BioHackrXiv metadata

This repository handles BioHackrXiv’s metadata (through RDF and JSON). Note that paper.md publications get cached here, so as to keep a stable record.

https://biohackrxiv.org/ is a scholarly publication service for biohackathons and codefests where papers are generated from markdown templates (see markdown example). In this repository we parse the metadata from the paper.md headers and turn that into JSON-LD and RDF for processing and searches.

The (JSON-LD) output is a hierarchy of

• header
• events [1-n]
• publications [1-n]

See also the relevant mini publication for background etc.

Install

The scripts need:

• ruby

Generate JSON-LD

ruby ./bin/biohackr2json-ld.rb

Generate RDF

(Generating RDF will most likely change)

ruby ./bin/biohackr2rdf.rb

To test the generated TTL use

rapper -i turtle test/data/biohackrxiv.ttl

For the latest version see ./test/data/biohackrxiv.ttl

SPARQL

A SPARQL endpoint runs at http://sparql.genenetwork.org/sparql/.

This is a query that lists all contributors:

prefix bhx: <http://biohackerxiv.org/resource>

SELECT DISTINCT ?contributor
FROM    <https://BioHackrXiv.org/graph>
WHERE   {
  ?bh <http://purl.org/dc/terms/contributor> ?contributor
}

Note that the virtuoso endpoint itself can also generate JSON.