Global Biotic Interactions: Taxon Graph Patches

2018-11-24T05:04:33Z (GMT) by Poelen, Jorrit H.

Global Biotic Interactions: Taxon Graph Patch 20181123-01 

Abstract / Introduction 

On release of Encyclopedia of Life (EOL) v3 in
November 2018, an unspecified collection of EOL page ids (aka taxon concept ids)
were deprecated and no longer supported. This issue was
documented in https://github.com/jhpoelen/eol-globi-data/issues/383 . This
issue describes an EOL page https://eol.org/pages/216713 previously associated 
with Bees (Apis) was no longer available and generated a server error. 

Methods

To prevent pointing to no longer present EOL web pages from GloBI, 
an automated precedure was implemented to do the following. First, an EOL v3 taxon
archive ([1]) was compared against a list of EOL ids on GloBI's Taxon Graph
v0.3.8 ([2]) to create a list of EOL ids only present in GloBI's list. Then, all
no longer supported EOL ids were marked in taxonMap.tsv.gz and taxonCache.tsv.gz by
replacing the prefix "EOL:" to "EOL_V2:". Patch files were then generated using
the unix "diff" comment to document the changes between the original
taxonMap/taxonCache files. The procedure was captured as a bash script in
"create_patch.sh". 

To apply the patch, run the "patch" program against the original
taxonCache/taxonMap files with the .patch files on any linux-y system.

Patch files taxonMap.tsv.patch.gz and taxonCache.tsv.patch.gz were 
created using: create_patch.sh in period 2018-11-21/2018-11-23 .

Result/Discussion 

The resulting patches inform us that 27,087 of 103,638 (~26%)
EOL ids present in GloBI Taxon Graph v0.3.8 were no longer included in EOL v3. A
simular exercise can be performed to prune dead link pointing into EOL from
platforms like Wikidata. 

References

[1] "EOL Dynamic Hierarchy with landmark taxa",
https://opendata.eol.org/dataset/b6bb0c9e-681f-4656-b6de-39aa3a82f2de/resource/bac4e11c-28ab-4038-9947-02d9f1b0329f/download/eoldynamichierarchywithlandmarks.zip 
with hash://sha256/6a26e52adf1518eebac3556c05370396251ca3ec6a9059694b91a2549fc4013a .
Accessed on 2018-11-21 .  

[2] Poelen, Jorrit H. (2018). Global Biotic Interactions: Taxon Graph 
(Version 0.3.8) [Data set]. Zenodo. http://doi.org/10.5281/zenodo.1489121