Pathway (PPI) resources collected 2016-JUNE

human    yeast    mouse
Release 31 (01. Sept. 2015)

ConsensusPathDB-human integrates interaction networks in Homo sapiensincluding binary and complex protein-protein, genetic, metabolic,signaling, gene regulatory and drug-target interactions, as well as biochemical pathways. Data originate from currently 32 public resources for interactions (listed below) and interactions that we have curated from the literature. The interaction data are integrated in a complementary manner (avoiding redundancies), resulting in a seamless interaction network containing different types of interactions.

Current statistics:
unique physical entities: 158,523
unique interactions: 458,570
   gene regulations: 17,098
   protein interactions: 261,085
   genetic interactions: 443
   biochemical reactions: 21,070
   drug-target interactions: 158,874
pathways: 4,593

Licensing information:
The use of ConsensusPathDB is free for academic users. Commercial users should contact Dr. Atanas Kamburov (kamburov [at] molgen.mpg.de) or Dr. Ralf Herwig ( herwig [at] molgen.mpg.de ). Interaction data from ConsensusPathDB is available under the license terms of each of the contributing databases listed above.
Disclaimer:
Although best efforts are always applied, the developers of ConsensusPathDB do not assume any legal responsibility for correctness or usefulness of the information in ConsensusPathDB.
Acknowledgements:
ConsensusPathDB is being developed by the Bioinformatics group of the Vertebrate Genomics Department at the Max-Planck-Institute for Molecular Genetics in Berlin, Germany. The project was supported by the EMBRACE and CARCINOGENOMICS projects that are funded by the European Commission within its 6th Framework Programme under the thematic area “Life Sciences, Genomics and Biotechnology for Health” (LSHG-CT- 2004-512092 and LSHB-CT-2006-037712); 7th Framework Programme project APO-SYS (HEALTH-F4-2007-200767); German Federal Ministry of Education and Research within the 65 NGFN-2 program (SMP-Protein, FKZ01GR0472); Max Planck Society within its International Research School program (IMPRS-CBSC).

Pathway resources

Name URL Formats
KEGG1 http://www.genome.jp/kegg/ BioPAX, png, KGML
Reactome2 http://www.reactome.org/ BioPAX, png, pdf
Pathway Commons7 http://www.pathwaycommons.org/ BioPAX, Sif, png
PANTHER pathway3 http://www.pantherdb.org/pathway/ BioPAX, SBML
WikiPathways5 http://www.wikipathways.org/ BioPAX, svg, png, pdf, gpml
Nature/NCI PathwayInteractionDatabase63 http://pid.nci.nih.gov/ BioPAX, jpg, svg
BioCyc4 http://biocyc.org/ BioPAX, png, SBML
INOH84 http://inoh.hgc.jp/ BioPAX, INOH (xml)
Netpath85 http://www.netpath.org/ BioPAX, SBML, PSI-MI
PharmGKB86 http://www.pharmgkb.org/ BioPAX, pdf, gpml

Abbreviations: BioPAX, Biological Pathway Exchange; KGML, KEGG Markup Language; PSI-MI, Proteomics Standards Initiative Molecular Interaction; SBML, Systems Biology Markup Language; NCI, National Cancer Institute; INOH, Integrating Network Objects with Hierarchies; PharmGKB, Pharmacogenomics Knowledge Base; KEGG, Kyoto Encyclopedia of Genes and Genomes.

Source: http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4461095/?report=reader
Tools for visualization and analysis of molecular networks, pathways, and -omics data


Pathway mining and comparison

Pathway gene sets were generated based on the GeneCards platform (12), implementing the gene symbolization process allowing for comparison of pathway gene sets, from 12 different manually curated sources, including: Reactome (13), KEGG (14), PharmGKB (15), WikiPathways (16) QIAGEN, HumanCyc (17), Pathway Interaction Database (18), Tocris Bioscience, GeneGO, Cell Signaling Technologies (CST), R&D Systems and Sino Biological (seeTable 1). A binary matrix was generated for all 3125 pathways, where each column represents a gene indicated by 1 for presence in the pathway and 0 for absence. Additionally, six sources were analysed for their cumulative tallying of genes content, including: BioCarta (19), SMPDB (20), INOH (21), NetPath (22), EHMN (23) and SignaLink (24).

 

Source: http://database.oxfordjournals.org/content/2015/bav006.full
PathCards: multi-source consolidation of human biological pathways

 

 


 

Welcome to the Biological General Repository for Interaction Datasets

BioGRID is an interaction repository with data compiled through comprehensive curation efforts. Our current index is version 3.4.137 and searches 56,733 publications for 1,067,443 protein and genetic interactions, 27,501 chemical associations and 38,559 post translational modifications from major model organism species. All data are freely provided via our search index and available for download in standardized formats.

 


 

© STRING CONSORTIUM 2016

STRING is a database of known and predicted protein-protein interactions. The database contains information from numerous sources, including experimental repositories, computational prediction methods and public text collections. STRING is regularly updated and gives a comprehensive view on protein-protein interactions currently available.

(http://string-db.org/cgi/input.pl?UserId=rzPqTB1Yphqn&sessionId=TuuvRkt5g4Bh&input_page_show_search=off)
  • ORGANISMS
    2031
  • PROTEINS
    9.6 mio
  • INTERACTIONS
    184 mio


Pathway Commons (http://www.pathwaycommons.org) is a collection of publicly available pathway data from multiple organisms. Pathway Commons provides a web-based interface that enables biologists to browse and search a comprehensive collection of pathways from multiple sources represented in a common language, a download site that provides integrated bulk sets of pathway information in standard or convenient formats and a web service that software developers can use to conveniently query and access all data. Database providers can share their pathway data via a common repository. Pathways include biochemical reactions, complex assembly, transport and catalysis events and physical
Oxford University Press

Pathway Commons, a web resource for biological pathway data

 

 PCViz Logo

Pathway Viewer Web

PCViz is an open-source web-based network visualization tool that helps users queryPathway Commons and obtain details about genes and their interactions extracted from multiple pathway data resources.

It allows interactive exploration of the gene networks where users can:

  • expand the network by adding new genes of interest
  • reduce the size of the network by filtering genes or interactions based on different criteria
  • load cancer context to see the overall frequency of alteration for each gene in the network
  • download networks in various formats for further analysis or use in publication

PCViz is built and maintained by Memorial Sloan-Kettering Cancer Center and theUniversity of Toronto.

 ChiBE

BioPAX Editor Desktop

Ethan G. Cerami, Benjamin E. Gross, […], and Chris Sander

Additional article information

ABSTRACT

Pathway Commons (http://www.pathwaycommons.org) is a collection of publicly available pathway data from multiple organisms. Pathway Commons provides a web-based interface that enables biologists to browse and search a comprehensive collection of pathways from multiple sources represented in a common language, a download site that provides integrated bulk sets of pathway information in standard or convenient formats and a web service that software developers can use to conveniently query and access all data. Database providers can share their pathway data via a common repository. Pathways include biochemical reactions, complex assembly, transport and catalysis events and physical interactions involving proteins, DNA, RNA, small molecules and complexes. Pathway Commons aims to collect and integrate all public pathway data available in standard formats. Pathway Commons currently contains data from nine databases with over 1400 pathways and 687 000 interactions and will be continually expanded and updated.

Pathway Commons currently includes pathway and interaction information from nine sources

Data Source Format Size Updated Focus (species) Reference or URL
BioGRID PSI–MI 2.5 347 508 Interactions August 2010 (3.0.67) Model organisms (20)
Cancer Cell Map BioPAX L2 10 Pathways May 2006 Human http://cancer.cellmap.org
2104 Interactions
HPRD PSI–MI 2.5 40 618 Interactions 13 April 2010 Version 9 Human (21)
HumanCyc BioPAX L2 266 Pathways 16 June 2010 Version 14.1 Human (22)
4879 Interactions
IMID BioPAX L2 1729 Interactions March, 2009 Human http://www.sbcny.org/
IntAct PSI–MI 2.5 154 567 Interactions 8 August 2010 Version 3.1, r14760 All (23)
MINT PSI–MI 2.5 117 202 Interactions 28 July 2010 All (24)
NCI/Nature PID BioPAX L2 186 Pathways 10 August 2010 Human (25)
13 879 Interactions
Reactome BioPAX L2 1015 Pathways 18 June 2010 Version 33 Human (5)
5397 Interactions
All Integrated BioPAX L2 1477 Pathways Multiple http:///www.pathwaycommons.org
687 883 Interactions

New sources are periodically added and listed on the Pathway Commons website. Note that pathway and interaction statistics represent non-unique counts from source databases, as these records are not currently merged from multiple sources (only molecules are currently merged).


Data Sources (http://www.pathwaycommons.org/pc2/datasources)

Warehouse data (canonical molecules, ontologies) are converted to BioPAX utility classes, such as EntityReference, ControlledVocabulary, EntityFeature sub-classes, and saved as the initial BioPAX model, which forms the foundation for integrating pathway data and for id-mapping.

Pathway and binary interaction data (interactions, participants) are normalized next and merged into the database. Original reference molecules are replaced with the corresponding BioPAX warehouse objects.

Note:

Links to the access summary for Warehouse data sources are not provided below; however, the total number of requests minus errors will be fair estimate. Access statistics are computed from January 2014, except unique IP addresses, which are computed from November 2014.

Acknowledgment

The Pathway Commons team much appreciates the fundamental contribution of all the data providers, authors, Identifiers.org, all the open biological ontologies, the open-source projects and standards, which made creating of this integrated BioPAX web service and database feasible.

  Reactome

Reactome v56 (only ‘Homo sapiens.owl’) 31-Mar-2016 (BIOPAX)

URI: http://pathwaycommons.org/pc2/reactome

All names (for data filtering): reactome

Contains: 2007 pathways, 14427 interactions, 35835 participants

Access summary

Publication: Croft D, Mundo AF, Haw R, Milacic M, Weiser J, Wu G, Caudy M, Garapati P, Gillespie M, Kamdar MR, Jassal B, Jupe S, Matthews L, May B, Palatnik S, Rothfels K, Shamovsky V, Song H, Williams M, Birney E, Hermjakob H, Stein L, D’Eustachio P. The Reactome pathway knowledgebase. Nucleic Acids Res. 2014;42(database issue):d472-7 (PMID:24243840)

Availability: free

  NCI Pathway Interaction Database: Pathway

NCI Curated Human Pathways from PID (final); 27-Jul-2015 (BIOPAX)

URI: http://pathwaycommons.org/pc2/pid

All names (for data filtering): pid,nci pathway interaction database: pathway

Contains: 745 pathways, 14707 interactions, 10531 participants

Access summary

Publication: Schaefer CF, Anthony K, Krupa S, Buchoff J, Day M, Hannay T, Buetow KH. PID: the Pathway Interaction Database. Nucleic Acids Res. 2009;37(database issue):d674-9 (PMID:18832364)

Availability: free

  PhosphoSitePlus

PhosphoSite Kinase-substrate information; 15-Mar-2016 (BIOPAX)

URI: http://pathwaycommons.org/pc2/psp

All names (for data filtering): phosphosite,phosphositeplus

Contains: 27692 interactions, 15458 participants

Access summary

Publication: Hornbeck PV, Kornhauser JM, Tkachev S, Zhang B, Skrzypek E, Murray B, Latham V, Sullivan M. PhosphoSitePlus: a comprehensive resource for investigating the structure and function of experimentally determined post-translational modifications in man and mouse. Nucleic Acids Res. 2012;40(database issue):d261-70 (PMID:22135298)

Availability: free

  HumanCyc

HumanCyc 19.5; 27-Oct-2015; under license from SRI International, www.biocyc.org (BIOPAX)

URI: http://pathwaycommons.org/pc2/humancyc

All names (for data filtering): humancyc,biocyc

Contains: 302 pathways, 7102 interactions, 5896 participants

Access summary

Publication: Romero P, Wagg J, Green ML, Kaiser D, Krummenacker M, Karp PD. Computational prediction of human metabolic pathways from the complete human genome. Genome Biol. 2005;6(1):r2 (PMID:15642094)

Availability: free

  HPRD

HPRD PSI-MI Release 9; 13-Apr-2010 (PSI_MI)

URI: http://pathwaycommons.org/pc2/hprd

All names (for data filtering): hprd

Contains: 40595 interactions, 9844 participants

Access summary

Publication: Keshava Prasad TS, Goel R, Kandasamy K, Keerthikumar S, Kumar S, Mathivanan S, Telikicherla D, Raju R, Shafreen B, Venugopal A, Balakrishnan L, Marimuthu A, Banerjee S, Somanathan DS, Sebastian A, Rani S, Ray S, Harrys Kishore CJ, Kanth S, Ahmed M, Kashyap MK, Mohmood R, Ramachandra YL, Krishna V, Rahiman BA, Mohan S, Ranganathan P, Ramabadran S, Chaerkady R, Pandey A. Human Protein Reference Database–2009 update. Nucleic Acids Res. 2009;37(database issue):d767-72 (PMID:18988627)

Availability: academic

  PANTHER Pathway

PANTHER Pathways 3.4 on 18-May-2015 (auto-converted to human-only model) (BIOPAX)

URI: http://pathwaycommons.org/pc2/panther

All names (for data filtering): panther,panther pathway,pantherdb

Contains: 272 pathways, 4700 interactions, 6703 participants

Access summary

Publication: Mi H, Muruganujan A, Thomas PD. PANTHER in 2013: modeling the evolution of gene function, and other gene attributes, in the context of phylogenetic trees. Nucleic Acids Res. 2013;41(database issue):d377-86 (PMID:23193289)

Availability: free

  Database of Interacting Proteins

DIP (human), 14-01-2016 (PSI_MI)

URI: http://pathwaycommons.org/pc2/dip

All names (for data filtering): dip,database of interacting proteins

Contains: 8218 interactions, 4671 participants

Access summary

Publication: Salwinski L, Miller CS, Smith AJ, Pettit FK, Bowie JU, Eisenberg D. The Database of Interacting Proteins: 2004 update. Nucleic Acids Res. 2004;32(database issue):d449-51 (PMID:14681454)

Availability: free

  BioGRID

BioGRID Release 3.4.135 (human and the viruses), 24-Mar-2016 (PSI_MI)

URI: http://pathwaycommons.org/pc2/biogrid

All names (for data filtering): biogrid

Contains: 322538 interactions, 645241 participants

Access summary

Publication: Stark C, Breitkreutz BJ, Reguly T, Boucher L, Breitkreutz A, Tyers M. BioGRID: a general repository for interaction datasets. Nucleic Acids Res. 2006;34(database issue):d535-9 (PMID:16381927)

Availability: free

  IntAct

IntAct (human only; ‘negative’ files removed), 16-Feb-2016 (PSI_MI)

URI: http://pathwaycommons.org/pc2/intact

All names (for data filtering): intact

Contains: 150549 interactions, 403729 participants

Access summary

Publication: Orchard S, Ammari M, Aranda B, Breuza L, Briganti L, Broackes-Carter F, Campbell NH, Chavali G, Chen C, del-Toro N, Duesbury M, Dumousseau M, Galeota E, Hinz U, Iannuccelli M, Jagannathan S, Jimenez R, Khadake J, Lagreid A, Licata L, Lovering RC, Meldal B, Melidoni AN, Milagros M, Peluso D, Perfetto L, Porras P, Raghunath A, Ricard-Blum S, Roechert B, Stutz A, Tognolli M, van Roey K, Cesareni G, Hermjakob H. The MIntAct project–IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res. 2014;42(database issue):d358-63 (PMID:24234451)

Availability: free

  IntAct

IntAct Complex (human), 16-Feb-2016 (PSI_MI)

URI: http://pathwaycommons.org/pc2/intact_complex

All names (for data filtering): intact

Contains: 1452 participants

Access summary

Publication: Orchard S, Ammari M, Aranda B, Breuza L, Briganti L, Broackes-Carter F, Campbell NH, Chavali G, Chen C, del-Toro N, Duesbury M, Dumousseau M, Galeota E, Hinz U, Iannuccelli M, Jagannathan S, Jimenez R, Khadake J, Lagreid A, Licata L, Lovering RC, Meldal B, Melidoni AN, Milagros M, Peluso D, Perfetto L, Porras P, Raghunath A, Ricard-Blum S, Roechert B, Stutz A, Tognolli M, van Roey K, Cesareni G, Hermjakob H. The MIntAct project–IntAct as a common curation platform for 11 molecular interaction databases. Nucleic Acids Res. 2014;42(database issue):d358-63 (PMID:24234451)

Availability: free

  BIND

BIND (human), 15-Dec-2010 (PSI_MI)

URI: http://pathwaycommons.org/pc2/bind

All names (for data filtering): bind,biomolecular interaction network database

Contains: 35279 interactions, 74675 participants

Access summary

Publication: Bader GD, Betel D, Hogue CW. BIND: the Biomolecular Interaction Network Database. Nucleic Acids Res. 2003;31(1):248-250 (PMID:12519993)

Availability: free

  CORUM

CORUM (human), 17-Feb-2012 (PSI_MI)

URI: http://pathwaycommons.org/pc2/corum

All names (for data filtering): corum

Contains: 4401 participants

Access summary

Publication: Ruepp A, Waegele B, Lechner M, Brauner B, Dunger-Kaltenbach I, Fobo G, Frishman G, Montrone C, Mewes HW. CORUM: the comprehensive resource of mammalian protein complexes–2009. Nucleic Acids Res. 2010;38(database issue):d497-501(PMID:19884131)

Availability: academic

  TRANSFAC

Transctiption Factor Target data from Collection 3 in MSigDB (originally from: TRANSFAC Public, by BIOBASE, QIAGEN); version 7.4 (BIOPAX)

URI: http://pathwaycommons.org/pc2/transfac

All names (for data filtering): transfac

Contains: 427 pathways, 261624 interactions, 13276 participants

Access summary

Publication: Wingender E. The TRANSFAC project as an example of framework technology that supports the analysis of genomic regulation. Brief Bioinform. 2008;9(4):326-332 (PMID:18436575)

Availability: academic

  miRTarBase

Human miRNA-target gene relationships from MiRTarBase; v4.5, 01-NOV-2013 (converted 13-MAR-2015) (BIOPAX)

URI: http://pathwaycommons.org/pc2/mirtarbase

All names (for data filtering): mirtarbase

Contains: 5 pathways, 51214 interactions, 12775 participants

Access summary

Publication: Hsu SD, Tseng YT, Shrestha S, Lin YL, Khaleel A, Chou CH, Chu CF, Huang HY, Lin CM, Ho SY, Jian TY, Lin FM, Chang TH, Weng SL, Liao KW, Liao IE, Liu CC, Huang HD. miRTarBase update 2014: an information resource for experimentally validated miRNA-target interactions. Nucleic Acids Res. 2014;42(database issue):d78-85 (PMID:24304892)

Availability: academic

  DrugBank

DrugBank v4.3 converted to BioPAX from the original XML dump (BIOPAX)

URI: http://pathwaycommons.org/pc2/drugbank

All names (for data filtering): drugbank

Contains: 19297 interactions, 15854 participants

Access summary

Publication: Law V, Knox C, Djoumbou Y, Jewison T, Guo AC, Liu Y, Maciejewski A, Arndt D, Wilson M, Neveu V, Tang A, Gabriel G, Ly C, Adamjee S, Dame ZT, Han B, Zhou Y, Wishart DS. DrugBank 4.0: shedding new light on drug metabolism. Nucleic Acids Res. 2014;42(database issue):d1091-7 (PMID:24203711)

Availability: academic

  Recon X

Recon X: Reconstruction of the Human Genome, converted from SBML; 2.03  (BIOPAX)

URI: http://pathwaycommons.org/pc2/reconx

All names (for data filtering): recon x

Contains: 1 pathways, 10813 interactions, 8316 participants

Access summary

Publication: Thiele I, Swainston N, Fleming RM, Hoppe A, Sahoo S, Aurich MK, Haraldsdottir H, Mo ML, Rolfsson O, Stobbe MD, Thorleifsson SG, Agren R, Bölling C, Bordel S, Chavali AK, Dobson P, Dunn WB, Endler L, Hala D, Hucka M, Hull D, Jameson D, Jamshidi N, Jonsson JJ, Juty N, Keating S, Nookaew I, Le Novère N, Malys N, Mazein A, Papin JA, Price ND, Selkov E Sr, Sigurdsson MI, Simeonidis E, Sonnenschein N, Smallbone K, Sorokin A, van Beek JH, Weichart D, Goryanin I, Nielsen J, Westerhoff HV, Kell DB, Mendes P, Palsson BØ. A community-driven global reconstruction of human metabolism. Nat Biotechnol. 2013;31(5):419-425(PMID:23455439)

Availability: free

  Comparative Toxicogenomics Database

Comparative Toxicogenomics Database (human), 20150603 (BIOPAX)

URI: http://pathwaycommons.org/pc2/ctd

All names (for data filtering): ctd,comparative toxicogenomics database,ctdbase

Contains: 32722 pathways, 390428 interactions, 61031 participants

Access summary

Publication: Davis AP, Grondin CJ, Lennon-Hopkins K, Saraceni-Richards C, Sciaky D, King BL, Wiegers TC, Mattingly CJ. The Comparative Toxicogenomics Database’s 10th year anniversary: update 2015. Nucleic Acids Res. 2015;43(database issue):d914-20(PMID:25326323)

Availability: academic

  KEGG Pathway

KEGG 07/2011 (only human, hsa* files), converted to BioPAX by BioModels (http://www.ebi.ac.uk/biomodels-main/) team (BIOPAX)

URI: http://pathwaycommons.org/pc2/kegg

All names (for data filtering): kegg,kegg pathway

Contains: 122 pathways, 3566 interactions, 3355 participants

Access summary

Publication: Wrzodek C, Büchel F, Ruff M, Dräger A, Zell A. Precise generation of systems biology models from KEGG pathways. BMC Syst Biol. 2013;7(undefined):15 (PMID:23433509)

Availability: academic

  Small Molecule Pathway Database

Small Molecule Pathway Database 2.0, 07-Jul-2015 (BIOPAX)

URI: http://pathwaycommons.org/pc2/smpdb

All names (for data filtering): smpdb,small molecule pathway database

Contains: 1206 pathways, 4701 interactions, 4863 participants

Access summary

Publication: Jewison T, Su Y, Disfany FM, Liang Y, Knox C, Maciejewski A, Poelzer J, Huynh J, Zhou Y, Arndt D, Djoumbou Y, Liu Y, Deng L, Guo AC, Han B, Pon A, Wilson M, Rafatnia S, Liu P, Wishart DS. SMPDB 2.0: big improvements to the Small Molecule Pathway Database. Nucleic Acids Res. 2014;42(database issue):d478-84 (PMID:24203708)

Availability: free

  Integrating Network Objects with Hierarchies

INOH 4.0 (signal transduction and metabolic data), 22-MAR-2011 (BIOPAX)

URI: http://pathwaycommons.org/pc2/inoh

All names (for data filtering): inoh,integrating network objects with hierarchies

Contains: 774 pathways, 5432 interactions, 17142 participants

Access summary

Publication: Yamamoto S, Sakai N, Nakamura H, Fukagawa H, Fukuda K, Takagi T. INOH: ontology-based highly structured database of signal transduction pathways. Database (Oxford). 2011;2011(undefined):bar052 (PMID:22120663)

Availability: free

  NetPath

NetPath 12/2011 (BIOPAX)

URI: http://pathwaycommons.org/pc2/netpath

All names (for data filtering): netpath

Contains: 27 pathways, 6347 interactions, 3266 participants

Access summary

Publication: Kandasamy K, Mohan SS, Raju R, Keerthikumar S, Kumar GS, Venugopal AK, Telikicherla D, Navarro JD, Mathivanan S, Pecquet C, Gollapudi SK, Tattikota SG, Mohan S, Padhukasahasram H, Subbannayya Y, Goel R, Jacob HK, Zhong J, Sekhar R, Nanjappa V, Balakrishnan L, Subbaiah R, Ramachandra YL, Rahiman BA, Prasad TS, Lin JX, Houtman JC, Desiderio S, Renauld JC, Constantinescu SN, Ohara O, Hirano T, Kubo M, Singh S, Khatri P, Draghici S, Bader GD, Sander C, Leonard WJ, Pandey A. NetPath: a public resource of curated signal transduction pathways. Genome Biol. 2010;11(1):r3 (PMID:20067622)

Availability: free

  WikiPathways

WikiPathways – Community Curated Human Pathways; 29/09/2015 (human) (BIOPAX)

URI: http://pathwaycommons.org/pc2/wp

All names (for data filtering): wikipathways

Contains: 333 pathways, 9758 interactions, 9584 participants

Access summary

Publication: Pico AR, Kelder T, van Iersel MP, Hanspers K, Conklin BR, Evelo C. WikiPathways: pathway editing for the people. PLoS Biol. 2008;6(7):e184 (PMID:18651794)

Availability: free

  ChEBI

ChEBI Ontology v138, 01-Apr-2016 (WAREHOUSE)

All names (for data filtering): chebi

Publication: Hastings J, de Matos P, Dekker A, Ennis M, Harsha B, Kale N, Muthukrishnan V, Owen G, Turner S, Williams M, Steinbeck C. The ChEBI reference database and ontology for biologically relevant chemistry: enhancements for 2013. Nucleic Acids Res. 2013;41(database issue):d456-63 (PMID:23180789)

Availability: free

  SwissProt

UniProtKB/Swiss-Prot (human), 16-Mar-2015 (WAREHOUSE)

All names (for data filtering): uniprot,swissprot,uniprotkb

Publication: UniProt Consortium. Activities at the Universal Protein Resource (UniProt). Nucleic Acids Res. 2014;42(database issue):d191-8 (PMID:24253303)

Availability: free

  UniChem

Selected whole-source id-mapping files (to ChEBI) from UniChem (manually edited/fixed/sorted), 29-Dec-2015 (MAPPING)

All names (for data filtering): unichem

Publication: Chambers J, Davies M, Gaulton A, Hersey A, Velankar S, Petryszak R, Hastings J, Bellis L, McGlinchey S, Overington JP. UniChem: a unified chemical structure cross-referencing and identifier tracking system. J Cheminform. 2013;5(1):3 (PMID:23317286)

Availability: free


ConsensusPathDB—a database for integrating human functional interaction networks

ConsensusPathDB is a database system for the integration of human functional interactions. Current knowledge of these interactions is dispersed in more than 200 databases, each having a specific focus and data format. ConsensusPathDB currently integrates the content of 12 different interaction databases with heterogeneous foci comprising a total of 26 133 distinct physical entities and 74 289 distinct functional interactions (protein–protein interactions, biochemical reactions, gene regulatory interactions), and covering 1738 pathways. We describe the database schema and the methods used for data integration. Furthermore, we describe the functionality of the ConsensusPathDB web interface, where users can search and visualize interaction networks, upload, modify and expand networks in BioPAX, SBML or PSI-MI format, or carry out over-representation analysis with uploaded identifier lists with respect to substructures derived from the integrated interaction network. The ConsensusPathDB database is available at: http://cpdb.molgen.mpg.de

The MIPS Mammalian Protein-Protein Interaction Database

The MIPS Mammalian Protein-Protein Interaction Database is a collection of manually curated high-quality PPI data collected from the scientific literature by expert curators. We took great care to include only data from individually performed experiments since they usually provide the most reliable evidence for physical interactions.

http://mips.helmholtz-muenchen.de/proj/ppi/

Other PPI resources

There are plenty of interesting databases and other sites on protein-protein interactions. Currently we are aware of the following PPI resources:

Resource Comments
APID Agile Protein Interaction DataAnalyzer (Cancer Research Center, Salamanca, Spain)
BIND Biomolecular INteraction Network Database at the University of Toronto, Canada. No species restriction
CYGD PPI section of the Comprehensive Yeast Genome Database. Manually curated comprehensive S. cerevisiae PPI database at MIPS
DIP Database of Interacting Proteins at UCLA. No species restriction.
GRID General Repository for Interaction Datasets. Mount Sinai Hospital, Toronto, Canada
HIV Interaction DB Interactions between HIV and host proteins.
HPRD The Human Protein Reference Database. Institute of Bioinformatics, Bangalore, India and Johns Hopkins University, Baltimore, MD, USA.
HPID Human Protein Interaction Database. Department of computer Science and Information Engineering Inha University, Inchon, Korea
iHOP iHOP (Information Hyperlinked over Proteins). Protein association network built by literature mining
IntAct Protein interaction database at EBI. No species restriction.
InterDom Database of putative interacting protein domains. Institute for InfoComm Research, Singapore.
JCB PPI site at the Jena Centre for Bioinformatics, Germany
MetaCore Commercial software suite and database. Manually curated human PPIs (among other things). GeneGo
MINT Molecular INTeraction database at the Centro di Bioinformatica Moleculare, Universita di Roma, Italy.
MRC PPI links Commented list of links to PPI databases and resources maintained at the MRC Rosalind Franklin Cetre for Genomics Research, Cambridge, UK
OPHID The Online Predicted Human Interaction Database. Ontario Cancer Institute and University of Toronto, Canada.
Pawson Lab Information on protein-interaction domains.
PDZbase Database of PDZ mediated protein-protein interactions.
Predictome Predicted functional associations and interactions. Boston University.
Protein-Protein Interaction Server Analysis of protein-protein interfaces of protein complexes from PDB. University College of London, UK.
PathCalling Proteomics and PPI tool/database. CuraGen Corporation.
PIM Hybrigenics PPI data and tool, H. pylori. Free academic license available
RIKEN Experimental and literature PPIs in mouse.
STRING Protein networks based on experimental data and predictions at EMBL.
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