RDF converter for MedGen

This script converts a MedGen CSV file into RDF turtle.

Input files

MedGen source files are available at here. medgen_pubmed_link.txt and MedGen_HPO_OMIM_Mapping.txt are available at here. omim2gene_medgen file is available at here. Semantic Types Ontology is available at here.

Usage

Usage: ruby convert_rdf_medgen.rb [options] <file>
   -p, --prefixes print prefixes
   -n, --names NAMES.csv to RDF
   -d, --mgdef convert MGDEF.csv to RDF
   -s, --mgsty   convert MGSTY.csv to RDF
   -c, --mgconso convert MGCONSO.csv to RDF
   -r, --mgrel   convert MGREL_1.csv and MGREL_2.csv to RDF
   -a, --mgsat   convert MGSAT_1.csv and MGSAT_2.csv to RDF
   -u, --pubmed  convert medgen_pubmed_lnk.txt to RDF
   -m, --omim    convert MedGen_HPO_OMIM_Mapping.txt to RDF
   -l, --sty     UMLS Semantic Type Ontology"
   -g, --gene    convert omim2gene_medgen to RDF"
   -h, --help print help\n"

All options otherwise -p, -m, -l can be set exclusively. Only -p option can be used with other option. The -m and -l options must be specified in pairs.

Example:
   ruby rdf_coverter_medgen -p -d MGDEF.csv > mgdef.ttl
   ruby rdf_converter_medgen -m MedGen_HPO_OMIM_Mapping.txt -l umls_semantictypes.ttl