2024 | Paul W. Sternberg, Kimberly Van Auken, Qinghua Wang, Adam Wright, Karen Yook, Magdalena Zarowiecki, Valerio Arnaboldi, Andrés Becerra, Stephanie Brown, Scott Cain, Juancarlos Chan, Wen J. Chen, Jaehyoung Cho, Paul Davis, Stavros Diamantakis, Sarah Dyer, Dionysis Grigoriadis, Christian A. Grove, Todd Harris, Kevin Howe, Ranjana Kishore, Raymond Lee, Ian Longden, Manuel Luy paert, Hans-Michael Müller, Paulo Nuin, Mark Quinton-Tulloch, Daniela Raciti, Tim Schedl, Gary Schindelman, Lincoln Stein
WormBase has been the primary repository and knowledgebase for the genome and genetics of Caenorhabditis elegans and other nematodes for over two decades. The project aims to keep up with fast-paced research, integrate with other resources, and ensure sustainability. The current state of WormBase and its transition to the Alliance of Genome Resources (Alliance) are discussed, along with future plans. As an Alliance member, WormBase will continue to interact with the C. elegans community, develop new features, and curate key information from literature and large-scale projects.
WormBase has evolved from ACeDB in 2000 and has expanded significantly in breadth and depth. The project has undergone several leadership changes, with current staff remaining relatively constant. The Global Biodata Coalition has designated WormBase as a Core Global Biodata Resource. WormBase joined the Gene Ontology Consortium in 2003 and later contributed to the formation of the Alliance in 2016.
The transition of WormBase infrastructure to the Alliance is driven by the need for improvement, sustainability, and standardized services for gene comparison across biomedical models. The Alliance provides a flexible infrastructure, including a graph database (Neo4J) and a PostgreSQL relational database, allowing for rapid data propagation and harmonization. The current Neo4J database contains harmonized data types from WormBase, while the PostgreSQL database will serve as the primary curation database.
WormBase will continue to provide data to the Neo4J database until its retirement and will also provide data in LinkML format to the PostgreSQL database. Additional data types, including reagents, genome features, RNAi phenotype annotations, regulatory interactions, transcripts and proteins, chromosomes and genome assemblies, transcription factors, expression clusters, gene site-of-action data, and person and laboratory data, will be imported into the PostgreSQL database.
The transition to the Alliance will allow for more rapid propagation of curated data to the website, improved user experience, and better integration with other model organism databases. The Alliance will also provide a unified perspective on gene expression across multiple organisms, including human, mouse, rat, frogs, zebrafish, fruit fly, and yeast.
WormBase will continue to curate human disease models, including genes, alleles, genotypes, and strains associated with disease terms from the Disease Ontology. The project will also continue to curate genetic pathways, gene expression data, and interactions between genes and gene products. The WormBase UI will continue to provide a comprehensive set of tools and displays, including the Gene Ontology annotations, gene summaries, and gene page information.
The transition to the Alliance will also allow for more efficient literature acquisition and processing, with the Alliance Bibliography Central (ABC) providing a unified system for literature curation. The Alliance will also provide a new ontology browser, replacing the WormBase one, and will continue to support community curation through the ACKnowledge pipeline and other initiatives.WormBase has been the primary repository and knowledgebase for the genome and genetics of Caenorhabditis elegans and other nematodes for over two decades. The project aims to keep up with fast-paced research, integrate with other resources, and ensure sustainability. The current state of WormBase and its transition to the Alliance of Genome Resources (Alliance) are discussed, along with future plans. As an Alliance member, WormBase will continue to interact with the C. elegans community, develop new features, and curate key information from literature and large-scale projects.
WormBase has evolved from ACeDB in 2000 and has expanded significantly in breadth and depth. The project has undergone several leadership changes, with current staff remaining relatively constant. The Global Biodata Coalition has designated WormBase as a Core Global Biodata Resource. WormBase joined the Gene Ontology Consortium in 2003 and later contributed to the formation of the Alliance in 2016.
The transition of WormBase infrastructure to the Alliance is driven by the need for improvement, sustainability, and standardized services for gene comparison across biomedical models. The Alliance provides a flexible infrastructure, including a graph database (Neo4J) and a PostgreSQL relational database, allowing for rapid data propagation and harmonization. The current Neo4J database contains harmonized data types from WormBase, while the PostgreSQL database will serve as the primary curation database.
WormBase will continue to provide data to the Neo4J database until its retirement and will also provide data in LinkML format to the PostgreSQL database. Additional data types, including reagents, genome features, RNAi phenotype annotations, regulatory interactions, transcripts and proteins, chromosomes and genome assemblies, transcription factors, expression clusters, gene site-of-action data, and person and laboratory data, will be imported into the PostgreSQL database.
The transition to the Alliance will allow for more rapid propagation of curated data to the website, improved user experience, and better integration with other model organism databases. The Alliance will also provide a unified perspective on gene expression across multiple organisms, including human, mouse, rat, frogs, zebrafish, fruit fly, and yeast.
WormBase will continue to curate human disease models, including genes, alleles, genotypes, and strains associated with disease terms from the Disease Ontology. The project will also continue to curate genetic pathways, gene expression data, and interactions between genes and gene products. The WormBase UI will continue to provide a comprehensive set of tools and displays, including the Gene Ontology annotations, gene summaries, and gene page information.
The transition to the Alliance will also allow for more efficient literature acquisition and processing, with the Alliance Bibliography Central (ABC) providing a unified system for literature curation. The Alliance will also provide a new ontology browser, replacing the WormBase one, and will continue to support community curation through the ACKnowledge pipeline and other initiatives.