The pbg-ld software provides access to semantically integrated geno- & pheno-typic data on Solanaceae species (such as tomato and potato) and enables ranking of candidate genes associated with traits of interest.
1. Clone this repository.
git clone https://github.com/candYgene/pbg-ld.git
2. Start Docker service(s).
pbg-ld
- Virtuoso-based RDF store including datafdp
- FAIR Data Point (requires pbg-ld)grlc
- grlc WebAPI (requires pbg-ld)
cd pbg-ld
# list available services
docker-compose config --services
# start all services or one-by-one
docker-compose up -d # or add [SERVICE]
Alternatively, deploy the services on a remote server using Ansible Playbook.
ansible-playbook -i inventory playbook.yml
Note: grlc
API can be deployed with SPARQL queries stored
- locally (in the container)
git clone https://github.com/candYgene/queries.git
docker cp queries grlc:/home/grlc/
- remotely (in a GitHub repo)
Set the environment variables in docker-compose.yml
:
GRLC_GITHUB_ACCESS_TOKEN
GRLC_SERVER_NAME
(or CNAME, excluding URI schemehttp(s)//:
)GRLC_SPARQL_ENDPOINT
3. Access (meta)data in RDF.
- Virtuoso Conductor use for admin tasks (default account name/password:
dba/dba
) - Virtuoso Faceted Browser
- Virtuoso SPARQL endpoint
- grlc Web API using local or remote SPARQL queries
- FAIR Data Point API
RDF graphs:IRIs (A-Box)
- SGN:
http://solgenomics.net/genome/Solanum_lycopersicum
http://solgenomics.net/genome/Solanum_pennellii
http://solgenomics.net/genome/Solanum_tuberosum
- Ensembl:
http://plants.ensembl.org/Solanum_lycopersicum
http://plants.ensembl.org/Solanum_tuberosum
- UniProt:
http://www.uniprot.org/proteomes/Solanum_lycopersicum
http://www.uniprot.org/proteomes/Solanum_tuberosum
- QTLs:
http://europepmc.org
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