Category: The ISB

Executive Committee Candidates 2025

The election of three members of the International Society for Biocuration Executive Committee (ISB EC) will be held from September 22nd – October 3rd, 2025.

Emails will be sent to current members on September 25th. Only current members, as of September 21st, 2025, 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 four 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:

TBK Reddy

Position: Genomic Standards Group Lead

Affiliation: DOE Joint Genome Institute Lawrence Berkeley National Lab, Berkeley, CA, USA

Biosketch: Dr. T.B.K. Reddy has devoted more than 25 years to advancing the field of biocuration through leadership in the development and stewardship of internationally recognized biological databases. He began his career at The Jackson Laboratory, where he contributed to the Mouse Genome Database, one of the earliest and most influential model organism resources. He later directed curation efforts at the Tuberculosis Database (TBDB), integrating genomic and functional data to accelerate research on a critical global health challenge.

Since 2011, Dr. Reddy has led the Genomic Standards Group at the U.S. Department of Energy Joint Genome Institute (JGI), Lawrence Berkeley National Laboratory. In this role, he oversees the Genomes Online Database (GOLD), a flagship repository that provides curated metadata for genomes, metagenomes, and related projects worldwide. Under his guidance, GOLD has become a cornerstone for microbial genomics and microbiome research, setting benchmarks for data standards and interoperability.

Throughout his career, Dr. Reddy has championed the use of controlled vocabularies, metadata standards, and FAIR principles to ensure that curated data are accurate, discoverable, and reusable. He has co-authored numerous peer-reviewed papers, trained students and curators, and played an active role in the International Society for Biocuration community.

Motivation: I am motivated to serve on the ISB Executive Committee because I believe the future of biocuration depends on our ability to adapt quickly and stay relevant in an AI-centric scientific world. Over the past 25 years, I have led curation efforts at the Mouse Genome Database, the Tuberculosis Database, and now the Genomes Online Database (GOLD) at the DOE Joint Genome Institute. Across these projects, I have seen how curated metadata is not just infrastructure—it is the foundation that drives biological discovery. Today, AI and machine learning offer powerful opportunities, but their success depends on high-quality, standardized, and comprehensive metadata. If we continue with “business as usual,” we risk being left behind. I see ISB playing a critical role in preparing our community to respond to rapidly changing needs, from curating massive new datasets to adopting AI-assisted workflows that augment curator expertise.

On the Executive Committee, I will work to:

1) Position ISB at the forefront of AI-ready curation standards.

2) Expand community training that integrates both best practices and new tools.

3) Foster agility in ISB activities so we can meet emerging challenges and continue to accelerate discovery.

Kalpana Panneerselvam

Position: IntAct Team lead/Senior curator

Affiliation: EMBL-EBI, Hinxton, Cambridgeshire, UK

Biosketch: I began my biocuration career in 2009, working on projects involving the bioindexing of key terms from scientific publications. I then served as a curator for Ingenuity Variant Analysis (QIAGEN), where I focused on clinical variants and their associations with phenotypes, therapeutic interventions, population studies, and biomarkers relevant to clinical conditions and therapies.

Currently, I contribute to the IntAct database, specializing in the curation of molecular interaction data. My work emphasizes building contextual interactomes, including clinical contexts and tissue-specific interactions, as well as studying how clinical variants affect interactomes. I also curate detailed features such as binding domains involved in interactions, interaction kinetics, and the roles of inhibitors, agonists, and antagonists. In addition, I have been involved in mapping tissues and cell lines where interactions are detected into ontologies at their simplest context, with mappings shared to EFO for public access. I also contributed to the proposal for upgrading the XML-maker into a more user-friendly tool for generating IMEx-compliant high-throughput interaction data, ready for import into the curation pipeline.

Beyond curation, I have actively engaged in community outreach and training activities, particularly in the areas of molecular interaction network biology and data analysis.

Motivation: I see serving on the Executive Committee as an opportunity to give back to the community that has shaped my career, while working with colleagues to ensure that biocuration continues to grow as a recognized and valued discipline. I would be particularly interested in contributing to the committee’s efforts in coordinating micro-grant and fellowship submissions that support training and innovation in biocuration, as well as in preparing calls for hosting future Biocuration meetings to ensure global representation and inclusivity.

Susan Bello

Position: Senior Scientific Curator

Affiliation: Mouse Genome Informatics, The Jackson Laboratory, Bar Harbor, ME, USA

Biosketch: I have been a curator for Mouse Genome Informatics for over 20 years. While my research background was in oceanography and toxicology, I translated that experience into mouse phenotypes. I began by concentrating on curation of phenotypes and alleles developing an understanding of nomenclature standards and use of ontologies. Over time, I moved into work on ontology development for the Mammalian Phenotype, Human Disease, Vertebrate Trait, and UPheno ontologies. I’ve also been involved with website development, including the creation of the Human – Mouse: Disease Connection portal at MGI. With the advent of the Alliance of Genome Resources, I work as part of a team on the integration and harmonization of allele, phenotype, and disease curation across species. This project has included developing LinkML models to support curation needs across a wide range of species.

Motivation: I have been a member of the ISB since 2009 and have been on the ISB EC for the past 3 years, acting as chair of the EC for the past 2 years. On the EC, I have served on the Awards and Training & Outreach subcommittees throughout my tenure. On the Training & Outreach subcommittee, I’ve helped to identify additional groups of curators that could be brought into the ISB to expand our membership. I was part of the organizing committee for the 2025 Biocuration conference. I help to keep the ISB active on social media, especially on our Bluesky account. As chair I have worked to keep the many tasks of the EC progressing forward and to update procedures for the EC. I’ve also been involved with our interactions with the Global Biodata Coalition providing insights and feedback for their interactions with funders. In a second term on the EC, I hope to continue to increase the visibility of the work of biocurators, expand the membership of the ISB, and improve the broader communities understanding of the importance of and value added by the work of biocurators to hopefully increase support for biocuration.

Ranjana Kishore

Position: Biocurator, WormBase and Alliance of Genome Resources

Affiliation: Biology and Biological Engineering (BBE), California Institute of Technology, Pasadena, CA 91125

Biosketch: I am a biocuration scientist and life sciences professional with over 20 years of experience in the fields of biomedical curation and data management with an in-depth expertise in modeling, integration and display of biomedical data and automated methods of text summarization. I have contributed extensively and worked with widely used biomedical resources such as the Gene Ontology Consortium, WormBase, and groups such as EBI-EMBL and most recently with the Alliance of Genome Resources (Alliance). I have led several projects from conception to completion: biocuration of human models of disease for WormBase and automated text summarization of gene data that led to thousands of gene summaries for C. elegans and nine other nematode and parasitic species. More recently I led a similar effort at the Alliance which has resulted in thousands of gene summaries for nine major model organism species, now integrated into resources such as NCBI RefSeq, directly serving the broader scientific community. I will bring my experience working across diverse biocuration groups and multidisciplinary teams to the EC committee of the ISB to better achieve its goals.

Motivation: I am a biocuration scientist with over 20 years of experience in biomedical curation, data management, and integration of biological knowledge. What motivates me is the central role that biocuration plays in enabling discovery across the life sciences. I envision ISB as a hub for advancing both the science and the visibility of biocuration, particularly in this era of dwindling monetary funding and resources. I believe ISB can play a stronger role in fostering collaborations among diverse biocuration groups, promoting and sharing innovative methods and tools, and ensuring the sustainability and visibility of biocuration. Equally important, I will work to strengthen global partnerships, build relationships with user and publishing communities, improve documentation on standards and expand training and mentoring opportunities for early-career biocurators, with a strong commitment to equality, diversity, and inclusion. If elected to the ISB Executive Committee, I will work to increase interaction between biocurators by providing new forums for the exchange of ideas and experiences. I will bring to the EC not only my deep expertise and longstanding connections within the community, but also my strong communication skills—both written and spoken, extensive experience working in teams, and readiness to try new and bold ideas in order to fulfill and even enhance the goals of the ISB.

Biocuration 2026 Travel Awards

The International Society for Biocuration (ISB) is offering 5 in-person travel grants for the Biocuration 2026 Conference in Cape Town, South Africa.

In-person awards cover up to 2,700 CHF in expenses, paid as reimbursements following the conference, meaning that awardees must pay their expenses and send receipts (including any for currency exchange costs) to the ISB following the conference.

In person awardees are also required to submit a recent photograph and a written report (minimum 100 words) about the outcomes of their attendance. These will be posted on the ISB website, newsletter, ISB mailing list, and promoted on social media (Bluesky, LinkedIn, Mastodon).

All awardees are expected to present either a talk or poster at the conference.

If you are a current ISB member, please provide the email address associated with your ISB membership.

Deadline for applications: October 31st, 2025

Apply here

Annual General Meeting

October 27th, 2025

The International Society for Biocuration (ISB) will hold its Annual General Meeting (AGM) on Monday, October 27th, 2025 along with presentations by our two biocurator career award winners, Tiago Lubiana and Kimberly Van Auken.

Time: 4:00–6:00 pm CST / 3:00–5:00 pm GMT / 11:00 am–1:00 pm EDT / 8:00 am–10:00 am PDT

Note that daylight savings begins in Europe/UK on October 26th and daylight savings begins on November 2nd in the USA, so there’s a slightly different offset than usual. All canonical times for this event are based on European time!

Please fill out this form to register to attend by Sunday, October 26th, 2025 and receive the meeting link.

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.

Schedule (in CET):

  • 4:00pm Sue Bello: ISB Annual General Meeting
  • 4:30pm Open for questions and suggestions from attendees
  • 5:45pm Tiago Lubiana, winner of the Early Career Award
  • 5:10pm Kimberly Van Auken, winner of the Advanced Career Award

Register here You do not need to be an active ISB member to attend

Equity, Diversity, Inclusion and Accessibility Officer

The International Society for Biocuration (ISB) is committed to working to build an inclusive and diverse network of biocurators, ontologists, data stewards and others who work to improve the quality of data wherever they may work. The EDI subcommittee has worked hard to establish a set of guidelines to promote equity, diversity, inclusion, and accessibility for the society. With these guidelines in place and with the difficulty in maintaining an active committee in the past year the executive committee has decided to establish an Equity, Diversity, Inclusion and Accessibility Officer. 

This officer will be charged with:

  1. Acting as a point person for ISB members to communicate EDIA concerns.
  2. Reviewing applications for Biocuration conference organizers for any EDIA concerns.
  3. Working with the Biocuration conference liaison to ensure the annual conference is following EDIA guidelines.
  4. Acting as a point person to think ahead for any potential EDIA blindspots.

The past few years have seen the first Biocuration conference in India (2024), the first fully hybrid Biocuration conference (2025), and plans for the first Biocuration conference in Africa (2026). We fund travel fellowships to enable curators from low-income countries to attend Biocuration conferences, We have increased the number of available microgrants and inclusivity grants available to members this year to two of each type. We have also revised and updated our guidelines for conference organizers.

We thank Mary Ann Tuli and the members of the EDI committee for their tireless work over the years to guide the society policies to where they are now.

We thank Luana Licata for volunteering to be the inaugural EDIA Officer!

Archived Data Sets

Last week saw a flurry of messages about how to find archived data sets. This is the list of resources and links from those messages. The bulk of this list came from the Data Rescue Project (@datarescue2025.bsky.social) that was shared by Melissa Haendel. Please check the Data Rescue Project page for new updates. The Data Rescue Project now has a homepage https://www.datarescueproject.org/about-data-rescue-project/

Larger and Established Data / Website Efforts

End of Term Crawl 

  • The main coordinated effort to archive websites
  • Datasets have been more of a challenge, especially data embedded in databases.

EDGI

Public Environmental Data Project 

Harvard’s LIbrary Innovation Lab Team

ICPSR

  • Overview of ICPSR’s data rescue activities to date:
    • Downloaded ~2800 files from various sources requested by researchers; all the files ICPSR collected will soon be available via a dropbox link.
    • Examining CDC data dump from archive.org to assess what might be missing.
      • Ideally will also be a resource for those looking for data to see what is/isn’t available.
    • ICPSR staff and allies are generating metadata for each of the datasets we have so that we can make them available through an existing archive at ICPSR (DataLumos, openICPSR, or the Resource Center for Minority Data, depending on our timeline and some technical issues we’re working out)
  • ICPSR Data Lumos – They have the older version of a lot of major data, including a recent addition from the CDC.

IPUMS

  • They have data and have been working on cataloging efforts
  • Notification went out yesterday that they will share more soon.

Dryad

  • Generalist repository available to help with data publication, storage, and preservation.

Synapse

  • Generalist biology and biomedical data repository available to help with data publication, storage, and preservation.

Silencing Science Tracker

  • Joint initiative of the Sabin Center for Climate Change Law and the Climate Science Legal Defense Fund.
  • Tracks government attempts to restrict or prohibit scientific research, education or discussion, or the publication or use of scientific information.

OSF

  • Generalist repository for archiving, sharing, and storing all types of research outputs, not limited to preprints or only data.
  • OSF is available as an option for pre-prints of articles if, for some reason, they cannot be posted on official sources.
  • Many universities also have institutional repositories where research (articles, data, dissertations, etc) from that institution can be posted. They also have preservation mandates. An example is Penn’s ScholarlyCommons.

The Climate Mirror Project

  • Has NOAA data pulled during the 2017 data rescue.

Open Energy Data Initiative

  • A volunteer has pointed out that “key equity data” is missing from the Dept of Energy. Says they were able to find it on this site. Includes additional data from DOE.

Wayback Machine

Data Rescue Events

Smaller/Ad Hoc Rescue Efforts/ Data Archiving Activists

  • UCSB LSIT Data Mirroring
    • Mirrored and archived public data on locally hosted git server
    • Includes retrieved data sets from CDC, NIH, and NOAA
  • CDC Page on Internet Archive
    • A special archive created on IA of all CDC datasets publicly available as of January 28, 2025
    • uploaded by DataHoarders (we think)
  • Datasets in Dataverse
    • Data uploaded by the Climate Change and Health Research Coordinating Center (CAFE)
      • CAFE is looking for potentially non US based location to duplicate the contents of their collection
    • Includes CDC’s Social Vulnerability Index data.  
    • Most of what’s being placed here is data focusing on health and the environment.
    • DataRefuge from 2017 DataRefuge initiative can be opened for more deposits 
  • Safeguarding Research
    • Organizer is Henrik Schönemann; https://fedihum.org/@lavaeolus
    • There is a forum: https://safeguarding-research.discourse.group/ (admin = Henrik)
      • Based in EU, USA and global – got access to Update 1-2 PB (and more on the way) of storage & people willing to seed
      • Currently, we’ve got around 1TB of data backed up
        • Including >100.000 PDFs from academia.edu (“transgender”, “Queer Studies”, “intersex”, “nonbinary” etc. – see the forum for the full list)
        • 350GB web archive of CDC, including all 30.000 files from archive.cdc.gov And much more
        • “We’re working on providing a central index of archives, with metadata about who archived what, when, to be disseminated widely alongside torrent files and act as both a central point of coordination for archivers to assess what new work is needed, and a mass distribution channel.”
      • Possible contact to CERN, will update asap
  • Data Hoarder
    • A reddit community that is coordinating efforts to rescue data. 
  • Data Hoarding 
    • index of resources and archives related to data hoarding, web archival and self hosting. 
  • ArchiveTeam Warriors
    • They run a distributed crawler. Anyone can install it to help contribute.
    • US Federal Data page
    • Data is uploaded to Archive.org by volunteers
  • Data Liberation Project
    • Note: It looks like the project may have stalled in September 2024. Send info if you know more about them.
    • Run by BigLocalNews and MuckRock, which are good groups to follow.

Tools for Data Rescues

Library Guides to Data Rescues

Articles on current efforts

Articles for context

Existing Alternative Data Sources

Thanks to Brianne Dosch for suggesting the section and some of the bullets.

  • PolicyMap – offers a free tier that can be used to view basic information down to the tract-level, but more detailed data and functionality requires a subscription; available at some universities
  • FRED – They have some demographic data as well; free and open source
  • Census Reporter – is a free, open-source platform focused on making American Community Survey (ACS) data more accessible, including the recent upload of the 2022 1-Year ACS data
  • Esri – for mapping users, the GIS vendor publishes several U.S. Census Bureau data sets, including the ACS, through its ArcGIS Online Platform
  • IPUMS – Even when the government operates normally, many analysts turn to Minnesota Population Center products to access ACS, Current Population Survey microdata and Decennial Census data
  • Social Explorer – historical Census data and more; available at some universities
  • SimplyAnalytics – has internally processed American Community Surveys; available at some universities
  • American College of Obstetricians and Gynecologists – Hosting copies of immunization schedules and contraceptive use guidance from the CDC
  • https://www.ebi.ac.uk/ena/browser/home – The European Nucleotide Archive (ENA) provides a comprehensive record of the world’s nucleotide sequencing information, covering raw sequencing data, sequence assembly information and functional annotation. Mirrors SRA public data

Economic Indicators 

  • National League of Cities: Federal Grant Navigation Equity Dashboard 
    • This tool aggregated data from many sources – it seems to still be able to categorize disadvantaged communities (by environmental and economic standards), as well as other critical data denotations that are increasingly hard to access 
  • ALICE Economic Vitality Dashboard and Report (2022 w/ 2024 update)
    • This resource specifically provides data on work, housing, and community resources for households below the ALICE threshold (Asset Limited, Income Constrained, Employed). The data is provided by the U.S. Census Bureau’s Public Use Microdata Sample (PUMS, 202!) 
  • National Equity Atlas Dashboards
    • A data and policy tool that provides a detailed report card on racial and economic equity – this tool can provide a holistic Racial Equity Index snapchat of communities. The Atlas draws its data from a unique regional equity indicators database developed and maintained by two private institutions: PolicyLink and USC Equity Research Institute ERI.

Public Health 

  • County Health Rankings & Roadmaps (CHR&R)
    • A program of University of Wisconsin’s Population Health Institute, this data tool aims to highlight the symbiotic nature of health and equity by factoring in physical environment, social and economic indicators, clinical care, and health behaviors to health outcomes. 
      • They also recommend these additional health data platforms: 
  • City Health Dashboard
    • From NYU Langone Health, this platform provides 40+ measures of health and factors affecting health across five areas (Health Behaviors, Social and Economic Factors, Physical Environment, Health Outcomes, and Clinical Care) for 970+ cities across the U.S.

Biocuration 2025 Preliminary Schedule of Talks

Schedule of talks for April 7-9

DAY 1

Keynote: Tanya Berger-Wolf

Director of the Translational Data Analytics Institute, Director of Imageomics Institute, PI of AI and Biodiversity Change (ABC) Global Climate Center, Ohio State University.

Day 1, Session 1: Data Standards & Ontologies

  • Encouraging authors to use and cite data in public repositories; a publisher perspective.
    • Bastien Molcrette
    • Data Publications, Data Standards, Fair Data Principles, Public Data Resources
  • DO Spanish: enhancing DEI via a standardized workflow for translating ontology and website content
    • Lynn Schriml
    • Curation, Data Sharing, Disease, Ontologies
  • Harnessing Community Power for Long-Term Success of the Mondo Disease Ontology
    • Sabrina Toro
    • Curation, Data Standards, Disease, Ontologies
  • The Earth Metabolome Initiative Ontology  
    • Tarcisio Mendes de Farias
    • Data Modeling, Knowledge Graphs, Omics Data, Ontologies

Keynote: Nirav Merchant

Director of the Data Science Institute at University of Arizona, PI CyVerse

Day 1, Session 2: Artificial Intelligence

  • From Lab Bench to Web: A Strategy for Making Biomedical Data Findable and Accessible
    • Christina Parry
    • Data Standards, Fair Data Principles, Graph Databases, Repositories
  • Extending Ontology for Biomarkers of Aging using OLIVE
    • Hande Kucuk McGinty
    • Artificial Intelligence, Knowledge Graphs, Large Language Models, Ontologies
  • Building the Lighthouse: Guiding LLM-Powered Biocuration with Domain Knowledge and Context
    • Harry Caufield
    • Generative Artificial Intelligence, Large Language Models, Literature Mining, Ontologies
  • AI Curation Methods for NASA Scientific Data
    • Walter Alvarado
    • Artificial Intelligence, Curation, Large Language Models, Metadata
  • Plant Reactome: A plant pathways Knowledgebase and discovery platform
    • Sushma Naithani
    • Artificial Intelligence, Curation, Functional Gene Annotations, Knowledge Graphs

Day 1, Session 3: Data Sharing, Databases & Knowledgebases

  • Single-cell comparative transcriptomics for hundreds of species?
    • Frederic Bastian
    • Comparative Data, Curation, Data Standards, Gene Expression
  • Epitope-Driven Annotations in Protein Resources
    • Randi Vita
    • Database, ontology, protein, epitope
  • Towards FAIR Phenome: Indian Crop Phenome Database at Indian Biological Data Centre (IBDC)
    • Sonia Balyan
    • Data Sharing, Data Standards, Databases, Phenotypes
  • Making Rare Disease Data Available in the Rare Disease Cures Accelerator-Data and Analytics Platform 
    • Nicole Vasilevsky
    • Curation, Data Sharing, Disease, Fair Data Principles
  • Project ‘Shail’: Curating a mountain
    • Saurabh Raghuvanshi
    • Curation, Databases, Drug Discovery, Genomics 
  • Import of Human GWAS Data and Mapping of EFO to multiple ontologies at the Rat Genome Database
    • Stan Laulederkind
    • Curation, Disease, Genomics, Ontologies

DAY 2

Keynote: Paul Thomas

Director, Division of Bioinformatics, Director of the Gene Sequence, Function, and Health Laboratory Initiative, University of Southern California, PI Gene Ontology, PI PANTHER

Day 2, Session 1: Gene/Protein Functional Prediction 

  • DisProt: The Manually Curated Resource for Intrinsically Disordered Proteins
    • M. Victoria Nugnes
    • Curation, Databases, Ontologies, Proteins
  • A Large Scale Crowdsourcing of the Fifth Critical Assessment of Protein Function Annotation
    • Iddo Friedberg
    • Annotations, Artificial Intelligence, Functional Protein Annotations, Public Data Resources
  • New Synteny visualizations on Xenbase
    • Malcolm Fisher
    • Annotations, Comparative Data, Genomes, Synteny

Day 2, Session 2: Gene/Protein Functional Prediction

  • Cross-species quantification of function annotations provides insights into disease-associated uncharacterized human genes
    • Parnal Joshi
    • Annotations, Comparative Analysis, Data Analysis, Functional Protein Annotations
  • Leveraging the AlphaFold Database for enhanced protein function annotation
    • Paulyna Magaña
    • Annotations, Functional Protein Annotations, Protein Structure Prediction, Proteins
  • Leveraging Large Language Models for Gene Summary Generation at the Alliance of Genome Resources
    • Valerio Arnaboldi
    • Large Language Models, Literature Mining, Automated Gene Summaries, Text Summarization
  • Life Cycle Events for Protein Family Models: Birth, Maturation, Cloning, Retirement
    • Daniel Haft
    • Bacteria, Data Sharing, Functional Protein Annotations

Keynote: Andy Hickl

Chief Technology Officer, Allen Institute

Day 2, Session 3: Natural Language Processing 

  • Semi-automated curation of post-translational modification relationships using automated knowledge extraction and assembly
    • Benjamin Gyori
    • Artificial Intelligence, Curation, Databases, Literature Mining
  • Characterization and automated classification of sentences in the biomedical literature: a case study for biocuration of gene expression and protein kinase activity
    • Daniela Raciti
    • Curation, Machine Learning, Community Curation, Sentence Classification
  • Enhancing the SIB Literature Services with annotations to support biocuration
    • Deborah Caucheteur
    • Annotations, Curation, Data Analysis, Literature Mining
  • Protein structure enrichment through text mining
    • Melanie Vollmar
    • Annotations, Literature Mining, Natural Language Processing, Protein structures
  • Enhancing data annotation in ChEMBL for robust analyses
    • Sybilla Corbett
    • Annotations, Curation, Fair Data Principles, Natural Language Processing

Day 2, Session 4: Glycans 

  • Glycan Archetypes: definitions, implementations and applications for standardizing glycan structure data
    • Kiyoko Aoki-Kinoshita
    • Data Standards, Databases, Glycans, Ontologies
  • BiomarkerKB: Biomarker-centric data modeling and knowledge integration for translational research
    • Raja Mazumder
    • Curation, Databases, Glycans, Knowledge Graphs
  • Inferring Tissue and Cell-type Glycosyltransferase Specificity from Single-Cell Gene Expression Data
    • Nathan Edwards
    • Annotations, Glycans, Machine Learning

DAY 3

Keynote: Shannon Farrell

Data Curation Network/Univ. Minnesota

Day 3, Session 1: Data Curation 

  • It’s Now or Never: Delays in Biocuration Disproportionately Affect Understudied Proteins
    • An Phan
    • Curation, Data Analysis, Functional Gene Annotations, Literature Mining
  • How have standards in genomics evolved since the first microbial genome was published 3 decades ago?
    • Chris Hunter
    • Data Standards, Metadata, Ontologies, Repositories

Keynote: Sandra Orchard

ISB 2023 Exceptional Contribution to Biocuration Awardee, EMBL-European Bioinformatics Institute – UK

Day 3, Session 2: Data Curation Databases, Infrastructure, Literature Mining, Public Data Resources

  • The global biodata infrastructure: how, where, who, and what?
    • Chuck Cook
    • Databases, Infrastructure, Literature Mining, Public Data Resources

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.

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.

EC Election Candidates – 2023

The election of five members of the International Society for Biocuration Executive Committee (ISB EC) will be held from September 26 – October 03, 2023.

Emails will be sent to current members on 26th September. Only current members, as of 20 September 2023, 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 nine 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:

Sara Chuguransky

InterPro/Pfam Biocurator

Sequence Family Resources, EMBL-EBI, Hinxton (Cambridge), England

I studied biochemistry and did my PhD in Diabetes, bone disease and alendronate treatment, using animal models and cell cultures, along with cytology techniques to evaluate different conditions and effects of bone loss/maintenance in this disease, in the National University of La Plata (UNLP), Argentina. Then I changed the topic in my postdoctoral position at the LiDeB (Research and Development of Bioactives Laboratory) also at the UNLP, Argentina, working in drug repurposing epilepsy treatment, especially refractory epilepsy. I also made collaborations in drug repurposing studies for tropical neglected diseases projects such as malaria, Chagas’ disease and Leishmania. During this time, I came to the EBI as a REFRACT secondee, a Marie Slowdowska-Curie project which involves European and Latin-American institutions for research internships, to improve and expand the coverage of repetitive proteins. From January 2020, I’m a Pfam/InterPro biocurator at the EMBL-EBI, as part of the Sequence Families Team lead by Alex Bateman, where we maintain and check that information from InterPro member databases is up-to-date and accurate, increasing the protein universe coverage integrating new models and updating the current ones. As a Pfam curator, I create new models to fill in the gaps in protein sequences, we improve the existing ones as well as check and increase the grouping of these models into superfamilies. I am also involved in delivering training as part of EBI courses, workshops, and webinars (for example Structural Bioinformatics course, Bioinformatics resources for Protein Biology course, UniAndes and UCR Bioinformatics training course (Colombia), webinars at the EBI, etc).

For the past three years, I’ve been working in biocuration, a job that I really enjoy as it is interesting and challenging. I’ve been learning a lot as it is dynamic, involving tasks which make me expand my knowledge to cover several aspects of the biology to understand predictions and provide accurate and up-to-date information based on current knowledge. This role also gives me the opportunity of interacting with many other database members and attending to conferences and meetings where I met members from a wide range of resources to expand our network which is great to understand users and databases’ requirements, leading to improvement of our services. A clear example of this is the Gene Ontology Consortium, with which we keep a fluent and usual contact. Based on these interactions, we received valuable feedback to make Pfam and InterPro more accessible and useful for researchers and the biocuration community.

 I am a new member of ISB and relatively new in the biocuration field, so I believe that crosslinks with other members, establishing a fluent communication and interaction will enhance our strengths and make it easier for all of us, to improve our services for the good of the community. The biocuration role is not the most visible one, so promoting participation of people from different places in the world and databases, along with promotion of events, conferences and jobs would be great to support us, since our role is critical for the understanding and giving the biological sense to bioinformatic tools, to expand and assist the development of different areas, from agriculture to human diseases and treatments, bacterial system, etc. I’m enthusiastic and open to change and evolution in the field, being confident that networking and exchanges between the biocuration community members is key for improvement and expansion of all services, supporting each other for a common objective.

To the ISB, as an EC member, I can bring the commitment of promoting activities and events within the organisation to increase and promote members participation and networking. I can take care of administrative task related to organisation and promotion of events, grants applications or workshops, as well as helping with email monitoring and maintaining the website. I have used WordPress before, when we make posts/protein focus articles in InterPro, although I don’t have experience in PHP/HTML/CSS or development skills. I’m keen to learn about ISB dynamics and function, and to support the biocuration community to make it more interactive.

No conflicts of interest.

Marc E. Gillespie

Professor, Biocurator, Vice Provost

Reactome & St. John’s University, NY  USA

I am a Senior Vice Provost at St. John’s University in Queens, NY USA and a biocurator on the Reactome Project (reactome.org). I received a BA in zoology from the University of Vermont in 1989 and worked as a lab technician at Cold Spring Harbor Laboratory and New York University Medical Center. I was lucky enough to get into the University of Utah’s Molecular Biology Program and received my PhD in 1998. My post-doctoral fellowship was done at Memorial Sloan Kettering’s Sloan Kettering Institute in NYC, working in x-ray crystallography. I originally trained as a molecular biologist focused on protein biochemistry, transitioning to genomics, proteomics, toxicology, bioinformatics, and eventually biocuration. My work in biocuration began when I joined the Reactome Team in 2003, a fantastic group and time to start in biocuration, alongside running my own lab focused on toxicogenomics. As with many groups the Reactome curators grew with the biocuration field, inventing methods and practices as we moved along. I have continued to work within the biocuration community, meeting many of you along the way. During the pandemic I had the fortune to work with the COVID-19 Disease Mapping Group and helped lead our disease curation efforts on a new more pressing front. Despite administrative pressures I continue to curate and look forward to new opportunities to contribute.

My interest in joining the ISB leadership started with the 2014 Biocuration meeting. Along with Francis Ouellette and Robin Haw I had the chance to co-chair the 2014 Biocuration meeting in Toronto, CA, at a time when the ISB was growing. The diversity of the members and attendees at biocuration meetings is the strength and a challenge for the society. Working across platforms and fields during the pandemic reminded me again that biocuration is a big tent encompassing many different fields. Professionally (outside of my biocuration role) I work in these cross seams regularly. I believe that the need for biocuration will grow, and that the field needs leadership that can bring the benefits of the society to an expanding group of stakeholders, many of whom work in a curation role, but don’t know that the ISB is here to help them grow professionally. At a time when FAIR principles and appreciation and attribution of the work that biocurators do is growing we need clear and straightforward support for expanding the ranks of the society, I am very interested in expanding and defining the practicalities and benefits that ISB membership can bring. I think we must explore what other societies and fields we should be aligning with. The value of the ISB hinges on the support and resources that it provides new, mid-career, and experienced biocurators.

No conflicts of interest.

Charles Tapley Hoyt

Senior Scientist

Gyori Lab for Computational Biomedicine, Northeastern University, Boston, MA, USA

Dr. Charles Tapley Hoyt received his Ph.D. in Computational Life Sciences from the University of Bonn. His research interests cover the interface of biocuration, knowledge graphs, and machine learning with systems biology, networks biology, and drug discovery. He currently works remotely from Germany as a Senior Scientist in the Gyori Lab for Computational Biomedicine at Northeastern University. He is an advocate of open source software, reproducibility, and open science. His open source projects such as PyBEL and PyKEEN are used by several academic and industrial groups.

My work in biocuration supplements my primary interests in translational science and drug discovery. To this end, I am the primary curator and developer of several community datasets and databases such as the Bioregistry and Biomappings. I make frequent small contributions to other curated resources and promote the concept of the Drive-By Curation. I am also active in the development of community standards such as the Simple Standard for Sharing Ontology Mappings (SSSOM) and the Biological Expression Language (BEL) as well as participating in the OBO Foundry community. From proximity to many of its members, I joined the ISB during the pandemic, quickly became involved in the planning of the 2022 virtual and 2023 in-person conferences, and was later awarded the 2023 Excellence in Biocuration Early Career Award. Throughout these experiences, I have developed many meaningful professional and personal connections.

There are two grand issues within the ISB and the wider biocuration community that I believe joining the ISB Executive Committee will help address. The first issue is to improve the outreach of the ISB further than the typical nexus around North American, British, and Swiss research institutes. This issue became apparent to me during my service as the Biocuration 2023 co-chair as we were ineffective at identifying and communicating to researchers outside of this bubble and there were no institutional tools available from the ISB to help. I would like to use my time on the ISB EC to develop such tools. The second issue is to promote the longevity and sustainability of curated resources. The ISB is enriched with members who provide key resources to the community, which in turn pose the highest risk with respect to longevity and sustainability. Therefore, I envision the ISB as an excellent platform through which to educate and enable progress towards these lofty goals. This might be accomplished through workshops, development of societal guidelines, partnerships with publishers, etc. Following my time as the Biocuration 2023 co-chair, I have the less grand goal to better support future Biocuration conference organizers, both in terms of preparing additional material as well as donation of my time. While I have already volunteered in this capacity for the Biocuration 2024 conference in India, I believe that I can better serve in that role as a liaison to the ISB EC.

No conflicts of interest.

Luana Licata

Assistant Professor and MINT database coordinator 

Department of Biology, Tor Vergata University of Rome, Rome, Italy

I work as Assistant Professor in the Department of Biology at the Tor Vergata University of Rome, Italy and I am the scientific coordinator of MINT, the Molecular INTeraction database (ELIXIR Core Data Resources). I have been working for over 16 years both as a curator and a team coordinator of MINT and I am directly involved in the curation of SIGNOR, a database that collects experimental verified causal relationships between biological entities. I have collaborated with other research groups in the development, organisation and/or curation of several Bioinformatics Resources such as, virusMINT, Complex Portal, DISNOR, CancerGeneNet. I am involved in the development of PSI-MI standards and controlled vocabularies (Molecular Interaction Ontology of the Proteomics Standard Initiative) to enable the exchange and integration of molecular interaction data and I am the Ontology coordinator of the HUPO Proteomics Standards Initiative (PSI), Molecular Interaction group.

I am a member of ELIXIR Italy Training Team which has the aim to produce quality training in bioinformatics in order to achieve excellence in life science research. I am also a trainer in Bioinformatics courses on Network Biology, Bioinformatics tools to study protein-protein interactions and Use of Standards, Controlled Vocabularies and Ontologies. I have experience in organising biocuration meetings and I am a member of the International Society of Biocuration (ISB) and I am a member of the Steering committee ELIXIR Biocuration Focus Group.

Since 2018, I am a member of the International Society of Biocuration (ISB), I am also a member of the ELIXIR Biocuration Focus Group Steering committee. I had been involved in several biocuration activities and I have experience in organising biocuration meetings. I would like to bring my experience to support ISB to promote biocuration activities and jobs in academia and industry (particularly needed in Italy) via, for example, high quality training  and University courses. I am also interested in identifying biocurator literature support tools to improve the quality of work.

No conflicts of interest.

Frederique Lisacek

Group Leader

Proteome Informatics Group, SIB Swiss Institute of Bioinformatics, Geneva, CH

PhD in Computer Science (Artificial Intelligence) from the University Pierre & Marie Curie, Paris, France in 1984. From 1985 to 1998, held research positions in biology labs in France, Japan and Australia working on knowledge representation and predictive methods based on sequence analysis. Successively worked in two biotech companies leading projects on knowledge management and mining in Proteome Systems Ltd in Sydney, Australia (1999-2000) and in Geneva Bioinformatics (GeneBio) S.A, Switzerland (2001-2005). Joined the SIB Swiss Institute of Bioinformatics in the Proteome Informatics Group in 2006. Manages the group since 2008 driving knowledge discovery projects in proteomics and glycomics. Specialised in glycoinformatics since 2010.

Having been recruited in Geneva by Amos Bairoch  in 2001, I need not explain how familiar I have been with biocuration and its evolution over the past decades. My input has been steady over that period but not in the forefront; it encompasses contributions to text mining methods, ontology definition and database development. Since 2010, I have specialised in glycoscience a source of many bioinformatics challenges, somehow a niche research topic though slowly but surely expanding. Our issues span data standardisation, formalisation, and curation. Our community struggles to produce reliable computational solutions for we need to handle the sparsity and the heterogeneity of glycodata.

Chairing the scientific committee of Biocuration23 gave me the opportunity to take a broader view on data curation and interact more extensively with a diversity of biocurators. It also occurred to me more clearly that dissemination and reinforcement of biocuration requires constant and long-term effort. The team spirit that I shared with the Biocuration23 committees has convinced me that I could partake in pursuing the needed constructive endeavours within the Executive Committee. I could simply contribute my experience and energy.

No conflicts of interest.

Saurabh Raghuvanshi

Professor

Department of Plant Molecular Biology, University of Delhi South Campus, Benito juarez road, New Delhi-110021, India

With a background in plant molecular biology I had ventured in plant genomics and bioinformatics. I concentrated on doing pioneering work in establishing the genome level data analytics expertise at national level by working in the rice genome project, which was the first genome sequencing project of India. This was followed by the first microbial genome (mycobacterium indicus pranii) and several EST sequencing projects. Also actively participated in the Rice Annotation Project (RAP) jamboree (meeting in Tsukuba, Japan). Subsequently, as a proof of concept, our group developed data digitization models for experimental data from published research articles. These models use an organized multi-tiered schema of ontologies to digitize data from over 150 different experimental techniques. Continuing further towards increasing the national level competence, I worked as the project lead to establish the first life science data center in India i.e. the Indian Biological Data Center (ibdc.rcb.res.in).

On the other hand our group also works extensively on global miRNA mediated regulatory schemas with a combination of molecular biology and data analytics techniques.

We are further venturing towards developing AI/ML based dynamic regulatory models for miRNA mediated regulatory networks as well as developing predictive models to aid precision breeding.

The capacity to integrated various biological data sets is critical to generate knowledge and understand any organism at the ‘systems’ level. Globally, extensive efforts are done to develop systems that can integrate curate and analyze biological data sets. I would like to create emphasis on methods and schemas that will enable complete and semantic digitization of all types of experimental data sets. Currently, only a portion of the published experimental data is in a computer discoverable format. Even if it is digitized, due to lack of uniformity over thousands of experimental technique the data requires lot of manual intervention (curation) to make it discoverable and be integrated in semantic fashion. Unless all published experimental data is (i.e. every data point) is made discoverable from all aspects that it represents we will continue to struggle to achieve ‘systems’ level understanding.

I would also like to continue my efforts to strengthen the field of data analytics and biocuration in India. It needs to be much better organized and strengthened so that the national capacity can also contribute to the global efforts to understand organisms and ecosystems at ‘Systems’ level. To this end I have been making efforts at various levels. I have introduced an ‘open-elective’ masters program on ‘Data Analytics and Biocuration’ at Delhi University. Further, started a series of National workshops entitled ‘National Symposium on Database Development and Biocuration’ (http://genomeindia.org/nsddb). The establishment of the Indian Biological Data Center (https://ibdc.rcb.res.in) is a major milestone to this end. Subsequently, hosting the 17th Annual International Biocuration Conference in India for the first time would prove to be very beneficial in consolidating efforts at national level as well as generating an organic connect with the international community.

No conflicts of interest.

Leonore Reiser

Principal Biocuration Scientist

Phoenix Bioinformatics

I received my PhD in Plant Biology from UC Berkeley under the supervision of Dr Robert Fischer and completed a post doc in Plant Genetics under the supervision of Dr Sarah Hake. After completing my post doc I joined the staff of the Arabidopsis Information Resource (TAIR). As one of the founding curators I helped with the design of the database and UI for this database that serves a global community.  I was part of the initial effort to integrate plants into the Gene Ontology and early integration leading to the Plant Ontology. I spent about a decade working  on DEI programs in science at the Carnegie Institution of Science, the Molecular Sciences Institute and UC Berkeley while still maintaining my connection to TAIR as an occasional consulting curator. I returned to TAIR full time 8 years ago and continue to work primarily in the area of literature curation. I also serve as a co-PI on the AgBioData RCN and as a managing editor for the Arabidopsis section of microPublication.

My primary motivation is to increase representation of plant sciences within the ISB and promote more interactions/collaborations with plant biocurators and DBs. Many of the goals of our AgBioData RCN are relevant to biological databases in general (FAIRificaiton of data, definition of metadata and data standards, education and database sustainability.)

I serve as a managing editor for microPublication Biology, I am a co-PI of the AgBioData RCN and serve on several of the working groups. I am a full time curator for TAIR and a working mother.

TBK Reddy

Genomic Standards Group Lead

DOE Joint Genome Institute, Lawrence Berkeley National Laboratory, Berkeley, CA, USA.

As a resolute and passionate member of our esteemed society, I consistently demonstrated an unwavering commitment to the field of biocuration, including building and maintaining biological databases over the last 20+ years, enhancing scientific data quality, metadata standards and accessibility.
For the last 12 years I have been leading the Genomic Standards Group at the DOE Joint Genome Institute and maintaining Genomes OnLine Database (GOLD), a metadata management system for genome and metagenome projects from around the world. We develop and apply metadata standards, controlled vocabularies, standardized naming for metagenome samples and promote its use in the research community. We ensure the data we put in the public domain adheres to the standards and train students in metadata curation.

Starting with my postdoctoral project to run initial annotation of Dictyostelium discoideum genome and find analogs of human disease-causing genes in early 2001, I continued working in the biocuration field till date. My work and experience at the Mouse Genome Informatics (The Jackson Laboratory 2003-2008), Tuberculosis Database (Stanford School of Medicine 2008-2011) and GOLD (DOE Joint Genome Institute 2011 – current) provided me an opportunity to work on different aspects of biocuration as well as in the design and development of biological databases by interfacing between biologists, biocurators and software developers. In my role as a Scientific Data Curator, I have been responsible for the meticulous curation of complex biological data, ensuring accuracy, consistency, and compliance with established standards. Collaborating closely with multidisciplinary teams, I have spearheaded efforts to enhance data sharing and accessibility, bridging the gap between researchers and valuable information resources. I often describe my role as a translator of English to English at biological databases, to ensure clear communication between biologists, biocurators and software developers to get things done in an efficient manner.

I not only did hands on data curation, developed SOPs, trained career biocurators as well as high school and undergraduate student interns. With a deep-rooted passion for advancing the field of biocuration, I have contributed significantly to the development and implementation of innovative strategies that foster data integrity and dissemination.

My ability to connect with individuals from diverse backgrounds and disciplines makes me an ideal candidate for Executive Committee Member.
 
By serving on the Executive Committee of the ISB, I am dedicated to driving the organization’s mission to enhance the practice of biocuration globally. Through collaborative initiatives, strategic planning, and thought leadership, I am committed to elevating the role of biocuration in scientific research and discovery.

I plan to continue promoting training the next generation of Biocurators as well as promoting biocuration as a career choice. I will be a steadfast advocate for the interests of our members and a proactive contributor to shaping the future of biocuration to strengthen the foundation of our society and pave the way for continued progress and excellence in the field of biocuration.

No conflicts of interest.

Peter Uetz

Associate Professor

Center for Biological Data Science, Virginia Commonwealth University, Richmond, VA, USA

While I was a graduate student at EMBL (Heidelberg, 1993-1997) I witnessed the internet and the web pop into our lives. Although I was trained as a molecular biologist (sequencing a gene as a master’s student and studying protein function as a grad student), I have always been interested in biodiversity research. So, I took the opportunity and started the “EMBL Reptile Database” (now without the “EMBL” part) and later the Microbial Protein interaction database, still curating the former after nearly 30 years.

Officially, my lab has studied protein function until about 2020, mainly protein interaction networks, but after obtaining tenure I gave up the wet-lab work and now mostly work on taxonomic data (although I still teach a lab class on functional genomics).

Biocuration is a critical but undervalued part of the biomedical sciences. We need to strengthen its role in science and society at large, given the critical importance of data. I have had various roles and positions, ranging from database curator, citizen science advocate (e.g. iNaturalist), teacher, and meeting co-organizer (ISB, various herpetological societies), so I think I am in a good position to help develop ISB further. I also believe that my experience with a broad range of topics, from basic science to medical applications will help (I have had the genomes of most of my family members sequenced, after all 🙂

No conflicts of interest.

Annual General Meeting October 18, 2023

The slides, minutes and recording of this meeting can be found here.

You are invited to a virtual Annual General Meeting of the International Society for Biocuration on Wednesday, 18 October. The meeting will include presentations by our two biocurator career award winners, Nico Matentzoglu and Charlie Hoyt.

Time: 5 pm CET / 4 pm BST / 8 am PT / 11 pm ET

Please fill out this form to register to attend and receive the zoom meeting link. NOTE 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.

Program (CET times)

5.00pm Ruth Lovering (ISB EC Chair): ISB Annual General Meeting 

5:30pm Open for questions and suggestions from attendees

5:45pm Nico Matentzoglu, Excellence in Biocuration, Advanced Career Award

Presentation title: Closing the gap between effective Biocuration and meaningful ontology evolution

6:10pm Charlie Hoyt, Excellence in Biocuration, Early Career Award

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

Presentation Abstracts

Nico Matentzoglu, Excellence in Biocuration, Advanced Career Award

Presentation title: Closing the gap between effective Biocuration and meaningful ontology evolution

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.

Charlie Hoyt, Excellence in Biocuration, Early Career Award

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

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.

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