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Complex Portal 2022: new curation frontiers.

Birgit H M Meldal1, Livia Perfetto1,2, Colin Combe3

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Summary
This summary is machine-generated.

The Complex Portal database now includes a draft Escherichia coli complexome and over 1100 human macromolecular complexes, enhancing viral and immune system research. Data is now openly licensed (CC0) to encourage reuse and integration with semantic web tools.

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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.