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Elton nanopubs
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| #!/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. | |
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