Abstract
The IntAct molecular interaction database has created a new, free, open-source, manually curated resource, the Complex Portal (www.ebi.ac.uk/intact/complex), through which protein complexes from major model organisms are being collated and made available for search, viewing and download. It has been built in close collaboration with other bioinformatics services and populated with data from ChEMBL, MatrixDB, PDBe, Reactome and UniProtKB. Each entry contains information about the participating molecules (including small molecules and nucleic acids), their stoichiometry, topology and structural assembly. Complexes are annotated with details about their function, properties and complex-specific Gene Ontology (GO) terms. Consistent nomenclature is used throughout the resource with systematic names, recommended names and a list of synonyms all provided. The use of the Evidence Code Ontology allows us to indicate for which entries direct experimental evidence is available or if the complex has been inferred based on homology or orthology. The data are searchable using standard identifiers, such as UniProt, ChEBI and GO IDs, protein, gene and complex names or synonyms. This reference resource will be maintained and grow to encompass an increasing number of organisms. Input from groups and individuals with specific areas of expertise is welcome.
Highlights
Biological processes are driven by the interactions of proteins with other molecules in an organism
It has been built in close collaboration with other bioinformatics services and populated with data from ChEMBL, MatrixDB, PDBe, Reactome and UniProtKB
Complexes are annotated with details about their function, properties and complex-specific Gene Ontology (GO) terms
Summary
Biological processes are driven by the interactions of proteins with other molecules in an organism. The PRO consortium, by collaborating with the IntAct group, will contribute to both extend the number of complexes which are available as objects within the PRO hierarchy while making more richly annotated data on these entities available in a broader range of formats through the Complex Portal. Model organism groups, such as Saccharomyces Genome Database [11] and WormBase [12], are contributing expertise and curation effort within their organism of interest, while the MINT database is augmenting the resource with additional expertise on the composition of protein complexes. As indicated above, modelled or inferred complexes are clearly marked using the evidence ontology terms and may be filtered out from experimentally verified data using a simple query
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