This award, given biennial (next award will be in 2023), recognizes a person who has made exceptional contributions to the field of biocuration. The recipient is required to present a 30 minute talk at an International Biocuration Conference, with expenses paid by the ISB, or at a virtual Biocuration seminar. The nominee does not have to be an active ISB member, as the award will include ISB membership for 1 year
Voting will be open from 26 May – 6 June 2023
The list of nominees is below. Scroll down for detailed descriptions.
- Judith A. Blake, The Jackson Laboratory, ME USA (emeritus)
- Victoria Blake, Montana State University, USA
- Peter D’Eustachio, NYU Grossman School of Medicine, New York, NY, USA
- Pascale Gaudet, Swiss Institute of Bioinformatics, Switzerland
- Gloria I. Giraldo-Calderon, Eck Institute for Global Health, University Notre Dame, IN, USA
- Sandra Orchard, EBI, Hinxton, Cambridge, UK
- Jennifer R. Smith, Rat Genome Database at Medical College of Wisconsin, Milwaukee, WI USA
Judith A. Blake, The Jackson Laboratory, ME USA (emeritus)
It is our pleasure to nominate Dr. Judith A Blake for the ISB ‘Exceptional Contribution to Biocuration – Lifetime Achievement Award’. Dr. Blake spent most of her career at the Jackson Laboratory (JAX) in Bar Harbor, Maine, where she was a Principal Investigator for the Mouse Genome Informatics project that includes the Mouse Genome Database for the laboratory mouse providing integrated genetic, genomic, and functional data for the study of human diseases. At JAX, she nurtured many young scientists as well as summer research students each year.
In 1998, she and colleagues at other model organism databases (MODs) founded the Gene Ontology Consortium (GOC) as they recognized the need to create structured controlled vocabularies for molecular biology to allow comparison of data across different genomes and species. Dr. Blake was a PI of the GOC from its inception until her retirement in 2021. The GOC is the primary resource for curation and standardization of functional information for all life forms, providing the ability to computational investigate molecular biology information.
With the recent formation of the Alliance of Genome Resources and as one of the PIs of that group, Dr. Blake co-lead the Orthology Working Group at the Alliance of Genome Resources, developing criteria and integrating algorithms for the selection of orthology sets. Working with the Quest for Orthologs group, orthology specialists from Harvard’s DIOPT group, and representatives from numerous MODs, she helped spearhead the development of the Alliance orthology resources that are essential for data integration across organisms.
Dr. Blake managed the Nomenclature Coordinator for the International Committee on Standardized Genetic Nomenclature for Mice. Her background in evolutionary biology motivated her work to represent the relationships between genes across species whenever possible.
Dr Blake worked as a curator of biological information throughout her scientific career, starting as an assistant curator of museum herpetological collections as both an undergraduate and graduate student, and building to extend this curatorial paradigm to molecular and genomic information.
- 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. Gene ontology: tool for the unification of biology. The Gene Ontology Consortium. Nat Genet. 2000 May;25(1):25-9. PMID:10802651
- Alterovitz G, Xiang M, Hill DP, Lomax J, Liu J, Cherkassky M, Dreyfuss J, Mungall C, Harris MA, Dolan ME, Blake JA, Ramoni MF. Ontology engineering. Nat Biotechnol. 2010 Feb;28(2):128-30. PMID:20139945.
- Thomas PD, Wood V, Mungall CJ, Lewis SE, Blake JA; Gene Ontology Consortium. On the Use of Gene Ontology Annotations to Assess Functional Similarity among Orthologs and Paralogs: A Short Report. PLoS Comput Biol. 2012;8(2):e1002386. doi: 10.1371/journal.pcbi.1002386. Epub 2012 Feb 16. PMID:22359495
- Alliance of Genome Resources Consortium. Harmonizing model organism data in the Alliance of Genome Resources. Genetics. 2022 Apr 4;220(4):iyac022. PMID:35380658
- Blake JA, Baldarelli R, Kadin JA, Richardson JE, Smith CL, Bult CJ; Mouse Genome Database Group. Mouse Genome Database (MGD): Knowledgebase for mouse- human comparative biology. Nucleic Acids Res. 2021 Jan 8;49(D1):D981-D987. PMID:33231642
Victoria Blake, Montana State University, USA
Summary: I would like to nominate Dr. Victoria Blake for ISB’s Lifetime Achievement Award for her over 20 years of exceptional and continuous curation service. She performed curation for a company, Montana State University, and four centralized biological databases, including GrainGenes, the Hordeum Toolbox, the Triticeae Toolbox, and Soybase. Dr. Blake has been an Organizer/Abstract Coordinator in the International Plant and Animal Genome Conference since 1999 and taught graduate modules to teach curation at Montana State University.
Dr. Blake worked at Aquanautics / Advanced Oxygen systems to build a corporate database of literature and patents for artificial oxygen carriers.
GrainGenes (1999-2006). Contributed ~400 map sets, containing ~4000 maps, with over 100 thousand genetic markers). Developed the Community Curation workbook that catalogues barley QTL work.
Montana State University (2006-2011). Management, germplasm acquisition, maintenance, and evaluation of a demonstration hopyard and vineyard at the University Horticultural Farm.
The Triticeae ToolBox (2011-2015). A founding curator who worked closely with the research community to populate the wheat and barley databases in the first four years of the project with thousands of breeding lines, and results from the TCAP project.
SoyBase (2015-2017). Developed a method to translate the sequences named in publications as alleles of known genes into sequence objects. Records from over 100 papers were created.
GrainGenes. Curator (2017- present). Created database objects, with functional annotations for ~500,000 genes in the reference sequences for the small grains. Curation of over 1,000 QTL from literature and in partnership with Ag Canada.
- Blake VC, Wight CP, Yao E, Sen TZ. GrainGenes: Tools and Content to Assist Breeders Improving Oat Quality. Foods. 2022 Mar 23;11(7):914. doi: 10.3390/foods11070914. PMID: 35407001
- Blake VC, Woodhouse MR, Lazo GR, Odell SG, Wight CP, Tinker NA, Wang Y, Gu YQ, Birkett CL, Jannink JL, Matthews DE, Hane DL, Michel SL, Yao E, Sen TZ. GrainGenes: centralized small grain resources and digital platform for geneticists and breeders. Database (Oxford). 2019 Jan 1;2019:baz065. PMID: 31210272.
- Blake VC, Birkett C, Matthews DE, Hane DL, Bradbury P, Jannink JL. The Triticeae Toolbox: Combining Phenotype and Genotype Data to Advance Small-Grains Breeding. Plant Genome. 2016 Jul;9(2). doi: 10.3835/plantgenome2014.12.0099. PMID: 27898834.
- Blake VC, Kling JG, Hayes PM et al. (2012) The Hordeum toolbox: the Barley coordinated agricultural project genotype and phenotype resource. The Plant Genome, 5, 81–91. https://doi.org/10.3835/plantgenome2012.03.0002
- Carollo VL, Matthews DE, Lazo GR, Blake TK, Hummel DD, Lui N, Hane DL, Anderson OD (2005) GrainGenes 2.0 – An Improved Resource for the Small-Grains Community. Plant Physiology 139:643-651. PMID: 16219925
Peter D’Eustachio, Department of Biochemistry & Molecular Pharmacology, NYU Grossman School of Medicine, New York, NY USA
Peter has been involved with the Reactome Knowledgebase since 2002, developing standards and procedures for curation of pathway events and tight integration of Reactome annotation with material from community resources such as the Gene Ontology, ChEBI, UniProt, and Rhea, and more recently the Alliance of Genome Resources to support efficient annotation of biologically complex processes in formats that are widely accessible and interoperable. This interoperability extends to the use of Reactome annotations of human processes as starting points for efficiently annotating model organism versions of these processes in formats that themselves support easy and reliable data re-use. Peter’s direct contributions have centered on the development of Reactome curation standards, development of tools to align Reactome annotations with corresponding instances in resources such as Rhea, and the development of a strategy to export Reactome content into the GO-CAM format that is rapidly becoming a bioinformatics community standard. Peter’s knowledge of a wide range of biological processes and his understanding of the underlying biochemistry enables him to clearly explain the most logical solutions to many challenging problems. Many gold standard biological knowledgebases have benefited from his insightful and considered suggestions.
- D’Eustachio P. (2013) Pathway databases: making chemical and biological sense of the genomic data flood. Chem Biol. 20:629-635. PMID: 23706629
- Hill DP, D’Eustachio P, Berardini TZ, Mungall CJ, Renedo N, Blake JA (2016) Modeling biochemical pathways in the gene ontology. Database baw126. PMID: 27589964
- Good BM, Van Auken K, Hill DP, Mi H, Carbon S, Balhoff JP, Albou LP, Thomas PD, Mungall CJ, Blake JA, D’Eustachio P. (2021) Reactome and the Gene Ontology: Digital convergence of data resources. Bioinformatics. 37:3343–3348. PMID: 33964129
- Gillespie M, Jassal B, Stephan R, Milacic M, Rothfels K, Senff-Ribeiro A, Griss J, Sevilla C, Matthews L, Gong C, Deng C, Varusai T, Ragueneau E, Haider Y, May B, Shamovsky V, Weiser J, Brunson T, Sanati N, Beckman L, Shao X, Fabregat A, Sidiropoulos K, Murillo J, Viteri G, Cook J, Shorser S, Bader G, Demir E, Sander C, Haw R, Wu G, Stein L, Hermjakob H, D’Eustachio P (2022) The Reactome Pathway Knowledgebase 2022. Nucleic Acids Res. 50:D687-D692. PMID: 34788843
Pascale Gaudet, Swiss Institute of Bioinformatics, Switzerland
Pascale Gaudet has worked in the biocuration field for over 19 years first at DictyBase and more recently NextProt and the Gene Ontology Consortium. Pascale is currently the GO Project Manager and oversees all editorial content. She has worked continually not only to improve the Gene Ontology structure and formalisation, but also has driven the project to produce high quality phylogenetically inferred GO annotation using the PAINT annotation system. The PAINT annotations are much more specific than existing annotation from automated sources, because they can be refined on a family-by-family and even gene-by-gene basis. This system is now providing over 3.5 million annotation in the GOA annotation database.
Pascale is working constantly to refine legacy and dormant annotations across the ontology, and with multiple collaborating groups to refine the both ontology and annotation to ensure that both are fit for purpose. She is driving the coordination of overhauls in many areas of GO ontology including multi-species processes, transcription, chromatin remodeling, tacking each are with insight and attention to detail but never failing to see the bigger picture. She has been key to the communication between different interested groups and manages the numerous discussions with efficiency. This is work that almost every bench biologist depends on to some degree, but is largely unrecognised because it depends on thousands of incremental tasks that are not usually attributed or described in publications.
- Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, Livstone MS, Lewis SE, Thomas PD. Brief Bioinform. 2011 Sep;12(5):449-62. PMID: 21873635
- Gene Ontology representation for transcription factor functions. Gaudet P, Logie C, Lovering RC, Kuiper M, Lægreid A, Thomas PD. Biochim Biophys Acta Gene Regul Mech. 2021 Nov-Dec;1864(11-12):194752. PMID: 34461313
- The Gene Ontology resource: enriching a GOld mine. Gene Ontology Consortium. Nucleic Acids Res. 2021 Jan 8;49(D1):D325-D334. PMID: 33290552
- Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems. Thomas PD, Hill DP, Mi H, Osumi-Sutherland D, Van Auken K, Carbon S, Balhoff JP, Albou LP, Good B, Gaudet P, Lewis SE, Mungall CJ. Nat Genet. 2019 Oct;51(10):1429-1433. PMID: 31548717
- Accelerating annotation of articles via automated approaches: evaluation of the neXtA5 curation-support tool by neXtProt. Britan A, Cusin I, Hinard V, Mottin L, Pasche E, Gobeill J, Rech de Laval V, Gleizes A, Teixeira D, Michel PA, Ruch P, Gaudet P. Database (Oxford). 2018 Jan 1;2018:bay129. PMID: 30576492
Gloria I. Giraldo-Calderon, Department of Biological Sciences, Eck Institute for Global Health, University Notre Dame, IN, USA
VectorBase.org is one of 14 database repositories that comprise the VEuPathDB.org suite of bioinformatics dataset repositories. It accepts sequencing and population abundance datasets, from global scientific researchers studying vector-eukaryote host-pathogen interactions. Since VEuPathDB’s inception, these databases have grown substantially, and their graphical user interfaces have evolved, allowing not only submission and access to the datasets stored, but also refined searches and data analysis via a workflow simplified by the depiction of icons. Furthermore, VectorBase has a unique feature that permits users to display a map of population counts of selected arbovectors via a geographical information system interface. Since 2012, Dr. Giraldo-Calderon has facilitated the storage and access of vector abundance data, participated in VEuPathDB’s public outreach efforts (webinars, tutorials and workshops), and supported its global user base online. Thanks to Dr. Giraldo-Calderon’s efforts and dataset-related publications, the VectorBase repository is continuing to grow not only in size, but also in its importance as an online bioinformatics resource.
- Amos B, Aurrecoechea C, Barba M, Barreto A, Basenko EY, Bażant W, Belnap R, Blevins AS, Böhme U, Brestelli J, Brunk BP, Caddick M, Callan D, Campbell L, Christensen MB, Christophides GK, Crouch K, Davis K, DeBarry J, Doherty R, Duan Y, Dunn M, Falke D, Fisher S, Flicek P, Fox B, Gajria B, Giraldo-Calderón GI, Harb OS, Harper E, Hertz-Fowler C, Hickman MJ, Howington C, Hu S, Humphrey J, Iodice J, Jones A, Judkins J, Kelly SA, Kissinger JC, Kwon DK, Lamoureux K, Lawson D, Li W, Lies K, Lodha D, Long J, MacCallum RM, Maslen G, McDowell MA, Nabrzyski J, Roos DS, Rund SSC, Schulman SW, Shanmugasundram A, Sitnik V, Spruill D, Starns D, Stoeckert CJ, Tomko SS, Wang H, Warrenfeltz S, Wieck R, Wilkinson PA, Xu L, Zheng J. VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center. Nucleic Acids Res. 2022 Jan 7;50(D1):D898-D911. PMID: 34718728
- Giraldo-Calderón GI, Harb OS, Kelly SA, Rund SS, Roos DS, McDowell MA. VectorBase.org updates: bioinformatic resources for invertebrate vectors of human pathogens and related organisms. Curr Opin Insect Sci. 2022 Apr;50:100860. doi: 10.1016/j.cois.2021.11.008. Epub 2021 Dec 3. PMID: 34864248
- Rund, Samuel S. C., Braak, Kyle, Cator, Lauren, Copas, Kyle, Emrich, Scott J., Giraldo-Calderón, Gloria I., Johansson, Michael A., Heydari, Naveed, Hobern, Donald, Kelly, Sarah A., Lawson, Daniel, Lord, Cynthia, MacCallum, Robert M., Roche, Dominique G., Ryan, Sadie J., Schigel, Dmitry, Vandegrift, Kurt, Watts, Matthew, Zaspel, Jennifer M., & Pawar, Samraat. MIReAD, a minimum information standard for reporting arthropod abundance data. Scientific Data, 6 (1). PMID: 31024009
Sandra Orchard, EBI, Hinxton, Cambridge, UK
Sandra has worked tirelessly for the biocuration community for over 20 years. She is currently the Team Leader for Protein Function Content at UniProt (https://www.uniprot.org), and is therefore responsible for a major part of probably the most used biological database in the world. In this role, she also maintains two other key interfaces: the Complex Portal (https://www.ebi.ac.uk/complexportal/home) and the Enzyme Portal (https://www.ebi.ac.uk/enzymeportal/). Previously, Sandra led the IntAct molecular interaction database (https://www.ebi.ac.uk/intact/home) and managed the IMEx consortium of collaborating interaction databases. She has also been key in establishing standards within the proteomics community, and has made significant contributions to the InterPro database and the Gene Ontology. Sandra has always been a strong proponent of FAIR principles, education and the biocuration community: she has chaired and/or contributed to numerous biocuration-related committees; she established the first formal educational qualification in biocuration (PgCert at the University of Cambridge); and she has been a long-time supporter of the ISB, serving as treasurer from 2015-2018 and chair from 2018-2020. Sandra has published ~200 papers on biocuration methods, standards and databases, which serves as a measure of her impact and importance both to the biocuration community as well as to the researchers who depend on the many resources to which she has contributed.
- N. Del Toro et al., “The IntAct database: efficient access to fine-grained molecular interaction data,” Nucleic Acids Res., vol. 50, no. D1, pp. D648–D653, Jan. 2022. PMID: 34761267
- B. H. M. Meldal et al., “Complex Portal 2022: new curation frontiers,” Nucleic Acids Res., vol. 50, no. D1, pp. D578–D586, Jan. 2022 PMID: 34718729
- UniProt Consortium. (2021) UniProt: a worldwide hub of protein knowledge. Nucleic Acids Res. 49(D1): D480-D489. doi: 10.1093/nar/gkaa1100. PMID: 33237286
- Gene Ontology Consortium. (2021) The Gene Ontology resource: enriching a GOld mine. Nucleic Acids Res. 49(D1:) D325-D334. PMID: 33290552
- Perfetto L, Pastrello C, Del-Toro N, et al. (2020) The IMEx coronavirus interactome: an evolving map of Coronaviridae-host molecular interactions. Database (Oxford).2020. doi:10.1093/database/baaa096. PMID: 33206959
Jennifer R. Smith, Rat Genome Database at Medical College of Wisconsin, Milwaukee, WI USA
Jennifer R. Smith has made considerable contributions to the Rat Genome Database and to model organism biocuration for a significant portion of her scientific career. Her RGD efforts began in database development and curation and have expanded significantly to encompass all facets of the ever-growing RGD resource, as well as the Alliance of Genome Resources. As other databases and resources around the world have grown, Jennifer has been integral to the efforts to incorporate as much as is useful into RGD, to provide a comprehensive interactive resource. Within RGD Jennifer is an important component to curator jamboree sessions, training of newer curators, as well as webpage development and tools development/testing. While curation efforts are primary to RGD’s functionality, Jennifer is also involved with projects to upgrade user interfaces to make access and utilization of RGD’s extensive multi-species genomic and phenotypic datasets maximally functional. Additional efforts include importation and integration of diverse additional datasets such as genetic variant data on not just rat but also clinically relevant human variants, dog variants, and soon to be domestic pig. RGD would not be the premier rat data site without the extensive work of Jennifer R. Smith. As testament to her stature in the biocuration community, she has been included as a working group leader and active participant in the Alliance of Genome Resources, as well as the Somatic Cell Genome Editing (SCGE) program toolkit.
- Vedi M, Nalabolu HS, Lin CW, Hoffman MJ, Smith JR, Brodie K, De Pons JL, Demos WM, Gibson AC, Hayman GT, Hill ML, Kaldunski ML, Lamers L, Laulederkind SJF, Thorat K, Thota J, Tutaj M, Tutaj MA, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. MOET: a web-based gene set enrichment tool at the Rat Genome Database for multiontology and multispecies analyses. Genetics. 2022 Apr 4;220(4). PMID: 35380657.
- Kaldunski ML, Smith JR, Hayman GT, Brodie K, De Pons JL, Demos WM, Gibson AC, Hill ML, Hoffman MJ, Lamers L, Laulederkind SJF, Nalabolu HS, Thorat K, Thota J, Tutaj M, Tutaj MA, Vedi M, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. The Rat Genome Database (RGD) facilitates genomic and phenotypic data integration across multiple species for biomedical research. Mamm Genome. 2022 Mar;33(1):66-80. PMID: 34741192.
- Smith JR, Hayman GT, Wang SJ, Laulederkind SJF, Hoffman MJ, Kaldunski ML, Tutaj M, Thota J, Nalabolu HS, Ellanki SLR, Tutaj MA, De Pons JL, Kwitek AE, Dwinell MR, Shimoyama ME. The Year of the Rat: The Rat Genome Database at 20: a multi-species knowledgebase and analysis platform. Nucleic Acids Res. 2020 Jan 8;48(D1):D731-D742. PMID: 31713623.
- Laulederkind SJF, Hayman GT, Wang SJ, Hoffman MJ, Smith JR, Bolton ER, De Pons J, Tutaj MA, Tutaj M, Thota J, Dwinell MR, Shimoyama M. Rat Genome Databases, Repositories, and Tools. Methods Mol Biol. 2019;2018:71-96. PMID: 31228152.
- Smith JR, Park CA, Nigam R, Laulederkind SJ, Hayman GT, Wang SJ, Lowry TF, Petri V, Pons JD, Tutaj M, Liu W, Worthey EA, Shimoyama M, Dwinell MR. The clinical measurement, measurement method and experimental condition ontologies: expansion, improvements and new applications. J Biomed Semantics. 2013 Oct 8;4(1):26. PMID: 24103152.