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Scripts that Bio2RDF users have created to generate RDF versions of scientific datasets
branch: release3
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affymetrix single file output
biomodels fixed change in remote download location
bioportal id fix
chembl fixed wrong variable name
clinicaltrials fix for url bug in data
common reimport; required for sgd
ctd fixed qname error
dbpedia adding minor changes
dbsnp fixed typing
drugbank fixed dosing problem, category problem
genage fixed changes in columns; changed type uris; added annotations
genbank added describe individual to reference section
gendr fixed bug in variable name;added dashes for types, and annotations
goa added clearing function to goa
hgnc added previous symbol as a uri so it can be properly linked
homologene fixed output file name
interpro Update interpro.php
ipi removed old parsers
iproclass added counter
irefindex refactoring the irefindex interactions and groups
kegg more support for drug and disease fields
linkedSPLs add query result shorten URLs
lsr update to partially conform with HCLS specification
mesh added dataset description to mesh
mgi replaced resource with vocabulary prefix for types
ncbigene fixed orientation annotation to the start/stop positions
ndc changed to single file output
omim correctly parsing multi-valued snp list
orphanet added dataset description
pathwaycommons Finished updating pathwaycommons to release 3
pdb fixed problem with chemicalComponents not being added to the model
pharmgkb made offsides/twosides a separate parse
pubchem 2 updates to CTD, NCBI Gene, PubChem, PubMed, SABIO-RK and SGD script…
pubmed make sure file buffer is cleared
refseq added per file clear function
sabiork fixed bug in local file location
sgd added one file output as default
sider added spl extract
statistics bug fix
taxonomy full refactor
toxkb forgot to commit change of pubchem to pubchem_compound namespace
uniprot updated: requires a destination folder as a parameter for the download
unists added new r3 parser
wormbase fixed types and annotations
.gitignore added .log to list Update
runparser.php removed stats generation from parser


This Git repository holds all of the RDF converter scripts used to generate Bio2RDF linked data.


The majority of these scripts were created so as to run on Linux servers. Depending on the script you wish to run you will need:

The Bio2RDF API should be installed in the root directory of the project tree (i.e bio2rdf-scripts).


Each script is run independently. See README files inside each script directory.

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Licensed under MIT License, see license page for details.

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