Harmonizing model organism data in the Alliance of Genome Resources
Authors:   Alliance of Genome Resources Consortium, Agapite Julie , Albou Laurent-Philippe , Aleksander Suzanne A , Alexander Micheal , Anagnostopoulos Anna V , Antonazzo Giulia , Argasinska Joanna , Arnaboldi Valerio , Attrill Helen , Becerra Andrés , Bello Susan M , Blake Judith A , Blodgett Olin , Bradford Yvonne M , Bult Carol J , Cain Scott , Calvi Brian R , Carbon Seth , Chan Juancarlos , Chen Wen J , Michael Cherry J , Cho Jaehyoung , Christie Karen R , Crosby Madeline A , Davis Paul , da Veiga Beltrame Eduardo , De Pons Jeffrey L , D’Eustachio Peter , Diamantakis Stavros , Dolan Mary E , dos Santos Gilberto , Douglass Eric , Dunn Barbara , Eagle Anne , Ebert Dustin , Engel Stacia R , Fashena David , Foley Saoirse , Frazer Ken , Gao Sibyl , Gibson Adam C , Gondwe Felix , Goodman Josh , Sian Gramates L , Grove Christian A , Hale Paul , Harris Todd , Thomas Hayman G , Hill David P , Howe Douglas G , Howe Kevin L , Hu Yanhui , Jha Sagar , Kadin James A , Kaufman Thomas C , Kalita Patrick , Karra Kalpana , Kishore Ranjana , Kwitek Anne E , Laulederkind Stanley J F , Lee Raymond , Longden Ian , Luypaert Manuel , MacPherson Kevin A , Martin Ryan , 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 , Nalabolu Harika S , Nash Robert S , Ng Patrick , Nuin Paulo , Paddock Holly , Paulini Michael , Perrimon Norbert , Pich Christian , Quinton-Tulloch Mark , Raciti Daniela , Ramachandran Sridhar , Richardson Joel E , Gelbart Susan Russo , Ruzicka Leyla , Schaper Kevin , Schindelman Gary , Shimoyama Mary , Simison Matt , Shaw David R , Shrivatsav Ajay , Singer Amy , Skrzypek Marek , Smith Constance M , Smith Cynthia L , Smith Jennifer R , Stein Lincoln , Sternberg Paul W , Tabone Christopher J , Thomas Paul D , Thorat Ketaki , Thota Jyothi , Toro Sabrina , Tomczuk Monika , Trovisco Vitor , Tutaj Marek A , Tutaj Monika , Urbano Jose-Maria , Van Auken Kimberly , Van Slyke Ceri E , Wang Qinghua , Wang Shur-Jen , Weng Shuai , Westerfield Monte , Williams Gary , Wilming Laurens G , Wong Edith D , Wright Adam , Yook Karen , Zarowiecki Magdalena , Zhou Pinglei , Zytkovicz Mark 
Published: February 2022

Abstract
The Alliance of Genome Resources (the Alliance) is a combined effort of 7 knowledgebase projects: Saccharomyces Genome Database, WormBase, FlyBase, Mouse Genome Database, the Zebrafish Information Network, Rat Genome Database, and the Gene Ontology Resource. The Alliance seeks to provide several benefits: better service to the various communities served by these projects; a harmonized view of data for all biomedical researchers, bioinformaticians, clinicians, and students; and a more sustainable infrastructure. The Alliance has harmonized cross-organism data to provide useful comparative views of gene function, gene expression, and human disease relevance. The basis of the comparative views is shared calls of orthology relationships and the use of common ontologies. The key types of data are alleles and variants, gene function based on gene ontology annotations, phenotypes, association to human disease, gene expression, protein–protein and genetic interactions, and participation in pathways. The information is presented on uniform gene pages that allow facile summarization of information about each gene in each of the 7 organisms covered (budding yeast, roundworm Caenorhabditis elegans, fruit fly, house mouse, zebrafish, brown rat, and human). The harmonized knowledge is freely available on the alliancegenome.org portal, as downloadable files, and by APIs. We expect other existing and emerging knowledge bases to join in the effort to provide the union of useful data and features that each knowledge base currently provides.