PUBLICATION
Updates to the Alliance of Genome Resources Central Infrastructure
- Authors
- Alliance of Genome Resources Consortium
- ID
- ZDB-PUB-240330-2
- Date
- 2024
- Source
- Genetics 227(1): (Journal)
- Registered Authors
- Bradford, Yvonne, Fashena, David, Moxon, Sierra (fka Taylor), Paddock, Holly, Pich, Christian, Ramachandran, Sridhar, Ruzicka, Leyla, Singer, Amy, Van Slyke, Ceri E., Westerfield, Monte
- Keywords
- C. elegans, Drosophila, data integration, database, knowledgebase, mouse, software, text mining, yeast, zebrafish
- MeSH Terms
-
- Software
- Databases, Genetic*
- Mice
- Genomics*/methods
- Animals
- Genome
- PubMed
- 38552170 Full text @ Genetics
Citation
Alliance of Genome Resources Consortium (2024) Updates to the Alliance of Genome Resources Central Infrastructure. Genetics. 227(1):.
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, 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).
Genes / Markers
Expression
Phenotype
Mutations / Transgenics
Human Disease / Model
Sequence Targeting Reagents
Fish
Orthology
Engineered Foreign Genes
Mapping