Author: SusanBello

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.

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!

Pascale Gaudet and Sandra Orchard – Recipients of the 2023 Exceptional Contribution to Biocuration Award

It is our great pleasure to announce the recipients of the 2023 Exceptional Contribution to Biocuration Award, the voting this year resulted in a tie and thus we have two recipients:

Pascale Gaudet, Swiss Institute of Bioinformatics, Switzerland

Pascale Gaudet has worked in the biocuration field for over 19 years first at DictyBase and more recently NextProt and the Gene Ontology Consortium. Pascale is currently the GO Project Manager and oversees all editorial content. She has worked continually not only to improve the Gene Ontology structure and formalization, but also has driven the project to produce high quality phylogenetically inferred GO annotation using the PAINT annotation system. The PAINT annotations are much more specific than existing annotation from automated sources, because they can be refined on a family-by-family and even gene-by-gene basis. This system is now providing over 3.5 million annotation in the GOA annotation database.

Pascale is working constantly to refine legacy and dormant annotations across the ontology, and with multiple collaborating groups to refine the both ontology and annotation to ensure that both are fit for purpose. She is driving the coordination of overhauls in many areas of GO ontology including multi-species processes, transcription, chromatin remodeling, tacking each are with insight and attention to detail but never failing to see the bigger picture. She has been key to the communication between different interested groups and manages the numerous discussions with efficiency. This is work that almost every bench biologist depends on to some degree, but is largely unrecognized because it depends on thousands of incremental tasks that are not usually attributed or described in publications.

Sandra Orchard, EBI, Hinxton, Cambridge, UK

Sandra has worked tirelessly for the biocuration community for over 20 years. She is currently the Team Leader for Protein Function Content at UniProt (https://www.uniprot.org), and is therefore responsible for a major part of probably the most used biological database in the world. In this role, she also maintains two other key interfaces: the Complex Portal (https://www.ebi.ac.uk/complexportal) and the Enzyme Portal (https://www.ebi.ac.uk/enzymeportal/). Previously, Sandra led the IntAct molecular interaction database (https://www.ebi.ac.uk/intact) and managed the IMEx consortium of collaborating interaction databases. She has also been key in establishing standards within the proteomics community, and has made significant contributions to the InterPro database and the Gene Ontology. Sandra has always been a strong proponent of FAIR principles, education and the biocuration community: she has chaired and/or contributed to numerous biocuration-related committees; she established the first formal educational qualification in biocuration (PgCert at the University of Cambridge); and she has been a long-time supporter of the ISB, serving as treasurer from 2015-2018 and chair from 2018-2020. Sandra has published ~200 papers on biocuration methods, standards and databases, which serves as a measure of her impact and importance both to the biocuration community as well as to the researchers who depend on the many resources to which she has contributed.

Congratulations Pascale and Sandra!

Thank you to the Awards Committee:

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

Many thanks to ISB members for voting!

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