29 March 2024 | The Alliance of Genome Resources Consortium
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. 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). The Alliance has 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). Existing interactive data tables have been enhanced, and an interactive table of paralogs has been added to complement our representation of orthology. Species-specific "landing pages" have been implemented, and disease-specific portals are planned. A common community forum implemented in Discourse software is also available. The Alliance is working 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). The Alliance has implemented a web portal with landing pages for each model organism, and new features include a paralogy section populated with data from the Drosophila Research & Screening Center (DRSC), a JBrowse sequence detail widget, and a Model organism BLAST tool. AllianceMine is a sophisticated search and retrieval tool that offers a unified view of harmonized data. SimpleMine is a tool for biologists to get essential information for a list of genes without any command-line or programming skill. Pathway displays with metabolites (GO Causal Activity Models) have been implemented. The Alliance has developed a harmonized data model using LinkML to enable data harmonization. A persistent store architecture has been designed to handle most of the demands of the project, including curation, analysis, and display of the data. The Alliance has implemented a literature system, ABC, that supports curation and end users. Textpresso is a full-text literature search engine that gets power from its single-sentence scope, focus on a specific model organism, and categories of semantically or biologically related terms. The Alliance is developing AI/ML classifiers for determining whether papers returned from automated PubMed queries should be kept in their corpus or discarded. APIs are a key component of Alliance Central's data service infrastructure. The Alliance is committed to the long-term preservation of digital objects and resources. The Alliance has an outreach and interactions program, including a help desk, online documentation, and a community forum. The Alliance uses social media to engage with the user community. The Alliance is exploring the use of AI/ML in gene function summarization. The Alliance is also exploring the use of AI/ML in data harmonization and curation. The Alliance is working on improving the accuracy of geneThe 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. 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). The Alliance has 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). Existing interactive data tables have been enhanced, and an interactive table of paralogs has been added to complement our representation of orthology. Species-specific "landing pages" have been implemented, and disease-specific portals are planned. A common community forum implemented in Discourse software is also available. The Alliance is working 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). The Alliance has implemented a web portal with landing pages for each model organism, and new features include a paralogy section populated with data from the Drosophila Research & Screening Center (DRSC), a JBrowse sequence detail widget, and a Model organism BLAST tool. AllianceMine is a sophisticated search and retrieval tool that offers a unified view of harmonized data. SimpleMine is a tool for biologists to get essential information for a list of genes without any command-line or programming skill. Pathway displays with metabolites (GO Causal Activity Models) have been implemented. The Alliance has developed a harmonized data model using LinkML to enable data harmonization. A persistent store architecture has been designed to handle most of the demands of the project, including curation, analysis, and display of the data. The Alliance has implemented a literature system, ABC, that supports curation and end users. Textpresso is a full-text literature search engine that gets power from its single-sentence scope, focus on a specific model organism, and categories of semantically or biologically related terms. The Alliance is developing AI/ML classifiers for determining whether papers returned from automated PubMed queries should be kept in their corpus or discarded. APIs are a key component of Alliance Central's data service infrastructure. The Alliance is committed to the long-term preservation of digital objects and resources. The Alliance has an outreach and interactions program, including a help desk, online documentation, and a community forum. The Alliance uses social media to engage with the user community. The Alliance is exploring the use of AI/ML in gene function summarization. The Alliance is also exploring the use of AI/ML in data harmonization and curation. The Alliance is working on improving the accuracy of gene