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Data sources

This page is devoted to the data sources that form the foundation of DASMIweb.

DASMIweb currently has access to 36 distributed data sources. 10 of these provide interaction data that has been experimentally determined or curated from the scientific literature, 24 data sources contain computational predictions, and 2 data sources can be used for scoring the quality of interactions.

Data caching

Though it contradicts the decentralization principles of DASMI and DASMIweb, we temporarily cache 28 external datasets at our institute to make them available via DASMIweb. In the table below, you can identify these datasets by their 'Other details' tags.

Should you wish to download one of the temporarily cached datasets for offline analysis, please visit our download page. However, note that we will remove temporary caches and download options as soon as the original data providers render these unneccesssary by setting up respective data servers.

Importantly, we would like to cordially thank all providers of interaction data or interacion confidence scores that support the distributed system by setting up servers for their data.


The following 36 data sources are currently available via DASMIweb:

If you feel that you resource should also be mentioned here, or that your resource should not be mentioned here (i.e. should not be accessible via DASMIweb), please contact us

Name Link to resource Publication / description Data determination method Other details
MPIDBhttp://jcvi.org/mpidb/about.phpGoll et al. (2008). MPIDB: the microbial protein interaction database. Bioinformatics, 24(15):1743-1744;literature curated
IntActhttp://www.ebi.ac.uk/intact/site/index.jsfKerrien et al. (2007). IntAct-open source resource for molecular interaction data. Nucleic Acids Res, 35(Database issue):D561-D565.literature curated
iRefIndexhttp://irefindex.uio.no/wiki/iRefIndexRazick et al. (2008). iRefIndex: A consolidated protein interaction database with provenance. BMC Bioinformatics 2008, 9:405.literature curated
StringStringStringliterature curated
3didhttp://gatealoy.pcb.ub.es/3did/Stein et al. (2008). 3did Update: domain-domain and peptide-mediated interactions of known 3D structure. Nucleic Acids Res, 37(Database issue):D300-D304.crystal structure analysistemporarily cached
version: update, 2008-10-15
APMM1http://intelligent.eic.osaka-sandai.ac.jp/chenen/MDCinfer.htmWang et al. (2007). Analysis on multi-domain cooperation for predicting protein-protein interactions. BMC Bioinformactics, 8(1):391predictedfinal dataset
APMM2http://intelligent.eic.osaka-sandai.ac.jp/chenen/MDCinfer.htmWang et al. (2007). Analysis on multi-domain cooperation for predicting protein-protein interactions. BMC Bioinformactics, 8(1):391predictedfinal dataset
Bioversehttp://bioverse.compbio.washington.edu/McDermott et al. (2005). Functional annotation from predicted protein interaction networks. Bioinformatics, 21(15):3217-3226. predictedfinal dataset
CCSB-HI1http://vidal.dfci.harvard.edu/Rual et al. (2005). Towards a proteome-scale map of the human protein-protein interaction network. Nature, 437(7062):1173-1178.experimentalfinal dataset
DIMA-DPEAhttp://mips.gsf.de/genre/proj/dima2/Pagel et al. (2008). DIMA 2.0-predicted and known domain interactions. Nucleic Acids Res, 36, D651-D655.predictedtemporarily cached
version: 2.0, 2007-11-13
DIMA-DPROFhttp://mips.gsf.de/genre/proj/dima2/Pagel et al. (2008). DIMA 2.0-predicted and known domain interactions. Nucleic Acids Res, 36, D651-D655.predictedtemporarily cached
version: 2.0, 2007-11-13
DIMA-STRINGhttp://mips.gsf.de/genre/proj/dima2/Pagel et al. (2008). DIMA 2.0-predicted and known domain interactions. Nucleic Acids Res, 36, D651-D655.predictedtemporarily cached
version: 2.0, 2007-11-13
DIPhttp://dip.doe-mbi.ucla.edu/Salwinski et al. (2004). The Database of Interacting Proteins: 2004 update. Nucleic Acids Res, 32:D449-D451literature curatedtemporarily cached
version: 2009-01-26
Domain supporthttp://www.dasmi.deinteraction quality measure
DPEAhttp://genomebiology.com/2005/6/10/R89Riley et al. (2005). Inferring protein domain interactions from databases of interacting proteins. Genome Biol, 6(10):R89.predictedfinal dataset
FunSimMat2.1http://funsimmat.bioinf.mpi-inf.mpg.de/Schlicker and Albrecht. (2008). FunSimMat: a comprehensive functional similarity database. Nucleic Acids Res, 36, D434-D439. interaction quality measure
HiMAPhttp://www.himap.org/Rhodes et al. (2005). Probabilistic model of the human protein-protein interaction network. Nat Biotechnol, 23(8):951-959. predictedtemporarily cached
version: 2006-12-19
HiMAP-corehttp://www.himap.org/Rhodes et al. (2005). Probabilistic model of the human protein-protein interaction network. Nat Biotechnol, 23(8):951-959. predictedtemporarily cached
version: 2006-12-19
HomoMINThttp://mint.bio.uniroma2.it/HomoMINT/Welcome.doPersico et al. (2005). HomoMINT: an inferred human network based on orthology mapping of protein interactions discovered in model organisms. BMC Bioinformatics, 6 Suppl 4:S21.predictedtemporarily cached
version: 2009-03-05
HPRDhttp://www.hprd.orgKeshava Prasad et al. (2009). Human Protein Reference Database-2009 update. Nucleic Acids Res, 37(Database issue):D767-D772literature curatedtemporarily cached
2009-06-07
InterDomhttp://interdom.i2r.a-star.edu.sg/Ng et al. (2003). Integrative approach for computationally inferring protein domain interactions. Bioinformatics, 19(8):923-929.predictedtemporarily cached
version: v2, 2007-07-31
IPPRI-HChttp://bioinformatics.oxfordjournals.org/cgi/content/full/24/16/i35High confidence subset of Schelhorn et al. (2008). An integrative approach for predicting interactions of protein regions. Bioinformatics, 24(16):i35-i41.predicted
IPPRIhttp://bioinformatics.oxfordjournals.org/cgi/content/full/24/16/i35Schelhorn et al. (2008). An integrative approach for predicting interactions of protein regions. Bioinformatics, 24(16):i35-i41.predicted
LDSChttp://www.biomedcentral.com/1471-2105/7/269Lee et al. (2006). An integrated approach to the prediction of domain-domain interactions. BMC Bioinformatics, 7:269.predictedfinal dataset
LDSC-corehttp://www.biomedcentral.com/1471-2105/7/269Lee et al. (2006). An integrated approach to the prediction of domain-domain interactions. BMC Bioinformatics, 7:269.predictedfinal dataset
LLZhttp://bioinformatics.med.yale.edu/interaction/Liu et al. (2005). Inferring protein-protein interactions through high-throughput interaction data from diverse organisms. Bioinformatics, 21(15):3279-3285.predictedfinal dataset
LPhttp://genomebiology.com/2006/7/11/R104Guimaraes. et al. (2006). Predicting domain-domain interactions using a parsimony approach. Genome Biol, 7(11):R104. predictedfinal dataset
MDChttp://www.ncbi.nlm.nih.gov/pubmed/16169070Stelzl et al. (2005). A human protein-protein interaction network: a resource for annotating the proteome. Cell, 122(6):957-968.experimentalfinal dataset
OPHIDhttp://ophid.utoronto.ca/ophid/Brown and Jurisica (2005). Online predicted human interaction database. Bioinformatics, 21(9):2076-2082.predictedtemporarily cached
version: 2009-08-03
PInShttp://pins.ornl.gov/Bordner and Gorin (2008). Comprehensive inventory of protein complexes in the Protein Data Bank from consistent classification of interfaces. BMC Bioinformatics, 9:234.crystal structure analysisfinal dataset
POINThttp://insilico.csie.ntu.edu.tw:9999/point/Huang et al. (2004). POINT: a database for the prediction of protein-protein interactions based on the orthologous interactome. Bioinformatics, 20(17):3273-3276.predictedfinal dataset
RCDP50http://www.pubmedcentral.nih.gov/articlerender.fcgi?artid=1618801Jothi et al. (2006). Co-evolutionary analysis of domains in interacting proteins reveals insights into domain-domain interactions mediating protein-protein interactions. J Mol Biol, 362(4):861-75.predictedfinal dataset
RDFFhttp://www.ittc.ku.edu/~xwchen/PPI/random_forest_PPIChen et al. (2005). Prediction of protein-protein interactions using random decision forest framework. Bioinformatics, 21(24):4394-400.predictedfinal dataset
Sangerhttp://genomebiology.com/2004/5/9/R63Lehner and Fraser (2004). A first-draft human protein interaction map. Genome Biol, 5(9):R63. predictedfinal dataset
Sanger-corehttp://genomebiology.com/2004/5/9/R63Lehner and Fraser (2004). A first-draft human protein interaction map. Genome Biol, 5(9):R63. predictedfinal dataset
TWhttp://www.biomedcentral.com/1471-2164/7/122/abstractWuchty et al. (2006). Topology and weights in a protein domain interaction network-a novel way to predict protein interactions. BMC Genomcis, 7:122.predictedfinal dataset