Complex Portal 2022: new curation frontiers

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.

The 2022Nucleic Acids Researchdatabase issue and the online molecular biology database collection

“…Elsewhere, an Update paper from CAZy ( 51 ), the database of carbohydrate-active enzymes, reports significant increases in numbers of enzyme families alongside interface improvements including Krona charts ( 52 ) for taxonomic distributions of families. Finally, sister EBI resources for macromolecular interactions IntAct ( 53 ) and Complex Portal ( 54 ) each contribute an Update. IntAct has more than doubled in size since its previous publication and captures diverse information on binary molecular interactions, including a SARS-CoV-2 interactome, in particularly clean and appealing visualisations.…”

Composition structures and biologically meaningful logics: plausibility and relevance in bipartite models of gene regulation

“…First, we obtained a list of 1325 macromolecular complexes in H. sapiens from the EBI Complex Portal database [55], and the list of 1639 human TFs provided by Lambert et al [56] (see http://humantfs.ccbr.utoronto.ca/). Among the 1639 human TFs, we selected only those TFs that were reviewed in the SWISS-PROT protein database, resulting in a list of 1617 human TFs that was used for further analysis.…”

“…First, we obtained a list of 1325 macromolecular complexes in H. sapiens from the EBI Complex Portal database [55], and the list of 1639 human TFs provided by Lambert et al [56] (see http://humantfs.ccbr. utoronto.ca/).…”

The European Bioinformatics Institute (EMBL-EBI) in 2021

“…All EMBL-EBI data resources are continuously updated to ensure that they are relevant for the research community. EMBL-EBI databases that have had major updates are detailed in articles elsewhere in this issue of Nucleic Acids Research and include Ensembl ( 8 ), Ensembl Genomes ( 9 ), the Ensembl COVID-19 Browser ( 10 ), the European Variation Archive (EVA) ( 11 ), the European Genome-phenome Archive (EGA) ( 12 ), Expression Atlas ( 13 ), Complex Portal ( 14 ), IntAct ( 15 ), Reactome ( 16 ), and PRIDE ( 17 ). Here, we highlight some of the major developments that have been carried out over the last year in a number of other resources.…”