Global Biotic Interactions Taxon Graph Builder

Builds a new, up-to-date, Global Biotic Interaction Taxon Graph using a previously published taxon graph, nomer and elton.

For an example of a published taxon graph, please see doi:10.5281/zenodo.755513 .

Prerequisites

• make
• bash
• git
• internet connection

Build

To build a taxon graph, run:

$ git clone https://github.com/globalbioticinteractions/taxon-graph-builder
$ cd taxon-graph-builder
$ make
[...  hours later ...]
$ ls -1 dist/taxon-graph.tar.gz
dist/taxon-graph.tar.gz

Deploy

To deploy a GloBI taxon graph, you can use:

Maven

To package and deploy the taxon graph using a maven repository:

sudo mvn\
 --settings /etc/globi/.m2/settings.xml\
 deploy:deploy-file\
 -DartifactId=taxon\
 -DgroupId=org.globalbioticinteractions\
 -Dversion=[some version]\
 -Dfile=[some file path]\
 -Dpackaging=zip\
 -DrepositoryId=globi-datasets\
 -Durl=s3://globi/datasets

Zenodo

Create a Zenodo deposit (e.g., https://zenodo.org/record/4753955), then upload dist artifacts (excluding the prepackaged zip) using

ls -1 | xargs -L1 bash ~/zenodo-upload/zenodo_upload.sh [some deposit id]