Updates to the Alliance of Genome Resources central infrastructure
Authors:   The Alliance of Genome Resources Consortium, Aleksander Suzanne A , Anagnostopoulos Anna V , Antonazzo Giulia , Arnaboldi Valerio , Attrill Helen , Becerra Andrés , Bello Susan M , Blodgett Olin , Bradford Yvonne M , Bult Carol J , Cain Scott , Calvi Brian R , Carbon Seth , Chan Juancarlos , Chen Wen J , Cherry J Michael , Cho Jaehyoung , Crosby Madeline A , De Pons Jeffrey L , D’Eustachio Peter , Diamantakis Stavros , Dolan Mary E , dos Santos Gilberto , Dyer Sarah , Ebert Dustin , Engel Stacia R , Fashena David , Fisher Malcolm , Foley Saoirse , Gibson Adam C , Gollapally Varun R , Gramates L Sian , Grove Christian A , Hale Paul , Harris Todd , Hayman G Thomas , Hu Yanhui , James-Zorn Christina , Karimi Kamran , Karra Kalpana , Kishore Ranjana , Kwitek Anne E , Laulederkind Stanley J F , Lee Raymond , Longden Ian , Luypaert Manuel , Markarian Nicholas , Marygold Steven J , Matthews Beverley , McAndrews Monica S , Millburn Gillian , Miyasato Stuart , Motenko Howie , Moxon Sierra , Muller Hans-Michael , Mungall Christopher J , Muruganujan Anushya , Mushayahama Tremayne , Nash Robert S , Nuin Paulo , Paddock Holly , Pells Troy , Perrimon Norbert , Pich Christian , Quinton-Tulloch Mark , Raciti Daniela , Ramachandran Sridhar , Richardson Joel E , Gelbart Susan Russo , Ruzicka Leyla , Schindelman Gary , Shaw David R , Sherlock Gavin , Shrivatsav Ajay , Singer Amy , Smith Constance M , Smith Cynthia L , Smith Jennifer R , Stein Lincoln , Sternberg Paul W , Tabone Christopher J , Thomas Paul D , Thorat Ketaki , Thota Jyothi , Tomczuk Monika , Trovisco Vitor , Tutaj Marek A , Urbano Jose-Maria , Van Auken Kimberly , Van Slyke Ceri E , Vize Peter D , Wang Qinghua , Weng Shuai , Westerfield Monte , Wilming Laurens G , Wong Edith D , Wright Adam , Yook Karen , Zhou Pinglei , Zorn Aaron , Zytkovicz Mark 
Published: March 2024

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).