Table 1

Integrated databases

Database

Concept 1

Relation

Concept 2

Literature references

Number of relations


BioGRID [25]

Gene/protein

PPI

Gene/protein

Yes

29,566

CTD [26]

Compound

Association

Gene/protein

Yes

62,336

Compound

Association

Disease

Yes

5,438

Gene/protein

Association

Disease

Yes

8,123

DIP [27]

Gene/protein

PPI

Gene/protein

Yes

1,524

GOA [28]

Gene/protein

Annotation

Gene Ontology term

No

26,949

HPRD [29]

Gene/protein

PPI

Gene/protein

Yes

149,036

IntAct [30]

Gene/protein

PPI

Gene/protein

Yes

37,258

InterPro [31]

Gene/protein

Contains

Protein domain/repeat/region

No

26,652

Gene/protein

Is member of

Gene family

No

22,988

Gene/gene family/protein domain/repeat/region

Annotation

Gene Ontology term

No

18,446

KEGG [32]

Gene/protein

Is part of

Pathway

No

14,100

Gene/protein

Has metabolite

Compound

No

19,073

MeSH [33]

Disease

Belongs to

Disease (family)

No

21,282

MINT [34]

Gene/protein

PPI

Gene/protein

Yes

11,389

miR2Disease [35]

MicroRNA

Targets

Gene

Yes

2,615

MicroRNA

Association

Disease

Yes

344

NetworKIN [36]

Gene/protein

Phosphorylates

Gene/protein

No

2,811

OMIM Morbid Map [11]

Gene/protein

Association

Disease

Yes

6,199

OMIM [11]

Disease

Is related to

Disease

Yes

2,467

TarBase [37]

MicroRNA

Targets

Gene

No

858


Overview of the 21 publicly available curated databases used to create BioGraph's heterogeneous knowledge base. Specific concept types were extracted from the various databases and integrated into a central graph. Note that these represent relations selected for Homo sapiens only. OMIM's disease-disease relations have been added after the data freeze of March 2010. CTD, Comparative Toxicogenomics Database; DIP, Database of Interacting Proteins; GOA, Gene Ontology Annotations; HPRD, Human Protein Reference Database; KEGG, Kyoto Encyclopedia of Genes and Genomes; MeSH, Medical Subject Headings; MINT, Molecular Interactions Database; OMIM, Online Mendelian Inheritance in Man; PPI, protein-protein interaction.

Liekens et al. Genome Biology 2011 12:R57   doi:10.1186/gb-2011-12-6-r57

Open Data