hmw

Machine readable version of Mammal Species of the World volumes as transcribed by Plazi

:warning: experimental - please use at own risk.

methods / results / summary statistics / example record / R example / funding / references

Physical copies of Mammal Species of the World are a valuable taxonomic resource for mammals. This repository uses Plazi digitized taxonomic treatment versions of these physical copies to generate msw1.json/msw1.csv, and msw2.json/msw2.csv. For your convenience, the first 10 records can be found msw1-sample.json/msw1-sample.csv, msw2-sample.json/msw2-sample.csv. The json and csv files are derived from a Preston tracked version of Plazi's treatment bank available via https://github.com/plazi/treatments-xml. For specific versions of treatments-xml see:

Plazi Community. (2022). Plazi Treatments XML Archive hash://sha256/3cfd60b8b19e76d208377537835de92efdb5b945a6a71765b74ed2fe22298b42 hash://md5/594923284e3eb9965b8cbad149c76cd0f (hash://sha256/3cfd60b8b19e76d208377537835de92efdb5b945a6a71765b74ed2fe22298b42) [Data set]. Zenodo. https://doi.org/10.5281/zenodo.7443343

This work originates from the Biodiversity Data Hub working group of the CETAF Covid19 . For more information see https://globalbioticinteractions.org/covid19 .

Methods

The json files are roughly generated via:

# get the recent version of Plazi's treatments in xml format

# transform only MSW treatments into json using preston

preston track https://github.com/plazi/treatments-xml/archive/master.zip\
 | preston plazi-stream\
 | grep "Mammal Species of the World"\
 > msw.json

Separate the msw related treatment into msw1 and msw2. At time of writing Plazi had not yet transcribed MSW3 yet.

cat msw.json\
 | jq --compact-output 'select(.["docOrigin"] == "Mammal Species of the World (1 st Edition), Lawrence, Kansas, USA: Alien Press, Inc. & The Association of Systematics Collections")'\
 > msw1.json 

cat msw.json\ 
 | jq --compact-output 'select(.["docOrigin"] == "Mammal Species of the World (2 nd Edition), Washington and London: Smithsonian Institution Press")'\
 > msw2.json

csv files were generated using mlr via scripts like:

 cat msw2.json | mlr --ijson --ocsv cat > msw2.csv
 cat msw1.json | mlr --ijson --ocsv cat > msw1.csv

only including the verbatim texts extracted by Plazi -

 cat msw1.json | jq --compact-output --raw-output '.["verbatimText"]' > msw1-verbatim.txt
 cat msw2.json | jq --compact-output --raw-output '.["verbatimText"]' > msw2-verbatim.txt

Work in process. Please open an issue if you have questions / comments.