Database Commons

a catalog of worldwide biological databases

Molecular interactions are key drivers of biological function. Providing interaction resources to the research community is important since they allow functional interpretation and network-based analysis of molecular data. ConsensusPathDB (http://consensuspathdb.org) is a meta-database combining interactions of diverse types from 31 public resources for humans, 16 for mice and 14 for yeasts. Using ConsensusPathDB, researchers commonly evaluate lists of genes, proteins and metabolites against sets of molecular interactions defined by pathways, Gene Ontology and network neighborhoods and retrieve complex molecular neighborhoods formed by heterogeneous interaction types. Furthermore, the integrated protein-protein interaction network is used as a basis for propagation methods. Here, we present the 2022 update of ConsensusPathDB, highlighting content growth, additional functionality and improved database stability. For example, the number of human molecular interactions increased to 859 848 connecting 200 499 unique physical entities such as genes/proteins, metabolites and drugs. Furthermore, we integrated regulatory datasets in the form of transcription factor-, microRNA- and enhancer-gene target interactions, thus providing novel functionality in the context of overrepresentation and enrichment analyses. We specifically emphasize the use of the integrated protein-protein interaction network as a scaffold for network inferences, present topological characteristics of the network and discuss strengths and shortcomings of such approaches.

Knowledge of the various interactions between molecules in the cell is crucial for understanding cellular processes in health and disease. Currently available interaction databases, being largely complementary to each other, must be integrated to obtain a comprehensive global map of the different types of interactions. We have previously reported the development of an integrative interaction database called ConsensusPathDB (http://ConsensusPathDB.org) that aims to fulfill this task. In this update article, we report its significant progress in terms of interaction content and web interface tools. ConsensusPathDB has grown mainly due to the integration of 12 further databases; it now contains 215 541 unique interactions and 4601 pathways from overall 30 databases. Binary protein interactions are scored with our confidence assessment tool, IntScore. The ConsensusPathDB web interface allows users to take advantage of these integrated interaction and pathway data in different contexts. Recent developments include pathway analysis of metabolite lists, visualization of functional gene/metabolite sets as overlap graphs, gene set analysis based on protein complexes and induced network modules analysis that connects a list of genes through various interaction types. To facilitate the interactive, visual interpretation of interaction and pathway data, we have re-implemented the graph visualization feature of ConsensusPathDB using the Cytoscape.js library.

ConsensusPathDB is a meta-database that integrates different types of functional interactions from heterogeneous interaction data resources. Physical protein interactions, metabolic and signaling reactions and gene regulatory interactions are integrated in a seamless functional association network that simultaneously describes multiple functional aspects of genes, proteins, complexes, metabolites, etc. With 155,432 human, 194,480 yeast and 13,648 mouse complex functional interactions (originating from 18 databases on human and eight databases on yeast and mouse interactions each), ConsensusPathDB currently constitutes the most comprehensive publicly available interaction repository for these species. The Web interface at http://cpdb.molgen.mpg.de offers different ways of utilizing these integrated interaction data, in particular with tools for visualization, analysis and interpretation of high-throughput expression data in the light of functional interactions and biological pathways.

ConsensusPathDB is a database system for the integration of human functional interactions. Current knowledge of these interactions is dispersed in more than 200 databases, each having a specific focus and data format. ConsensusPathDB currently integrates the content of 12 different interaction databases with heterogeneous foci comprising a total of 26,133 distinct physical entities and 74,289 distinct functional interactions (protein-protein interactions, biochemical reactions, gene regulatory interactions), and covering 1738 pathways. We describe the database schema and the methods used for data integration. Furthermore, we describe the functionality of the ConsensusPathDB web interface, where users can search and visualize interaction networks, upload, modify and expand networks in BioPAX, SBML or PSI-MI format, or carry out over-representation analysis with uploaded identifier lists with respect to substructures derived from the integrated interaction network. The ConsensusPathDB database is available at: http://cpdb.molgen.mpg.de.