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Harmonizing model organism data in the Alliance of Genome Resources
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 ben...
Formato: | Online Artículo Texto |
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Lenguaje: | English |
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Oxford University Press
2022
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Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8982023/ https://www.ncbi.nlm.nih.gov/pubmed/35380658 http://dx.doi.org/10.1093/genetics/iyac022 |
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collection | PubMed |
description | 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. |
format | Online Article Text |
id | pubmed-8982023 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2022 |
publisher | Oxford University Press |
record_format | MEDLINE/PubMed |
spelling | pubmed-89820232022-04-05 Harmonizing model organism data in the Alliance of Genome Resources Genetics Knowledgebase and Database Resources 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. Oxford University Press 2022-02-25 /pmc/articles/PMC8982023/ /pubmed/35380658 http://dx.doi.org/10.1093/genetics/iyac022 Text en © The Author(s) 2022. Published by Oxford University Press on behalf of Genetics Society of America. https://creativecommons.org/licenses/by/4.0/This is an Open Access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/), which permits unrestricted reuse, distribution, and reproduction in any medium, provided the original work is properly cited. |
spellingShingle | Knowledgebase and Database Resources Harmonizing model organism data in the Alliance of Genome Resources |
title | Harmonizing model organism data in the Alliance of Genome Resources |
title_full | Harmonizing model organism data in the Alliance of Genome Resources |
title_fullStr | Harmonizing model organism data in the Alliance of Genome Resources |
title_full_unstemmed | Harmonizing model organism data in the Alliance of Genome Resources |
title_short | Harmonizing model organism data in the Alliance of Genome Resources |
title_sort | harmonizing model organism data in the alliance of genome resources |
topic | Knowledgebase and Database Resources |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8982023/ https://www.ncbi.nlm.nih.gov/pubmed/35380658 http://dx.doi.org/10.1093/genetics/iyac022 |
work_keys_str_mv | AT harmonizingmodelorganismdataintheallianceofgenomeresources |