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BioPAX is a standard language for integration, exchange, visualization and analysis of biological pathway data. BioPAX supports data exchange between pathway data groups and thus reduces the complexity of interchange between data formats by providing an accepted standard format for pathway data. By offering a standard, with well-defined semantics for pathway representation, BioPAX allows pathway databases and software to interact more efficiently. In addition, BioPAX enables the development of pathway visualization from databases and facilitates analysis of experimentally generated data through combination with prior knowledge. The BioPAX effort is coordinated closely with that of other pathway related standards initiatives namely; PSI-MI, SBML, CellML, and SBGN in order to deliver a compatible standard in the areas where they overlap.

This project contains the BioPAX specification, documentation, Paxtools Java API and the BioPAX validator.

You can download file releases of Biological Pathway Exchange Language project from List of release files

List of release files

File/Folder Name	File Type	Size	Date	Download Count
Latest 5 files
paxtools.pdf	application/pdf; charset=binary	220.6 KB	2013-05-22 18:27	0
biopax-validator-3.0.1-all.zip	application/zip; charset=binary	83.5 MB	2013-05-21 14:36	0
paxtools-4.2.0-no-jena.jar	application/zip; charset=binary	5.1 MB	2013-05-19 06:38	0
paxtools-4.2.0.jar	application/zip; charset=binary	13.2 MB	2013-05-19 06:38	0
webprotege-projects-20130309.zip	application/zip; charset=binary	57.6 KB	2013-04-09 16:47	0
All Files
paxtools
paxtools.pdf	application/pdf; charset=binary	220.6 KB	2013-05-22 18:27	0
paxtools-4.2.0-no-jena.jar	application/zip; charset=binary	5.1 MB	2013-05-19 06:38	0
paxtools-4.2.0.jar	application/zip; charset=binary	13.2 MB	2013-05-19 06:38	0
README-PAXTOOLS.txt	text/plain; charset=us-ascii	0.4 KB	2013-04-08 16:02	7
paxtools-4.1.6.jar	application/zip; charset=binary	16.1 MB	2013-01-27 13:39	0
paxtools-4.1.6-no-jena.jar	application/zip; charset=binary	8.0 MB	2013-01-27 13:22	0
python-readme.txt	text/plain; charset=us-ascii	1.6 KB	2011-09-09 16:45	6
pythonPaxtoolsExample.py	text/x-java; charset=us-ascii	3.7 KB	2011-09-09 16:45	3
validator
biopax-validator-3.0.1-all.zip	application/zip; charset=binary	83.5 MB	2013-05-21 14:36	0
README-VALIDATOR.txt	text/plain; charset=us-ascii	10.5 KB	2013-03-27 00:36	0
biopax-validator-2.2.0.zip	application/zip; charset=binary	18.4 MB	2012-11-15 01:53	0
biopax-validator-2.0.0.zip	application/zip; charset=binary	37.0 MB	2011-11-16 21:43	0
other
webprotege-projects-20130309.zip	application/zip; charset=binary	57.6 KB	2013-04-09 16:47	0
Level3updateWorkshopNov2009.ppt	application/vnd.ms-office; charset=binary	411.0 KB	2013-03-31 06:35	0
IntroducingTheBioPAXValidatorNov2009.pdf	application/pdf; charset=binary	251.2 KB	2013-03-31 06:35	0
BioPAXTutorialNov2009.ps	application/postscript; charset=utf-8	25.2 MB	2013-03-31 06:35	0
BioPAXTutorialNov2009.ppt	application/vnd.ms-office; charset=binary	7.0 MB	2013-03-31 06:35	0
BioPAXTutorialNov2009.pdf	application/pdf; charset=binary	6.5 MB	2013-03-31 06:35	0
BioPAXISMB2010_NADIA.pdf	application/pdf; charset=binary	2.8 MB	2013-03-31 06:35	0
README.md	text/plain; charset=us-ascii	0.3 KB	2013-03-31 06:22	0
HARMONY2011
Van_Iersel_combine_layout_wkgrp.pdf	application/pdf; charset=binary	147.7 KB	2013-03-27 22:33	0
SED-ML_Presentation-bergmann.pdf	application/pdf; charset=binary	3.4 MB	2013-03-27 22:33	0
sbml-status-2011-04-21_MH.pdf	application/pdf; charset=binary	3.0 MB	2013-03-27 22:33	0
SBGNQuiz-Emek.pdf	application/pdf; charset=binary	22.8 KB	2013-03-27 22:33	0
RobinHaw2011_Outreach_Harmony.ppt	application/vnd.ms-office; charset=binary	1.6 MB	2013-03-27 22:33	0
SBGNMLInDetails.pdf	application/pdf; charset=binary	652.9 KB	2013-03-27 22:33	0
RichardAdams-SEDML_Harmony.pdf	application/pdf; charset=binary	1.5 MB	2013-03-27 22:33	0
NLN_kisao.pdf	application/pdf; charset=binary	748.6 KB	2013-03-27 22:33	0
Nadia_MakingBioPAXSPARQLHarmony.pdf	application/pdf; charset=binary	1.2 MB	2013-03-27 22:33	0
Monday_InstallingBuildingLibSBML.pptx	application/zip; charset=binary	2.8 MB	2013-03-27 22:33	0
mhucka-sbml-overview-2011-04-17.pdf	application/pdf; charset=binary	3.3 MB	2013-03-27 22:33	0
libSBML_Tutorial_Getting-started.ppt	application/vnd.ms-office; charset=binary	825.5 KB	2013-03-27 22:33	0
mhucka-poster-intro-2011-04-17.pdf	application/pdf; charset=binary	4.1 MB	2013-03-27 22:33	0
libSBML_Intro_HARMONY_2011.ppt	application/vnd.ms-office; charset=binary	441.5 KB	2013-03-27 22:33	0
HARMONYSBGNPD-StuartM.pptx	application/zip; charset=binary	275.4 KB	2013-03-27 22:33	0
JSBML-HARMONY_2011.pptx	application/zip; charset=binary	1.3 MB	2013-03-27 22:33	0
HARMONY-SBGN-Le_Novere.pdf	application/pdf; charset=binary	558.0 KB	2013-03-27 22:33	0
HARMONY-ModelsForAll-NLeN.pdf	application/pdf; charset=binary	425.2 KB	2013-03-27 22:33	0
HARMONY-ER-Le_Novere.pdf	application/pdf; charset=binary	868.5 KB	2013-03-27 22:33	0
Harmony_presentation_SBML2OWL_MD.pdf	application/pdf; charset=binary	1.5 MB	2013-03-27 22:33	0
DavidNickersonCellML-SED-ML.pdf	application/pdf; charset=binary	1.3 MB	2013-03-27 22:33	0
BioPAXHarmony-Intro.pptx	application/zip; charset=binary	848.1 KB	2013-03-27 22:33	0
BioPAXOverviewHarmony2011.pdf	application/pdf; charset=binary	58.6 KB	2013-03-27 22:33	0
AndreaWIP-HarmonyNotes.pdf	application/pdf; charset=binary	2.9 MB	2013-03-27 22:33	0
agenda-slide-sbml-day-2011-04-21_MH.pdf	application/pdf; charset=binary	58.5 KB	2013-03-27 22:33	0
intro-lenovere-2011-04-19.mov	video/quicktime; charset=binary	17.3 MB	2013-03-27 22:33	0
huaiyu-sbgn-af-2011-04-19.mp3	audio/mpeg; charset=binary	16.0 MB	2013-03-27 22:33	0
sbgn-pd-moodie-2011-04-19.mov	video/quicktime; charset=binary	42.4 MB	2013-03-27 22:33	0
intro-lenovere-2011-04-19.mp3	audio/mpeg; charset=binary	13.3 MB	2013-03-27 22:33	0
lenovere-sbgn-1.mp3	audio/mpeg; charset=binary	26.3 MB	2013-03-27 22:33	0
lenovere-sbgn.mp3	audio/mpeg; charset=binary	26.3 MB	2013-03-27 22:33	0
martijn-libsbgn-2011-04-19.mp3	audio/mpeg; charset=binary	15.2 MB	2013-03-27 22:33	0
sbgn-pd-moodie-2011-04-19.mp3	audio/mpeg; charset=binary	47.7 MB	2013-03-27 22:33	0
website_files
RodchenkovNov2009.pdf	application/pdf; charset=binary	251.2 KB	2010-02-11 20:38	3
paxtools_Demir_Nov2009.pot	application/vnd.ms-office; charset=binary	270.5 KB	2010-02-11 20:38	2
Level3updateWorkshopNov2009.ppt	application/vnd.ms-office; charset=binary	411.0 KB	2010-02-11 20:37	0
BioPAXTutorialNov2009.pdf	application/pdf; charset=binary	6.5 MB	2010-02-11 20:29	2
examples
StatesAndGenericsProposal.owl	application/xml; charset=utf-8	125.3 KB	2010-01-26 18:08	1
INOHFeadbackAndExamples.doc	application/msword; charset=binary	693.0 KB	2010-01-26 18:08	0
psimi.owl	application/xml; charset=us-ascii	53.0 KB	2010-01-26 18:08	7
amaze_conceptual.pdf	application/pdf; charset=binary	19.8 KB	2010-01-26 18:07	0
amaze.pprj	text/plain; charset=us-ascii	196.4 KB	2010-01-26 18:07	0
amaze.owl	application/xml; charset=us-ascii	71.7 KB	2010-01-26 18:06	0
bind.asn.txt	text/plain; charset=us-ascii	92.8 KB	2010-01-05 17:37	2
geneticInteractions-GRID-eg-biopax.pprj	text/plain; charset=us-ascii	121.6 KB	2010-01-05 16:48	0
geneticInteractions-GRID-eg-biopax.owl	application/xml; charset=us-ascii	14.1 KB	2010-01-05 16:48	1
geneticInteractions-Flybase-eg-biopax.pprj	text/plain; charset=us-ascii	123.3 KB	2010-01-05 16:48	13
geneticInteractions-Flybase-eg-biopax.owl	application/xml; charset=us-ascii	9.5 KB	2010-01-05 16:47	7
geneticInteractions-biopax.pprj	text/plain; charset=us-ascii	118.6 KB	2010-01-05 16:47	0
geneticInteractions-biopax.owl	application/xml; charset=utf-8	128.9 KB	2010-01-05 16:47	3
geneticInteractions-BIND-eg-biopax.pprj	text/plain; charset=us-ascii	121.4 KB	2010-01-05 16:47	1
geneticInteractions-BIND-eg-biopax.owl	application/xml; charset=us-ascii	14.9 KB	2010-01-05 16:46	0
SampleOntology.owl	application/xml; charset=us-ascii	8.3 KB	2010-01-04 22:39	0
pathwayBOF.ppt	application/vnd.ms-office; charset=binary	945.0 KB	2010-01-26 18:08	1
nettab2007bader.pdf	application/pdf; charset=binary	4.2 MB	2010-01-26 18:07	0
sbml-level-2-v1.pdf	application/pdf; charset=binary	507.5 KB	2010-01-26 18:07	0
biopax
biopaxpaper-Feb25-2010.zip	application/zip; charset=binary	5.4 MB	2013-03-31 06:12	0
BioPAX-Archive.zip	application/zip; charset=binary	24.5 MB	2013-03-31 06:10	0
README.md	text/plain; charset=us-ascii	31 B	2013-03-31 05:58	0
level2
Level2.zip	application/zip; charset=binary	50.0 KB	2011-09-14 16:12	0
level3
Level3-1.0.zip	application/zip; charset=binary	14.4 MB	2011-09-14 16:12	1
cy_plugins
cpath2.jar	application/zip; charset=binary	1.8 MB	2010-08-27 21:31	1
biopax.jar	application/zip; charset=binary	1.3 MB	2010-08-27 21:27	1