Jonas Almeida to Keynote at SWAT4LS

Jonas Almeida will give a keynote at SWAT4LS.

Title: Development of Integrative Bioinformatics Applications using Cloud Computing resources and Knowledge Organization Systems (KOS).

Summary: In response to the increasingly data intensive and increasingly heterogeneous sources involved in large scale biomedical initiatives, such as The Cancer Genome Atlas (TCGA), NCI's Specialized Programs of Research Excellence (SPOREs) and NHLBI's Proteomics Centers, we have had to move to abstract logical frameworks to develop applications that make use of more distributed computational resources. As a result, we embarked on a 6 year effort to increase the abstraction level of our data structures by relying on the diadic predicated nature of RDF (Wang 2005) to facilitate both our ability to represent fast changing biological data and to let the domain experts themselves participate in its constant re-definition (Almeida 2006). Fast forward to 2010 and a Knowledge Organization System, S3DB (Almeida 2010) is in place as a logical framework for a computational ecosystem assessable via SPARQL endpoints, such as http://tcga.s3db.org. In the process we found out, like many others, that the collaborative involvement of domain experts puts peculiar pressures on the software development environment. Specifically, that it clashes with the conventional stand alone executable application model we were used to. In response we moved to use code injection (javascript) and other distributed features of the modern web browser as a development platform, as in clinical trial initiatives such as http://aguia.googlecode.com and visualization of biomolecular data as in http://cnviewer.googlecode.com, and distributed computing in http://quanah.googlecode.com.


Wang X, R Gorlitsky, and JS Almeida (2005) From XML to RDF: How Semantic Web Technologies Will Change the Design of ‘Omic’ Standards. Nature Biotechnology, Sep;23(9):1099-103 [PMID:16151403].

Almeida JS, C Chen, R Gorlitsky, R Stanislaus, M Aires-de-Sousa, P Eleutério, JA Carriço, A Maretzek, A Bohn, A Chang, F Zhang, R Mitra, GB Mills, X Wang, HF Deus (2006) Data integration gets 'Sloppy'. Nature Biotechnology 24(9):1070-1071. [PMID:16964209].

Almeida JS, Deus HF, Maass W. (2010) S3DB core: a framework for RDF generation and management in bioinformatics infrastructures. BMC Bioinformatics. 2010 Jul 20;11(1):387. [PMID 20646315]