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Project Description

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.

System Requirements

Operating System: OS Independent

Download Package list

Latest 5 files
Name Size Date Download count
biopax-validator-5.0.0-SNAPSHOT-all.zip 59.8 MB 2019-11-14 14:59 0
biopax-validator-4.0.0-all.zip 100.7 MB 2018-09-14 11:19 0
paxtools-5.1.0.jar 12.1 MB 2018-09-13 02:48 2
biopax-validator-4.0.0-SNAPSHOT-all.zip 100.7 MB 2018-04-25 12:54 11
paxtools-5.0.1.jar 12.0 MB 2017-05-09 08:03 2
All Files
validator
biopax-validator-5.0.0-SNAPSHOT-all.zip59.8 MB2019-11-14 14:590
biopax-validator-4.0.0-all.zip100.7 MB2018-09-14 11:190
biopax-validator-4.0.0-SNAPSHOT-all.zip100.7 MB2018-04-25 12:5411
README-VALIDATOR.txt10.3 KB2014-05-14 22:302
biopax-validator-3.0.3-all.zip84.7 MB2013-12-20 06:178
biopax-validator-2.2.0.zip18.4 MB2012-11-15 09:528
paxtools
paxtools-5.1.0.jar12.1 MB2018-09-13 02:482
paxtools-5.0.1.jar12.0 MB2017-05-09 08:032
paxtools-5.0.0.jar12.0 MB2017-04-27 10:145
paxtools-4.3.1.jar25.1 MB2015-09-30 03:317
paxtools-4.3.1-no-jena.jar16.3 MB2015-09-29 04:0910
paxtools-4.3.0-no-jena.jar13.7 MB2014-11-06 04:286
paxtools-4.3.0.jar21.8 MB2014-11-06 04:283
paxtools-4.2.1-no-jena.jar5.8 MB2013-11-05 00:503
paxtools-4.2.1.jar14.0 MB2013-11-05 00:5016
paxtools.pdf222.5 KB2013-06-28 01:3025
paxtools-4.2.0-no-jena.jar5.1 MB2013-05-19 13:386
paxtools-4.2.0.jar13.2 MB2013-05-19 13:385
README-PAXTOOLS.txt0.4 KB2013-04-08 23:0210
paxtools-4.1.6.jar16.1 MB2013-01-27 21:391
paxtools-4.1.6-no-jena.jar8.0 MB2013-01-27 21:222
python-readme.txt1.6 KB2011-09-09 23:4520
pythonPaxtoolsExample.py3.7 KB2011-09-09 23:457
other
cytoscape2_plugins
README.md0.4 KB2015-01-15 04:457
cpath2.jar1.8 MB2010-08-28 04:312
biopax.jar1.3 MB2010-08-28 04:275
webprotege-projects-20130309.zip57.6 KB2013-04-09 23:476
Level3updateWorkshopNov2009.ppt411.0 KB2013-03-31 13:353
IntroducingTheBioPAXValidatorNov2009.pdf251.2 KB2013-03-31 13:3519
BioPAXTutorialNov2009.ps25.2 MB2013-03-31 13:343
BioPAXTutorialNov2009.ppt7.0 MB2013-03-31 13:283
BioPAXTutorialNov2009.pdf6.5 MB2013-03-31 13:2625
BioPAXISMB2010_NADIA.pdf2.8 MB2013-03-31 13:2430
README.md0.3 KB2013-03-31 13:223
HARMONY2011
SED-ML_Presentation-bergmann.pdf3.4 MB2013-03-28 05:3330
Van_Iersel_combine_layout_wkgrp.pdf147.7 KB2013-03-28 05:3330
sbml-status-2011-04-21_MH.pdf3.0 MB2013-03-28 05:3314
SBGNMLInDetails.pdf652.9 KB2013-03-28 05:3322
SBGNQuiz-Emek.pdf22.8 KB2013-03-28 05:3337
RobinHaw2011_Outreach_Harmony.ppt1.6 MB2013-03-28 05:331
NLN_kisao.pdf748.6 KB2013-03-28 05:3324
RichardAdams-SEDML_Harmony.pdf1.5 MB2013-03-28 05:3320
Nadia_MakingBioPAXSPARQLHarmony.pdf1.2 MB2013-03-28 05:3326
Monday_InstallingBuildingLibSBML.pptx2.8 MB2013-03-28 05:331
mhucka-poster-intro-2011-04-17.pdf4.1 MB2013-03-28 05:3324
mhucka-sbml-overview-2011-04-17.pdf3.3 MB2013-03-28 05:3324
libSBML_Tutorial_Getting-started.ppt825.5 KB2013-03-28 05:336
JSBML-HARMONY_2011.pptx1.3 MB2013-03-28 05:333
libSBML_Intro_HARMONY_2011.ppt441.5 KB2013-03-28 05:332
HARMONYSBGNPD-StuartM.pptx275.4 KB2013-03-28 05:331
HARMONY-SBGN-Le_Novere.pdf558.0 KB2013-03-28 05:3343
HARMONY-ER-Le_Novere.pdf868.5 KB2013-03-28 05:3324
HARMONY-ModelsForAll-NLeN.pdf425.2 KB2013-03-28 05:3320
Harmony_presentation_SBML2OWL_MD.pdf1.5 MB2013-03-28 05:3321
BioPAXOverviewHarmony2011.pdf58.6 KB2013-03-28 05:3317
DavidNickersonCellML-SED-ML.pdf1.3 MB2013-03-28 05:3317
BioPAXHarmony-Intro.pptx848.1 KB2013-03-28 05:333
AndreaWIP-HarmonyNotes.pdf2.9 MB2013-03-28 05:3328
agenda-slide-sbml-day-2011-04-21_MH.pdf58.5 KB2013-03-28 05:3320
intro-lenovere-2011-04-19.mov17.3 MB2013-03-28 05:333
huaiyu-sbgn-af-2011-04-19.mp316.0 MB2013-03-28 05:332
sbgn-pd-moodie-2011-04-19.mov42.4 MB2013-03-28 05:333
intro-lenovere-2011-04-19.mp313.3 MB2013-03-28 05:331
lenovere-sbgn-1.mp326.3 MB2013-03-28 05:331
lenovere-sbgn.mp326.3 MB2013-03-28 05:333
martijn-libsbgn-2011-04-19.mp315.2 MB2013-03-28 05:331
sbgn-pd-moodie-2011-04-19.mp347.7 MB2013-03-28 05:321
website_files
RodchenkovNov2009.pdf251.2 KB2010-02-12 04:3823
paxtools_Demir_Nov2009.pot270.5 KB2010-02-12 04:384
Level3updateWorkshopNov2009.ppt411.0 KB2010-02-12 04:372
BioPAXTutorialNov2009.pdf6.5 MB2010-02-12 04:2933
examples
StatesAndGenericsProposal.owl125.3 KB2010-01-27 02:083
INOHFeadbackAndExamples.doc693.0 KB2010-01-27 02:086
psimi.owl53.0 KB2010-01-27 02:0813
amaze_conceptual.pdf19.8 KB2010-01-27 02:0733
amaze.pprj196.4 KB2010-01-27 02:074
amaze.owl71.7 KB2010-01-27 02:0664
bind.asn.txt92.8 KB2010-01-06 01:378
geneticInteractions-GRID-eg-biopax.pprj121.6 KB2010-01-06 00:482
geneticInteractions-GRID-eg-biopax.owl14.1 KB2010-01-06 00:484
geneticInteractions-Flybase-eg-biopax.pprj123.3 KB2010-01-06 00:4816
geneticInteractions-Flybase-eg-biopax.owl9.5 KB2010-01-06 00:4714
geneticInteractions-biopax.pprj118.6 KB2010-01-06 00:476
geneticInteractions-biopax.owl128.9 KB2010-01-06 00:4711
geneticInteractions-BIND-eg-biopax.pprj121.4 KB2010-01-06 00:472
geneticInteractions-BIND-eg-biopax.owl14.9 KB2010-01-06 00:464
SampleOntology.owl8.3 KB2010-01-05 06:392
pathwayBOF.ppt945.0 KB2010-01-27 02:087
nettab2007bader.pdf4.2 MB2010-01-27 02:0711
sbml-level-2-v1.pdf507.5 KB2010-01-27 02:0731
biopax
biopaxpaper-Feb25-2010.zip5.4 MB2013-03-31 13:122
BioPAX-Archive.zip24.5 MB2013-03-31 13:108
README.md31 B2013-03-31 12:583
level2
Level2.zip50.0 KB2011-09-14 23:1214
level3
Level3-1.0.zip14.4 MB2011-09-14 23:12102