Complex Portal 2022: new curation frontiers.

Birgit H M Meldal,Pablo Porras,Kalpana Panneerselvam,Henning Hermjakob,Anjali Shrivastava,Juri Rappsilber,Tiago Lubiana,Livia Perfetto,Sandra Orchard,Egon Willighagen,Colin Combe,Gabriela Bindea,João Vitor Ferreira Cavalcante,Bernhard Mlecnik,Elisabeth Barrera,Hema Bye-A-Jee,Noemi Del-Toro,Edith Wong,Andra Waagmeester

doi:10.1093/nar/gkab991

Abstract

The Complex Portal (www.ebi.ac.uk/complexportal) is a manually curated, encyclopaedic database of macromolecular complexes with known function from a range of model organisms. It summarizes complex composition, topology and function along with links to a large range of domain-specific resources (i.e. wwPDB, EMDB and Reactome). Since the last update in 2019, we have produced a first draft complexome for Escherichia coli, maintained and updated that of Saccharomyces cerevisiae, added over 40 coronavirus complexes and increased the human complexome to over 1100 complexes that include approximately 200 complexes that act as targets for viral proteins or are part of the immune system. The display of protein features in ComplexViewer has been improved and the participant table is now colour-coordinated with the nodes in ComplexViewer. Community collaboration has expanded, for example by contributing to an analysis of putative transcription cofactors and providing data accessible to semantic web tools through Wikidata which is now populated with manually curated Complex Portal content through a new bot. Our data license is now CC0 to encourage data reuse. Users are encouraged to get in touch, provide us with feedback and send curation requests through the ‘Support’ link.

Highlights

Protein complexes, stable functional assemblies consisting of two or more associated polypeptide chains, are responsible for driving and regulating many cellular processes
By combining inferred complexes from hu.MAP 2.0 [32], curated complexes from CORUM [33] and curated physical interaction data from IntAct [this volume NAR paper] and BioGrid [34] with a selected set of transcription-related Gene Ontology terms we have identified more than 1500 putative transcription cofactors. 415 of these are already participants of complexes in Complex Portal, and the remaining proteins will be curated into Complex Portal if they are identified as components of complexes
With the completion of the draft complexomes for S. cerevisiae and E. coli we are fully focusing on completing a first draft of the human complexome

Summary

Introduction

Stable functional assemblies consisting of two or more associated polypeptide chains, are responsible for driving and regulating many cellular processes. We have made updates to the ComplexTab format, adding a ‘UniProt ID-only’ column that lists the UniProt accession numbers (and their stoichiometry) for the protein participants of complexes, including those that are part of subcomplexes and molecule sets.

Results

Conclusion