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author:("besaa, Paolo")
1.  OWL model of clinical trial eligibility criteria compatible with partially-known information 
Background
Clinical trials are important for patients, for researchers and for companies. One of the major bottlenecks is patient recruitment. This task requires the matching of a large volume of information about the patient with numerous eligibility criteria, in a logically-complex combination. Moreover, some of the patient’s information necessary to determine the status of the eligibility criteria may not be available at the time of pre-screening.
Results
We showed that the classic approach based on negation as failure over-estimates rejection when confronted with partially-known information about the eligibility criteria because it ignores the distinction between a trial for which patient eligibility should be rejected and trials for which patient eligibility cannot be asserted. We have also shown that 58.64% of the values were unknown in the 286 prostate cancer cases examined during the weekly urology multidisciplinary meetings at Rennes’ university hospital between October 2008 and March 2009.
We propose an OWL design pattern for modeling eligibility criteria based on the open world assumption to address the missing information problem. We validate our model on a fictitious clinical trial and evaluate it on two real clinical trials. Our approach successfully distinguished clinical trials for which the patient is eligible, clinical trials for which we know that the patient is not eligible and clinical trials for which the patient may be eligible provided that further pieces of information (which we can identify) can be obtained.
Conclusions
OWL-based reasoning based on the open world assumption provides an adequate framework for distinguishing those patients who can confidently be rejected from those whose status cannot be determined. The expected benefits are a reduction of the workload of the physicians and a higher efficiency by allowing them to focus on the patients whose eligibility actually require expertise.
doi:10.1186/2041-1480-4-17
PMCID: PMC3852288  PMID: 24034867
2.  OpenKnowledge for peer-to-peer experimentation in protein identification by MS/MS 
Background
Traditional scientific workflow platforms usually run individual experiments with little evaluation and analysis of performance as required by automated experimentation in which scientists are being allowed to access numerous applicable workflows rather than being committed to a single one. Experimental protocols and data under a peer-to-peer environment could potentially be shared freely without any single point of authority to dictate how experiments should be run. In such environment it is necessary to have mechanisms by which each individual scientist (peer) can assess, locally, how he or she wants to be involved with others in experiments. This study aims to implement and demonstrate simple peer ranking under the OpenKnowledge peer-to-peer infrastructure by both simulated and real-world bioinformatics experiments involving multi-agent interactions.
Methods
A simulated experiment environment with a peer ranking capability was specified by the Lightweight Coordination Calculus (LCC) and automatically executed under the OpenKnowledge infrastructure. The peers such as MS/MS protein identification services (including web-enabled and independent programs) were made accessible as OpenKnowledge Components (OKCs) for automated execution as peers in the experiments. The performance of the peers in these automated experiments was monitored and evaluated by simple peer ranking algorithms.
Results
Peer ranking experiments with simulated peers exhibited characteristic behaviours, e.g., power law effect (a few dominant peers dominate), similar to that observed in the traditional Web. Real-world experiments were run using an interaction model in LCC involving two different types of MS/MS protein identification peers, viz., peptide fragment fingerprinting (PFF) and de novo sequencing with another peer ranking algorithm simply based on counting the successful and failed runs. This study demonstrated a novel integration and useful evaluation of specific proteomic peers and found MASCOT to be a dominant peer as judged by peer ranking.
Conclusion
The simulated and real-world experiments in the present study demonstrated that the OpenKnowledge infrastructure with peer ranking capability can serve as an evaluative environment for automated experimentation.
doi:10.1186/1759-4499-3-3
PMCID: PMC3377912  PMID: 22192521

Results 1-2 (2)