Abstract
BackgroundOsteoporosis is a common, complex disease of bone with a strong heritable component, characterized by low bone mineral density, microarchitectural deterioration of bone tissue and an increased risk of fracture. Due to limited drug selection for osteoporosis and increasing morbidity, mortality of osteoporotic fractures, osteoporosis has become a major health burden in aging societies. Current researches for identifying specific loci or genes involved in osteoporosis contribute to a greater understanding of the pathogenesis of osteoporosis and the development of better diagnosis, prevention and treatment strategies. However, little is known about how most causal genes work and interact to influence osteoporosis. Therefore, it is greatly significant to collect and analyze the studies involved in osteoporosis-related genes. Unfortunately, the information about all these osteoporosis-related genes is scattered in a large amount of extensive literature. Currently, there is no specialized database for easily accessing relevant information about osteoporosis-related genes and miRNAs.MethodsWe extracted data from literature abstracts in PubMed by text-mining and manual curation. Moreover, a local MySQL database containing all the data was developed with PHP on a Windows server.ResultsOsteoporosAtlas (http://biokb.ncpsb.org/osteoporosis/), the first specialized database for easily accessing relevant information such as osteoporosis-related genes and miRNAs, was constructed and served for researchers. OsteoporosAtlas enables users to retrieve, browse and download osteoporosis-related genes and miRNAs. Gene ontology and pathway analyses were integrated into OsteoporosAtlas. It currently includes 617 human encoding genes, 131 human non-coding miRNAs, and 128 functional roles. We think that OsteoporosAtlas will be an important bioinformatics resource to facilitate a better understanding of the pathogenesis of osteoporosis and developing better diagnosis, prevention and treatment strategies.
Highlights
Osteoporosis is a common skeletal disease under strong genetic control (Ralston & De Crombrugghe, 2006), whose characteristics are low bone mineral density (BMD), microarchitectural deterioration of bone tissue and increased risk of fracture (Kanis et al, 1994)
The precision, recall, F-measure of our bio-entity recognizer for identifying gene/protein were respectively 0.959, 0.802 and 0.874, indicating it is of great performance for entity recognition
All osteoporosis-related genes and their relevant information were deposited into a local MySQL database
Summary
Osteoporosis is a common skeletal disease under strong genetic control (Ralston & De Crombrugghe, 2006), whose characteristics are low bone mineral density (BMD), microarchitectural deterioration of bone tissue and increased risk of fracture (Kanis et al, 1994). Osteoporosis is a common, complex disease of bone with a strong heritable component, characterized by low bone mineral density, microarchitectural deterioration of bone tissue and an increased risk of fracture. Current researches for identifying specific loci or genes involved in osteoporosis contribute to a greater understanding of the pathogenesis of osteoporosis and the development of better diagnosis, prevention and treatment strategies. There is no specialized database for accessing relevant information about osteoporosis-related genes and miRNAs. Methods. OsteoporosAtlas (http://biokb.ncpsb.org/osteoporosis/), the first specialized database for accessing relevant information such as osteoporosis-related genes and miRNAs, was constructed and served for researchers. We think that OsteoporosAtlas will be an important bioinformatics resource to facilitate a better understanding of the pathogenesis of osteoporosis and developing better diagnosis, prevention and treatment strategies
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