EXCELLENCE IN BIOCURATION ADVANCED CAREER AWARD 2025

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 25 June – 23 July 2025

NOMINEES

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

  • Laurel Cooper, Oregon State University, USA
  • Steven Marygold, University of Cambridge, UK
  • Saurabh Raghuvanshi, University of Delhi, India
  • Kimberly Van Auken, California Institute of Technology, USA
  • Egon L. Willighagen, Maastricht University, Netherlands

Detailed Descriptions

Laurel Cooper, Oregon State University, USA

Laurel Cooper has a degree in Agronomy and a Ph.D. in Plant Physiology and Molecular Biology, from the University of Alberta, Canada. Since 2014, Laurel has been Project Coordinator and Scientific Curator with the Planteome Project (formerly the Plant Ontology Project), working primarily on developing reference ontologies for plant sciences and fostering open science. She has lead outreach and training efforts by co-organizing more than 30 workshops with scopes ranging from regional to international, engaging diverse audiences and expanding the Planteome project’s visibility and impact. Laurel collaborates with a large number of groups who are developing their own vocabularies for use in plant breeding projects around the world, integrating these with the Planteome Ontologies. Over her career, Laurel has authored or co-authored 34 peer-reviewed publications, 10 conference proceedings and three book chapters, covering a wide variety of topics in ontologies, plant molecular biology, genetics, and plant genomics. These publications reflect both her leadership in original research and her ongoing collaborative work across multidisciplinary teams.

Publications

  • Cooper L, Elser J, Laporte M-A, Arnaud E, Jaiswal P. (2024) Planteome 2024 Update: Reference Ontologies and Knowledgebase for Plant Biology. Nucleic Acids Research 52: D1548-D1555. DOI:10.1093/nar/gkad1028
  • Clarke* JL, Cooper* L, Poelchau* MF, Berardini TZ, Elser J, Farmer AD, Ficklin S, Kumari S, Laporte M-A, Nelson RT, Sadohara R, Selby P, Thessen AE, Whitehead B, Sen TZ. (2023) Data Sharing and Ontology Use Among Agricultural Genetics, Genomics, and Breeding Databases and Resources of the AgBioData Consortium. Database 2023. DOI:10.1093/database/baad076
  • Thessen AE, Cooper L, Swetnam TL, Hegde H, Reese J, Elser J, Jaiswal P. (2023) Using Knowledge Graphs to Infer Gene Expression in Plants. Frontiers in Artificial Intelligence. DOI:10.3389/frai.2023.1191122
  • Cooper L, LaPorte M-A, Elser JL, Blake VC, Sen TZ, Mungall CJ, Arnaud E, Jaiswal P (2020) The Plant Trait Ontology Links Wheat Traits for Crop Improvement and Genomics. In: Proceedings of the 11th International Conference on Biomedical Ontologies (ICBO 2020). CEUR Workshop Proceedings Vol-2807. Sept. 17th, 2020. Virtual
  • Cooper L, Meier A, Laporte M-A, Elser JL, Mungall C, Sinn BT, Cavaliere D, Carbon S, Dunn NA, Smith B, Qu B, Preece J, Zhang E, Todorovic S, Gkoutos G, Doonan JH, Stevenson DW, Arnaud E, Jaiswal P. (2018). The Planteome Database: An Integrated Resource for Reference Ontologies, Plant Genomics and Phenomics. Nucleic Acids Research 46:D1168–D1180. DOI:10.1093/nar/gkx1152
  • Cooper L, Walls RL, Elser J, Gandolfo MA, Stevenson DW, Smith B, Preece J, Athreya B, Mungall CJ, Rensing S, Hiss M, Lang D, Reski R, Berardini TZ, Li D, Huala E, Schaeffer M, Menda N, Arnaud E, Shrestha R, Yamazaki Y, Jaiswal P. (2013). The Plant Ontology as a Tool for Comparative Plant Anatomy and Genomic Analyses. Plant and Cell Physiology 54: e1–e1. DOI: 10.1093/pcp/pcs163

Steven Marygold, University of Cambridge, UK

Steven has been a curator and the group coordinator at the Cambridge (UK) site of FlyBase (flybase.org) for almost 20 years. In this time, he has initiated many innovative projects to improve the content, quality and display of Drosophila data in FlyBase. Principle among these are: modernization of bibliography updates, systematic revisions to gene nomenclature, establishment of Gene Group pages to provide easy access to sets of related genes, a comprehensive annotation review of ~4,000 enzyme encoding genes, the systematic cataloguing of all ncRNA genes and their submission to RNAcentral, and numerous enhancements to the FlyBase website.
Steven is passionate about data coordination – all his work within FlyBase is done in conjunction with colleagues at partner databases to maximise the efficiency, accuracy and consistency of data curation and presentation. To this end, he has established productive collaborations with UniProtKB, RNAcentral, Alliance of Genome Resources, HGNC, Reactome, BioCyc, ENA, Ensembl, Sequence Ontology and Disease Ontology. Steven is also a major contributor to the Gene Ontology (GO) consortium, having submitted >1,000 tickets to the GO issue trackers, and working as a GO editor.
Steven is currently leading a project to create a new, high-quality genome-scale metabolic models (GSMMs) for Drosophila, taking advantage of his improvements to the GO itself and the GO annotation of Drosophila enzymes. This work has already produced a new computed GSMM within the BioCyc framework (called FlyCyc). Ongoing work focusses on manual creation of GO causal activity models (GO CAMs) for all Drosophila metabolic pathways, and the production of corresponding pathway reports on FlyBase.

Publications

  • Öztürk-Çolak A, Marygold SJ, Antonazzo G, Attrill H, Goutte-Gattat D, Jenkins VK, Matthews BB, Millburn G, dos Santos G, Tabone CJ, the FlyBase Consortium (2024) FlyBase: updates to the Drosophila genes and genomes database. Genetics 227(1) iyad211 DOI:10.1093/genetics/iyad211
  • Marygold SJ (2023) FlyCyc: Pathway/Genome Database of the model organism Drosophila melanogaster. https://biocyc.org/organism-summary?object=FLY
  • Marygold SJ and the FlyBase Consortium (2023) Exploring FlyBase Data Using QuickSearch. Current Protocols 3:e731. DOI:10.1002/cpz1.731
  • Garapati PV, Zhang J, Rey AJ and Marygold SJ (2019) Towards comprehensive annotation of Drosophila melanogaster enzymes in FlyBase. Database 2019 bay144 DOI:10.1093/database/bay144
  • 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(D1):D786-92. DOI:10.1093/nar/gkv1046
  • Marygold SJ, Leyland PC, Seal RL, Goodman JL, Thurmond J, Strelets VB, Wilson RJ; FlyBase consortium (2013) FlyBase: improvements to the bibliography. Nucleic Acids Res. 41(Database issue):D751-D757 DOI:10.1093/nar/gks1024

Saurabh Raghuvanshi, University of Delhi, India

My submission is based on my sustained long-term efforts to establish the field of Biocuration in India. The journey initiated when I joined ‘Rice Genome Project’ in India as a Scientist (bioinformatics). Worked hard to establish the Genome analytics lab (first in India) and performed all genome assemblies/annotations (BAC/PAC) at the center. Later, participated in a short training at CSHL, New York (W. Richard McCombie) and subsequently represented India in the annotation jamborees (RAP1 and RAP2) in Tsukuba. This is where I realized the pivotal nature of Biocuration. Few years later I established my own lab (Univ. of Delhi) and worked on semantic digitization of experimental data, among other things. Several years later (2021), got the opportunity to establish (as Project Head) the first national life science data center of India i.e. Indian Biological Data Center (IBDC), which has multiple data portals for nucleotide, metabolic, proteomic and phenotyping data. IBDC played a pivotal role in consolidating and analyzing national COVID19 genomic surveillance data during the pandemic. Recently, data of the first 10,000 Indian human genomes (GenomeIndia project) at IBDC was released by Honorable Prime Minister of India.
I also put in efforts to popularize Biocuration in India by organizing ‘National Symposium on Database Development and Biocuration’ (NSDDB 2018 and 2019) followed by the 17th International Biocuration Conference (2024) for the first time in India. Further, I have been offering (since 2019) an ‘open elective’ course on ‘Data analytics and Biocuration’ at the post-graduate level.

Publications

  • Bhattacharyya, C., Subramanian, K., Uppili, B. GenomeIndia Consortium et. al. (2025) Mapping genetic diversity with the GenomeIndia project. Nat. Genet . https://doi.org/10.1038/s41588-025-02153-x.
  • Gour P, Garg P, Jain R, Joseph SV, Tyagi AK, Raghuvanshi S. (2013) Manually curated database of rice proteins. Nucleic Acids Res. 42(1): D1214-21.
  • The Rice annotation project. (2008) The Rice Annotation Project Database (RAP-DB): 2008 update. Nucleic Acids Res., 1028-1033.
  • The rice annotation project (2007). Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana. Genome Research, 17: 175-183.
  • International Rice Genome Sequencing Consortium (2005). Map based sequence of the rice genome. (Authors from UDSC) S. Raghuvanshi, A. Mohanty, A. K. Bharti, A. Gaur, V. Gupta, D.Kumar, V. Ravi, S. Vij, A. Kapur, Parul Khurana, Paramjit Khurana, J. P. Khurana, A. K. Tyagi. Nature, 436; 793-800.

Kimberly Van Auken, California Institute of Technology, USA

Kimberly Van Auken’s career reflects deep expertise, sustained innovation, and dedicated service to the biocuration community. With a foundation in C. elegans genetics and early experience in protein annotation, she has made impactful contributions to multiple high-profile projects, including WormBase, the Gene Ontology (GO) Consortium, and the Alliance of Genome Resources. Her pioneering efforts in applying text mining to GO curation, particularly through the use of Textpresso and participation in BioCreative challenges, exemplify her forward-thinking approach to improving curation efficiency and quality.

As co-manager of the GO annotation group, Kimberly helped lead the development of the Noctua curation tool and the creation of GO-Causal Activity Models (GO-CAMs), transforming how biological processes are modeled and curated. Her leadership in transitioning WormBase literature infrastructure to the Alliance and her current role as lead of the Literature Working Group underscore her ability to guide large-scale, collaborative initiatives. She is also a member of the Alliance AI working group and a core contributor to the AI-assisted ACKnowledge community curation platform, promoting broader engagement in data annotation.

In addition to her technical achievements, Kimberly is a dedicated mentor and educator who actively supports community curation and biocuration training. She is a dependable and proactive colleague, known for her thoughtful collaboration and forward-looking vision. Her contributions continue to shape the standards, tools, and community practices that support high-quality biocuration.

Publications

  • Van Auken K, Jaffery J, Chan J, Müller HM, Sternberg PW. Semi-automated curation of protein subcellular localization: a text mining-based approach to Gene Ontology (GO) Cellular Component curation. BMC Bioinformatics. 2009 Jul 21;10:228. doi: 10.1186/1471-2105-10-228. PMID: 19622167; PMCID: PMC2719631.
  • Van Auken K, Fey P, Berardini TZ, Dodson R, Cooper L, Li D, Chan J, Li Y, Basu S, Muller HM, Chisholm R, Huala E, Sternberg PW; WormBase Consortium. Text mining in the biocuration workflow: applications for literature curation at WormBase, dictyBase and TAIR. Database (Oxford). 2012 Nov 17;2012:bas040. doi: 10.1093/database/bas040. PMID: 23160413; PMCID: PMC3500519.
  • 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. Gene Ontology Causal Activity Modeling (GO-CAM) moves beyond GO annotations to structured descriptions of biological functions and systems. Nat Genet. 2019 Oct;51(10):1429-1433. doi: 10.1038/s41588-019-0500-1. PMID: 31548717; PMCID: PMC7012280.
  • Arnaboldi V, Raciti D, Van Auken K, Chan JN, Müller HM, Sternberg PW. Text mining meets community curation: a newly designed curation platform to improve author experience and participation at WormBase. Database (Oxford). 2020 Jan 1;2020:baaa006. doi: 10.1093/database/baaa006. PMID: 32185395; PMCID: PMC7078066.
  • Prakash SJ, Van Auken KM, Hill DP, Sternberg PW. Semantic representation of neural circuit knowledge in Caenorhabditis elegans. Brain Inform. 2023 Nov 10;10(1):30. doi: 10.1186/s40708-023-00208-5. Erratum in: Brain Inform. 2024 May 15;11(1):13. doi: 10.1186/s40708-024-00226-x. PMID: 37947958; PMCID: PMC10638142.

Egon L. Willighagen, Maastricht University, Netherlands

Egon is a champion for FAIR and open science in chemistry, biology, and the information sciences. He was a community staple of Science Twitter and now on its successor in the Fediverse (egonw@social.edu.nl). A few of his career highlights include:

His earliest contributions included work on the Chemistry Development Kit (CDK), an important open source software package for cheminformatics and his related work in chemometrics. He participated in Blue Obelisk, an effort to promote interoperability between chemistry software and data and was recognized by their yearly award in 2007. He continued his work in FAIR and linked data by developing ChEMBL RDF and integrating chemical data in the semantic web / linked open data world in the OpenPHACTS project.

Later, he served as Editor-in-Chiefs at the Journal of Cheminformatics where he promoted code sharing and the more detailed annotation of citations using CiTO. These interests persist through his contributions to Wikidata and Scholia as a frontend for bibliometrics scientometrics.

Finally, he works on the WikiPathways project with interest in systems biology modeling, adverse outcome pathways, and the integration with pathway modeling resources, where he proactively made contributions to many external resources and notably contributed to the COVID19 Disease Maps initiative.

Egon is an exceptional scientist and biocurator as his interests range widely, he is highly proactive in engaging many communities, and he has an inhuman amount of energy!

Publications