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A roadmap for the functional annotation of protein families: a community perspective.
de Crécy-Lagard, Valérie; Amorin de Hegedus, Rocio; Arighi, Cecilia; Babor, Jill; Bateman, Alex; Blaby, Ian; Blaby-Haas, Crysten; Bridge, Alan J; Burley, Stephen K; Cleveland, Stacey; Colwell, Lucy J; Conesa, Ana; Dallago, Christian; Danchin, Antoine; de Waard, Anita; Deutschbauer, Adam; Dias, Raquel; Ding, Yousong; Fang, Gang; Friedberg, Iddo; Gerlt, John; Goldford, Joshua; Gorelik, Mark; Gyori, Benjamin M; Henry, Christopher; Hutinet, Geoffrey; Jaroch, Marshall; Karp, Peter D; Kondratova, Liudmyla; Lu, Zhiyong; Marchler-Bauer, Aron; Martin, Maria-Jesus; McWhite, Claire; Moghe, Gaurav D; Monaghan, Paul; Morgat, Anne; Mungall, Christopher J; Natale, Darren A; Nelson, William C; O'Donoghue, Seán; Orengo, Christine; O'Toole, Katherine H; Radivojac, Predrag; Reed, Colbie; Roberts, Richard J; Rodionov, Dmitri; Rodionova, Irina A; Rudolf, Jeffrey D; Saleh, Lana; Sheynkman, Gloria.
Affiliation
  • de Crécy-Lagard V; Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA.
  • Amorin de Hegedus R; Genetics Institute, University of Florida, Gainesville, FL 32611, USA.
  • Arighi C; Department of Computer and Information Sciences, University of Delaware, Newark, DE 19713, USA.
  • Babor J; Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA.
  • Bateman A; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.
  • Blaby I; US Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Blaby-Haas C; Biology Department, Brookhaven National Laboratory, Upton, NY 11973, USA.
  • Bridge AJ; Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva 4 CH-1211, Switzerland.
  • Burley SK; RCSB Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.
  • Cleveland S; Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA.
  • Colwell LJ; Departmenf of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
  • Conesa A; Spanish National Research Council, Institute for Integrative Systems Biology, Paterna, Valencia 46980, Spain.
  • Dallago C; TUM (Technical University of Munich) Department of Informatics, Bioinformatics & Computational Biology, i12, Boltzmannstr. 3, Garching/Munich 85748, Germany.
  • Danchin A; School of Biomedical Sciences, Li KaShing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, SAR Hong Kong 999077, China.
  • de Waard A; Research Collaboration Unit, Elsevier, Jericho, VT 05465, USA.
  • Deutschbauer A; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Dias R; Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA.
  • Ding Y; Department of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 32610, USA.
  • Fang G; NYU-Shanghai, Shanghai 200120, China.
  • Friedberg I; Department of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA.
  • Gerlt J; Institute for Genomic Biology and Departments of Biochemistry and Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
  • Goldford J; Physics of Living Systems, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
  • Gorelik M; Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA.
  • Gyori BM; Laboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA.
  • Henry C; Mathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA.
  • Hutinet G; Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA.
  • Jaroch M; Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA.
  • Karp PD; Bioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA.
  • Kondratova L; Genetics Institute, University of Florida, Gainesville, FL 32611, USA.
  • Lu Z; National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), 8600 Rockville Pike, Bethesda, MD 20817, USA.
  • Marchler-Bauer A; National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), 8600 Rockville Pike, Bethesda, MD 20817, USA.
  • Martin MJ; European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.
  • McWhite C; Lewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA.
  • Moghe GD; Plant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
  • Monaghan P; Department of Agricultural Education and Communication, University of Florida, Gainesville, FL 32611, USA.
  • Morgat A; Swiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva 4 CH-1211, Switzerland.
  • Mungall CJ; Environmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
  • Natale DA; Georgetown University Medical Center, Washington, DC 20007, USA.
  • Nelson WC; Biological Sciences Division, Pacific Northwest National Laboratories, Richland, WA 99354, USA.
  • O'Donoghue S; School of Biotechnology and Biomolecular Sciences, University of NSW, Sydney, NSW 2052, Australia.
  • Orengo C; Department of Structural and Molecular Biology, University College London, London WC1E 6BT, UK.
  • O'Toole KH; New England Biolabs, Ipswich, MA 01938, USA.
  • Radivojac P; Khoury College of Computer Sciences, Northeastern University, Boston, MA 02115, USA.
  • Reed C; Department of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA.
  • Roberts RJ; New England Biolabs, Ipswich, MA 01938, USA.
  • Rodionov D; Sanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
  • Rodionova IA; Department of Bioengineering, Division of Engineering, University of California at San Diego, La Jolla, CA 92093-0412, USA.
  • Rudolf JD; Department of Chemistry, University of Florida, Gainesville, FL 32611, USA.
  • Saleh L; New England Biolabs, Ipswich, MA 01938, USA.
  • Sheynkman G; Department of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.
Database (Oxford) ; 20222022 08 12.
Article in En | MEDLINE | ID: mdl-35961013
ABSTRACT
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.
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Proteins / Genomics Language: En Journal: Database (Oxford) Year: 2022 Document type: Article Affiliation country: Estados Unidos
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Full text: 1 Collection: 01-internacional Database: MEDLINE Main subject: Proteins / Genomics Language: En Journal: Database (Oxford) Year: 2022 Document type: Article Affiliation country: Estados Unidos