Table 4.

Databases and their access policies considered for the requirement clusters of data bridges

Data providers	Summary of main access restrictions and policies
Requirement cluster: Imaging bridge	See: Additional file 1: Table S1
Mouse tissue imaging data (Infrafrontier), Human tumour tissue data (BBMRI/ FIMM), MitoCheck (cell-based RNAi screens), WebMicroscope (mouse and human image data sets), Ensembl, ArrayExpress, Phenotator, MitoCheck	Restricted access, data linking only possible, if the data provider gives permission based on the availability of informed consents, consent form which permits such a research may be required, application to the steering committee or principal investigator, Images are owned by image generator
Requirement cluster: Phenotypic bridge	See: Additional file 1: Table S2
EuroPhenome, IMPC, Gene Expression Atlas (GXA), ArrayExpress, ChEMBL, Metabolights, Reactome, CERM datasets, Biobank/BBMRI (University of Graz, Austria)	Predominantly open access, open restricted for private data (pre-publication/ unpublished), open access, when data is used for research purposes, biobank with restricted access (access rules include project application and approval committee)
Requirement cluster: Personalised Medicine bridge	See: Additional file 1: Table S3
ICGC (International Cancer Genome Consortium), TCGA (The Cancer Genome Atlas), EGA (European Genome-phenome Archive), Cosmic (Catalogue of somatic mutations in cancer), GEO (Gene Expression Omnibus), Array-Express, ChEMBL, Reactome, Ensembl, Drugbank, Pharmgkb, BioSD, Biobanks (BBMRI), EU-OPENSCREEN, ECRIN (CTIM), FIMM Institute for Molecular Medicine Finland (EATRIS)	Open access and data with and without restricted access, different policies apply, controlled access datasets means access control, Data Access Compliance Office (DACO) handles requests from scientists for access to controlled data, requirement for user certification via Data Access Request, download of datasets must be approved by the specified Data Access Committee (DAC), requires users to sign a Data Access Agreement (DAA), which details the terms and conditions of use for each dataset, all controlled access downloadable datasets are encrypted, restricted access usually for pre-published/unpublished data
Requirement cluster: Structural Data bridge	See: Additional file 1: Table S4
UniProt, AmiGO (Gene Ontology database), EMDB (Electron Microscopy Data Bank), IntAct (Molecular Interaction Database), GenBank (NCBI), ELIXIR, BMB database	All are open access
Requirement cluster: Biosample data bridge	See: Additional file 1: Table S5
	Mainly restricted access. Open access for aggregated anonymised information or metadata about samples, for data access researcher has to apply to Data Access Committee (DAC) of biobank and has to agree to use data only for research, which has been specified between biobank and researcher, and not to try to identify patients