Complex Portal 2022: new curation frontiers

B.H.M. Meldal; L. Perfetto; C. Combe; T. Lubiana; J.V.F. Cavalcante; H. Bye-A-Jee; A. Waagmeester; N. Del-Toro; A. Shrivastava; E. Barrera; E. Wong; B. Mlecnik; G. Bindea; K. Panneerselvam; E. Willighagen; J. Rappsilber; P. Porras; H. Hermjakob; S. Orchard

doi:10.1093/nar/gkab991

Complex Portal 2022: new curation frontiers

B.H.M. Meldal, L. Perfetto, C. Combe, T. Lubiana, J.V.F. Cavalcante, H. Bye-A-Jee, A. Waagmeester, N. Del-Toro, A. Shrivastava, E. Barrera, E. Wong, B. Mlecnik, G. Bindea, K. Panneerselvam, E. Willighagen, J. Rappsilber, P. Porras, H. Hermjakob^*, S. Orchard^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › Academic › peer-review

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.

Original language	English
Pages (from-to)	D578-D586
Number of pages	9
Journal	Nucleic Acids Research
Volume	50
Issue number	D1
DOIs	https://doi.org/10.1093/nar/gkab991
Publication status	Published - 7 Jan 2022

Keywords

GENE ONTOLOGY
PROTEIN
CYTOSCAPE
TOOL

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10.1093/nar/gkab991Licence: CC BY

Cite this

Meldal, B. H. M., Perfetto, L., Combe, C., Lubiana, T., Cavalcante, J. V. F., Bye-A-Jee, H., Waagmeester, A., Del-Toro, N., Shrivastava, A., Barrera, E., Wong, E., Mlecnik, B., Bindea, G., Panneerselvam, K., Willighagen, E., Rappsilber, J., Porras, P., Hermjakob, H., & Orchard, S. (2022). Complex Portal 2022: new curation frontiers. Nucleic Acids Research, 50(D1), D578-D586. https://doi.org/10.1093/nar/gkab991

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title = "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.",

keywords = "GENE ONTOLOGY, PROTEIN, CYTOSCAPE, TOOL",

author = "B.H.M. Meldal and L. Perfetto and C. Combe and T. Lubiana and J.V.F. Cavalcante and H. Bye-A-Jee and A. Waagmeester and N. Del-Toro and A. Shrivastava and E. Barrera and E. Wong and B. Mlecnik and G. Bindea and K. Panneerselvam and E. Willighagen and J. Rappsilber and P. Porras and H. Hermjakob and S. Orchard",

note = "Funding Information: European Molecular Biology Laboratory, European Bioin-formatics Institute (EMBL-EBI); Open Targets [OTAR-044, OTAR-048]; National Eye Institute; National Human Genome Research Institute; National Heart, Lung, and Blood Institute; National Institute of Allergy and Infectious Diseases; National Institute of Diabetes and Digestive and Kidney Diseases; National Institute of General Medical Sciences; by National Cancer Institute; National Institute On Aging; National Institute of Mental Health of the National Institutes of Health [U24HG007822 to S.O., H.B.]; National Human Genome Research Institute [U41HG002273 to S.O., H.B.]; National Institute of General Medical Sciences [R01GM080646 to S.O., H.B., P20GM103446 to S.O., H.B.] (the content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health); Wellcome Trust [218294 to C.C, J.R.]; Wellcome Centre for Cell Biology is supported by core funding from the Wellcome Trust [203149]; INSERM [to G.B., B.M.]; S{\~a}o Paulo Research Foundation [2019/26284-1 to T.L.]; Alfred P. Sloan Foundation [G-2019-11458 to E.W.]; National Institute of General Medical Sciences [R01 GM089820 to A.W.]. Funding for open access charge: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI). Conflict of interest statement. None declared. Publisher Copyright: {\textcopyright} The Author(s) 2021.",

year = "2022",

month = jan,

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doi = "10.1093/nar/gkab991",

language = "English",

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Meldal, BHM, Perfetto, L, Combe, C, Lubiana, T, Cavalcante, JVF, Bye-A-Jee, H, Waagmeester, A, Del-Toro, N, Shrivastava, A, Barrera, E, Wong, E, Mlecnik, B, Bindea, G, Panneerselvam, K, Willighagen, E, Rappsilber, J, Porras, P, Hermjakob, H & Orchard, S 2022, 'Complex Portal 2022: new curation frontiers', Nucleic Acids Research, vol. 50, no. D1, pp. D578-D586. https://doi.org/10.1093/nar/gkab991

TY - JOUR

T1 - Complex Portal 2022: new curation frontiers

AU - Meldal, B.H.M.

AU - Perfetto, L.

AU - Combe, C.

AU - Lubiana, T.

AU - Cavalcante, J.V.F.

AU - Bye-A-Jee, H.

AU - Waagmeester, A.

AU - Del-Toro, N.

AU - Shrivastava, A.

AU - Barrera, E.

AU - Wong, E.

AU - Mlecnik, B.

AU - Bindea, G.

AU - Panneerselvam, K.

AU - Willighagen, E.

AU - Rappsilber, J.

AU - Porras, P.

AU - Hermjakob, H.

AU - Orchard, S.

N1 - Funding Information: European Molecular Biology Laboratory, European Bioin-formatics Institute (EMBL-EBI); Open Targets [OTAR-044, OTAR-048]; National Eye Institute; National Human Genome Research Institute; National Heart, Lung, and Blood Institute; National Institute of Allergy and Infectious Diseases; National Institute of Diabetes and Digestive and Kidney Diseases; National Institute of General Medical Sciences; by National Cancer Institute; National Institute On Aging; National Institute of Mental Health of the National Institutes of Health [U24HG007822 to S.O., H.B.]; National Human Genome Research Institute [U41HG002273 to S.O., H.B.]; National Institute of General Medical Sciences [R01GM080646 to S.O., H.B., P20GM103446 to S.O., H.B.] (the content is solely the responsibility of the authors and does not necessarily represent the official views of the National Institutes of Health); Wellcome Trust [218294 to C.C, J.R.]; Wellcome Centre for Cell Biology is supported by core funding from the Wellcome Trust [203149]; INSERM [to G.B., B.M.]; São Paulo Research Foundation [2019/26284-1 to T.L.]; Alfred P. Sloan Foundation [G-2019-11458 to E.W.]; National Institute of General Medical Sciences [R01 GM089820 to A.W.]. Funding for open access charge: European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI). Conflict of interest statement. None declared. Publisher Copyright: © The Author(s) 2021.

PY - 2022/1/7

Y1 - 2022/1/7

N2 - 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.

AB - 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.

KW - GENE ONTOLOGY

KW - PROTEIN

KW - CYTOSCAPE

KW - TOOL

U2 - 10.1093/nar/gkab991

DO - 10.1093/nar/gkab991

M3 - Article

C2 - 34718729

SN - 0305-1048

VL - 50

SP - D578-D586

JO - Nucleic Acids Research

JF - Nucleic Acids Research

IS - D1

ER -