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Am J Physiol Renal Physiol. 2014 Sep 15;307(6):F747-55. doi: 10.1152/ajprenal.00012.2014. Epub 2014 Jul 23.

A knowledge base of vasopressin actions in the kidney.

Author information

1
Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland;
2
Departments of Electrical and Computer Engineering and Computer Science, Western Michigan University, Kalamazoo, Michigan.
3
Faculty of Medicine, Chulalongkorn University, Bangkok, Thailand; and.
4
Epithelial Systems Biology Laboratory, National Heart, Lung, and Blood Institute, National Institutes of Health, Bethesda, Maryland; knep@helix.nih.gov.

Abstract

Biological information is growing at a rapid pace, making it difficult for individual investigators to be familiar with all information that is relevant to their own research. Computers are beginning to be used to extract and curate biological information; however, the complexity of human language used in research papers continues to be a critical barrier to full automation of knowledge extraction. Here, we report a manually curated knowledge base of vasopressin actions in renal epithelial cells that is designed to be readable either by humans or by computer programs using natural language processing algorithms. The knowledge base consists of three related databases accessible at https://helixweb.nih.gov/ESBL/TinyUrls/Vaso_portal.html. One of the component databases reports vasopressin actions on individual proteins expressed in renal epithelia, including effects on phosphorylation, protein abundances, protein translocation from one subcellular compartment to another, protein-protein binding interactions, etc. The second database reports vasopressin actions on physiological measures in renal epithelia, and the third reports specific mRNA species whose abundances change in response to vasopressin. We illustrate the application of the knowledge base by using it to generate a protein kinase network that connects vasopressin binding in collecting duct cells to physiological effects to regulate the water channel protein aquaporin-2.

KEYWORDS:

ENaC; aquaporin-2; database; urea channel

PMID:
25056354
PMCID:
PMC4166727
DOI:
10.1152/ajprenal.00012.2014
[Indexed for MEDLINE]
Free PMC Article

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