EXCELLENCE IN BIOCURATION ADVANCED CAREER AWARD 2023

The Advanced Career Award recognizes biocurators who have been involved in a biocuration-relevant field for 7 years or more. The nominees will have made sustained contributions to the field of biocuration. The recipient will be required to present a 15 minute talk at a virtual Biocuration seminar and will be sent a prize of 500 CHF. 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

NOMINEES

The list of nominees is below. Scroll down for detailed descriptions.

  • Helen Attrill, FlyBase, University of Cambridge, UK
  • Omar Harb, VEuPathDB, University of Pennsylvania, PA, USA
  • Nico Matentzoglu, Monarch Initiative, Semanticly, Greece
  • Rob Nash, Saccharomyces Genome Database, Stanford University, CA, USA
  • Susan Tweedie, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK
  • Shur-Jen Wang, Rat Genome Database at Medical College of Wisconsin, WI USA

Detailed Descriptions

Helen Attrill, FlyBase, University of Cambridge, UK

Helen is the lead GO curator at FlyBase. In this position she made extensive and far-reaching improvements to the GO curation at FlyBase, especially in terms of improving the quality of the GO annotation set – being as fond of removing annotations as she is at adding them. She has contributed to many targeted curation projects, often coupling GO curation to the provision resources for the fly research community, for example Gene Groups and Signaling Pathway resources. She has been involved in countless projects within the Gene Ontology Consortium (GOC), contributing to the formulation of curation guidelines in different contexts, such as leading an effort on how to annotate data from high-throughput studies, and more recently focusing on ncRNA annotation guidelines. Helen collaborates with many additional teams, such as the Alliance of Genome Resources, the Complex Portal and UniProt. Her collaborations with the Drosophila RNAi Screening Center (DRSC) at Harvard have been crucial to ensure that novel tools, such as the new PANGEA enrichment tool, provide maximal utility for the Drosophila community.

Helen is an exceptional biocurator who understands the requirements for ‘whole organism’ curation and identifies and targets the curation gaps required to summarize an organism’s biology, and to prioritise multiple projects. She is also has a particular interest in science outreach, delivering hands-on scientific activities for children.

  • Publications
    • Attrill H, Gaudet P, Huntley RP, Lovering RC, Engel SR, Poux S, Van Auken KM, Georghiou G, Chibucos MC, Berardini TZ, Wood V, Drabkin H, Fey P, Garmiri P, Harris MA, Sawford T, Reiser L, Tauber R, Toro S; Gene Ontology Consortium. (2019) Annotation of gene product function from high-throughput studies using the Gene Ontology. Database (Oxford), 2019:baz007. PMID: 30715275
    • Rey AJ, Attrill H, Marygold SJ; FlyBase Consortium. (2018) Using FlyBase to Find Functionally Related Drosophila Genes. Methods Mol Biol. 1757, 493-512. PMID: 29761468
    • Attrill H, Falls K, Goodman JL, Millburn GH, Antonazzo G, Rey AJ, Marygold SJ, FlyBase consortium. (2016) FlyBase: establishing a Gene Group resource for Drosophila melanogaster. Nucleic Acids Res 44 (Database issue), D786-92. PMID: 26467478
    • Thurmond J, Goodman JL, Strelets VB, Attrill H, Gramates LS, Marygold SJ, Matthews BB, Millburn G, Antonazzo G, Trovisco V, Kaufman TC, Calvi BR; FlyBase Consortium. (2019) FlyBase 2.0: the next generation. Nucleic Acids Res. 47 (Database Issue), D759-D765. PMID: 30364959
    • Hu Y, Comjean A, Attrill H, Antonazzo G, Thurmond J, Chen W, Li F, Chao T, Mohr SE, Brown NH, Perrimon N; PANGEA: a new gene set enrichment tool for Drosophila and common research organisms. Nucleic Acids Res 2023:gkad331. PMID: 36865134

Omar Harb, VEuPathDB, University of Pennsylvania, PA, USA

VEuPathDB.org is a suite of 14 database repositories that accept sequencing and population abundance datasets, from global scientific researchers studying vector-eukaryote host-pathogen interactions. Since its 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. Since June 2008, Dr. Harb, as a member of the VEuPathDB organization, has been at the forefront of its outreach, as a host of webinars announcing repository updates, online tutorials, managing annual in-person workshops, and coordinating its global customer support. As the cost of gene sequencing technologies continues to drop, and FAIR principles for scientific data storage become the norm, more datasets will become available, and VEuPathDB will continue to grow not only in size, but also as an indispensable bioinformatics resource, thanks to the outreach efforts of Dr. Harb.

  • Publications
    • Harb OS, Roos DS. The Eukaryotic Pathogen Databases: a functional genomic resource integrating data from human and veterinary parasites Methods Mol Biol. 2015;1201:1-18. PMID: 25388105
    • 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. PMID: 34864248.

Nico Matentzoglu, Monarch Initiative, Semanticly, Greece

Nico is celebrated in the bio-ontology and biocuration community as a passionate promoter of open science and a champion of curators and ontology editors. He generously shares his extensive knowledge of semantic and ontology engineering, and works tirelessly to drive complex collaborations involving many different stakeholders.

Nico co-leads the OBO Academy, which brings together extensive yet highly accessible training material on ontologies and related topics through collaboratively authored online material as well as curated seminars, tutorials, and courses. This material has been used extensively by many curators to help them master everything from ontology development to writing queries to retrieve biological data.

Thanks to Nico’s vision and technical oversight, the Ontology Development Kit (ODK) has enabled the editors of dozens of bio-ontologies to utilize powerful automated workflows for maintaining, QC-ing, and releasing their products with ease. The ODK has had a huge positive impact on ontology standardization.

Nico leads the development of the widely used Simple Standard for Sharing Ontological Mappings (SSSOM), involving years of painstaking standards work, driving consensus on key design and modeling issues. He also led the efforts to unify multiple phenotype ontologies (Mammalian (MP), Zebrafish (ZP), Human (HPO), Ontology of Biological Attributes (OBA) through common design patterns.

Nico has recruited and encouraged a diverse range of contributors (researchers, government officials, clinicians as well as ontology developers) to grow and unite our community, promote open science, and provide mentorship. He is the ultimate team player and demonstrates unwavering positive energy and dedication to our community.

Rob Nash, Saccharomyces Genome Database, Stanford University, CA, USA

Rob Nash has been a biocurator since before being a “biocurator” was cool. Rob started out at Ingenuity as a “Content Scientist”, before joining Saccharomyces Genome Database in 2003. Now a seasoned Senior Biocuration Scientist, Rob is a “full-stack” biocurator, making invaluable contributions to SGD and the field of biocuration as a whole. Working at SGD requires biocuration at the cutting edge, as the yeast community regularly breaks scientific barriers in both method and knowledge. The mid-2000s saw dramatic increases in protein-related data and genome-wide phenotypic screens. Rob led efforts to improve the integration of experimental information and sequence-based protein predictions, and the development of new phenotype curation methods and controlled-vocabulary system (Ascomycete Phenotype Ontology). More recently, Rob was instrumental in the development of a curation system for functional complementation. Rob’s careful curation work in all aspects of biocuration (literature, function, phenotype, disease, etc.) is complemented by his dedication to outreach. For years, Rob has been an invited instructor at the annual Cold Spring Harbor Yeast Genetics & Genomics course, where his teaching skills have garnered an ongoing opportunity to teach incoming scientists about genome-based methods of analysis facilitated by SGD. At conferences, Rob is a familiar presence at the SGD table, where users are always happy to see him. On the job, Rob regularly trains incoming curators, and is known for his cell biology expertise, attention to detail, patience, and tolerance. SGD and the field of biocuration are fortunate to have Rob Nash, whose efforts deserve to be celebrated.

  • Publications
    • Nash RS, Weng S, Karra K, Wong ED, Engel SR, Cherry JM; SGD Project (2020) Incorporation of a unified protein abundance dataset into the Saccharomyces genome database. Database (Oxford). 2020 Jan 1 [PMID: 32128557]
    • Skrzypek MS, Nash RS, Wong ED, MacPherson KA, Hellerstedt ST, Engel SR, Karra K, Weng S, Sheppard TK, Binkley G, Simison M, Miyasato SR, Cherry JM (2018) Saccharomyces genome database informs human biology. Nucleic Acids Res. 2018 Jan 4; 46:D736-D742. [PMID: 29140510]
    • Hellerstedt ST, Nash RS, Weng S, Paskov KM, Wong ED, Karra K, Engel SR, Cherry JM (2017) Curated protein information in the Saccharomyces Genome Database. 2017 Mar 11; pii: bax011. [PMID: 28365727]
    • Costanzo MC, Skrzypek MS, Nash R, Wong E, Binkley G, Engel SR, Hitz B, Hong EL, Cherry JM, and the Saccharomyces Genome Database Project. (2009) New mutant phenotype data curation system in the Saccharomyces Genome Database. Database. [PMID: 20157474]
    • Nash R, Weng S, Hitz B, Balakrishnan R, Christie KR, Costanzo MC, Dwight SS, Engel SR, Fisk DG, Hirschman JE, Hong EL, Livstone MS, Oughtred R, Park J, Skrzypek M, Theesfeld CL, Binkley G, Dong Q, Lane C, Miyasato S, Sethuraman A, Schroeder M, Dolinski K, Botstein D, Cherry JM (2007) Expanded protein information at SGD: new pages and proteome browser. Nucleic Acids Res 35(Database issue):D468-71. [PMID: 17142221]

Susan Tweedie, EMBL-EBI, Wellcome Genome Campus, Hinxton, UK

Susan has been working in biocuration since she joined the FlyBase group at the University of Cambridge in 2006. There she was the team’s dedicated Gene Ontology (GO) curator. Susan added signficantly to the number of GO terms curated for fly genes, particularly for those orthologous to disease-causing human genes, and worked directly on GO by editing terms and relationships within the ontology. In 2014 she switched from Drosophila to human when she joined the HUGO Gene Nomenclature Committee (HGNC), to work on naming human genes. In her 9 years with the HGNC Susan has contributed substantially to numerous projects, including many efforts which involved considerable discussions with the community, such as standardising the nomenclature of selenoproteins and stabilising the nomenclature of thousands of genes associated with human phenotypes. As well as continuing to contribute to GO on a smaller scale, since the formation of the Vertebrate Gene Nomenclature Committee in 2016, Susan has also been contributing to naming genes in multiple gene groups across key verterbrate species. She has also served the ISB as a member of the Award Committee, Nominating Committee, and Conference Organising Committee at various timepoints over the years. Susan’s exceptional drive for clarity and consistency, always with the user in mind, has greatly helped to develop and improve the outputs of FlyBase, GO, and the HGNC and VGNC over the span of her career.

  • Publications
    • FlyBase: enhancing Drosophila Gene Ontology annotations. Tweedie S, Ashburner M, Falls K, Leyland P, McQuilton P, Marygold S, Millburn G, Osumi-Sutherland D, Schroeder A, Seal R, Zhang H; FlyBase Consortium. Nucleic Acids Res. 2009 Jan;37(Database issue):D555-9. PMID: 18948289
    • FlyBase portals to human disease research using Drosophila models. Millburn GH, Crosby MA, Gramates LS, Tweedie S; FlyBase Consortium. Dis Model Mech. 2016 Mar;9(3):245-52. PMID: 26935103
    • Selenoprotein Gene Nomenclature. Gladyshev VN, Arnér ES, Berry MJ, Brigelius-Flohé R, Bruford EA, Burk RF, Carlson BA, Castellano S, Chavatte L, Conrad M, Copeland PR, Diamond AM, Driscoll DM, Ferreiro A, Flohé L, Green FR, Guigó R, Handy DE, Hatfield DL, Hesketh J, Hoffmann PR, Holmgren A, Hondal RJ, Howard MT, Huang K, Kim HY, Kim IY, Köhrle J, Krol A, Kryukov GV, Lee BJ, Lee BC, Lei XG, Liu Q, Lescure A, Lobanov AV, Loscalzo J, Maiorino M, Mariotti M, Sandeep Prabhu K, Rayman MP, Rozovsky S, Salinas G, Schmidt EE, Schomburg L, Schweizer U, Simonović M, Sunde RA, Tsuji PA, Tweedie S, Ursini F, Whanger PD, Zhang Y. J Biol Chem. 2016 Nov 11;291(46):24036-24040. PMID: 27645994
    • Guidelines for human gene nomenclature. Bruford EA, Braschi B, Denny P, Jones TEM, Seal RL, Tweedie S. Nat Genet. 2020 Aug;52(8):754-758. PMID: 32747822
    • Genenames.org: the HGNC and VGNC resources in 2021. Tweedie S, Braschi B, Gray K, Jones TEM, Seal RL, Yates B, Bruford EA. Nucleic Acids Res. 2021 Jan 8;49(D1):D939-D946. PMID: 33152070

Shur-Jen Wang, Rat Genome Database at Medical College of Wisconsin, WI USA

Dr. Shur-Jen Wang has made considerable contributions to the Rat Genome Database (RGD) and to the model organism database community for a significant portion of her scientific career. Dr. Wang joined RGD in 2009, began in curation, and currently is involved in many facets of the ever-growing RGD resource. One primary focus continues to be rat strain curation and nomenclature. In the years that Dr. Wang has been a curator at RGD, the database increased from <2400 rat strains to >4100, with report pages for collected information. Strains are curated from literature or submitted by researchers, and curated for source, derivation, and other data. Through collaborative efforts with other global biodata resources, Dr. Wang has been integral to establishing standardized nomenclature, ontologies and data harmonization (including Alliance of Genome Resources, Gene Ontology Consortium). Dr. Wang was closely involved in the development of RGD’s curator training process and comprehensive curation manual to ensure that all curators follow rigorous standards. She mentors newer curators and takes part in monthly sessions in which papers are discussed to ensure curation consistency within RGD. Additional efforts include development and testing of innovative data interactivity and analysis tools, such as RGD’s curated phenotype data warehouse, PhenoMiner. Dr. Wang has presented data and tools on behalf of RGD at many domestic and international meetings. Simply put, RGD would not be a premier model organism knowledgebase without the considerable work of Dr. Shur-Jen Wang and she is an ideal candidate for this award.

  • Publications
    • Wang SJ, Brodie KC, De Pons JL, Demos WM, Gibson AC, Hayman GT, Hill ML, Kaldunski ML, Lamers L, Laulederkind SJF, Nalabolu HS, Thota J, Thorat K, Tutaj MA, Tutaj M, Vedi M, Zacher S, Smith JR, Dwinell MR, Kwitek AE. Ontological Analysis of Coronavirus Associated Human Genes at the COVID-19 Disease Portal. Genes (Basel). 2022 Dec 7;13(12):2304. PMID: 36553571
    • Vedi M, Smith JR, Thomas Hayman G, Tutaj M, Brodie KC, De Pons JL, Demos WM, Gibson AC, Kaldunski ML, Lamers L, Laulederkind SJF, Thota J, Thorat K, Tutaj MA, Wang SJ, Zacher S, Dwinell MR, Kwitek AE. 2022 updates to the Rat Genome Database: a Findable, Accessible, Interoperable, and Reusable (FAIR) resource. Genetics. 2023 May 4;224(1):iyad042. PMID: 36930729
    • Gene Ontology Consortium; Aleksander SA, Balhoff J, Carbon S, Cherry JM, Drabkin HJ, Ebert D, Feuermann M, Gaudet P, Harris NL, et al. The Gene Ontology knowledgebase in 2023. Genetics. 2023 May 4;224(1):iyad031. PMID: 36866529.
    • Alliance of Genome Resources Consortium. Harmonizing model organism data in the Alliance of Genome Resources. Genetics. 2022 Apr 4;220(4):iyac022. PMID: 35380658.
    • Wang SJ, Laulederkind SJF, Zhao Y, Hayman GT, Smith JR, Tutaj M, Thota J, Tutaj MA, Hoffman MJ, Bolton ER, De Pons J, Dwinell MR, Shimoyama M. Integrated curation and data mining for disease and phenotype models at the Rat Genome Database. Database (Oxford). 2019 Jan 1;2019:baz014. PMID: 30753478.

News