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pbg-ld

Linked Data Platform for Plant Breeding & Genomics

https://github.com/candygene/pbg-ld

Science Score: 67.0%

This score indicates how likely this project is to be science-related based on various indicators:

  • ✓
    CITATION.cff file
    Found CITATION.cff file
  • ✓
    codemeta.json file
    Found codemeta.json file
  • ✓
    .zenodo.json file
    Found .zenodo.json file
  • ✓
    DOI references
    Found 5 DOI reference(s) in README
  • ✓
    Academic publication links
    Links to: science.org, zenodo.org
  • ○
    Academic email domains
  • ○
    Institutional organization owner
  • ○
    JOSS paper metadata
  • ○
    Scientific vocabulary similarity
    Low similarity (9.5%) to scientific vocabulary

Keywords

genome-annotation genomics linked-data plant-sciences qtl rdf solanaceae sparql traits triples
Last synced: 6 months ago · JSON representation ·

Repository

Linked Data Platform for Plant Breeding & Genomics

Basic Info
Statistics
  • Stars: 2
  • Watchers: 1
  • Forks: 5
  • Open Issues: 16
  • Releases: 3
Topics
genome-annotation genomics linked-data plant-sciences qtl rdf solanaceae sparql traits triples
Created almost 9 years ago · Last pushed about 2 years ago
Metadata Files
Readme License Citation Zenodo

README.md

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

DOI Published in PeerJ CI

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

Install & deploy

1. Clone this repository.

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

2. Start Docker service(s).

```bash 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.

bash ansible-playbook -i inventory playbook.yml

Note: grlc API can be deployed with SPARQL queries stored

  • locally (in the container)

bash 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.

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

Owner

  • Name: candYgene
  • Login: candYgene
  • Kind: organization
  • Location: Netherlands

Software repositories of the candYgene project (Prediction of candidate genes for traits using interoperable genome annotations)

Citation (CITATION.cff) 

# YAML 1.2
---
authors: 
  - 
    affiliation: "Netherlands eScience Center"
    family-names: Kuzniar
    given-names: Arnold
    orcid: https://orcid.org/0000-0003-1711-7961
  - 
    affiliation: "Netherlands eScience Center"
    family-names: Martinez-Ortiz
    given-names: Carlos
    orcid: https://orcid.org/0000-0001-5565-7577
  - 
    affiliation: "Wageningen University and Research"
    family-names: Singh
    given-names: Gurnoor
    orcid: https://orcid.org/0000-0003-1615-4197
cff-version: "1.0.3"
date-released: 2023-02-23
doi: 10.5281/zenodo.1458168
keywords:
  - "plant breeding"
  - "Solanaceae"
  - "genomics"
  - "genome annotation"
  - "QTL"
  - "trait"
  - "Sol Genomics Network"
  - "Europe PMC"
  - "UniProt"
  - "Ensembl Plants"
  - "Linked Data"
  - "FAIR Data"
  - "Virtuoso"
  - "RDF"
  - "SPARQL"
  - "Web API"
license: Apache-2.0
message: "If you use this software, please cite it using these metadata."
repository-code: "https://github.com/candYgene/pbg-ld"
title: "pbg-ld"
version: "1.1.0"

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