OsteoChondroDB: a database about biomolecular chondral- bone development in physiological and diseased conditions

Abstract

Motivations Current researches on osteochondral tissue focus on understanding the biomolecular mechanisms of bone/cartilage development [1,2], which helps in understanding the onset of the related genetics diseases [3] and prompt the development of new approaches for tissue engineering [4]. Nowadays, regulation of tissue formation and remodelling is not completely understood, especially when dealing with the process of differentiation into bone and cartilage or with tissues affected by complex pathologies. Concerning the biomolecular mechanisms of bone formation, to authors’ knowledge the only data collection existing is the Skeletal Gene Database [5], a list of genes involved in the bone metabolism accompanied by PubMed [6] references to scientific papers. This database consists of a pdf file, which describes and annotates many genes involved in osteochondrial development in a simple, but static way. Other data are sparse in literature, although a rationalization of the available information about bone pathologies has been done by OMIM [7]. In order to overcome this limitation, authors designed a database, the OsteoChondroDB, by employing a vertical data integration strategy to connect tissue specific information referred to diverse biomolecular levels. In particular, the database stores information about bone development in physiological conditions together with data about osteochondral pathologies, which helps in highlighting pathways of differentiation and tissue maintaining. The resource aims at collecting and organizing data, to facilitate mining of active components in bone tissue cells. The resource is intended to be a reference knowledge base for research studies about the genetics of bone and cartilage pathologies, with the aim of improving the knowledge about physiological pathways involved in the development of this tissue. Moreover it represents a support for tissue engineering, to identify always better methods to grow cells on biomaterial scaffolds, and for new therapies identification, proposing molecules as possible targets for drug treatments of bone diseases.