Run the Bio2RDF parsers

You can run any of the Bio2RDF scripts using runparser.php which should be inside your bio2rdf-scripts directory. Every Bio2RDF script may require a different set parameters to correctly execute them. For example:

php runparser.php 

Will display the complete list of Bio2RDF parsers that you can run:

  *parser=clinicaltrials|hgnc|sgd|pdb|pubmed|sabiork|affymetrix|pubchem|pharmgkb|lsr|drugbank|omim|mesh|interpro|ncbigene|irefindex|sider|mgi|homologene|genbank|taxonomy|chembl|wormbase|ctd|uniprot|dbsnp|ndc|biomodels|genage|ipi|pathwaycommons|biopax|refseq|bioportal|iproclass|goa|unists
    description: bio2rdf parser to run

If for example you wish to run the MeSh parser:

php runparser.php parser=mesh download=true files=all indir=/path/to/data/download/mesh/  outdir=/path/to/data/rdf/mesh/

Replace /path/to with the corresponding path to your data/download directory The resulting RDF files will be stored in the /path/to/data/rdf/mesh directory