Bio2RDF-scripts

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

Requirements

See the wiki for details.

Licensed under MIT License, see license page for details.

Name	Name	Last commit message	Last commit date
Latest commit micheldumontier Merge pull request #475 from micheldumontier/master Jan 15, 2021 02a94c3 · Jan 15, 2021 History 1,946 Commits
.github/workflows	.github/workflows	fix env example in workflow	Jan 15, 2021
affymetrix	affymetrix	update	Nov 24, 2015
biomodels	biomodels	fixed change in remote download location	Sep 11, 2013
bioportal	bioportal	Update bioportal.php	Dec 27, 2020
chembl	chembl	fixed merge error	Oct 29, 2018
clinicaltrials	clinicaltrials	Update clinicaltrials.php	Dec 25, 2020
common	common	replaced empty string initialisation to array	Jun 1, 2020
ctd	ctd	changed ctd output files to new standard	Jun 30, 2020
dailymed	dailymed	limited dailymed parser	Jun 30, 2020
dbpedia	dbpedia	adding minor changes	Apr 19, 2012
dbsnp	dbsnp	fixed dbsnp query bug	Dec 1, 2015
drugbank	drugbank	Update drugbank.php	Dec 27, 2020
genage	genage	updated genage parser	Nov 30, 2015
genbank	genbank	added describe individual to reference section	Aug 15, 2013
gendr	gendr	removed automatic processing of gendr gene expression data, which req…	Dec 1, 2015
goa	goa	Merge branch 'r5' of https://github.com/bio2rdf/bio2rdf-scripts	Dec 25, 2020
hgnc	hgnc	revised gene family related triples	Dec 23, 2020
homologene	homologene	fixed output file name	Aug 13, 2014
interpro	interpro	removed html tags, extra spaces, and escaped special chars in abstract	Jun 1, 2020
ipi	ipi	removed old parsers	Aug 23, 2013
iproclass	iproclass	added counter	Nov 12, 2014
irefindex	irefindex	update the path and version number of the latest entry	Jun 1, 2020
kegg	kegg	resolved merge conflict	Jun 30, 2020
linkedSPLs	linkedSPLs	update linkedSPLs done	Aug 7, 2017
lsr	lsr	Update lsr.php	Jan 14, 2021
mesh	mesh	changes to download urls; fixes to record processor	Jun 2, 2020
mgi	mgi	Update mgi.php	Jan 14, 2021
miriam	miriam	resolved merge conflict	Jun 30, 2020
ncbigene	ncbigene	removed files no longer available; changed output file names	Jun 1, 2020
ndc	ndc	updated download file location	Jun 1, 2020
omim	omim	Update omim.php	Dec 24, 2020
orphanet	orphanet	id fixes; addition of prevalence parser	May 27, 2020
pathwaycommons	pathwaycommons	Finished updating pathwaycommons to release 3	Aug 12, 2013
pdb	pdb	Bump junit from 4.7 to 4.13.1 in /pdb	Oct 13, 2020
pharmgkb	pharmgkb	Update pharmgkb.php	Dec 26, 2020
pubchem	pubchem	2 updates to CTD, NCBI Gene, PubChem, PubMed, SABIO-RK and SGD script…	Aug 8, 2013
pubmed	pubmed	update to pubmed script	Jul 20, 2020
refseq	refseq	ignore the http links	Jan 19, 2016
sabiork	sabiork	fixed bug in local file location	Jun 5, 2014
sgd	sgd	Update sgd.php	Jan 14, 2021
sider	sider	fixed the namespace declaration for meddra concept -it's actually a u…	Oct 14, 2015
statistics	statistics	Merge branch 'release3' of github.com:micheldumontier/bio2rdf-scripts…	Aug 13, 2015
taxonomy	taxonomy	Update taxonomy.php	Dec 26, 2020
toxkb	toxkb	forgot to commit change of pubchem to pubchem_compound namespace	Aug 8, 2012
uniprot	uniprot	updated: requires a destination folder as a parameter for the download	Sep 27, 2013
unists	unists	added new r3 parser	Aug 15, 2013
wormbase	wormbase	updates to wormbase	Jun 1, 2020
.gitignore	.gitignore	Add data/ folder to .gitignore	Jan 12, 2021
.gitmodules	.gitmodules	remove submodule	Jan 12, 2021
MIT-LICENSE.txt	MIT-LICENSE.txt	Update MIT-LICENSE.txt	Jan 24, 2014
README.md	README.md	update readme file to remove submodule docs	Jan 12, 2021
composer.json	composer.json	update to composer	Jun 30, 2020
runparser.php	runparser.php	removed redundant parameter	Sep 16, 2015

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