Table 1.

Comparison of omic data repositories for three different diseases [cancer, inflammatory bowel disease, and rheumatoid arthritis]

Disease	Database	URL	Omic layers available	Downloadability?	Data format [raw/ processed]
IBD	HMP2/IBDMDB	https://ibdmdb.org/	Proteomics, host tissue transcriptomics, 16S gut microbiome profiling, metagenomes, viromics, metabolites, serology, metatranscriptomes	Yes	Both raw and processed
	Dutch IBD biobank	https://1000ibd.org/; https://ega-archive.org/studies/EGAS00001002702	Genetics, 16S gut microbiome profiling [faeces and intestinal biopsies], faecal metagenomics	Yes	Raw only
	International Inflammatory Bowel Disease Genetics Consortium [IIBDGC]	https://www.ibdgenetics.org/downloadshtml	Genetics	No	-
	NIHR IBD bioresource	https://www.ibdbioresource.nihr.ac.uk/index.php/resources/applying-for-access-to-the-ibd-bioresource-panel-2/	Genetics	No	-
	PRISM	https://www.ncbi.nlm.nih.gov/bioproject/PRJNA400072/	WGS gut microbiome profiling, LC- MS metabolomics	Yes	Raw only
	UK Biobank	https://www.ukbiobank.ac.uk/	Genetics	No	-
Cancer	ArrayMap	http://www.arraymap.org	Copy number data	No	-
	BCNTBbp	https://www.breastcancertissuebank.org/bioinformatics	Genomics, methylomics, transcriptomics, proteomics and microRNA	No	-
	BRCA Share	http://www.umd.be/BRCA2/	Genomic variants on the BRCA1 and BRCA2 genes	Yes	Processed only
	BreCAN-DB	http://14.139.32.56/	Somatic DNA breakpoint profiles mapped using whole genome sequencing data	Yes	Raw only
	Cancer PPD	http://crdd.osdd.net/raghava/cancerppd/	Lists of proteins and peptides with anti-cancer activities	Yes	Processed only
	Cancer RNA-Seq Nexus	http://syslab4.nchu.edu.tw/	Expression of long non-coding RNAs and miRNAs	No	-
	Cancer3D	http://www.cancer3d.org/search	Map of cancer missense mutations on protein structures	Yes	Processed only
	cBioPortal	https://www.cbioportal.org/	Mutations, copy numbers, mRNA and protein expression	Yes	Both raw and processed
	COSMIC	https://cancer.sanger.ac.uk/cosmic/	Mutations and their annotations	Yes	Both raw and processed
	Database of Germline p53 Mutations	http://kolweb.lf2.cuni.cz//projects/germline_mut_p53.htm	Detailed annotations of p53 mutations	Yes	Processed only
	intOGen	https://www.intogen.org/search	Mutational cancer driver genes	Yes	Processed only
	Lnc2Cancer	http://www.bio-bigdata.com/lnc2cancer/home.jsp	Expression of cancer associated long non-coding RNAs	No	-
	MethHC	http://methhc.mbc.nctu.edu.tw/php/index.php	DNA methylation, gene expression, microRNA methylation, microRNA expression	Yes	Both raw and processed
	MOKCa	http://strubiol.icr.ac.uk/extra/mokca/	Map of cancer mutations and their phenotypic effects	No	-
	MutationAligner	http://www.mutationaligner.org/	Mutation ‘hotspots’ identified in protein domains	Yes	Processed only
	Network of Cancer Genes	http://ncg.kcl.ac.uk/index.php	Duplicated loci and expression of protein-coding cancer genes	Yes	Both raw and processed
	TCGA	https://portal.gdc.cancer.gov/	RNA-seq, methylation, genotyping, miRNA-seq, whole-exome high- throughput DNA sequencing	Yes	Both raw and processed
	TCGA Splice Seq	http://projects.insilico.us.com/TCGASpliceSeq/	Cross-tumour and tumour-normal alterations in mRNA splicing patterns in cancer	Yes	Processed only
Rheumatoid arthritis	Biogps	http://biogps.org/dataset/tag/rheumatoid%20arthritis/	Gene expression	Yes	Both raw and processed
	Gene Expression Omnibus	https://www.ncbi.nlm.nih.gov/geo/	Gene expression	Yes	Both raw and processed
	Array Express	https://www.ebi.ac.uk/arrayexpress/	Gene expression	Yes	Raw only
	PMID: 23143596	https://pubmed.ncbi.nlm.nih.gov/23143596/	Genetics	Yes	Both raw and processed
	PMID: 22446963	https://pubmed.ncbi.nlm.nih.gov/22446963/	Genetics	Yes	Both raw and processed
	RADB	http://www.bioapp.org/RADB/	RA-related genetic polymorphisms extracted from published papers	Yes	Processed only

IBD, inflammatory bowel disease; LC-MS, Liquid Chromatography-Mass Spectrometry; RA, rheumatoid arthritis; WGS , whole genome sequencing.