jvarkit

BioToRDF

Last commit

Build a RDF database for human from misc sources

Usage

This program is now part of the main jvarkit tool. See jvarkit for compiling.

Usage: java -jar dist/jvarkit.jar bio2rdf  [options] Files

Usage: bio2rdf [options] Files
  Options:
    --genes
      Limit to those genes names , separated with comma (for debugging)
      Default: <empty string>
    -h, --help
      print help and exit
    --helpFormat
      What kind of help. One of [usage,markdown,xml].
    --min-stringdb-combined-score
      Discard interaction with stringdb combined score < 'x'
      Default: 990
    -o, --out
      Output file. Optional . Default: stdout
    --version
      print version and exit
    -D
      parameters. -Dkey1=value1  -Dkey2=value2 ...
      Syntax: -Dkey=value
      Default: {GO_OWL=http://purl.obolibrary.org/obo/go.owl, STRINGDB_LINK=https://stringdb-static.org/download/protein.links.v{STRINGDB_RELEASE}/9606.protein.links.v{STRINGDB_RELEASE}.txt.gz, HPO_PHENOTYPE_TO_GENE=https://github.com/obophenotype/human-phenotype-ontology/releases/download/v2023-04-05/phenotype_to_genes.txt, BASE_NCBI_REFSEQ=https://ftp.ncbi.nlm.nih.gov/refseq/H_sapiens/RefSeqGene, NCBI_GENE_INFO=https://ftp.ncbi.nlm.nih.gov/gene/DATA/GENE_INFO/Mammalia/Homo_sapiens.gene_info.gz, STRINGDB_RELEASE=11.5, GFF3_GRCH38=https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_{GENCODE_RELEASE}/gencode.v{GENCODE_RELEASE}.annotation.gff3.gz, STRINGDB_PROTEIN_ALIASES=https://stringdb-static.org/download/protein.aliases.v{STRINGDB_RELEASE}/9606.protein.aliases.v{STRINGDB_RELEASE}.txt.gz, GFF3_GRCH37=https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_{GENCODE_RELEASE}/GRCh37_mapping/gencode.v{GENCODE_RELEASE}lift37.annotation.gff3.gz, GENCODE_RELEASE=43, NCBI_GENE_GO=https://ftp.ncbi.nlm.nih.gov/gene/DATA/gene2go.gz}

Keywords

Creation Date

20220427

Source code

https://github.com/lindenb/jvarkit/tree/master/src/main/java/com/github/lindenb/jvarkit/tools/bio2rdf/BioToRDF.java

Contribute

License

The project is licensed under the MIT license.

Citing

Should you cite bio2rdf ? https://github.com/mr-c/shouldacite/blob/master/should-I-cite-this-software.md

The current reference is:

http://dx.doi.org/10.6084/m9.figshare.1425030

Lindenbaum, Pierre (2015): JVarkit: java-based utilities for Bioinformatics. figshare. http://dx.doi.org/10.6084/m9.figshare.1425030

motivation

build RDF file to build a RDF database.

usage

$ java -jar dist/jvarkit.jar bio2rdf | gzip > bio2rdf.rdf.gz

Example queries:

Example

find all the descendant of GO:0045823

PREFIX rdfs: <http://www.w3.org/2000/01/rdf-schema#>
PREFIX rdf: <http://www.w3.org/1999/02/22-rdf-syntax-ns#>
PREFIX dc: <http://purl.org/dc/elements/1.1/>


SELECT ?subClass ?label ?desc WHERE { 
        ?subClass rdfs:subClassOf* <http://purl.obolibrary.org/obo/GO_0045823> . 
        ?subClass dc:title ?label . 
        ?subClass dc:description ?desc . 
    }

$ arq --data=/home/me/bio2rdf.rdf.gz --query query.sparql
subClass label desc
http://purl.obolibrary.org/obo/GO_0045823 “GO:0045823” “positive regulation of heart contraction”
http://purl.obolibrary.org/obo/GO_0001989 “GO:0001989” “positive regulation of the force of heart contraction involved in baroreceptor response to decreased systemic arterial blood pressure”
http://purl.obolibrary.org/obo/GO_0010460 “GO:0010460” “positive regulation of heart rate”
http://purl.obolibrary.org/obo/GO_0001996 “GO:0001996” “positive regulation of heart rate by epinephrine-norepinephrine”
http://purl.obolibrary.org/obo/GO_0086024 “GO:0086024” “adenylate cyclase-activating adrenergic receptor signaling pathway involved in positive regulation of heart rate”
http://purl.obolibrary.org/obo/GO_0003065 “GO:0003065” “positive regulation of heart rate by epinephrine”
http://purl.obolibrary.org/obo/GO_0003112 “GO:0003112” “positive regulation of heart rate by neuronal epinephrine”
http://purl.obolibrary.org/obo/GO_0003111 “GO:0003111” “positive regulation of heart rate by circulating epinephrine”
http://purl.obolibrary.org/obo/GO_0003066 “GO:0003066” “positive regulation of heart rate by norepinephrine”
http://purl.obolibrary.org/obo/GO_0003114 “GO:0003114” “positive regulation of heart rate by circulating norepinephrine”
http://purl.obolibrary.org/obo/GO_0003113 “GO:0003113” “positive regulation of heart rate by neuronal norepinephrine”
http://purl.obolibrary.org/obo/GO_0001988 “GO:0001988” “positive regulation of heart rate involved in baroreceptor response to decreased systemic arterial blood pressure”
http://purl.obolibrary.org/obo/GO_0060452 “GO:0060452” “positive regulation of cardiac muscle contraction”
http://purl.obolibrary.org/obo/GO_0003099 “GO:0003099” “positive regulation of the force of heart contraction by chemical signal”
http://purl.obolibrary.org/obo/GO_0003061 “GO:0003061” “positive regulation of the force of heart contraction by norepinephrine”
http://purl.obolibrary.org/obo/GO_0003110 “GO:0003110” “positive regulation of the force of heart contraction by neuronal norepinephrine”
http://purl.obolibrary.org/obo/GO_0003109 “GO:0003109” “positive regulation of the force of heart contraction by circulating norepinephrine”
http://purl.obolibrary.org/obo/GO_0003059 “GO:0003059” “positive regulation of the force of heart contraction by epinephrine”
http://purl.obolibrary.org/obo/GO_0003087 “GO:0003087” “positive regulation of the force of heart contraction by neuronal epinephrine”
http://purl.obolibrary.org/obo/GO_0003088 “GO:0003088” “positive regulation of the force of heart contraction by circulating epinephrine”
http://purl.obolibrary.org/obo/GO_0001997 “GO:0001997” “positive regulation of the force of heart contraction by epinephrine-norepinephrine”
http://purl.obolibrary.org/obo/GO_0003090 “GO:0003090” “positive regulation of the force of heart contraction by neuronal epinephrine-norepinephrine”
http://purl.obolibrary.org/obo/GO_0003089 “GO:0003089” “positive regulation of the force of heart contraction by circulating epinephrine-norepinephrine”
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