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Scripts that Bio2RDF users have created to generate RDF versions of scientific datasets
Java PHP HTML Ruby Web Ontology Language Python Other
Branch: release3
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affymetrix single file output
biomodels fixed change in remote download location
bioportal changed the ontology uri
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 process other snp lists
drugbank fixed addlist function; salts; hgnc replace
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 changed predicate for reaction to rpair role
linkedSPLs edit readme
lsr update to partially conform with HCLS specification
mesh added dataset description to mesh
mgi parse out the alleles
ncbigene Merge branch 'release3' of…
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 uri encoding bug
pharmgkb made offsides/twosides a separate parse
pubchem 2 updates to CTD, NCBI Gene, PubChem, PubMed, SABIO-RK and SGD script…
pubmed up
refseq quick fix for uniprotkb/swiss-prot dbxref parse problem #416
sabiork fixed bug in local file location
sgd added more domains for SGD
sider added spl extract
statistics bug fix
taxonomy remove the default gi2taxid file processing
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 untrack xml outputs 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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