From multiallele fish to nonstandard environments, how ZFIN assigns phenotypes, human disease models, and gene expression annotations to genes

Bradford, Yvonne M.; Slyke, Ceri E. Van; Howe, Douglas G.; Fashena, David; Frazer, Ken; Martin, R. D.; Paddock, Holly; Pich, Christian; Ramachandran, Sridhar; Ruzicka, Leyla; Singer, Amy; Taylor, Ryan; Tseng, Wei-Chia; Westerfield, Monte

doi:10.1093/genetics/iyad032

Cited by 5 publications

(3 citation statements)

References 57 publications

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“…2022 ), Mouse Genome Database ( Ringwald et al . 2022 ), the Zebrafish Information Network ( Bradford et al . 2023 ), Rat Genome Database ( Vedi et al .…”

Section: Introductionmentioning

confidence: 99%

Updates to the Alliance of Genome Resources central infrastructure

Aleksander,

Anagnostopoulos,

Antonazzo

et al. 2024

Genetics

Self Cite

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The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively-studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast, C. elegans, Drosophila, zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium. The project is in a rapid development phase to harmonize knowledge, store it, analyze it, and present it to the community through a web portal, direct downloads, and Application Programming Interfaces (APIs). Here we focus on developments over the last two years. Specifically, we added and enhanced tools for browsing the genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching of the literature (Textpresso), and sequence similarity searching (SequenceServer). We enhanced existing interactive data tables and added an interactive table of paralogs to complement our representation of orthology. To support individual model organism communities, we implemented species-specific “landing pages” and will add disease-specific portals soon; in addition, we support a common community forum implemented in Discourse software. We describe our progress towards a central persistent database to support curation, the data modeling that underpins harmonization, and progress towards a state-of-the art literature curation system with integrated Artificial Intelligence and Machine Learning (AI/ML).

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“…2022 ), Mouse Genome Database ( Ringwald et al . 2022 ), the Zebrafish Information Network ( Bradford et al . 2023 ), Rat Genome Database ( Vedi et al .…”

Section: Introductionmentioning

confidence: 99%

Updates to the Alliance of Genome Resources central infrastructure

Aleksander,

Anagnostopoulos,

Antonazzo

et al. 2024

Genetics

Self Cite

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show abstract

“…Knowledge Centers also are responsible for organism-specific user support activities and for providing access to data types not yet supported by Alliance Central. The founding Alliance Knowledge Centers are Saccharomyces Genome Database (Engel et al 2022 ), WormBase (Davis et al 2022 ), FlyBase (Gramates et al 2022 ), Mouse Genome Informatics (Ringwald et al 2022 ), the Zebrafish Information Network (Bradford et al 2023 ), Rat Genome Database (Vedi et al 2023 ), and the Gene Ontology Consortium (Gene Ontology et al 2023 ). The newest member, Xenbase (Fisher et al 2023 ), joined the Alliance consortium in 2022.…”

Section: Introductionmentioning

confidence: 99%

The alliance of genome resources: transforming comparative genomics

Bult,

Sternberg

2023

Mamm Genome

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Comparing genomic and biological characteristics across multiple species is essential to using model systems to investigate the molecular and cellular mechanisms underlying human biology and disease and to translate mechanistic insights from studies in model organisms for clinical applications. Building a scalable knowledge commons platform that supports cross-species comparison of rich, expertly curated knowledge regarding gene function, phenotype, and disease associations available for model organisms and humans is the primary mission of the Alliance of Genome Resources (the Alliance). The Alliance is a consortium of seven model organism knowledgebases (mouse, rat, yeast, nematode, zebrafish, frog, fruit fly) and the Gene Ontology resource. The Alliance uses a common set of gene ortholog assertions as the basis for comparing biological annotations across the organisms represented in the Alliance. The major types of knowledge associated with genes that are represented in the Alliance database currently include gene function, phenotypic alleles and variants, human disease associations, pathways, gene expression, and both protein–protein and genetic interactions. The Alliance has enhanced the ability of researchers to easily compare biological annotations for common data types across model organisms and human through the implementation of shared programmatic access mechanisms, data-specific web pages with a unified “look and feel”, and interactive user interfaces specifically designed to support comparative biology. The modular infrastructure developed by the Alliance allows the resource to serve as an extensible “knowledge commons” capable of expanding to accommodate additional model organisms.

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“…Knowledge Centers also are responsible for organism-specific user support activities and for providing access to data types not yet supported by Alliance Central. The founding Alliance Knowledge Centers are Saccharomyces Genome Database (Engel et al 2022), WormBase (Davis et al 2022), FlyBase (Gramates et al 2022), Mouse Genome Database (Ringwald et al 2022), the Zebrafish Information Network (Bradford et al 2023), Rat Genome Database (Vedi et al 2023), and the Gene Ontology Consortium (Gene Ontology Consortium 2023). The newest member, Xenbase (Fisher et al, 2023), joined the Alliance consortium in 2022.…”

Section: Introductionmentioning

confidence: 99%

Updates to the Alliance of Genome Resources Central Infrastructure Alliance of Genome Resources Consortium

Aleksander,

Anagnostopoulos,

Antonazzo

et al. 2023

Preprint

Self Cite

View full text Add to dashboard Cite

The Alliance of Genome Resources (Alliance) is an extensible coalition of knowledgebases focused on the genetics and genomics of intensively-studied model organisms. The Alliance is organized as individual knowledge centers with strong connections to their research communities and a centralized software infrastructure, discussed here. Model organisms currently represented in the Alliance are budding yeast,C. elegans,Drosophila, zebrafish, frog, laboratory mouse, laboratory rat, and the Gene Ontology Consortium. The project is in a rapid development phase to harmonize knowledge, store it, analyze it, and present it to the community through a web portal, direct downloads, and APIs. Here we focus on developments over the last two years. Specifically, we added and enhanced tools for browsing the genome (JBrowse), downloading sequences, mining complex data (AllianceMine), visualizing pathways, full-text searching of the literature (Textpresso), and sequence similarity searching (SequenceServer). We enhanced existing interactive data tables and added an interactive table of paralogs to complement our representation of orthology. To support individual model organism communities, we implemented species-specific “landing pages” and will add disease-specific portals soon; in addition, we support a common community forum implemented in Discourse. We describe our progress towards a central persistent database to support curation, the data modeling that underpins harmonization, and progress towards a state-of-the art literature curation system with integrated Artificial Intelligence and Machine Learning (AI/ML).

show abstract

From multiallele fish to nonstandard environments, how ZFIN assigns phenotypes, human disease models, and gene expression annotations to genes

Cited by 5 publications

References 57 publications

Updates to the Alliance of Genome Resources central infrastructure

Updates to the Alliance of Genome Resources central infrastructure

The alliance of genome resources: transforming comparative genomics

Updates to the Alliance of Genome Resources Central Infrastructure Alliance of Genome Resources Consortium

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