ArticleDatabase : the journal of biological databases and curation2022
A roadmap for the functional annotation of protein families: a community perspective.
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Article in Database : the journal of biological databases and curation, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 39 papers.
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39 citing papers in PubMed, 60 citations in OpenAlex.
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Authors and funding
59 authors at 20 institutions in 9 countries.
Valérie de Crécy-LagardDepartment of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA.ORCID 0000-0002-9955-3785
Rocio Amorin de HegedusGenetics Institute, University of Florida, Gainesville, FL 32611, USA.
Cecilia ArighiDepartment of Computer and Information Sciences, University of Delaware, Newark, DE 19713, USA.ORCID 0000-0002-0803-4817
Jill BaborDepartment of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA.
Alex BatemanEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.ORCID 0000-0002-6982-4660
Ian BlabyUS Department of Energy Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.ORCID 0000-0002-1631-3154
Crysten Blaby-HaasBiology Department, Brookhaven National Laboratory, Upton, NY 11973, USA.
Alan J BridgeSwiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva 4 CH-1211, Switzerland.ORCID 0000-0003-2148-9135
Stephen K BurleyRCSB Protein Data Bank, Institute for Quantitative Biomedicine, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA.ORCID 0000-0002-2487-9713
Stacey ClevelandDepartment of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA.
Lucy J ColwellDepartmenf of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW, UK.
Ana ConesaSpanish National Research Council, Institute for Integrative Systems Biology, Paterna, Valencia 46980, Spain.ORCID 0000-0001-9597-311X
Christian DallagoTUM (Technical University of Munich) Department of Informatics, Bioinformatics & Computational Biology, i12, Boltzmannstr. 3, Garching/Munich 85748, Germany.ORCID 0000-0003-4650-6181
Antoine DanchinSchool of Biomedical Sciences, Li KaShing Faculty of Medicine, The University of Hong Kong, 21 Sassoon Road, Pokfulam, SAR Hong Kong 999077, China.ORCID 0000-0002-6350-5001
Anita de WaardResearch Collaboration Unit, Elsevier, Jericho, VT 05465, USA.ORCID 0000-0002-9034-4119
Adam DeutschbauerEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Raquel DiasDepartment of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA.
Yousong DingDepartment of Medicinal Chemistry, Center for Natural Products, Drug Discovery and Development, University of Florida, Gainesville, FL 32610, USA.ORCID 0000-0001-8610-0659
Gang FangNYU-Shanghai, Shanghai 200120, China.
Iddo FriedbergDepartment of Veterinary Microbiology and Preventive Medicine, Iowa State University, Ames, IA 50011, USA.ORCID 0000-0002-1789-8000
John GerltInstitute for Genomic Biology and Departments of Biochemistry and Chemistry, University of Illinois at Urbana-Champaign, Urbana, IL 61801, USA.
Joshua GoldfordPhysics of Living Systems, Massachusetts Institute of Technology, Cambridge, MA 02139, USA.
Mark GorelikDepartment of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA.
Benjamin M GyoriLaboratory of Systems Pharmacology, Harvard Medical School, Boston, MA 02115, USA.ORCID 0000-0001-9439-5346
Christopher HenryMathematics and Computer Science Division, Argonne National Laboratory, Argonne, IL 60439, USA.
Geoffrey HutinetDepartment of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA.
Marshall JarochDepartment of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA.
Peter D KarpBioinformatics Research Group, SRI International, Menlo Park, CA 94025, USA.
Liudmyla KondratovaGenetics Institute, University of Florida, Gainesville, FL 32611, USA.
Zhiyong LuNational Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), 8600 Rockville Pike, Bethesda, MD 20817, USA.ORCID 0000-0001-9998-916X
Aron Marchler-BauerNational Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), 8600 Rockville Pike, Bethesda, MD 20817, USA.
Maria-Jesus MartinEuropean Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Hinxton CB10 1SD, UK.
Claire McWhiteLewis-Sigler Institute for Integrative Genomics, Princeton University, Princeton, NJ 08540, USA.
Gaurav D MoghePlant Biology Section, School of Integrative Plant Science, Cornell University, Ithaca, NY 14853, USA.
Paul MonaghanDepartment of Agricultural Education and Communication, University of Florida, Gainesville, FL 32611, USA.
Anne MorgatSwiss-Prot group, SIB Swiss Institute of Bioinformatics, Centre Medical Universitaire, Geneva 4 CH-1211, Switzerland.
Christopher J MungallEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.ORCID 0000-0002-6601-2165
Darren A NataleGeorgetown University Medical Center, Washington, DC 20007, USA.
William C NelsonBiological Sciences Division, Pacific Northwest National Laboratories, Richland, WA 99354, USA.
Seán O'DonoghueSchool of Biotechnology and Biomolecular Sciences, University of NSW, Sydney, NSW 2052, Australia.
Christine OrengoDepartment of Structural and Molecular Biology, University College London, London WC1E 6BT, UK.
Katherine H O'TooleNew England Biolabs, Ipswich, MA 01938, USA.
Predrag RadivojacKhoury College of Computer Sciences, Northeastern University, Boston, MA 02115, USA.ORCID 0000-0002-6769-0793
Colbie ReedDepartment of Microbiology and Cell Sciences, University of Florida, Gainesville, FL 32611, USA.
Richard J RobertsNew England Biolabs, Ipswich, MA 01938, USA.
Dmitri RodionovSanford Burnham Prebys Medical Discovery Institute, La Jolla, CA 92037, USA.
Irina A RodionovaDepartment of Bioengineering, Division of Engineering, University of California at San Diego, La Jolla, CA 92093-0412, USA.ORCID 0000-0002-6500-2758
Jeffrey D RudolfDepartment of Chemistry, University of Florida, Gainesville, FL 32611, USA.
Lana SalehNew England Biolabs, Ipswich, MA 01938, USA.
Gloria SheynkmanDepartment of Molecular Physiology and Biological Physics, University of Virginia, Charlottesville, VA, USA.ORCID 0000-0002-4223-9947
Francoise Thibaud-NissenNational Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), 8600 Rockville Pike, Bethesda, MD 20817, USA.
Paul D ThomasDepartment of Population and Public Health Sciences, University of Southern California, Los Angeles, CA 90033, USA.ORCID 0000-0002-9074-3507
Peter UetzCenter for Biological Data Science, Virginia Commonwealth University, Richmond, VA 23284, USA.
David VallenetLABGeM, Génomique Métabolique, CEA, Genoscope, Institut François Jacob, Université d'Évry, Université Paris-Saclay, CNRS, Evry 91057, France.ORCID 0000-0001-6648-0332
Erica Watson CarterDepartment of Plant Pathology, University of Florida Citrus Research and Education Center, 700 Experiment Station Rd., Lake Alfred, FL 33850, USA.
Peter R WeigeleNew England Biolabs, Ipswich, MA 01938, USA.ORCID 0000-0003-3696-4541
Valerie WoodDepartment of Biochemistry, University of Cambridge, Cambridge CB2 1GA, UK.ORCID 0000-0001-6330-7526
Elisha M Wood-CharlsonEnvironmental Genomics and Systems Biology Division, Lawrence Berkeley National Laboratory, Berkeley, CA 94720, USA.
Jin XuDepartment of Plant Pathology, University of Florida Citrus Research and Education Center, 700 Experiment Station Rd., Lake Alfred, FL 33850, USA.
University of Florida · USLawrence Berkeley National Laboratory · USNew England Biolabs (United States) · USNational Institutes of Health · USEuropean Bioinformatics Institute · GBFlorida Department of Citrus · USSanford Burnham Prebys Medical Discovery Institute · USSIB Swiss Institute of Bioinformatics · CHUniversity of Cambridge · GBArgonne National Laboratory · USBrookhaven National Laboratory · USCentre National de la Recherche Scientifique · FRConsejo Superior de Investigaciones Científicas · ESCornell University · USGeorgetown University · USHarvard University · USInstitute of Structural and Molecular Biology · GBIowa State University · USLiving Systems (United States) · USNew York University Shanghai · CN
Funding
Women's Oncology Program - WONP30CA044579 · NCI · UNIVERSITY OF VIRGINIA CHARLOTTESVILLE · PI Dina Gould Halme · 1987 to 2026
$72.1MUncovering the functional diversification mechanisms of transcription factor isoforms involved in stem cell differentiationR35GM142647 · NIGMS · UNIVERSITY OF VIRGINIA · PI SHEYNKMAN, GLORIA · 2021 to 2025
$2.1MQuery Log Analysis for Improving User Access to NCBI Web ServicesZIALM010022 · NLM · NATIONAL LIBRARY OF MEDICINE · PI LU, ZHIYONG · 2022 to 2022
$1.8MNCI NIH HHS P30 CA044579NIGMS NIH HHS R35 GM142647
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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GenomicsProteinsBase SequenceComputational BiologyGenomeMolecular Sequence AnnotationProteins
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