Scripts that Bio2RDF users have created to generate RDF versions of scientific datasets
Java PHP HTML Ruby Web Ontology Language Python Other
Latest commit 3d21e00 Jan 30, 2017 @ningyifan ningyifan committed on GitHub Merge pull request #451 from bio2rdf/release3
linkedSPLs - add testing cases for example queries
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affymetrix update Nov 24, 2015
biomodels fixed change in remote download location Sep 11, 2013
bioportal fixed premature end of parse due to blank entry May 19, 2016
chembl merged release3 Feb 2, 2016
clinicaltrials edit clinicaltrials.php to trigger empty files Jan 30, 2016
common reimport; required for sgd May 2, 2014
ctd added 'map' to kegg pathway identifiers, to conform with source #440 Apr 12, 2016
dbpedia adding minor changes Apr 19, 2012
dbsnp fixed dbsnp query bug Dec 1, 2015
drugbank MD5 Hash Drugbank Mixture URIs Nov 1, 2016
genage updated genage parser Nov 30, 2015
genbank added describe individual to reference section Aug 15, 2013
gendr removed automatic processing of gendr gene expression data, which req… Dec 1, 2015
goa removed pdb and uniprot from list, captured missing associations Aug 12, 2015
hgnc added extra vega column to hgnc parser Aug 11, 2015
homologene fixed output file name Aug 13, 2014
interpro added a check for the example list Oct 8, 2015
ipi removed old parsers Aug 23, 2013
iproclass added counter Nov 12, 2014
irefindex simplify column id and includes a column fix for aliases Jul 22, 2016
kegg fixed multi entry parsing error #432 Mar 29, 2016
linkedSPLs linkedSPLs - add testing cases for example queries Jan 30, 2017
lsr update May 27, 2015
mesh no parsing of supplemental records that lack id and name (only a few) Dec 1, 2015
mgi accomodating current bug in mgi sequence data file; added a few more … Oct 8, 2015
miriam initial import Jun 22, 2015
ncbigene use limited set of organisms by default for ncbigene Dec 4, 2015
ndc changed to single file output Aug 13, 2014
omim filelisting fix Aug 13, 2015
orphanet added dataset description Jul 17, 2014
pathwaycommons Finished updating pathwaycommons to release 3 Aug 12, 2013
pdb fixed uri encoding bug Mar 16, 2015
pharmgkb fix for multiple control and cell types #442 Apr 12, 2016
pubchem 2 updates to CTD, NCBI Gene, PubChem, PubMed, SABIO-RK and SGD script… Aug 8, 2013
pubmed parse the mesh ids out of the xml files #433 Mar 29, 2016
refseq replaced deprecated split with explode; added passive ftp connection Dec 1, 2015
sabiork fixed bug in local file location Jun 5, 2014
sgd added domain mappings; changed default bioportal ontology location Aug 12, 2015
sider fixed the namespace declaration for meddra concept -it's actually a u… Oct 14, 2015
statistics Merge branch 'release3' of… Aug 13, 2015
taxonomy comment out testing line Dec 4, 2015
toxkb forgot to commit change of pubchem to pubchem_compound namespace Aug 8, 2012
uniprot updated: requires a destination folder as a parameter for the download Sep 27, 2013
unists added new r3 parser Aug 15, 2013
wormbase update for ws249 Sep 16, 2015
.gitignore remove java bin from repo, update gitignore Jan 20, 2017
MIT-LICENSE.txt Update MIT-LICENSE.txt Jan 24, 2014 Update May 13, 2016
runparser.php removed redundant parameter Sep 16, 2015


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


See the wiki for details.

Licensed under MIT License, see license page for details.