PathwayCommons v12 on Virtuoso 7

This repository launches a VOS server and populates it with the PathwayCommons (v12) dump. Modular addition of other graphs (e.g. NextProt, below) is also supported.

Installation (Linux)

1. Edit docker-compose.yml with your system parameters. Users should pay special attention to the following:
   • Memory usage settings defined in environment:VIRT_Parameters_*. Consult the VOS Performance Tuning documentation for more information.
   • Ensure that container_name: is unique, to avoid conflicts.
   • Ensure that ports: are unused and that downstream clients are pointed correctly.
2. Open a terminal inside this directory and run docker-compose up -d:
   • Ensure that <user> has permission to run docker containers or has sudo access.

RDF Compliance:

• SPARQL 1.1 inference is supported for all prefixes via the Mapping Pipeline on the rdf_mappers.vad extension.

Description of pre-loading scripts (scripts/)

Scripts are loaded in alphabetical order, they are informally grouped by numeric prefixes.

1. 01-get-vad.sh: fetches http-accessible VAD packages
   • Additional VAD packages are described in VOS VAD Packages
2. 02-vad-install.sql: call vad_install on the downloaded packages
   • Note that Virtuoso Conductor is automatically installed and not explicitly listed here.
3. 11-bulkload-biopax.sql: download and BioPax schema from biopax.org and load the RDF/XML file (biopax-level3.owl) into target graph http://www.biopax.org/release/biopax-level3.owl
4. 21-get-pcv12.sh: download the PC v12 RDF dump (PathwayCommons12.All.BIOPAX.owl.gz) from PathwayCommons.org
5. 22-bulkload-pcv12.sql: call the RDF Bulk Loader on the previously-downloaded RDF dump
   • Bulk loading is heavily dependent on the memory performance parameters defined above.

Optional pre-loading scripts

Remove the *.norun suffix to enable.

1. 31-get-nextprot.sh.norun: download the RDF dump of the current NextProt release from nextprot.org
2. 32-bulkload-nextprot.sql.norun: call the RDF Bulk loader on the RDF dump