Data Integration Solution for Organ-Specific Studies: An Application for Oral Biology - Biomedical Engineering Systems and Technologies - page 386

We presented Oralome as a set of tools combining a database, web services and
user interface, useful for joining specific results from several major databases, such as
UniProt or NCBI. This framework generated a database, web services and a web ap-
plication where users can access the downloaded data.
Finally, we proposed OralCard as an example of a web application that takes ad-
vantages of the Oralome functionalities. It works as a search engine where the re-
searcher can input any searched-for item, concerning the field of oral biology. It uses
the Oralome database and some of the new web standards to present specific informa-
tion regarding a protein (JavaScript, AJAX and CSS).
Some of the advantages of the Oralome approach are reduction of the time and re-
sources involved in searching, processing and curating information, as well as facili-
tating the use of algorithms to retrieve biologically meaningful results. As a particular
example of Oralome use, OralCard offers the advantage of gathering several major
external tools in one single web application, making it easier and more comfortable
for researchers to access important information regarding one specific protein. Using
the oral cavity as a particular case study, we have shown how it can be used to obtain
a fully functional tool that enables both interactive categorization and exploration.
We believe this project will be a valuable resource for investigators to clarify the
oral cavity biology, identify molecular disease markers, develop diagnostic tests and
improve prognosis, as well as providing invaluable help in discovering new therapeu-
tic agents.
Acknowledgements. This work was supported by the European Community's Se-
venth Framework Programme (FP7/2007-2013), under grant agreement no. 200754
(GEN2PHEN project), and from Fundação para a Ciência e Tecnologia, FCT, under
grant agreement PTDC/EIA-CCO/100541/2008. Joel P. Arrais is funded by FCT
grant SFRH/BPD/79044/2011.
References
1. Cherry, J.M., et al.: SGD: Saccharomyces genome database. Nucleic Acids Re-
search 26(1), 73 (1998)
2. Mering, C., et al.: STRING: a database of predicted functional associations between pro-
teins. Nucleic Acids Research 31(1), 258 (2003)
3. Maglott, D., et al.: Entrez Gene: gene-centered information at NCBI. Nucleic Acids Re-
search 33(suppl. 1), D54 (2005)
4. Bairoch, A., et al.: The universal protein resource (UniProt). Nucleic Acids Research
33(suppl. 1), D154 (2005)
5. Humbertclaude, V., et al.: G.P.9.10 Clinical development of the French UMD-DMD data-
base. Neuromuscular Disorders 17(9-10), 817-818 (2007)
6. Fokkema, I.F.A.C., den Dunnen, J.T., Taschner, P.E.M.: LOVD: Easy creation of a locus
specific sequence variation database using an “LSDB in a box” approach. Human Muta-
tion 26(2), 63-68 (2005)
7. D O'Connor, B., et al.: GMODWeb: a web framework for the Generic Model Organism
Database. Genome Biology 9(6), R102 (2008)
8. Swertz, M., et al.: The MOLGENIS toolkit: rapid prototyping of biosoftware at the push of
a button. BMC Bioinformatics 11(suppl. 12), S12 (2010)