Database Commons

a catalog of biological databases

e.g., animal; RNA; Methylation; China

Database Profile

PTR

General information

URL: http://www.ars.usda.gov/Services/docs
Full name:
Description: The use of swine in biomedical research has increased dramatically in the last decade. Diverse genomic- and proteomic databases have been developed to facilitate research using human and rodent models. Current porcine gene databases, however, lack the robust annotation to study pig models that are relevant to human studies and for comparative evaluation with rodent models. Furthermore, they contain a significant number of errors due to their primary reliance on machine-based annotation. To address these deficiencies, a comprehensive literature-based survey was conducted to identify certain selected genes that have demonstrated function in humans, mice or pigs.
Year founded: 2017
Last update:
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Country/Region: United States
Data type:
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Contact information

University/Institution: United States Department Of Agriculture
Address: United States Department of Agriculture, Agricultural Research Service, Beltsville Human Nutrition Research Center, Diet, Genomics and Immunology Laboratory, Beltsville, MD, USA.
City: maryland
Province/State:
Country/Region: United States
Contact name (PI/Team): Dawson HD
Contact email (PI/Helpdesk): Harry.Dawson@ars.usda.gov

Publications

28830355
The porcine translational research database: a manually curated, genomics and proteomics-based research resource. [PMID: 28830355]
Dawson HD, Chen C, Gaynor B, Shao J, Urban JF.

BACKGROUND: The use of swine in biomedical research has increased dramatically in the last decade. Diverse genomic- and proteomic databases have been developed to facilitate research using human and rodent models. Current porcine gene databases, however, lack the robust annotation to study pig models that are relevant to human studies and for comparative evaluation with rodent models. Furthermore, they contain a significant number of errors due to their primary reliance on machine-based annotation. To address these deficiencies, a comprehensive literature-based survey was conducted to identify certain selected genes that have demonstrated function in humans, mice or pigs.
RESULTS: The process identified 13,054 candidate human, bovine, mouse or rat genes/proteins used to select potential porcine homologs by searching multiple online sources of porcine gene information. The data in the Porcine Translational Research Database (( http://www.ars.usda.gov/Services/docs.htm?docid=6065 ) is supported by >5800 references, and contains 65 data fields for each entry, including >9700 full length (5' and 3') unambiguous pig sequences, >2400 real time PCR assays and reactivity information on >1700 antibodies. It also contains gene and/or protein expression data for >2200 genes and identifies and corrects 8187 errors (gene duplications artifacts, mis-assemblies, mis-annotations, and incorrect species assignments) for 5337 porcine genes.
CONCLUSIONS: This database is the largest manually curated database for any single veterinary species and is unique among porcine gene databases in regard to linking gene expression to gene function, identifying related gene pathways, and connecting data with other porcine gene databases. This database provides the first comprehensive description of three major Super-families or functionally related groups of proteins (Cluster of Differentiation (CD) Marker genes, Solute Carrier Superfamily, ATP binding Cassette Superfamily), and a comparative description of porcine microRNAs.

BMC Genomics. 2017:18(1) | 13 Citations (from Europe PMC, 2021-01-16)

Ranking

All databases:
1748/4728 (63.05%)
Expression:
335/865 (61.387%)
1748
Total Rank
13
Citations
3.25
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Record metadata

Created on: 2018-01-29
Curated by:
Alia Rafique [2018-04-16]
zhang yang [2018-01-28]