Complex Portal 2022: new curation frontiers

Area of Science:

• Biochemistry
• Molecular Biology
• Bioinformatics

Background:

• The Complex Portal is a manually curated database detailing macromolecular complex composition, topology, and function across model organisms.
• It serves as a central hub, linking to essential resources like wwPDB, EMDB, and Reactome.

Purpose of the Study:

• To update and expand the Complex Portal with new data, including a draft complexome for Escherichia coli and an increased number of human complexes.
• To enhance data visualization and accessibility, including improvements to ComplexViewer and integration with semantic web tools via Wikidata.
• To promote data reuse through a new CC0 data license and encourage community feedback and contributions.

Main Methods:

• Manual curation of macromolecular complex data from various model organisms.
• Development of a draft complexome for Escherichia coli.
• Expansion of the human complexome, focusing on viral protein targets and immune system components.
• Enhancements to the ComplexViewer interface for improved protein feature display and participant table visualization.
• Integration with Wikidata for semantic web accessibility through a new bot.
• Adoption of a Creative Commons Zero (CC0) data license.

Main Results:

• A first draft complexome for Escherichia coli has been generated.
• The Saccharomyces cerevisiae complexome has been maintained and updated.
• Over 40 coronavirus complexes and more than 1100 human complexes have been added.
• The human complexome now includes approximately 200 complexes relevant to viral interactions or immune system functions.
• ComplexViewer display and participant table coordination have been improved.
• Community contributions have expanded, including analysis of transcription cofactors and Wikidata population.
• The Complex Portal data is now available under a CC0 license.

Conclusions:

• The Complex Portal continues to be a vital, expanding resource for macromolecular complex information.
• Recent updates significantly enhance coverage of bacterial, viral, and human systems, particularly for immunology and virology research.
• Improved data visualization, accessibility via semantic web tools, and an open data license foster broader data reuse and community engagement.