Biomedical Engineering Reference
In-Depth Information
Although this effort to create long-lasting hubs of biomedical data has been very
successful, we should not ignore the major contribution that many, more specific,
databases make to the current state of science. They are of special interest for small
communities that share common research interests. The UMD-DMD database [5],
specialized in Duchenne Muscular Dystrophy, is one example.
Being aware of the redundancy of features shared by many of those databases, and
of the lack of technical expertise regarding the curators, several frameworks have
been proposed to ease the task of deploying new databases. Examples include LOVD
[6], specialized in annotating locus-specific databases, GMODWeb [7] for organism-
specific databases, or Molgenis [8] which allows deployment of more generic bio-
medical databases. Despite the validity of those frameworks, there is none focused on
simulating the behaviour of a single human organ or set of adjacent organs. This need
to partition the data of the “whole” human system is relevant because, on the one
hand, it reduces the time and resources involved in searching, processing and curating
information, and on the other, it facilitates the use of algorithms to retrieve biological-
ly meaningful results.
The main objective of this project was the development of a web information sys-
tem that can collect genotypic information about oral health and that can be useful
both for researchers and dentists. A comprehensive integrated resource of the saliva
proteins, currently missing in the field of oral biology, would enable researchers to
understand the basic constituents, diversity and variability of the salivary proteome,
allowing definition and characterization of the human oral physiome. This goal was
achieved at two levels: (1) Oralome for the application developer, which consists of a
proprietary database, and a set of tools to retrieve biomolecular information from the
major platforms like NCBI (National Center for Biotechnology Information) and
UniProt; (2) for the end-user, a web portal (OralCard) directed to researchers and
dentists, with a set of tools for searching and filtering data from the database, and the
possibility to add new information.
Through OralCard web portal, users are able to perform their queries and search
among a list of provided results. For each entity, users will be able to consult and ana-
lyse a list of dependencies and information retrieved from other major databases. To
demonstrate the usefulness of this project, we also present its application in the oral
cavity research domain. A platform designed to integrate protein data related to this
field will be implemented. This will include salivary proteins obtained in proteomic
studies by different research groups, as well as proteins potentially produced and ex-
creted by microorganisms assigned to the oral cavity. The ultimate goal is to present a
tool for the community that contains accurate, manually curated and updated data re-
garding the oral cavity, to enable interaction studies, categorization and exploration.
We expect this work to be a valuable resource for investigators aiming to clarify
oral biology, identify molecular disease markers, develop diagnostic tests and im-
prove prognosis, as well as providing information for the design of biological path-
ways preparing the ground for the discovery of new therapeutic agents.
2
Motivation
The oral cavity consists of a complex ecosystem where a variety of proteins from
numerous origins are present. Being able to estimate the impact of the interactions
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