sbd-data-landscape-opendata

This repository is about SbD4Nano Landscape data from openly licensed resources. Internally, the project has a larger collection of data, including data that cannot be shared. This repository are the tools needed to collect the RDF behind our public SPARQL endpoint and the basis of an eBook:

• SPARQL endpoint: https://sbd4nanolandscape.rdf.bigcat-bioinformatics.org/
• eBook: https://h2020-sbd4nano.github.io/sbd-data-book/

Requirements

A Ubuntu or Debian system, e.g. with the Windows Linux Subsystem.

• wget
• roqet
• jq
• npm
• Groovy 4.x (not available as Debian/Ubuntu package)

Install the Debian/Ubuntu packages with:

sudo apt install wget rasqal-utils jq

Install ROBOT:

wget https://github.com/ontodev/robot/releases/download/v1.9.3/robot.jar
curl https://raw.github.com/ontodev/robot/master/bin/robot > robot

Get a copy of the eNanoMapper ontology and convert it with ROBOT to Turtle:

wget https://github.com/enanomapper/ontologies/releases/download/v9.0/enanomapper-full.owl
sh ./robot convert --input enanomapper-full.owl --output enanomapper-full.ttl

How to run

First, check the fetchData.sh file in this repository. Then, run these commands:

sh fetchData.sh
make validation
sh fetchShapes.sh
make statistics
make | tee shexValidation.log

Make the open.ttl

Run the fetchData.sh file to download all data. This script also defines the files that are open-licensed and which ones are not. Next, run the following commands to create the open.ttl:

make open.ttl

Status

The following repositories use GitHub Actions to collect data. Here are their status badges:

• h2020-sbd4nano/sbd-data-ambit
• h2020-sbd4nano/sbd-data-aopwiki
• h2020-sbd4nano/sbd-data-elixir-biotools
• h2020-sbd4nano/sbd-data-fdp
• h2020-sbd4nano/sbd-data-nanocommons
• h2020-sbd4nano/sbd-data-nanowiki
• h2020-sbd4nano/sbd-data-riskgone
• h2020-sbd4nano/sbd-data-vhp4safety