EXCELLENCE IN BIOCURATION EARLY CAREER AWARD 2024

The Early Career Award recognizes biocurators who have been involved in a biocuration-relevant field for less than 7 years. The nominees are in a non-leadership position and 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 27 June – 25 July 2024

NOMINEES

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

  • Robert Giessmann, Institute for Globally Distributed Open Research and Education (IGDORE), Technical University Berlin, Germany
  • Scott V. Nguyen, American Type Culture Collection, University Blvd, Manassas, Virginia, USA
  • Maria Victoria Nugnes, University of Padova, Italy
  • Umasri Sankarlal, Freelance Biocurator, India

Detailed descriptions

Robert Giessmann, Institute for Globally Distributed Open Research and Education (IGDORE), Germany

Robert is the community facilitator and creator of the openTECR database (https://github.com/opentecr/opentecr). This community creates an open database that simplifies access to and sharing of thermodynamic data for biochemical reaction, built by and for modellers and experimentalists alike.

Robert earns his living with other things, but voluntarily took up the effort to reach out to scientists interested in biothermodynamics. While everyone agreed that a database like openTECR would make sense, there was no momentum to make it happen as a collective, and Robert worked solitarily on the project from 2021 on. He collected >1000 primary publications, and visited many libraries to digitize old scientific articles himself. To grow a community, in late 2023 Robert received mentorship in Open Life Science’s “Open Seeds” program. He presented the project at several conferences, ran a globe-spreading online hackathon and finally, in 2024, invited the global biocuration community to community-curate the data. This invitation attracted 17 curators who contributed a total of 100 working hours over 4 months, all voluntarily; now 40 people are on openTECR’s mailing list. From time to time, Robert works in the lab to generate new data and publishes his lab notes immediately online under an open license.

Robert believes that the next wave of life science databases should be hosted in the open, with open data, open infrastructure, and open code. He is currently exploring how git and GitHub/Lab can serve as a replacement to traditional databases, including quality control and linking to other databases by CI/CD actions.

Scott V. Nguyen, American Type Culture Collection, University Blvd, Manassas, Virginia, USA

Scott is a senior biocurator for the American Type Culture Collection Genome Portal (AGP). He ensures the pedigree of genome assemblies in the AGP are directly sourced to physical materials in the repository. Sequencing data is also paired with historical metadata within the nearly century old collection that spans handwritten notes to corresponding letters from depositors to modern digital records.
Scott is also a volunteer biocurator for the Yersinia section of EnteroBase (https://enterobase.warwick.ac.uk/species/index/yersinia), a genomic database for enteric pathogens that provides core genome multilocus sequencing typing (cgMLST) to help researchers identify population structures for important pathogens.
Prior to joining the ATCC as a biocurator, Scott curated epidemiological metadata and submitted nearly 6500 SARS-CoV-2 genomes to the GISAID database on behalf of the District of Columbia Public Health Laboratory. These genomes and associated metadata helped inform epidemiologists of current SARS-CoV-2 trends within the Washington, DC metropolitan region. In addition to contributing to GISAID, he also actively researched emerging coronavirus lineages and discovered three new variants for the SARS-CoV-2 Pango lineages.
One Pango variant, the XD Delta-Omicron recombinant, was monitored by the WHO as a variant under monitoring (VUM) in 2022 (https://www.nytimes.com/2022/03/11/science/deltacron-coronavirus-variant.html). Through this work, he also informally works with other SARS-CoV-2 variant hunters across the globe and helps volunteer scientists gain access to the GISAID database to help track emerging variants (https://x.com/LongDesertTrain/status/1783670135103926697). Additionally, he mentored undergraduate interns as a volunteer with the Metropolitan Washington Council of Governments to monitor SARS-CoV-2 trends within the Washington, DC area with GISAID data.

  • Publications
    • The ATCC genome portal: 3,938 authenticated microbial reference genomes. Genomics and Proteomics. Scott V Nguyen, Nikhita P Puthuveetil, Joseph R Petrone, Jade L Kirkland, Kaitlyn Gaffney, Corina L Tabron, Noah Wax, James Duncan, Stephen King, Robert Marlow, Amy L Reese, David A Yarmosh, Hannah H McConnell, Ana S Fernandes, John Bagnoli, Briana Benton, Jonathan L Jacobs. Microbiol Resour Announc. PMID:38289057
    • Rapid characterization of a Delta-Omicron SARS-CoV-2 recombinant detected in Europe. Preprint. https://doi.org/10.21203/rs.3.rs-1502293/v1

Maria Victoria Nugnes, University of Padova, Italy

Maria Victoria is a Research Fellow at the University of Padova and the primary expert curator of the DisProt database. Throughout her career as a biocurator, she has demonstrated exceptional dedication, remarkable skill, and a profound impact on the quality and content growth of the DisProt database over the past three years. Her contributions include the manual curation of over 800 intrinsically disordered proteins (IDPs), more than 4,000 disordered regions, and 1,200 publications (https://apicuron.org/curators/0000-0001-8399-7907). She has also reviewed more than 1,500 disordered regions. Additionally, she contributes to constructing thematic datasets for the characterization of IDPs in biological processes and diseases, including the dataset for the Critical Assessment of IDPs prediction (CAID) – Round 2. She contributes to updating Gene Ontology and IDPs Ontology, with new terms for disorder states and functions. She is co-first author of the latest DisProt publication (Aspromonte MC, Nugnes MV et al., NAR 2023) and a collaborator in defining best practices (Quaglia F et al., Database 2023) for the curation of IDPs in DisProt. Victoria is the Minimal Reporting Requirements Coordinator of the HUPO-PSI IDP Working Group. In addition, she has also made significant contributions to the community of curators, both in their engagement and in their training. She is very careful with their education, constantly involved in virtual and in-person training sessions on curation activities. These include a recorded Spanish DisProt Biocuration course in ELIXIR-SI eLearning platform, Virtual training and Workshop in 4th REFRACT Annual Latin America Visit.

  • Publications
    • Best practices for the manual curation of intrinsically disordered proteins in DisProt. Federica Quaglia, Anastasia Chasapi, Maria Victoria Nugnes, Maria Cristina Aspromonte, Emanuela Leonardi, Damiano Piovesan, Silvio C E Tosatto. Database (Oxford). PMID:38507044
    • PED in 2024: improving the community deposition of structural ensembles for intrinsically disordered proteins. Hamidreza Ghafouri, Tamas Lazar, Alessio Del Conte, Luiggi G Tenorio Ku; PED Consortium; Peter Tompa, Silvio C E Tosatto, Alexander Miguel Monzon. Nucleic Acids. Res. PMID:37904608
    • DisProt in 2024: improving function annotation of intrinsically disordered proteins.
    • Nucleic Acids Res. Maria Cristina Aspromonte, Maria Victoria Nugnes, Federica Quaglia, Adel Bouharoua; DisProt Consortium; Silvio C E Tosatto, Damiano Piovesan. PMID:37904585

Umasri Sankarlal, Freelance Biocurator, India

Her career started in 2004 and the role given to her was to enter data for building comprehensive databases for biomarkers, biological pathways, and chemical compounds from scientific literatures. They were not familiar with “Biocuration” or role of “Biocurator” then, yet she has honed my skills in interpreting curated data and have been a major significant contributor to Fruiteomics, SNP, GeneSeq, Pathway, and neurology-specific databases.
During her career break between 2007 and 2010, she worked for a client as a freelance mentor about the Ontology concept to their developers, shared ideas on developing an ontology for online databases, and supported them with the necessary datasets for their project. She was also working as a consultant with Thomson Reuters, Chennai on their drug Forecasting database.
After her career break, she joined another Bio-IT firm and worked to develop drug target ontology at a higher level that was used in developing a platform for effective information retrieval, extraction, and visualisation from scientific literature. This method and platform were patented, and she is one of the authors. She was one of the contributors to developing “DrugMechDB,” a curated database of drug mechanisms. Presently, she is volunteering as a member of the “ClinGen Intellectual Disability and Autism Gene Curation Working Group panel” and publishing the curated genes on the ClinGen portal.
Even though she switched her career to the IT industry by 2015, she is proud to make significant contributions to Biocuration whenever she gets an opportunity.

  • Publications

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