Harmonizing model organism data in the Alliance of Genome Resources
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.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Feb 25, 2022
- Source ID
- 10.1093/genetics/iyac022
Entities
People
- Adam C Gibson
- Adam Wright
- Ajay Shrivatsav
- Alliance Of Genome Resources Consortium
- Amy Singer
- Andrés Becerra
- Anna V Anagnostopoulos
- Anne E Kwitek
- Anne Eagle
- Anushya Muruganujan
- Barbara Dunn
- Beverley Matthews
- Brian R Calvi
- Carol J. Bult
- Ceri E Van Slyke
- Christian A Grove
- Christian Pich
- Christopher J Tabone
- Christopher J. Mungall
- Clare Smith
- Cynthia L Smith
- Daniela Raciti
- David Fashena
- David P. Hill
- David R Shaw
- Douglas G Howe
- Dustin Ebert
- Edith D Wong
- Eduardo Da Veiga Beltrame
- Eric Douglass
- Felix Gondwe
- G Thomas Hayman
- Gary Schindelman
- Gary Williams
- Gilberto Dos Santos
- Gillian Millburn
- Giulia Antonazzo
- Hans-michael Muller
- Harika S Nalabolu
- Helen Attrill
- Holly Paddock
- Howie Motenko
- Ian Longden
- J. Michael Cherry
- Jaehyoung Cho
- James A Kadin
- Jeffrey L De Pons
- Jennifer R Smith
- Joanna Argasinska
- Joel E Richardson
- Jose-maria Urbano
- Josh Goodman
- Juancarlos Chan
- Judith A Blake
- Julie Agapite
- Jyothi Thota
- Kalpana Karra
- Karen R. Christie
- Karen Yook
- Ken Frazer
- Ketaki Thorat
- Kevin A Macpherson
- Kevin L Howe
- Kevin Schaper
- Kimberly Van Auken
- L Sian Gramates
- Laurens G Wilming
- Laurent-philippe Albou
- Leyla Ruzicka
- Lincoln Stein
- Madeline A Crosby
- Magdalena Zarowiecki
- Manuel Luypaert
- Marek A Tutaj
- Marek Skrzypek
- Mark Quinton-tulloch
- Mark Zytkovicz
- Mary E Dolan
- Mary Shimoyama
- Matt Simison
- Michael Paulini
- Micheal Alexander
- Monica S Mcandrews
- Monika Tomczuk
- Monika Tutaj
- Monte Westerfield
- Norbert Perrimon
- Olin Blodgett
- Patrick Kalita
- Patrick Ng
- Paul D. Thomas
- Paul H Davis
- Paul Hale
- Paul W. Sternberg
- Paulo Nuin
- Peter D’eustachio
- Pinglei Zhou
- Qinghua Wang
- Ranjana Kishore
- Raymond Lee
- Robert S Nash
- Ryan Martin
- Sabrina Toro
- Sagar Jha
- Saoirse Foley
- Scott Cain
- Seth Carbon
- Shuai Weng
- Shur-jen Wang
- Sibyl Gao
- Sierra Moxon
- Sridhar Ramachandran
- Stacia R Engel
- Stanley J F Laulederkind
- Stavros Diamantakis
- Steven J Marygold
- Stuart Miyasato
- Susan M. Bello
- Susan Russo Gelbart
- Suzanne A Aleksander
- Thomas C Kaufman
- Todd Harris
- Tremayne Mushayahama
- Valerio Arnaboldi
- Vitor Trovisco
- Wen J Chen
- Yanhui Hu
- Yvonne M Bradford
Organizations
- Eunice Kennedy Shriver National Institute of Child Health and Human Development
- Medical Research Council
- National Heart, Lung, and Blood Institute
- National Human Genome Research Institute