globalbioticinteractions/nomer 0.1.0

Published May 31, 2018 | Version 0.1.0

Software Open

Features

Introduce command replace to replace matched values according defined schemas. By default, input expects ids in first columns and names in second. The output schema is the same. Added examples in readme.
Introduce matcher globi-taxon-rank. This matcher takes taxonomic rank names and attempts to match them against wikidata taxon rank items. Wikidata itself is mined for "common names" for taxonomic ranks in various languages. The taxonomic rank information is cached locally after first use.
Exposed individual matchers used by globi-enrich matcher. These include but are not limited to taxonomic lookup at Atlas of Living Australia, National Biodiversity Network, NCBI, ITIS, EOL, WoRMS and more.
Added a stopword remover as part of the globi-correct matcher.

Improvements

Various updates to documentation.
Added more information to the output of the matchers command.
Point default taxon cache to GloBI Taxon Cache 0.3.2 at http://doi.org/10.5281/zenodo.1250572 .
Remove progress reporting with .. Probably best to use a program like pv in combination with *nix pipes to report on progress.
Upgrade to globi libs v0.9.18 .

Bug fixes

make sure to include empty ncbi taxon path/id/rank elements to avoid inconsistent taxonomic path lengths.

Files

Name	Size	Download all
globalbioticinteractions/nomer-0.1.0.zip md5:5a3759eb086c227619a963f3689358e7	10.9 MB	Preview Download

Is supplement to: https://github.com/globalbioticinteractions/nomer/tree/0.1.0 (URL)