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.
- Edit
docker-compose.ymlwith 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.
- Memory usage settings defined in
- Open a terminal inside this directory and run
docker-compose up -d:- Ensure that
<user>has permission to run docker containers or hassudoaccess.
- Ensure that
- SPARQL 1.1 inference is supported for all prefixes via the Mapping Pipeline on the rdf_mappers.vad extension.
Scripts are loaded in alphabetical order, they are informally grouped by numeric prefixes.
01-get-vad.sh: fetches http-accessible VAD packages- Additional VAD packages are described in VOS VAD Packages
02-vad-install.sql: callvad_installon the downloaded packages- Note that Virtuoso Conductor is automatically installed and not explicitly listed here.
11-bulkload-biopax.sql: download and BioPax schema from biopax.org and load the RDF/XML file (biopax-level3.owl) into target graphhttp://www.biopax.org/release/biopax-level3.owl21-get-pcv12.sh: download the PC v12 RDF dump (PathwayCommons12.All.BIOPAX.owl.gz) from PathwayCommons.org22-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.
Remove the *.norun suffix to enable.
31-get-nextprot.sh.norun: download the RDF dump of the current NextProt release from nextprot.org32-bulkload-nextprot.sql.norun: call the RDF Bulk loader on the RDF dump