This script converts a MedGen CSV file into RDF turtle.
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: 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