This software provides semantically integrated genotypic/phenotypic data on animals to enable ranking of candidate genes associated with traits of interest (e.g. nipple quantity in pig).

1. Clone this git repo.

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

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

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

• Pig QTLdb: http://www.animalgenome.org/QTLdb/pig
• Ensembl: http://www.ensembl.org/pig, http://www.ensembl.org/human
• UniProt: http://www.uniprot.org/proteomes/pig
• OMIM: http://bio2rdf.org/omim_resource:bio2rdf.dataset.omim.R4

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
• VT: http://purl.obolibrary.org/obo/vt.owl
• CMO: http://purl.obolibrary.org/obo/cmo.owl
• LPT: http://purl.bioontology.org/ontology/LPT
• LBO: http://purl.bioontology.org/ontology/LBO
• Uniprot Core: http://purl.uniprot.org/core/

Further details can be found on the wiki.