Linked Data Platform for Plant Breeding & Genomics
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README.md

Linked Data Platform for Plant Breeding & Genomics

Build Status

This software provides semantically integrated genotypic/phenotypic data on plants to enable ranking of candidate genes associated with traits of interest (e.g. fruit ripening in tomato).

1. Clone this git repo.

git clone https://github.com/candYgene/pbg-ld.git

2. Start a Docker container with Virtuoso Universal Server & ingest data in RDF.

cd pbg-ld/src
make all # with defaults: CONTAINER_NAME=virtuoso and CONTAINER_PORT=8890 (in development)
make -e all CONTAINER_NAME=pbg-ld CONTAINER_PORT=80 # override defaults (in production)

Note: other make rules: pull-image, build-image, start-srv, stop-srv, restart-srv, install-pkgs, get-rdf, import-rdf, update-rdf, post-install and clean.

3. Login to running Virtuoso instance for admin tasks.

Use dba for both account name and password.

4. Run queries via Virtuoso SPARQL endpoint or browse data via Faceted Browser (no login required).

RDF graphs:IRIs (A-Box)

  • SGN:
    • http://solgenomics.net/genome/Solanum_lycopersicum
    • http://solgenomics.net/genome/Solanum_pennellii
  • Ensembl: http://plants.ensembl.org/Solanum_lycopersicum
  • UniProt: http://www.uniprot.org/proteomes/Solanum_lycopersicum
  • QTLs: http://europepmc.org/articles

RDF graphs:IRIs (T-Box)

  • FALDO: http://biohackathon.org/resource/faldo.rdf
  • SO[FA]: http://purl.obolibrary.org/obo/so.owl
  • SIO: http://semanticscience.org/ontology/sio.owl
  • RO: http://purl.obolibrary.org/obo/ro.owl
  • GO: http://purl.obolibrary.org/obo/go.owl
  • UniProt Core: http://purl.uniprot.org/core/
  • PO: http://purl.obolibrary.org/obo/po.owl
  • TO: http://purl.obolibrary.org/obo/to.owl
  • SPTO: http://purl.bioontology.org/ontology/SPTO
  • PATO: http://purl.obolibrary.org/obo/pato.owl

Further details can be found on the wiki.