The following GraphML files have been generated from BIOPAX using Pax2Graphml. They can be directly used for biological regulation analysis.
Pax2Graphml
| bank | GRAPHML(gz) | nodes | edges | reactions | substrats | products | activators | inhibitors | creation | size | site | source | details |
|---|---|---|---|---|---|---|---|---|---|---|---|---|---|
| pc_filtered | GRAPHML | 119,285 | 167,515 | 55,184 | 83,782 | 66,056 | 16,939 | 738 | 05/17/2021 | 23.2MB | merged regulation banks (reactome,pid,kegg,humancyc,inoh,intact_complex,corum,msigdb,netpath,panther,pathbank,psp,reconx) | ||
| detailed | GRAPHML | 175,262 | 639,945 | 85,750 | 84,496 | 95,743 | 52,009 | 407,697 | 05/17/2021 | 36.7MB | BIOPAX (399M) | All Pathway Commons BIOPAX sources | |
| corum | GRAPHML | 13,664 | 19,434 | 3,786 | 15,648 | 3,786 | 0 | 0 | 05/17/2021 | 1.6MB | BIOPAX (8.5M) | corum | |
| ctd | GRAPHML | 44,639 | 98,993 | 19,814 | 18,538 | 19,073 | 35,077 | 26,305 | 05/17/2021 | 4.6MB | site | BIOPAX (134M) | Curated chemical-gene interactions from Comparative Toxicogenomics Database, MDI Biological Laboratory, and NC State University; 26-Jun-2019; converted with http://github.com/PathwayCommons/ctd-to-biopax |
| humancyc | GRAPHML | 5,733 | 11,890 | 1,778 | 3,875 | 4,455 | 3,560 | 0 | 05/17/2021 | 963.3KB | site | BIOPAX (9.5M) | HumanCyc 21; 2017; under license from SRI International, www.biocyc.org |
| inoh | GRAPHML | 4,315 | 7,409 | 2,188 | 4,247 | 3,162 | 0 | 0 | 05/17/2021 | 577.0KB | site | BIOPAX (16M) | INOH 4.0 (signal transduction and metabolic data), 22-MAR-2011 |
| intact_complex | GRAPHML | 2,187 | 2,869 | 563 | 2,306 | 563 | 0 | 0 | 05/17/2021 | 241.5KB | BIOPAX (3.8M) | intact_complex | |
| kegg | GRAPHML | 3,133 | 7,041 | 1,560 | 3,488 | 3,553 | 0 | 0 | 05/17/2021 | 340.4KB | site | BIOPAX (4.9M) | KEGG 07/2011 (only human, hsa* files), converted to BioPAX by BioModels (http://www.ebi.ac.uk/biomodels) team |
| mirtarbase | GRAPHML | 32,727 | 395,703 | 15,064 | 0 | 15,064 | 0 | 380,639 | 05/17/2021 | 8.5MB | site | BIOPAX (97M) | Human miRNA-target gene relationships from MiRTarBase; v7.0, 15-SEP-2017, converted in Apr-2018 with http://github.com/PathwayCommons/mirtarbase-to-biopax |
| msigdb | GRAPHML | 23,840 | 11,920 | 11,920 | 0 | 11,920 | 0 | 0 | 05/17/2021 | 1.6MB | site | BIOPAX (30M) | MSigDB v5.2 (XML), human C3 TFT motif gene sets, 09-2016; converted with http://github.com/PathwayCommons/msigdb-to-biopax |
| netpath | GRAPHML | 840 | 704 | 348 | 532 | 172 | 0 | 0 | 05/17/2021 | 56.5KB | site | BIOPAX (4.7M) | NetPath 12/2011 |
| panther | GRAPHML | 3,766 | 5,263 | 1,662 | 2,914 | 2,165 | 142 | 42 | 05/17/2021 | 440.8KB | site | BIOPAX (7.6M) | PANTHER Pathways 3.6.3 on 25-Mar-2019 (auto-converted to human-only model) |
| pathbank | GRAPHML | 4,375 | 7,954 | 1,442 | 3,612 | 3,113 | 1,229 | 0 | 05/17/2021 | 549.2KB | site | BIOPAX (5.9M) | Pathbank BioPAX data (primary, human pathway data only) |
| pid | GRAPHML | 9,403 | 14,827 | 4,495 | 6,613 | 4,544 | 3,233 | 437 | 05/17/2021 | 1.2MB | site | BIOPAX (12M) | NCI Curated Human Pathways from PID (final); 27-Jul-2015 |
| psp | GRAPHML | 14,426 | 11,275 | 11,275 | 5,630 | 5,645 | 0 | 0 | 05/17/2021 | 8.0MB | site | BIOPAX (23M) | PhosphoSite Kinase-substrate information; 19-Aug-2019 |
| reactome | GRAPHML | 31,718 | 46,541 | 11,404 | 27,210 | 15,358 | 3,717 | 256 | 05/17/2021 | 4.5MB | site | BIOPAX (47M) | Reactome v69 (only 'Homo_sapiens.owl') 28-May-2019 |
| reconx | GRAPHML | 6,956 | 20,485 | 2,821 | 7,722 | 7,689 | 5,074 | 0 | 05/17/2021 | 1.0MB | BIOPAX (6.3M) | reconx |
Tested with the following python packages: Pax2Graphml, graph-tool, NetworkX, igraph. The sizes given for gz compressed files.
Data processed with Pax2Graphml.
Input sources from Pathway Commons v 12 (PC): https://www.pathwaycommons.org/archives/PC2/v12/