A roadmap for the functional annotation of protein families: a community perspective
Valérie De Crecy-Lagard
(1)
,
Rocio Amorin De Hegedus
(1)
,
Cecilia Arighi
(2)
,
Jill Babor
(1)
,
Alex Bateman
(3)
,
Iyan Blaby
(4)
,
Crysten Blaby-Haas
(5)
,
Alen J. Bridge
(6)
,
Stephen K. Burley
(7)
,
Stacey Cleveland
(1)
,
Lucy J. Colwell
(8)
,
Ana Conesa
(9, 10)
,
Christian Dallago
(11)
,
Antoine Danchin
(12)
,
Anita De Waard
(13)
,
Adam Deutschbauer
(14, 4)
,
Raquel Dias
(1)
,
Yousong Ding
(1)
,
Gang Fang
(15)
,
Iddo Friedberg
(16)
,
John Gerlt
(17)
,
Joshua Goldford
(18)
,
Mark Gorelik
(1)
,
Benjamin M. Gyori
(19)
,
Christopher Henry
(20)
,
Geoffroy Hutinet
(1)
,
Marshall Jaroch
(1)
,
Peter D. Karp
(21)
,
Liudmyla Kondratova
(1)
,
Zhiyong Lu
(22)
,
Aron Marchler-Bauer
(23, 22)
,
Maria-Jesus Martin
(3)
,
Claire Mcwhite
(24)
,
Gaurav D. Moghe
(25)
,
Paul Monaghan
(1)
,
Anne Morgat
(26)
,
Christopher J. Mungall
(27)
,
Darren A. Natale
(28)
,
William C. Nelson
(29)
,
Seán O'Donoghue
(30)
,
Christine Orengo
(31)
,
Katherine H. O'Toole
(32)
,
Pedrag Radivojac
(33)
,
Colbie Reed
(1)
,
Richard J. Roberts
(32)
,
Dimitri Rodionov
(34)
,
Irina A. Rodionova
(34, 35)
,
Jeffey D. Rudolf
(1)
,
Lana Saleh
(32)
,
Gloria Sheynkman
(36)
,
Françoise Thibaud-Nissen
(22)
,
Paul D. Thomas
(37)
,
Peter Uetz
(38)
,
David Vallenet
(39)
,
Erika Watson Carter
(1)
,
Peter R. Weigele
(32)
,
Valerie Wood
(8)
,
Elisha M. Wood-Charlson
(27)
,
Jin Xu
(40, 1)
1
UF -
University of Florida [Gainesville]
2 CIS - Department of Computer and Information Sciences [Newark]
3 EMBL-EBI - European Bioinformatics Institute [Hinxton]
4 LBNL - Lawrence Berkeley National Laboratory [Berkeley]
5 BNL - Brookhaven National Laboratory [Upton, NY]
6 Swiss-Prot Group
7 RU - Rutgers, The State University of New Jersey [New Brunswick]
8 CAM - University of Cambridge [UK]
9 i2sysbio - Institute for Integrative Systems Biology [Valencia]
10 CSIC - Spanish National Research Council [Santiago de Compostela]
11 TUM - Technische Universität Munchen - Technical University Munich - Université Technique de Munich
12 School of Biomedical Sciences
13 Elsevier
14 UC Berkeley - University of California [Berkeley]
15 NYU Shanghai
16 ISU - Iowa State University
17 UIUC - University of Illinois at Urbana-Champaign [Urbana]
18 MIT - Massachusetts Institute of Technology
19 HMS - Harvard Medical School [Boston]
20 MCS - Mathematics and Computer Science Division [ANL]
21 SRI International
22 NCBI - National Center for Biotechnology Information
23 NIH - National Institutes of Health [Bethesda, MD, USA]
24 Lewis-Sigler Institute for Integrative Genomics
25 School of Integrative Plant Science [CALS]
26 SIB - Swiss Institute of Bioinformatics [Genève]
27 EGSB - Environmental Genomics and Systems Biology Division [LBNL Berkeley]
28 Georgetown University Medical Center
29 PNNL - Pacific Northwest National Laboratory
30 UNSW - University of New South Wales [Sydney]
31 UCL - University College of London [London]
32 New England Biolabs
33 Khoury College of Computer Sciences [Boston]
34 Sanford Burnham Prebys Medical Discovery Institute
35 UC San Diego - University of California [San Diego]
36 University of Virginia
37 USC - University of Southern California
38 VCU - Virginia Commonwealth University
39 LABGeM - Analyse Bio-Informatique pour la Génomique et le Métabolisme
40 Anhui Institute of Optics and Fine Mechanics
2 CIS - Department of Computer and Information Sciences [Newark]
3 EMBL-EBI - European Bioinformatics Institute [Hinxton]
4 LBNL - Lawrence Berkeley National Laboratory [Berkeley]
5 BNL - Brookhaven National Laboratory [Upton, NY]
6 Swiss-Prot Group
7 RU - Rutgers, The State University of New Jersey [New Brunswick]
8 CAM - University of Cambridge [UK]
9 i2sysbio - Institute for Integrative Systems Biology [Valencia]
10 CSIC - Spanish National Research Council [Santiago de Compostela]
11 TUM - Technische Universität Munchen - Technical University Munich - Université Technique de Munich
12 School of Biomedical Sciences
13 Elsevier
14 UC Berkeley - University of California [Berkeley]
15 NYU Shanghai
16 ISU - Iowa State University
17 UIUC - University of Illinois at Urbana-Champaign [Urbana]
18 MIT - Massachusetts Institute of Technology
19 HMS - Harvard Medical School [Boston]
20 MCS - Mathematics and Computer Science Division [ANL]
21 SRI International
22 NCBI - National Center for Biotechnology Information
23 NIH - National Institutes of Health [Bethesda, MD, USA]
24 Lewis-Sigler Institute for Integrative Genomics
25 School of Integrative Plant Science [CALS]
26 SIB - Swiss Institute of Bioinformatics [Genève]
27 EGSB - Environmental Genomics and Systems Biology Division [LBNL Berkeley]
28 Georgetown University Medical Center
29 PNNL - Pacific Northwest National Laboratory
30 UNSW - University of New South Wales [Sydney]
31 UCL - University College of London [London]
32 New England Biolabs
33 Khoury College of Computer Sciences [Boston]
34 Sanford Burnham Prebys Medical Discovery Institute
35 UC San Diego - University of California [San Diego]
36 University of Virginia
37 USC - University of Southern California
38 VCU - Virginia Commonwealth University
39 LABGeM - Analyse Bio-Informatique pour la Génomique et le Métabolisme
40 Anhui Institute of Optics and Fine Mechanics
Antoine Danchin
- Fonction : Auteur
- PersonId : 21434
- IdHAL : adanchin
- ORCID : 0000-0002-6350-5001
- IdRef : 026810441
David Vallenet
- Fonction : Auteur
- PersonId : 800108
- IdHAL : david-vallenet
- ORCID : 0000-0001-6648-0332
- IdRef : 114897573
Résumé
Over the last 25 years, biology has entered the genomic era and is becoming a science of ‘big data’. Most interpretations of genomic analyses rely on accurate functional annotations of the proteins encoded by more than 500 000 genomes sequenced to date. By different estimates, only half the predicted sequenced proteins carry an accurate functional annotation, and this percentage varies drastically between different organismal lineages. Such a large gap in knowledge hampers all aspects of biological enterprise and, thereby, is standing in the way of genomic biology reaching its full potential. A brainstorming meeting to address this issue funded by the National Science Foundation was held during 3–4 February 2022. Bringing together data scientists, biocurators, computational biologists and experimentalists within the same venue allowed for a comprehensive assessment of the current state of functional annotations of protein families. Further, major issues that were obstructing the field were identified and discussed, which ultimately allowed for the proposal of solutions on how to move forward.
Domaines
Sciences du Vivant [q-bio]
Origine : Publication financée par une institution