lunedì 20 settembre 2010

Registrations to SWAT4LS are now open

Registrations to SWAT4LS are now open and accessible at:

Places are limited. We suggest to book in advance. A limited number of additional places will be made available after the early registration deadline.

sabato 11 settembre 2010

Ontotext to sponsor SWAT4LS 2010

SWAT4LS is generously sponsored by Ontotext

Ontotext is a leading technology company that develops robust engines for analysis and management of text and data. It is a proven, competent and cost-effective, partner in:

  • Development of tools and solutions based on semantic technologies

  • Software engineering, performance optimization, ontology design

  • Analysis, evaluation, feasibility studies based on cutting-edge expertise

Our life sciences and health care platform facilitates semantic integration of heterogeneous data sources by employing inference rules and state-of-the-art text mining algorithms. The platform is capable of telling whether “kidney malfunction” is an adverse event or a symptom and will not be confused by the multiple coding systems. We offer customer specific information extraction services that will enrich you internal company knowledge with new facts that are “hidden” in the unstructured experimental data, clinical trials and literature. Our platform supports very powerful search that enable efficient reasoning over structures and extracted information, thus fostering discovery of previously unidentified correlations between varied biological, medical and chemical entities.

Ontotext delivers highly efficient and scalable semantic infrastructure that significantly reduces the cost of combining internal company knowledge with public information. Building a system to integrate and efficiently query 5 billion statements of semantic data on a USD 10K hardware is no longer a dream – it is Ontotext!

Ontotext /
135 Tsarigradsko Shosse, Sofia 1784, Bulgaria
T: +359 2 974 6160,

domenica 5 settembre 2010

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 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 and visualization of biomolecular data as in, and distributed computing in

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]