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
