> https://opendata.eol.org/dataset/b6bb0c9e-681f-4656-b6de-39aa3a82f2de/resource/bac4e11c-28ab-4038-9947-02d9f1b0329f/download/eoldynamichierarchywithlandmarks.zip <br> with hash://sha256/6a26e52adf1518eebac3556c05370396251ca3ec6a9059694b91a2549fc4013a .<br> Accessed on 2018-11-21 .  </p> <p>[2] Poelen, Jorrit H. (2018). Global Biotic Interactions: Taxon Graph <br> (Version 0.3.8) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.1489121</p>