Table 2

Index contents of the current DIPSBC example installation
Data type Source File format Nr. of entries Description
Protein mass spectra PRIDE acc. 8538 mzData 745 Peptide tandem mass spectra (Homo sapiens) with identifications
DNA microarrays GEO acc. GSE3325 MINiML 19 Prostate cancer study; chip platform: Affymetrix U133 Plus 2.0 arrays (Homo sapiens)
GEO acc. GSE1133 MINiML 438 Novartis gene atlas 2004 (mouse and human arrays)
GEO acc. GSE10204, GSE11193 MINiML 80 Genetic functional basics of water-binding- capacity in pork; chip platform: Affymetrix Porcine Whole Genome Array
Studies MPI Berlin XML 'study' 7 Summary tables of statistical analyses
Test result tables MPI Berlin STAT-ML 94497 Results of statistical analyses of microarray experiments
Microsatellite markers / phenotypes University Bonn XML 'pigs' 873 Pig marker and trait values
Molecular interactions IntAct PSI-MI 5915 Yeast-2-hybrid datasets from Rual et al. and Stelzl et al.
CPDB XML 'cpdb' 46454 Interactions involving genes, proteins, and compounds; source: ConsensusPathDB
Molecular Models BioModels SBML 699 Mathematical models of gene regulatory pathways
Synonyms pig Affymetrix XML 'synonyms' 24123 Pig genome annotations
Synonyms human Affymetrix XML 'synonyms' 54675 Homo sapiens genome annotations
Protein sequences Uniprot FASTA 16.5 mio. Protein sequences (FASTA format)
Publications PubMed XML 'pubmed' 18.2 mio. Publications in PubMed starting from 1970
Foswiki pages DIPSBC TXT 26 Web pages within the DIPBSC platform
Total nr. of entries 34.970.538

The index contains a large collection of different data types, including protein mass spectra, DNA microarray experiments, molecular interactions, protein sequences and Pubmed abstracts, amongst others. In total about 35 million records are indexed and thus searchable.

Dreher et al.

Dreher et al. BMC Bioinformatics 2012 13:85   doi:10.1186/1471-2105-13-85

Open Data