Document Type

Article

Publication Date

5-7-2024

Keywords

JMG, Animals, Databases, Genetic, Genomics, Software, Genome, Mice

JAX Source

Genetics. 2024;227(1):iyae049.

ISSN

1943-2631

PMID

38552170

DOI

https://doi.org/10.1093/genetics/iyae049

Grant

The core funding for the Alliance is from the National Human Genome Research Institute and the National Heart, Lung and Blood Institute (U24HG010859). The curation of data and their harmonization is supported by National Human Genome Research Institute grants U24HG002659 (ZFIN), U24HG002223 (WormBase), U41HG000739 (FlyBase), U24HG001315 (SGD), U24HG000330 (MGD), P41HD064556 (Xenbase), U24HG011851 (Reactome + GO), and U41HG012212 (GO Consortium), as well as grant R01HL064541 from the National Heart, Lung and Blood Institute (RGD), P41HD062499 from the Eunice Kennedy Shriver National Institute of Child Health and Human Development (GXD), and the Medical Research Council UK grant MR/L001020/ 1 (WormBase). Additional effort was supported by the U.S. Department of Energy (DOE DE-AC02-05CH11231. Curation tools are supported in part by the National Library of Medicine NLM R01LM013871.

Abstract

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, Caenorhabditis 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 2 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 toward a central persistent database to support curation, the data modeling that underpins harmonization, and progress toward a state-of-the-art literature curation system with integrated artificial intelligence and machine learning (AI/ML).

Creative Commons License

Creative Commons Attribution 4.0 International License
This work is licensed under a Creative Commons Attribution 4.0 International License.

Download

Share

COinS