Standardized pipelines support and facilitate integration of diverse datasets at the Rat Genome Database. Database (Oxford) 2025 Jan 22;2025
Date
01/22/2025Pubmed ID
39841812Pubmed Central ID
PMC11753291DOI
10.1093/database/baae132Scopus ID
2-s2.0-85216608239 (requires institutional sign-in at Scopus site) 1 CitationAbstract
The Rat Genome Database (RGD) is a multispecies knowledgebase which integrates genetic, multiomic, phenotypic, and disease data across 10 mammalian species. To support cross-species, multiomics studies and to enhance and expand on data manually extracted from the biomedical literature by the RGD team of expert curators, RGD imports and integrates data from multiple sources. These include major databases and a substantial number of domain-specific resources, as well as direct submissions by individual researchers. The incorporation of these diverse datatypes is handled by a growing list of automated import, export, data processing, and quality control pipelines. This article outlines the development over time of a standardized infrastructure for automated RGD pipelines with a summary of key design decisions and a focus on lessons learned.
Author List
Smith JR, Tutaj MA, Thota J, Lamers L, Gibson AC, Kundurthi A, Gollapally VR, Brodie KC, Zacher S, Laulederkind SJF, Hayman GT, Wang SJ, Tutaj M, Kaldunski ML, Vedi M, Demos WM, De Pons JL, Dwinell MR, Kwitek AEAuthors
Melinda R. Dwinell PhD Associate Dean, Professor in the Physiology department at Medical College of WisconsinAnne E. Kwitek PhD Professor in the Physiology department at Medical College of Wisconsin
Monika Tutaj Research Scientist II in the Physiology department at Medical College of Wisconsin
Shur-Jen Wang Research Scientist II in the Physiology department at Medical College of Wisconsin
MESH terms used to index this publication - Major topics in bold
AnimalsDatabases, Genetic
Genome
Genomics
Rats
