Complex Portal 2018: extended content and enhanced visualization tools for macromolecular complexes

By B. Meldal, Hema Bye-A-Jee, L. Gajdos, Zuzana Hammerová, Aneta Horácková, F. Melicher, L. Perfetto, Daniel Pokorný, M. Rodríguez-López, Alzbeta Türková and 8 more. 2018

120 citations recorded by the source corpus.

Abstract The Complex Portal (www.ebi.ac.uk/complexportal) is a manually curated, encyclopaedic database that collates and summarizes information on stable, macromolecular complexes of known function. It captures complex composition, topology and function and links out to a large range of domain-specific resources that hold more detailed data, such as PDB or Reactome. We have made several significant improvements since our last update, including improving compliance to the FAIR data principles by providing complex-specific, stable identifiers that include versioning. Protein complexes are now available from 20 species for download in standards-compliant formats such as PSI-XML, MI-JSON and ComplexTAB or can be accessed via an improved REST API. A component-based JS front-end framework has been implemented to drive a new website and this has allowed the use of APIs from linked services to import and visualize information such as the 3D structure of protein complexes, its role in reactions and pathways and the co-expression of complex components in the tissues of multi-cellular organisms. A first draft of the complete complexome of Saccharomyces cerevisiae is now available to browse and download.

Subfields: Information Systems, Information Systems and Management, Molecular Biology

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In Molecular Biology

Citations in the corpus

The Gene Ontology Resource: 20 years and still GOing strong (2018, background): “GO imports subsets of these external ontologies that include information about anatomical structures, cell types, chemicals and taxonomic groupings: Uberon (14), Protein Ontology (15), Plant Ontology (16) (23) and MetaCyc (24).”
WikiPathways: connecting communities (2020, methodology): “Recently, mappings to the EBI Complex Portal (27) and IUPHAR/BPS Guide to PHARMACOLOGY (28) have been added to the identifier mapping framework BridgeDb (29) which is integrated with WikiPathways.”
The STRING database in 2021: customizable protein–protein networks, and functional characterization of user-uploaded gene/measurement sets (2020, background): “These include pathways annotated in KEGG (41), Reactome (42) and Meta-Cyc (43), as well as protein complexes defined at the EBI Complex Portal (44) or by the Gene Ontology Consortium (45).”