COMPARTMENTS: unification and visualization of protein subcellular localization evidence

TLDR

Protein subcellular localization is essential for understanding protein function, yet current data are fragmented across manual curation, high‑throughput screens, and sequence‑based predictions, requiring consultation of multiple databases. COMPARTMENTS was created to unify these disparate sources, including literature mining, into a single resource. The resource is automatically updated, maps evidence to common protein identifiers and Gene Ontology terms, assigns confidence scores by evidence type and source, and visualizes the integrated data on a schematic cell. Database URL: http://compartments.jensenlab.org.

Abstract

Information on protein subcellular localization is important to understand the cellular functions of proteins. Currently, such information is manually curated from the literature, obtained from high-throughput microscopy-based screens and predicted from primary sequence. To get a comprehensive view of the localization of a protein, it is thus necessary to consult multiple databases and prediction tools. To address this, we present the COMPARTMENTS resource, which integrates all sources listed above as well as the results of automatic text mining. The resource is automatically kept up to date with source databases, and all localization evidence is mapped onto common protein identifiers and Gene Ontology terms. We further assign confidence scores to the localization evidence to facilitate comparison of different types and sources of evidence. To further improve the comparability, we assign confidence scores based on the type and source of the localization evidence. Finally, we visualize the unified localization evidence for a protein on a schematic cell to provide a simple overview. Database URL: http://compartments.jensenlab.org.