Searching and Extracting Data from the EMBL-EBI Complex Portal

  • Birgit H.  M. MeldalEmail author
  • Sandra Orchard
Part of the Methods in Molecular Biology book series (MIMB, volume 1764)


The Complex Portal ( is an encyclopedia of macromolecular complexes. Complexes are assigned unique, stable IDs, are species specific, and list all participating members with links to an appropriate reference database (UniProtKB, ChEBI, RNAcentral). Each complex is annotated extensively with its functions, properties, structure, stoichiometry, tissue expression profile, and subcellular location. Links to domain-specific databases allow the user to access additional information and enable data searching and filtering. Complexes can be saved and downloaded in PSI-MI XML, MI-JSON, and tab-delimited formats.

Key words

Complex portal Protein-protein interactions Database Bioinformatics Protein function Protein structure Molecular pathways 



This work was supported by European Molecular Biology Laboratories core funding, BBSRC Midas Grant (BB/L024179/1), and the Wellcome Trust (WT101477MA) (Complex Viewer, as part of PRIDE Atlas). We thank Mila Rodrigues and Luana Perfetto for their curation efforts, Maximilian Koch for developing the website, Xavier Watkins and Sangya Pundir for their user experience design expertise, and Colin Combe for writing ComplexViewer for this project.


  1. 1.
    Meldal BHM, Forner-Martinez O, Costanzo MC, Dana J, Demeter J, Dumousseau M, Dwight SS, Gaulton A, Licata L, Melidoni AN, Ricard-Blum S, Roechert B, Skyzypek MS, Tiwari M, Velankar S, Wong ED, Hermjakob H, Orchard S (2015) The complex portal–an encyclopaedia of macromolecular complexes. Nucleic Acids Res 43(Database issue):D479–D484. CrossRefPubMedGoogle Scholar
  2. 2.
    The UniProt Consortium (2017) UniProt: the universal protein knowledgebase. Nucleic Acids Res 45(D1):D158–D169. CrossRefGoogle Scholar
  3. 3.
    Hastings J, Owen G, Dekker A, Ennis M, Kale N, Muthukrishnan V, Turner S, Swainston N, Mendes P, Steinbeck C (2016) ChEBI in 2016: improved services and an expanding collection of metabolites. Nucleic Acids Res 44(D1):D1214–D1219. CrossRefPubMedGoogle Scholar
  4. 4.
    The RNAcentral Consortium (2017) RNAcentral: a comprehensive database of non-coding RNA sequences. Nucleic Acids Res 45(D1):D128–D134. CrossRefGoogle Scholar
  5. 5.
    Ashburner M, Ball CA, Blake JA, Botstein D, Butler H, Cherry JM, Davis AP, Dolinski K, Dwight SS, Eppig JT, Harris MA, Hill DP, Issel-Tarver L, Kasarskis A, Lewis S, Matese JC, Richardson JE, Ringwald M, Rubin GM, Sherlock G (2000) Gene ontology: tool for the unification of biology. The gene ontology consortium. Nat Genet 25(1):25–29CrossRefPubMedPubMedCentralGoogle Scholar
  6. 6.
    Gene Ontology Consortium (2015) Gene ontology consortium: going forward. Nucleic Acids Res 43(Database issue):D1049–D1056. CrossRefGoogle Scholar
  7. 7.
    Bento AP, Gaulton A, Hersey A, Bellis LJ, Chambers J, Davies M, Krüger FA, Light Y, Mak L, McGlinchey S, Nowotka M, Papadatos G, Santos R, Overington JP (2014) The ChEMBL bioactivity database: an update. Nucleic Acids Res 42(Database issue):D1083–D1090. CrossRefPubMedGoogle Scholar
  8. 8.
    Lawson CL, Patwardhan A, Baker ML, Hryc C, Garcia ES, Hudson BP, Lagerstedt I, Ludtke SJ, Pintilie G, Sala R, Westbrook JD, Berman HM, Kleywegt GJ, Chiu W (2016) EMDataBank unified data resource for 3DEM. Nucleic Acids Res 44(D1):D396–D403. CrossRefPubMedGoogle Scholar
  9. 9.
    Burley SK, Berman HM, Kleywegt GJ, Markley JL, Nakamura H, Velankar S (2017) Protein data bank (PDB): the single global macromolecular structure archive. Methods Mol Biol 2017(1607):627–641. CrossRefGoogle Scholar
  10. 10.
    Fleischmann A, Darsow M, Degtyarenko K, Fleischmann W, Boyce S, Axelsen KB, Bairoch A, Schomburg D, Tipton KF, Apweiler R (2004) IntEnz, the integrated relational enzyme database. Nucleic Acids Res 32(Database issue):D434–D437CrossRefPubMedPubMedCentralGoogle Scholar
  11. 11.
    Launay G, Salza R, Multedo D, Thierry-Mieg N, Ricard-Blum S (2015) MatrixDB, the extracellular matrix interaction database: updated content, a new navigator and expanded functionalities. Nucleic Acids Res 43(Database issue):D321–D327. CrossRefPubMedGoogle Scholar
  12. 12.
    Fabregat A, Sidiropoulos K, Garapati P, Gillespie M, Hausmann K, Haw R, Jassal B, Jupe S, Korninger F, McKay S, Matthews L, May B, Milacic M, Rothfels K, Shamovsky V, Webber M, Weiser J, Williams M, Wu G, Stein L, Hermjakob H, D'Eustachio P (2016) The reactome pathway knowledgebase. Nucleic Acids Res 44(D1):D481–D487. CrossRefPubMedGoogle Scholar
  13. 13.
    Orchard S, Kerrien S, Abbani S, Aranda B, Bhate J, Bidwell S, Bridge A, Briganti L, Brinkman FS, Cesareni G, Chatr-aryamontri A, Chautard E, Chen C, Dumousseau M, Goll J, Hancock RE, Hannick LI, Jurisica I, Khadake J, Lynn DJ, Mahadevan U, Perfetto L, Raghunath A, Ricard-Blum S, Roechert B, Salwinski L, Stümpflen V, Tyers M, Uetz P, Xenarios I, Hermjakob H (2012) Protein interaction data curation: the international molecular exchange (IMEx) consortium. Nat Methods 9(4):345–350. CrossRefPubMedPubMedCentralGoogle Scholar
  14. 14.
    Chibucos MC, Mungall CJ, Balakrishnan R, Christie KR, Huntley RP, White O, Blake JA, Lewis SE, Giglio M (2014) Standardized description of scientific evidence using the evidence ontology (ECO). Database (Oxford) 2014:bau075. CrossRefGoogle Scholar
  15. 15.
    Combe CW, Sivade MD, Hermjakob H, Heimbach J, Meldal BHM, Micklem G, Orchard S, Rappsilber J (2017) ComplexViewer: visualization of curated macromolecular complexes. Bioinformatics. 33(22):3673–3675. PMID:29036573. CrossRefPubMedPubMedCentralGoogle Scholar
  16. 16.
    Malone J, Holloway E, Adamusiak T, Kapushesky M, Zheng J, Kolesnikov N, Zhukova A, Brazma A, Parkinson H (2010) Modeling sample variables with an experimental factor ontology. Bioinformatics 26(8):1112–1118. CrossRefPubMedPubMedCentralGoogle Scholar
  17. 17.
  18. 18.
    Köhler S, Vasilevsky NA, Engelstad M, Foster E, McMurry J, Aymé S, Baynam G, Bello SM, Boerkoel CF, Boycott KM, Brudno M, Buske OJ, Chinnery PF, Cipriani V, Connell LE, Dawkins HJ, DeMare LE, Devereau AD, de Vries BB, Firth HV, Freson K, Greene D, Hamosh A, Helbig I, Hum C, Jähn JA, James R, Krause R, F Laulederkind SJ, Lochmüller H, Lyon GJ, Ogishima S, Olry A, Ouwehand WH, Pontikos N, Rath A, Schaefer F, Scott RH, Segal M, Sergouniotis PI, Sever R, Smith CL, Straub V, Thompson R, Turner C, Turro E, Veltman MW, Vulliamy T, Yu J, von Ziegenweidt J, Zankl A, Züchner S, Zemojtel T, Jacobsen JO, Groza T, Smedley D, Mungall CJ, Haendel M, Robinson PN (2017) The human phenotype ontology in 2017. Nucleic Acids Res 45(D1):D865–D876. CrossRefPubMedGoogle Scholar
  19. 19.
    Europe PMC Consortium (2015) Europe PMC: a full-text literature database for the life sciences and platform for innovation. Nucleic Acids Res 43(Database issue):D1042–D1048. CrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.European Molecular Biology LaboratoriesEuropean Bioinformatics Institute (EMBL-EBI)CambridgeUK

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