Executive Committee 2024 Election Winners

As announced at the Annual General Meeting earlier this week, we would like to congratulate the following three individuals who have been elected by members of the International Society for Biocuration to serve on the society’s Executive Committee from 2024:

  1. M. Victoria Nugnes (University of Padua)
  2. Sonia Balyan (Indian Biological Data Centre)
  3. Peter Uetz (Virginia Commonwealth University)

We would also like to thank the election officer, Harry Caufield, and the nominating committee for making this election run smoothly:

  1. Sabrina Toro (Chair)
  2. Pascale Gaudet
  3. Silvio Tosatto
  4. Saurabh Raghuvanshi
  5. Raja Mazumder

More information on the Executive Committee can be found here.

Alliance of Genome Resources Webinar – An Introduction to the Alliance

Carol Bult (0000-0001-9433-210X) will present An Introduction to the Alliance on September 19th, 2024. This will cover searching the Alliance, gene pages, and disease pages and will include a Q & A session. This is the first in an ongoing series.

Register by September 18 to receive the Zoom URL. You can find the registration link here: https://www.alliancegenome.org/news/webinar-an-introduction-to-the-alliance

Executive Committee Candidates – 2024

The election of three members of the International Society for Biocuration Executive Committee (ISB EC) will be held from September 25th – October 2nd, 2024.

Emails will be sent to current members on September 26th. Only current members, as of September 24th, 2024, who receive this email will be allowed to vote. Please note that if you are an ISB member and do not receive the email, please contact us at isb@biocurator.org.

We thank all of the following seven candidates for agreeing to stand for election to the Executive Committee (EC). Information about the candidates standing for election to the Executive Committee (EC) is available below:

Sonia Balyan

Position: Scientist

Affiliation: Indian Biological Data Centre, Regional Centre for Biotechnology, Faridabad, India

Biosketch: As a dedicated scientist specializing in plant molecular biology, biotechnology, and bioinformatics, my career is rooted in cutting-edge research and the crucial field of biocuration. With over 7 years of post-Ph.D. experience, I have developed deep expertise in managing and curating complex biological data, particularly in plant genomics and phenomics. My work is driven by a commitment to transforming raw data into accessible, well-annotated resources that are indispensable for advancing agricultural research and promoting environmental sustainability.

At the Indian Biological Data Centre (IBDC) in Faridabad, where I currently serve as a Scientist, I have played a pivotal role in pioneering initiatives that enhance the utility of big data. A cornerstone of my career has been the development of the Indian Crop Phenome Database, a unique resource designed to archive crop phenome data and ensure it adheres to FAIR principles (Findable, Accessible, Interoperable, Reusable). I am currently spearheading the Indian Functional Genomics DataBank (IFGDb) project, which aims to create a comprehensive repository for functional genomics data, as well as the Indian Research Data Archive (IRDA), a repository for the archival of diverse research data. Additionally, I lead the genomics module of the Multiomics Analysis Toolbox at IBDC, a groundbreaking platform that facilitates the analysis of multidimensional biological data to unravel the complexities of life sciences research. These initiatives not only advance biological sciences but also highlight the essential role of biocuration in ensuring that data-driven research is both meaningful and impactful.

My contributions have been recognized within the scientific community through several publications in good-impact journals, including training and outreach activities. My passion for science communication is further evident in my role as the host of the Beyond Shodh podcast, where I engage with leading Scientists/researchers to share their research, vision and journeys to a broader audience. Through my work in biocuration, I strive to bridge the gap between data and discovery, empowering researchers to unlock new insights that drive innovation in biological sciences and beyond.

Motivation: As a scientist at India’s first Biological Data Centre, I have been actively involved in structuring and archiving our nation’s invaluable biological data. This work has deepened my understanding of the essential role biocuration plays in not just preserving data, but in making it accessible and impactful for the global scientific community. My experience has fueled a strong commitment to upholding the highest standards of data integrity and usability—values I will bring to the ISB Executive Committee.

In 2024, I led the local organizing committee for the 17th Annual International Biocuration Conference in India, where I gained firsthand experience in fostering global collaboration and advancing biocuration practices. This role provided me with a comprehensive understanding of the field’s challenges and opportunities, equipping me to contribute effectively to ISB’s strategic initiatives.

As the host of Beyond Shodh, I have actively engaged with scientists across India, highlighting the journeys of pioneers in STEM. I also manage outreach for the Indian Biological Data Centre, focusing on engaging and motivating researchers about the importance of FAIR data and data stewardship. I am passionate about expanding ISB’s outreach efforts, ensuring biocuration’s significance is effectively communicated to emerging scientists and policymakers. My goal is to strengthen the global integration of diverse datasets, particularly from underrepresented regions, to build a more inclusive and comprehensive biocuration community.

Marija Milacic

Position: Scientific Associate/Biocurator

Affiliation: Computational Biology, Ontario Institute for Cancer Research, Toronto, Ontario, Canada

Biosketch: My training and wet lab experience involve an undergraduate degree in Molecular Biology and Physiology from the University of Belgrade, where I took part in human papillomavirus research, doctoral degree in Molecular and Medical Genetics from the University of Toronto, where I studied childhood cancer retinoblastoma, and postdoctoral training at the Centre for Addiction and Mental Health in Toronto, where I studied genetics of autism spectrum disorders. My career in biocuration started in 2011, when I joined the Ontario Institute for Cancer Research and became part of the Reactome curation team. Becoming a biocurator enabled me to apply my skillset to building and maintaining a repository of biological pathways used by researchers globally. It also provided me with an insight into the importance of standardized representation of knowledge in biology and medical research, where open and continuous communication between researchers, publishers, and biocurators is key. I would like to continue my career in the field of biocuration because I believe that systematization and synthesis of knowledge is crucial for the ethical advancement of basic and applied biological sciences.

Motivation: As an ISB member for ten years now and a biocurator for more than thirteen years, I greatly appreciate the ISB’s efforts in bringing together biocurators from many different areas of biology, providing professional guidance, and improving the visibility of this profession. It would be an honor to contribute to the ISB as a member of its Executive Committee. As a biocurator of a peer-reviewed pathway database, I would bring to the Executive Committee experience in the areas of data visualization and community curation. The areas within the ISB that I would like to see developed are Training, Outreach, and Communication, and the IT Infrastructure.

Maria Victoria Nugnes

Position: Senior biocurator and trainer of the DisProt database (https://disprot.org/)

Affiliation: BioComputing UP Lab (https://protein.bio.unipd.it/) at University of Padua, Italy

Biosketch: I am a senior biocurator for DisProt (https://disprot.org/), database of manually curated intrinsically disordered proteins (IDPs) from literature, working both remotely from my country, Argentina, and in person at Silvio Tosatto’s lab at the University of Padova, in Italy. In this role, I curate and revise contributions from over 40 community curators spanning various countries from all over the world. I first joined DisProt as a curator in 2021 and have been focused on biocuration as my primary research interest since then. Over the course of the last two years, I assumed leadership responsibilities also for database thematic datasets and I have had the opportunity to manually curate over 1,200 publications. In addition to my curation duties, I design and deliver training materials and sessions for DisProt biocurators. My training sessions are conducted both remotely and in person, with recent sessions held in Argentina and Chile. My work is driven by a passion for enhancing our understanding of IDPs and supporting the global community of biocurators.

Motivation: My career in biocuration is dedicated to improving the quality and accessibility of biological data, particularly concerning intrinsically disordered proteins (IDPs). I am from Argentina, where I work mainly remotely from, and I am deeply committed to helping people from lower-middle-income countries gain access to the tools, knowledge, and support needed to excel in biocuration.

If given the opportunity to serve on the ISB Executive Committee, I will bring:

Expertise in IDP Curation: My extensive experience with the DisProt database, best practices, ontologies and standards, that will help me to provide valuable insights into the curation processes.

Commitment to Education and Training: I am passionate about supporting and mentoring fellow curators. I have conducted numerous training sessions in English and in Spanish, both virtual and in-person, including a Spanish-language DisProt Biocuration course on the ELIXIR-SI eLearning platform. I aim to expand these educational initiatives to benefit curators worldwide.

Dedication to Collaboration and Community Building: My involvement in international projects, such as HUPO Proteomics Standards Initiative and Gene Ontology, have fostered strong collaborative skills and I am dedicated to building a supportive and connected biocuration community.

Within ISB, I would like to focus on the following areas:

  • Enhanced Training and Support: Develop comprehensive and accessible training programs, including multilingual options, to support curators from diverse backgrounds and regions in their career progression, especially those from lower-middle-income countries.
  • Standardization and Best Practices: Advocate for the adoption of standardized curation practices across databases, facilitating data integration and interoperability.
  • Community Engagement and Collaboration: Strengthen the global biocuration community by encouraging collaborative projects and networks, fostering a sense of common goal and mutual support among curators.

I am deeply honored to be this year’s recipient of the ISB Excellence in Biocuration Early Career Award 2024. This recognition increases even more my dedication to supporting and uplifting the global biocuration community. I am eager to contribute to the ISB Executive Committee, bringing enthusiasm, dedication, and a collaborative spirit to support and elevate our biocuration community even further.

Santhi Ramachandran

Position: Curator

Affiliation: GWAS Catalogue Curator, Cambridge, UK

Biosketch: I have been working in the field of biocuration since 2012, with a primary focus on variant curation. Over the years, I have gained extensive experience by working with prominent organizations and now at EMBL-EBI. My work has provided me with a strong foundation in biocuration practices, and I have also had the opportunity to engage with users of the curated data, gaining a deeper understanding of its practical applications in research and healthcare. This interaction has shaped my approach to curation, ensuring that the data we provide is accurate, reliable, and impactful for both scientific and societal advancement.

Motivation: I am motivated to run for a position on the ISB Executive Committee due to my decade-long experience in biocuration and my desire to contribute to the field’s growth. Over the past decade, I have worked with various organizations, including my current role at EMBL-EBI, where I have developed expertise in curating high-quality, impactful data. This experience has deepened my understanding of the complexities of biocuration and its vital role in supporting research and healthcare. I believe that the success of biocuration depends not only on data accuracy but also on how effectively this data is applied in real-world settings.

As a member of the ISB Executive Committee, I aim to contribute to the broader advancement of biocuration by leveraging my strong background in curation and my insights into the evolving needs of data users. I am particularly eager to promote stronger connections between curators and end-users, enhancing the practical impact of curated data. Additionally, I would advocate for expanding training programs and resources to support the next generation of biocurators, ensuring that ISB continues to lead the way in this critical field. Through these efforts, I hope to enhance the impact of biocuration within the scientific community.

Umasri Sankarlal

Position: Freelance Biocurator

Affiliation: Freelancer

Biosketch: My career started as a Biocurator participating in various projects involved in building comprehensive databases for Biomarker, Biological Pathway and Chemical compounds. Since 2004, my passion in biocuration has been growing, and volunteered myself wherever I got an opportunity. During my career break, I worked as freelance ontology mentor to developers, shared ideas on developing an ontology for online databases and supporting with necessary datasets for their project. I worked as short time Consulting Analyst with Thomson Reuters, Chennai on their Drug Forecasting database. Even though working a full-time employee in IT firm, I volunteer to be a member of ClinGen Intellectual Disability and Autism Gene curation working group panel and publishing the curated genes after my office hours.

Motivation: I nominate for a position in Equity, Diversity and Inclusion Committee. In my 20 years of work experience as a Biocurator, Patent analyst, IT Operation Analyst, Autosys Specialist and currently as Software Quality Analyst acquired technical skills with the help of diverse expertise team I worked with in various companies. I have always been treated equally without any gender bias and got motivated at my work place. The team have included people from various cultures and countries, and always supported in sharing their expertise knowledge to improve my career. Now it is my turn to return their kindness to others who need encouragement and support. Apart from doing at my current workplace, the role as a member of EDI committee in ISB will be more meaningful and have impact in Biocuration field.

Peter Uetz

Position: Associate Professor

Affiliation: Center for Biological Data Science, School of Life Sciences, Richmond, VA, USA

Biosketch: I have started the Reptile Database in 1996 when I was a graduate student at EMBL, Heidelberg, Germany. Since then, the database has become one of the most comprehensive biodiversity databases worldwide (being one of 160 databases in the Catalogue of Life consortium). I have also founded the Microbial Protein Interaction database, now a part of IntAct. After being an investigator at The Institute for Genomic Research (TIGR) and the Venter Institute (JCVI) for about 5 years I was hired as associate professor at VCU in Richmond, Va, in 2011. I am teaching courses in functional genomics and bioinformatics there, training students in biodiversity data-related curation and processing. The database and various papers about it have been cited 4000-5000 times.

Motivation: Biocuration is an undervalued part of biomedical sciences and I feel strongly that its role needs to be better promoted and students trained in this field. While all biomedical scientists are using various databases, they rarely appreciate the huge amount of work required to establish and maintain these data sources. My long career experience in database curation and promotion will help the ISB to promote and advance the field, although I am currently focusing on biodiversity data, an area that has been underrepresented at ISB, hence one of my goals is to strengthen the links to biodiversity and other biological sub-disciplines that are not well covered by ISB.

Huajin Wang

Position: Senior Librarian

Affiliation: Carnegie Mellon University

Biosketch: I am a Cell Biologist turned information professional and open science advocate. As a Senior Librarian at Carnegie Mellon University Libraries, I provide consultation and develop programs that help research communities make their research data and outputs more open, reproducible, and reusable, foster collaboration across disciplinary boundaries, and engage stakeholders to build a healthy data ecosystem. I have been in consulting roles for data curation and management on many research projects. As a life sciences researcher, I have collaborated with biologists, clinicians, and data scientists on many successful research projects in areas spanning membrane trafficking, lipid metabolism, bioinformatics, and management and analysis of multimodal datasets. I completed my PhD in Cell Biology at University of Alberta, postdoctoral research at Yale/Harvard, and independent research at Carnegie Mellon University. I was a co-founder and Director of the Open Science & Data Collaborations Program at CMU. I served a senior leadership role at the Center for Open Science to drive culture change in research communities with technology, community building, services, and thought leadership. I am a member of the Data Curation Network, FORCE11, and other organizations that contribute to the scholarly data ecosystem. I am also on the Advisory Committee of the UK Reproducibility Network (UKRN).

Affiliation: The biggest asset that makes me an excellent fit for the Executive Committee is my rich and multifaceted experience with data in the many roles I play – a scientist, a data steward, a community builder, and a strategic leader. During my career as a scientist, I worked with large varieties of research data and data formats, and deeply appreciated the value of well curated, open datasets. When I move into a librarian and open science role, it has been my mission to help researchers make data more open and reusable so that the results are more reproducible. I co-founded the Open Science & Data Collaborations program at CMU, and served as the Director of Program at the Center for Open Science (the nonprofit running OSF). In these roles, I helped researchers and communities navigate data sharing, stewardship and curation. I oversaw the strategy and execution of training and consulting services, launched community engagement and outreach initiatives, and supported communities and stakeholders to adopt data sharing infrastructure and best practices. The communities I worked with span a wide range of life sciences fields including neuroscience, cancer biology, genomics, and virology, with an emphasis on early career researchers and under represented groups.

Announcement for the 2024 Annual General Meeting (AGM)

The International Society for Biocuration (ISB) will hold its Annual General Meeting (AGM) on Tuesday, October 29th, 2024 along with presentations by our two biocurator career award winners, Sushma Naithani and Maria Victoria Nugnes.

Time:

  • 3:00–5:00 pm CET (Central European)
  • 2:00–4:00 pm GMT (British)
  • 10:00 am–12:00 pm EST (Eastern)
  • 8:00–10:00 am PST (Pacific)

Note that daylight savings begins in Europe/UK on October 27th, 2024 and daylight savings begins on November 3rd, 2024 in the USA, so there’s a slightly different offset than usual. All canonical times for this event are based on European time!

Schedule (in CET):

This meeting will be recorded, by attending the meeting you are agreeing to be recorded. The recording will be available on the ISB website after the meeting.

2025 Applications for Travel Fellowships

Submit applications using the Travel Fellowship Application Form

Application deadline extended until 5:00 PM Eastern Time November 25th, 2024

There are 1 in-person (low-income country only) and 5 virtual awards remaining.

Applications are open until 5:00 PM Eastern Time, October 31st, 2024.

For the 2025 conference in Kansas City, the ISB will offer 4 In-Person Travel Fellowships covering up to 2,500 CHF in costs. The ISB will also offer 5 Virtual Travel Fellowships covering the the cost of early bird member or non-member virtual registration for the conference.

The award notification will be sent via email at least 3 months before the conference will take place.

Announcement for winners of “Excellence in Biocuration Awards 2024”

The International Society for Biocuration (ISB) would like to congratulate the recipients of the 2024 Excellence in Biocuration Early and Advanced Career awards:

  • Early – Maria Victoria Nugnes from the University of Padova
  • Advanced – Sushma Naithani from Oregon State University

Thank you to the Award Subcommittee:

Parul Gupta 

Sue Bello

Sara Chuguransky

Thank you to all the ISB members who participated in the voting.

2024 Nominations for the Excellence in Biocuration Advanced Career Award

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 27 June – 25 July 2024

NOMINEES

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

  • Peter D’Eustachio, NYU Grossman School of Medicine, New York, USA
  • Steven Marygold, FlyBase, Cambridge, UK
  • Sushma Naithani, Plant Reactome Knowledgebase, Oregon, USA
  • Achchuthan Shanmugasundram, Genomics England Limited, London, UK
  • Peter Uetz, Center for Biological Data Science, Virginia, USA

Detailed Descriptions

Peter D’Eustachio, NYU Grossman School of Medicine, New York, 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.

Publications

  • 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

Steven Marygold, FlyBase, Cambridge, UK

Steven is a curator, nomenclature advisor and the group coordinator at FlyBase (Cambridge UK) with a special interest in enzymes, metabolism, ncRNAs and gene groups. Steven’s team established the gene group resource https://academic.oup.com/nar/article/44/D1/D786/2502590 and has worked systematically to improve the annotation of many classes of genes at FlyBase including most recently tRNAs, snoRNAs, and reviewing all ~3700 enzyme-encoding genes. He collaborates widely with many other data resources including the Alliance of Genome Resources member databases, UniProt, Rhea, Reactome, RNACentral and members of the fly community. Steven is also a major contributor to the Gene Ontology Consortium, and his work here is improving the representation of enzymes and metabolism across species in in both the ontology and annotation.

  • Publications
    • The UDP-Glycosyltransferase Family in Drosophila melanogaster: Nomenclature Update, Gene Expression and Phylogenetic Analysis Ahn, S.-J., Marygold, S.J. Frontiers in Physiology, 2021, 12, 648481 PMID: 33815151
    • The DNA polymerases of Drosophila melanogaster Marygold, S.J., Attrill, H., Speretta, E., …Rong, Y., Yamaguchi, M. Fly, 2020, 14(1-4), pp. 49–61 PMID: 31933406
    • Towards comprehensive annotation of Drosophila melanogaster enzymes in FlyBase Garapati, P.V., Zhang, J., Rey, A.J., Marygold, S.J. Database, 2019, 2019 PMID: 30689844
    • Using FlyBase to find functionally related drosophila genes Rey, A.J., Attrill, H., Marygold, S.J. Methods in Molecular Biology, 2018, 1757, pp. 493–512 PMID: 29761468
    • The translation factors of Drosophila melanogaster Marygold, S.J., Attrill, H., Lasko, P. Fly, 2017, 11(1), pp. 65–74 PMID: 27494710

Sushma Naithani, Plant Reactome Knowledgebase, Oregon, USA

Dr. Sushma Naithani is an Associate Professor Senior Research at Oregon State University. Naithani is the Lead biocurator of the Plant Reactome knowledgebase ((https://plantreactome.gramene.org), a pathway portal of the Gramene database. Since 2012, she has led the biocuration of plant pathways and served as outreach and training coordinator for database users. In addition, Naithani has led the development and biocuration of species-specific metabolic network for strawberry (FragariaCyc) and grapevine (VitisCyc) and contributed to the biocuration of maize-specific metabolic network MaizeCyc— all Cyc databases are available at http://pathways.cgrb.oregonstate.edu/metabolic.html. Naithani has trained 20 undergraduate students at Oregon State University on gene and pathway biocuration; conducted two in-person community curation workshops; and two online biocuration training workshops for the graduate students. Naithani also made significant contribution to Gene Ontology, and Grapevine Information system. From 2022-present, Naithani also serves as the Steering Committee Member for the AgBiodata consortium (https://www.agbiodata.org), a consortium of agricultural biological databases and associated resources. Naithani co-organized the ‘Ontologies and Systems Biology workshop’ at the annual Plant and Animal Genome conference (2014-2024). Naithani’s involvement in promoting equity and diversity within the scientific community is evident through her service on the ISB Equity, Diversity, and Inclusion (EDI) committee from 2021 to 2022. Notably, she chaired the ‘Addressing Implicit or Unconscious Bias Workshop’ at the 14th Annual Biocuration Conference in 2021. In subsequent years, she co-chaired the 15th Annual Biocuration Conference in 2022 (virtual) and served on the Scientific Committee for the 17th Annual Biocuration Conference held in India in 2023.

  • Publications
    • Gupta P., J. Elser, E. Hooks, P. D’Eustachio, P. Jaiswal and S. Naithani (2024). Plant Reactome Knowledgebase: empowering plant pathway exploration and OMICS data analysis. Nucleic Acids Res., 52 (D1): D1538-D1547. doi:10.1093/nar/gkad1052. PMID: 37986220
    • Gene Ontology Consortium (2023). The Gene Ontology Knowledgebase in 2023. Genetics, doi: 10.1093/genetics/iyad031 PMID: 36866529
    • Tello-Ruiz M.K., S. Naithani, P. Gupta, A. Olson, S. Wei, J. Preece, Y. Jiao, B. Wang, K. Chougule, P. Garg, J. Elser, S. Kumari, V. Kumar, B. Contreras-Moreira, G. Naamati, N. George, J. Cook, D. Bolser, P. D’Eustachio, L.D. Stein, A. Gupta, W. Xu, J. Regala, I. Papatheodorou, P.J Kersey, P. Flicek, C. Taylor, P. Jaiswal, and D. Ware (2021). Gramene 2021: harnessing the power of comparative genomics and pathways for plant research. Nucleic Acids Res. 49 (D1): D1452-D1463. doi: 10.1093/nar/gkaa979 PMID: 33170273
    • Harper L., J. Campbell, E.K.S. Cannon, S. Jung, M. Poelchau, R. Walls, C. Andorf, E. Arnaud, T. Berardini, C. Birkett, S. Cannon, J. Carson, B. Condon, L. Cooper, N. Dunn, C. G. Elsik, A. Farmer, S.P. Ficklin, D. Grant, E. Grau, N. Herndon, Z.-L. Hu, J. Humann, P. Jaiswal, C. Jonquet, M.-A. Laporte, P. Larmande, G. Lazo, F. McCarthy, N. Menda, C. Mungall, M. Munoz-Torres, S. Naithani, et al. (2018). AgBioData consortium recommendations for sustainable genomics and genetics databases for agriculture. Database, 2018:1-32, doi: 10.1093/database/bay088 PMID: 30239679
    • Naithani S., R. Raja, E.N. Waddell, J. Elser, S. Gouthu, L.G. Deluc and P. Jaiswal (2014). VitisCyc, a metabolic pathways knowledgebase for grapevine (Vitis vinifera). Frontiers in Plant Science, 5: 1, doi: 10.3389/fpls.2014.00644. PMID: 25538713

Achchuthan Shanmugasundram, Genomics England Limited, London, UK

Achchuthan began his biocuration journey as a PhD student at the University of Liverpool, where he manually curated metabolic pathways for Apicomplexan parasites and developed a web database. Following a brief postdoctoral period focusing on genome annotation and curation, he returned to Liverpool as a biocurator, working on the genomes of neglected tropical parasites and fungal pathogens in the non-model organism database VEuPathDB. During this time, he played a pivotal role in developing VEuPathDB’s framework for phenotypic curation of fungal pathogens by leveraging existing OBO Foundry ontologies.

A strong proponent for data standardisation and sharing, Achchuthan often worked as the sole biocurator at VEuPathDB. He actively collaborated with other resources to better represent the taxon-specific biology of neglected species in ontologies such as Gene Ontology (GO). His contributions included submitting VEuPathDB’s annotations to GO and coordinating the integration of curated data from other resources into VEuPathDB.

Achchuthan contributed to outreach efforts, educating users on the importance of curated datasets, working on standardisation and integration of user curated datasets, and developing SOPs and frameworks for community curation of gene functions and phenotypic datasets in VEuPathDB. He also embedded curation and ontologies into his genomics teaching at Liverpool.

Achchuthan is currently working with Genomics England’s PanelApp, curating gene-disease associations within gene panels. His focus has always been on the complete data cycle, ensuring appropriate representation of curated data by contributing to the development and testing of new features. Despite transitioning through various roles, curation has remained at the heart of his career.

  • Publications
    • Shanmugasundram, A. Increasing gene coverage for developmental disorders in PanelApp using the Gene2Phenotype database. Genomics England bioinformatics blog series. 2 May 2024; https://www.genomicsengland.co.uk/blog/increasing-gene-coverage-for-developmental-disorders-in-panelapp-using-the-gene2phenotype-database.
    • Basenko, EY., Shanmugasundram, A., Boehme, U., Starns, D., Wilkinson, PA., Davison, HR., et al. What is new in FungiDB: a web-based bioinformatics platform for omics-scale data analysis for fungal and oomycete species. Genetics. 2024; 227(1): iyae035. PMID: 38529759.
    • Alvarez-Jarreta, J., Amos, B., Aurrecoechea, C., Bah, S., Barba, M., Barreto, A., et al. VEuPathDB: the eukaryotic pathogen, vector and host bioinformatics resource center in 2023. Nucleic Acids Research. 2024; 52(D1): D808-D816. PMID: 37953350.
    • Shanmugasundram, A., Starns, D., Boehme, U., Amos, B., Wilkinson, PA., Harb, OS., et al. TriTrypDB: An integrated functional genomics resource for kinetoplastida. PLoS Neglected Tropical Diseases. 2023; 17(1): e0011058. PMID: 36656904.
    • Shanmugasundram, A., Gonzalez-Galarza, FF., Wastling, JM., Vasieva, O., Jones, AR. Library of Apicomplexan Metabolic Pathways: a manually curated database for metabolic pathways of apicomplexan parasites. Nucleic Acids Research. 2013; 41(D1): D706-D713. PMID: 23193253.

Peter Uetz, Center for Biological Data Science, Virginia, USA

The nominee has founded the EMBL Reptile Datatabase as a graduate student in 1995. It was thus one of the first biodiversity databases worldwide. Uetz has been its lead curator since its inception for almost 30 years. After the last contributor to the database, Ramu Chenna, had left EMBL, the database moved to TIGR in 2008 and then to an independent site in 2010. Uetz has curated about 50,000 papers over the past 30 years for a database that receives more than 2000 queries per day and has been cited more than 4,000 times in the scientific literature. He has also trained numerous student curators, programmers, and other volunteers who have helped to maintain the database. The Reptile Database is now a key contributor and collaborator of many other data sources, such as the NCBI Taxonomy, iNaturalist (a citizen science project), IUCN (Red List of threatened species), the Catalogue of Life, and others. Uetz has published about a dozen papers about the database and its history. The database contains descriptions of ~12,000 species of reptiles, >20,000 images, geographic and taxonomic information, as well as links to about 55,000 references online. The nominee also maintains a mailing list of about 5,000 people who receive regular updates on reptile taxonomy and topics related to the Reptile Database. More recently, work on the database included the establishment of standardized vocabularies (ontologies), the use of AI such as ChatGPT for data mining, and collaborations on image analysis and automated species recognition.

  • Publications
    • Uetz, P. & Etzold, T. 1996 The EMBL/EBI Reptile Database. Herpetological Review 27: 174-175
    • Uetz, P. & Stylianou, A. 2018 The original descriptions of reptiles and their subspecies. Zootaxa 4375 (2): 257-264, https://doi.org/10.11646/zootaxa.4375.2.5
    • Uetz P, Cherikh S, Shea G, Ineich I, Campbell PD, Doronin IV, Rosado J, Wynn A, Tighe KA, Mcdiarmid R, Lee JL, Köhler G, Ellis R, Doughty P, Raxworthy CJ, Scheinberg L, Resetar A, Sabaj M, Schneider G, Franzen M, Glaw F, Böhme W, Schweiger S, Gemel R, Couper P, Amey A, Dondorp E, Ofer G, Meiri S, Wallach V. 2019 A global catalog of primary reptile type specimens. Zootaxa 4695 (5): 438–450, https://doi.org/10.11646/zootaxa.4695.5.2
    • Uetz P, Koo MS, Aguilar R, Brings E, Catenazzi A, Chang AT, Chaitanya R, Freed P, Gross J, Hammermann M, Hosek J, Lambert M, Sergi Z, Spencer CL, Summers K, Tarvin R, Vredenburg VT, Wake DB 2021 A Quarter Century of Reptile and Amphibian Databases. Herpetological Review 52 (2): 246-255
    • Uetz, P.; Darko, Y.A.; Voss, O. 2023 Towards digital descriptions of all extant reptile species. Megataxa 010 (1): 027–042, https://doi.org/10.11646/megataxa.10.1.6

Excellence in Biocuration Early Career Award 2024 Nominations

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

Call for Proposals to host the 2026 International Biocuration Conference.

Dear Colleagues,

The Executive Committee of the International Society for Biocuration (ISB) would like to once again invite tenders to host the 19th International Biocuration Conference in Europe during the Northern Spring or Summer of 2026.

Individuals and organizations interested in applying may do so by sending a proposal to the ISB Executive Committee (intsocbio@gmail.com) on or before August 31st, 2024. 

The successful bidder will be notified by October 1st, 2024. The ISB Executive Committee will publicly announce the selected organization or individuals during the 18th International Biocuration Conference, held in Kansas City, MO, USA in April, 2025.

Format:

Proposals should be short; length should not exceed one side of an A4 or US letter size sheet, using 11 point font. The proposal should contain:

  • The name and institution of the local organizer
  • Details of the proposed venue for at least 150 participants, if the venue has less space please provide plans for hybrid attendance. Typical numbers have not exceeded 350 participants.
  • The range of dates available for the conference. Previous conferences typically have 3-4 days of main conference agenda and 1-2 days of workshops. Dates should not overlap with local holidays.
  • A brief outline of a strategic plan to attract a broad range of participants from the Biocuration community
  • As fair gender representation is positively encouraged by the ISB; we would also like to know how the applicant intends to accomplish this.

In a continued effort to bring our meeting to curators in all geographic regions, we strongly encourage ISB members in Europe and Africa to put forward proposals to bring the ISB meeting to your region once again, or for the first time!

REGIONS ROTATION: 

  • North and South America
  • Europe and Africa
  • Asia and Australasia

This Call for Applications is also available on the ISB website at https://www.biocuration.org/events-and-conferences. For more information about the ISB and our previous conferences, please visit http://www.biocuration.org.

We look forward to hearing from you!

Your colleagues at the ISB Executive Committee.

2024 Travel Grant Applications

Description

The ISB provides conference travel grants for biocurators, software engineers, students, etc. whose work contributes to biocuration.

All conference participants associated with biocuration can apply; however, priority will be given to students and those in junior posts, as well as to applicants from low to middle-income countries or countries suffering from natural and humanitarian disasters. The award
committee will aim to choose awardees from a range of countries distributed in different continents, with around 2/3rd of the awards ring-fenced for low to middle-income countries and countries suffering from natural and humanitarian disasters. Previous recipients can apply again; however, they will be given a lower priority.

As the 17th International Biocuration Conference, will be held in Faridabad, India the ISB is supporting 5 International travel grants with a maximum of 3,000 CHF to cover travel expenses (e.g. hotel, flight, subsistence and ground transportation) and 6 travel grants with a maximum of 500 CHF for applicants working in India.

Application requirements

The applicant does not have to be an active ISB member, as the travel award will include ISB membership for 1 year.

The applicant must have submitted an abstract for a presentation/poster and only applicants who have had the abstract accepted for either a presentation or a poster by the conference organising/scientific committee will be eligible for a travel award. In addition, the applicant must agree to give either a presentation or a poster if they are successful in their application, or the award will be withdrawn.

Only the presenting author from a multi-author abstract may apply for a travel grant.

Once notified of a successful application, the recipient must register for the conference and arrange their travel themselves.

The recipient must agree to provide a photo of themselves before the meeting and provide a short summary of their current role and how they benefited from the conference after attending the conference. The photo will be included in the slides circulating during interval breaks. Both the photo and summary will be uploaded to the ISB website, circulated in the ISB Newsletter, and distributed via other online formats.

An individual can only be awarded a travel grant a maximum of once every 3 years and can receive no more than 2 travel grants.
Application

The applicant must explain why they are requesting travel funds and how attending the ISB annual conference will benefit their career.

The deadline for application will be determined by the date of each conference.

Applications for the 17th International Biocuration Conference in Faridabad, India ( 5th March to 8th March 2024 ) are now open. The first round of applications are closed and a second round of applications are now open.

Apply here, open for applications from 30 October,

  • Deadline date: Friday, 01 December 2023.
  • Deadline time: 5pm GMT / 9:30pm India Standard Time.

Notification

The award notification will be sent via email at least 3 months before the conference will take place. For the 17th International Biocuration Conference notifications of award will be sent in November 2023.

Updates for 2024 Travel Awards (India Conference)

  • Applications for travel awards will open 4 months before the conference and will be open for one month. 
  • Award recipients will be required to have an accepted abstract at the conference and register to attend the conference, or the award will be withdrawn.
  • Being a member of the ISB is not a requirement to apply for or receive a travel grant. The travel award recipients will also receive a free ISB membership for one year.
  • We will offer 11 travel fellowships:
    • 2 awards for applicants from any area of the world (each 3,000 CHF maximum)
    • 3 awards for applicants from low-income countries: global north and global south (each 3,000 CHF maximum)
    • 6 awards for applicants working in India (each 500 CHF maximum)
  • The ISB Awards subcommittee will review the applications, with consideration of our priority criteria (as listed above in the description) and inform the awardees within 2 weeks of the closing date.
  • We will reopen the application deadline if there are any unassigned travel grants.

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