Updates to the Alliance of Genome Resources central infrastructure

作者：Suzi Aleksander, Anna V. Anagnostopoulos, Giulia Antonazzo, Valerio Arnaboldi, Helen Attrill, Andrés Becerra, Susan M Bello, Olin Blodgett, Yvonne M. Bradford, Carol J. Bult, Scott Cain, Brian R. Calvi, Seth J Carbon, Juancarlos Chan, Wen J. Chen, J. Michael Cherry, Jaehyoung Cho, Madeline A. Crosby, Jeff De Pons, Peter D’Eustachio, Stavros Diamantakis, Mary Eileen Dolan, Gilberto dos Santos, Sarah C. Dyer, Dustin Ebert, Stacia R. Engel, David S. Fashena, Malcolm E Fisher, Saoirse Foley, Adam C Gibson, Varun Reddy Gollapally, L. Sian Gramates, Christian A Grove, Paul Hale, Todd W. Harris, G. Thomas Hayman, Yanhui Hu, Christina James‐Zorn, Kamran Karimi, Kalpana Karra, Ranjana Kishore, Anne E. Kwitek, Stanley J. F. Laulederkind, Raymond Lee, Ian Longden, Manuel Luypaert, Nicholas Markarian, Steven J Marygold, Beverley B. Matthews, Monica S. McAndrews, Gillian Millburn, Stuart R. Miyasato, Howie Motenko, Sierra A. Taylor Moxon, Hans‐Michael Müller, Chris Mungall, Anushya Muruganujan, Tremayne Mushayahama, Robert S Nash, Paulo A.S. Nuin, Holly Paddock, Troy J. Pells, Norbert Perrimon, Christian Pich, Mark J. Quinton-Tulloch, Daniela Raciti, Sridhar Ramachandran, Joel E. Richardson, Susan Russo Gelbart, Leyla Ruzicka, Gary Schindelman, David Richard Shaw, Gavin J. Sherlock, Ajay Shrivatsav, Amy Singer, Constance M. Smith, Cynthia L. Smith, Jennifer R. Smith, Lincoln Stein, Paul W. Sternberg, Christopher J. Tabone, Paul D. Thomas, Ketaki Thorat, Jyothi Thota, Monika Tomczuk, Vítor Trovisco, Marek Tutaj, Jose-Maria Urbano, Kimberly M. Van Auken, Ceri E. Van Slyke, Peter D. Vize, Qinghua Wang, Shuai Weng, Monte Westerfield, Laurens G. Wilming, Edith D. Wong, Adam Wright, Karen Yook, Pinglei Zhou, Aaron M. Zorn, Mark Zytkovicz · 发表于：Genetics · 年份：2024 · DOI：10.1093/genetics/iyae049 · 被引用次数：73 · 研究领域：Biomedical Text Mining and Ontologies、Genetics, Bioinformatics, and Biomedical Research、Genomics and Rare Diseases

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, ...