candYgene / pbg-ld

Linked Data Platform for Plant Breeding & Genomics

pbg-ld: Linked Data Platform for Plant Breeding & Genomics

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.

Prerequisites

• Docker CE
• Docker Compose
• Ansible

Install & deploy

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 data
• fdp - 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 scheme http(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

Overview of datasets

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