The Translational Medicine Ontology and Knowledge Base: driving personalized medicine by bridging the gap between bench and bedside

Background: Translational medicine requires the integration of knowledge using heterogeneous data from health care to the life sciences. Here, we describe a collaborative effort to produce a prototype Translational Medicine Knowledge Base (TMKB) capable of answering questions relating to clinical practice and pharmaceutical drug discovery. Results: We developed the Translational Medicine Ontology (TMO) as a unifying ontology to integrate chemical, genomic and proteomic data with disease, treatment, and electronic health records. We demonstrate the use of Semantic Web technologies in the integration of patient and biomedical data, and reveal how such a knowledge base can aid physicians in providing tailored patient care and facilitate the recruitment of patients into active clinical trials. Thus, patients, physicians and researchers may explore the knowledge base to better understand therapeutic options, efficacy, and mechanisms of action. Conclusions: This work takes an important step in using Semantic Web technologies to facilitate integration of relevant, distributed, external sources and progress towards a computational platform to support personalized medicine. Availability: TMO can be downloaded from http://code.google.com/p/translationalmedicineontology and TMKB can be accessed at http://tm.semanticscience.org/sparql

Interlinking educational data to web of data

With the proliferation of educational data on the Web, publishing and interlinking eLearning resources have become an important issue nowadays. Educational resources are exposed under heterogeneous Intellectual Property Rights (IPRs) in different times and formats. Some resources are implicitly related to each other or to the interest, cultural and technical environment of learners. Linking educational resources to useful knowledge on the Web improves resource seeking. This becomes crucial for moving from current isolated eLearning repositories towards an open discovery space, including distributed resources irrespective of their geographic and system boundaries. Linking resources is also useful for enriching educational content, as it provides a richer context and other related information to both educators and learners. On the other hand, the emergence of the so-called "Linked Data" brings new opportunities for interconnecting different kinds of resources on the Web of Data. Using the Linked Data approach, data providers can publish structured data and establish typed links between them from various sources. To this aim, many tools, approaches and frameworks have been built to first expose the data as Linked Data formats and to second discover the similarities between entities in the datasets. The research carried out for this PhD thesis assesses the possibilities of applying the Linked Open Data paradigm to the enrichment of educational resources. Generally speaking, we discuss the interlinking educational objects and eLearning resources on the Web of Data focusing on existing schemas and tools. The main goals of this thesis are thus to cover the following aspects: -- Exposing the educational (meta)data schemas and particularly IEEE LOM as Linked Data -- Evaluating currently available interlinking tools in the Linked Data context -- Analyzing datasets in the Linked Open Data cloud, to discover appropriate datasets for interlinking -- Discussing the benefits of interlinking educational (meta)data in practice

LIMES M/R: Parallelization of the LInk discovery framework for MEtric Spaces using the Map/Reduce paradigm

The World Wide Web is the most important information space in the world. With the change of the web during the last decade, today’sWeb 2.0 offers everybody the possibility to easily publish information on the web. For instance, everyone can have his own blog, write Wikipedia articles, publish photos on Flickr or post status messages via Twitter. All these services on the web offer users all around the world the opportunity to interchange information and interconnect themselves with other users. However, the information, as it is usually published today, does not offer enough semantics to be machine-processable. As an example, Wikipedia articles are created using the lightweight Wiki markup language and then published as HyperText Markup Language (HTML) files whose semantics can easily be captured by humans, but not machines