Category: Award Recipient

Recipient of the 2023 Excellence in Biocuration Early Career Award

Democratizing Biocuration, or, How I Learned to Love the Drive-by Curation

Charles Tapley Hoyt, Laboratory of Systems Pharmacology Harvard Medical School, MA, USA

Abstract: The increasing reliance of artificial intelligence applications in biomedicine on reliable structured data, metadata, and knowledge accentuates the need for effective, sustainable biocuration. While there has been a historical disconnect between such consumers and biocurators, the looming paradigm shift towards the open code, open data, and open infrastructure (O3) principles presents an opportunity to engage and empower consumers to contribute to the maintenance and ongoing development of the resources they use. In this talk, I will reflect on how biocuration became an important facet of my job as a systems and networks biologist interested in translational research as I became more aware of the importance of data quality and provenance. Notably, I will highlight the concept of the drive-by curation and how it fits into a more community-oriented future vision for biocuration.

Nico Matentzoglu – Recipient of the 2023 Excellence in Biocuration Advanced Career Award

Closing the gap between effective Biocuration and meaningful ontology evolution

Nico Matentzoglu, Monarch Initiative, Semanticly, Greece

Effective Biocuration is dependent on controlled vocabularies such as biomedical ontologies. From the perspective of biocurators, it is of central importance to get new terms integrated into the ontology as soon as they are needed. From the perspective of the users who want to exploit the ontology for analysing their data, however, it is key that the integrated term is carefully curated into the ontological structure, which is difficult and time-consuming. This provides a dilemma for ontology developers who, on the one side, are expected to respond quickly to curation requests, but on the other side are tasked to provide a reliable resource for the community. In this talk, I will describe a strategy based on change languages, design patterns and templates that could be used to “outsource” some of the ontology curation to biocurators, thereby creating a drastically reduced effort and subsequently much tighter turnaround time for new (and changed) term requests. I will discuss the importance of such community contributions to open ontology projects and hope to convince the biocuration community to engage more closely with the ontology curation process. 

Announcement for 2023 winners of “Excellence in Biocuration Awards”

We are pleased to announce winners of “Excellence in Biocuration Award” for the year 2023 in two categories:

Charlie is in 3/4 profile playing a guitar with his mouth open singing into a mic with an orange covering. He is wearing a black t-shirt and orange slacks.

Early Career Award – Charles Tapley Hoyt, Laboratory of Systems Pharmacology Harvard Medical School, MA, USA

Charlie has been so amazingly busy in such a short amount of time. He is a Research Fellow at Harvard Medical School and the primary curator, developer, and maintainer of several community datasets and databases.These include Bioregistry, which promotes standardization of prefixes, CURIEs, and URIs when used to reference entities/concepts in the life sciences. He contributes to Biomappings, which provides mappings between named biological entities. He created Chemical Roles Graph, which curates mechanistic relations between small molecules and biological processes, pathways, and diseases in an ontological framework. He is a frequent contributor to other curated datasets, and promotes the concept of the Drive-by Curation and of progressive governance models to enable community curation and strengthen project sustainability.

Charlie actively contributes to community efforts; he is an active member of the OBO Foundry ontology community, focusing on promoting standardization of semantics, better curation and coding practices through continuous integration/continuous development and social workflows, promotes more granular attribution and explicit/transparent licensing to better enable reuse.

He contributes to standards development including the SSSOM standard, a simple standard for sharing ontology mappings that includes explicit semantics and provenance, and is a member of Biological Expression Language (BEL), a domain-specific language for representing causal, correlative, and associative relationships between biomedical entities as well as their associated contextual and provenance annotations.

He has mentored a large number of students at the Institute for Algorithms and Scientific Computing (SCAI) and is frequently available to lend support to public projects such as PyBEL and PyKEEN.

Charlie is actively engaged in the Biocuration community and co-chaired the most recent Biocuration 2023 conference in Padova, Italy and participated in the organizing committee of the Virtual Biocuration 2022 Conference. His charisma, enthusiasm and energy are invaluable to our community. His enthusiasm and energy are rare and he deserves to be celebrated.

Advanced Career Award – Nicolas Matentzoglu, Monarch Initiative, Semanticly, Greece

The head and shoulders of Nico appear in front of a background of blue sky and green trees. Nico is wearing a dark blue shirt.

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.

Thank you to the Award subcommittee:

  • Nicole Vasilevsky
  • Parul Gupta
  • Susan Bello
  • Ruth Lovering

Many thanks to the ISB members for voting!

2023 Travel Grant Awardees

Travel Grant Awardees – 16th Annual International Biocuration Conference

The ISB are pleased to award fellowships to the following six members to attend the forthcoming ISB conference. These grants help cover travel expenses associated with attending the conference e.g. accommodation, flights and ground transportation.

Congratulations to you all!

Yukie Akune is a postdoctoral bioinformatician in the Glycosciences Laboratory at Imperial College, London, UK directed by Professor Ten Feizi and Dr Yan Liu. Dr Akune and her collaborators at the Complex Carbohydrate Research Center in Atlanta, Georgia have developed the Carbohydrate micro-Array Analysis and Reporting Tool (CarbArrayART), for storing, processing and presenting glycan array data, as well as data submission to the international GlyGen glycan microarray repository that has been developed with her input. She is committed to establishing data-mining systemsin the field of glycan recognition including definitions of parameters for curation and annotation of published glycan microarray dataon diverse glycan-recognition systems in health and disease.
Shasank Sekhar Swain (post-doctoral researcher, Regional Medical Center (ICMR), Bhubaneswar, India) introduced a novel ‘hybrid drug’ concept using chemical conjugationbetween phytochemicals and clinically inactive or obsolete drugs during his doctoral research work. Currently, he is working on developing a greater number of potential hybrid drug candidates against bacteria, mycobacteria, cancer, etc. As an early-career research scientist in bioinformatics, he uses widely available computer-aided drug discovery platforms and bioinformatics tools to select the most drug-able hybrid drugs prior to synthesis and clinical experiments in order to reduce the resources and costs associated with traditional hit-and-trial drug discovery methods.
Dominik Martinat is a PhD student at the Department of Physical Chemistry of Palacky University in Olomouc, Czech Republic. The focus of his study is an integration of biomedical databases. The main project he participates in is MolMeDB (Molecules On Membrane Database).
Anna Spackova, is a PhD student at Palacky University in Olomouc, Czech Republic, Department of Physical Chemistry. Anna is also a bioinformatician and her research involves mainly tools connected to protein structure especially to protein tunnels, that link the surface with active sites of the protein. Her main focus is the the MOLEonline tool together with the ChannelsDB database.
Nishad Thalhath is a doctoral candidate in Information Science and a member of the Metadata Laboratory at the School of Library, Media and Information Studies, University of Tsukuba, Japan.His research interests include metadata standards, knowledge graphs, and (meta)data interoperability. Before becoming a doctoral student, he worked as a developer, engineer and consultant in various IT and ITES projects. He currently works as a part-time researcher in the Laboratory for Large-Scale Biomedical Data Technology, RIKEN Center for Integrative Medical Sciences, Japan, where he develops and manages the metadata and integration systems for omics data.
Karina Martinez, is a graduate student in the Bioinformatics and Molecular Biochemistry MS program at The George Washington University in Washington, DC and is a member of the GlyGen data management team. She is working on curating glycan expression levels in the presence and absence of disease from the literature. She expects this effort to result in a set of publicly available datasets designed for bioinformatic and machine learning applications. She is also working in the biomarker curation space to create a comprehensive dataset of glycan biomarkers which will present new opportunities for data mining.

Announcement for winners of “Excellence in Biocuration Awards”

We are pleased to announce winners of “Excellence in Biocuration Award” for the year 2022 in two categories:

Early Career Award – Shirin Saverimuttu, SciBite Limited, Wellcome Genome Campus Hinxton, Cambridge, UK

Shirin started her biocuration career in 2019 at University College London (UCL) as a Gene Ontology biocurator. As a biocurator at UCL, she focussed on the curation of microRNAs and helped to develop a resource for more consistent annotation of microRNAs. During this time, she helped master students with their annotation projects. After being awarded a COST grant she spent a week in Italy with Dr Panni, Università della Calabria, where she exchanged information about microRNA annotation. In late 2020, Shirin joined the Polygenic Score (PGS) Catalog at EMBL-EBI as an intern biocurator and got trained to identify suitable PGS publications and extract polygenic scores from them, along with relevant metadata, for inclusion in the PGS Catalog. Later, she continued to work as a full time biocurator for both the PGS Catalog and GWAS Catalog at EMBL-EBI. Since 2021, Shirin has been working at SciBite as a scientific curator. At SciBite, she is involved in developing ontologies for customers as well as updating SciBite’s pre-existing vocabularies. Shirin enjoys working as a biocurator and would like to thank the ISB community for this recognition.

Advanced Career Award – Antonia Lock, European Bioinformatics Institute, Hinxton, Cambridge, UK

Following a PhD in molecular biology, Antonia started her career as a curator at the PomBase database in 2011. From 2016, she split her time to work with the drug discovery company Healx. From 2020, she started working full time biocurator at UniProt. Antonia has enjoyed being part of a varied range of projects over her career from curating model and pathogenic organisms to human, drugs, and diseases, developing new procedures, encouraging community data submissions, and problem-solving data display and software specification. Antonia is proud to have developed standards to describe metadata for genome-wide HTP data sets, mapped controlled vocabularies to ontologies, and done ground-work curation for a genetic disorder with drugs currently in clinical trial. In all her roles she has promoted the efficient use of curated data by training users, students, and novice curators.

Thank you to the Award subcommittee:

  • Parul Gupta (Chair)
  • Ruth Lovering
  • Randi Vita
  • Caio Cesar De Carvalho
  • Rama Balakrishnan

          Many Thanks to ISB members for voting!