DIPSBC - data integration platform for systems biology collaborations

BMC Bioinformatics

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.

ISSN: 1471-2105