Elton nanopubs

exportNanoPubs.sh

#!/bin/bash
#
# Example of how to create trustry nanopubs from species interaction data using elton and nanopub-java
#

echo download elton tool...
curl -L "https://github.com/globalbioticinteractions/elton/releases/download/0.4.1/elton.jar" > elton.jar
echo download elton tool done.

# you can also use https://github.com/globalbioticinteractions/elton-archive to retrieve archived datasets from the internet archive
echo get bird diets ...
java -jar elton.jar update hurlbertlab/dietdatabase
echo get bird diets done.

echo export nanopubs...
java -jar elton.jar nanopubs hurlbertlab/dietdatabase | gzip > nanopubs.trig.gz
echo export nanopubs done.

# print first 5 nanopubs - one nanopub per line
zcat nanopubs.trig.gz | head -n 5

echo get nanopub-java tool...
curl -L "https://github.com/Nanopublication/nanopub-java/releases/download/nanopub-1.14/nanopub-1.14-jar-with-dependencies.jar" > np.jar
echo get nanopub-java tool done.

echo checking nanopubs...
java -jar np.jar check nanopubs.trig.gz
echo checking nanopubs done.

echo make trustry nanopubs...
java -jar np.jar mktrusty nanopubs.trig.gz
echo make trustry nanopubs done.

echo checking trustry nanopubs...
java -jar np.jar check trustry.nanopubs.trig.gz
echo checking trustry nanopubs done.