Extending the Foundational Model of Anatomy with Automatically Acquired Spatial Relations

Formal ontologies have made significant impact in bioscience over the last ten years. Among them, the Foundational Model of Anatomy Ontology (FMA) is the most comprehensive model for the spatio-structural representation of human anatomy. In the research project MEDICO we use the FMA as our main source of background knowledge about human anatomy. Our ultimate goals are to use spatial knowledge from the FMA (1) to improve automatic parsing algorithms for 3D volume data sets generated by Computed Tomography and Magnetic Resonance Imaging and (2) to generate semantic annotations using the concepts from the FMA to allow semantic search on medical image repositories. We argue that in this context more spatial relation instances are needed than those currently available in the FMA. In this publication we present a technique for the automatic inductive acquisition of spatial relation instances by generalizing from expert-annotated volume datasets

Named Graphs as a Mechanism for Reasoning About Provenance

Named Graphs is a simple, compatible extension to the RDF abstract syntax that enables statements to be made about RDF graphs. This approach is in contrast to earlier attempts such as RDF reification, or knowledge-base specific extensions including quads and contexts. In this paper we demonstrate the use of Named Graphs and our experiences developing new kinds of semantic web application that build on Named Graphs for digital signatures, provenance, and semantic reasoning. We present a working example based on the Named Graphs for Jena (NG4J) API, from which we developed a semantic version control system for Software Engineering capable of reasoning about Named Graph-based provenance. We go on to discuss the implications of Named Graphs for Description Logics and semantic inference strategies

CONGAS: a collaborative ontology development framework based on Named GrAphS

The process of ontology development involves a range of skills and know-how often requiring team work of different people, each of them with his own way of contributing to the definition and formalization of the domain representation. For this reason, collaborative development is an important feature for ontology editing tools, and should take into account the different characteristics of team participants, provide them with a dedicated working environment allowing to express their ideas and creativity, still protecting integrity of the shared work. In this paper we present CONGAS, a collaborative version of the Knowledge Management and Acquisition platform Semantic Turkey which, exploiting the potentialities brought by recent introduction of context management into RDF triple graphs, offers a collaborative environment where proposals for ontology evolution can emerge and coexist, be evaluated by team users, trusted across different perspectives and eventually converged into the main development stream

Designing an automated clinical decision support system to match clinical practice guidelines for opioid therapy for chronic pain

Abstract Background Opioid prescribing for chronic pain is common and controversial, but recommended clinical practices are followed inconsistently in many clinical settings. Strategies for increasing adherence to clinical practice guideline recommendations are needed to increase effectiveness and reduce negative consequences of opioid prescribing in chronic pain patients. Methods Here we describe the process and outcomes of a project to operationalize the 2003 VA/DOD Clinical Practice Guideline for Opioid Therapy for Chronic Non-Cancer Pain into a computerized decision support system (DSS) to encourage good opioid prescribing practices during primary care visits. We based the DSS on the existing ATHENA-DSS. We used an iterative process of design, testing, and revision of the DSS by a diverse team including guideline authors, medical informatics experts, clinical content experts, and end-users to convert the written clinical practice guideline into a computable algorithm to generate patient-specific recommendations for care based upon existing information in the electronic medical record (EMR), and a set of clinical tools. Results The iterative revision process identified numerous and varied problems with the initially designed system despite diverse expert participation in the design process. The process of operationalizing the guideline identified areas in which the guideline was vague, left decisions to clinical judgment, or required clarification of detail to insure safe clinical implementation. The revisions led to workable solutions to problems, defined the limits of the DSS and its utility in clinical practice, improved integration into clinical workflow, and improved the clarity and accuracy of system recommendations and tools. Conclusions Use of this iterative process led to development of a multifunctional DSS that met the approval of the clinical practice guideline authors, content experts, and clinicians involved in testing. The process and experiences described provide a model for development of other DSSs that translate written guidelines into actionable, real-time clinical recommendations.http://deepblue.lib.umich.edu/bitstream/2027.42/78267/1/1748-5908-5-26.xmlhttp://deepblue.lib.umich.edu/bitstream/2027.42/78267/2/1748-5908-5-26.pdfhttp://deepblue.lib.umich.edu/bitstream/2027.42/78267/3/1748-5908-5-26-S3.TIFFhttp://deepblue.lib.umich.edu/bitstream/2027.42/78267/4/1748-5908-5-26-S2.TIFFhttp://deepblue.lib.umich.edu/bitstream/2027.42/78267/5/1748-5908-5-26-S1.TIFFPeer Reviewe

Evaluation of 17-mm St. Jude Medical Regent prosthetic aortic heart valves by rest and dobutamine stress echocardiography

BACKGROUND: The prosthesis used for aortic valve replacement in patients with small aortic root can be too small in relation to body size, thus showing high transvalvular gradients at rest and/or under stress conditions. This study was carried out to evaluate rest and Dobutamine stress echocardiography (DSE) hemodynamic response of 17-mm St. Jude Medical Regent (SJMR-17 mm) in relatively aged patients at mean 24 months follow-up. METHODS AND RESULTS: The study population consisted of 19 patients (2 men, 17 women, mean age 69.2 ± 7.3 years). All patients underwent rest Doppler echocardiography before and after surgery and basal and DSE at follow up (infused at rate of 5 micrg/Kg/min and increased by 5 microg/Kg/min at 5 min intervals up to 40 microg/Kg/min). The following parameters were evaluated at rest and/or under DSE: heart rate (HR), ejection fraction (EF), cardiac output (CO), peak and mean velocity and pressure gradients (MxV, MnV, MxPG, MnPG), effective orifice area (EOA), indexed EOA (EOAi), left ventricular mass (LVM), indexed LVM (LVMi), Velocity Time Integral at left ventricular outflow tract (VTI LVOT) and transvalvular (Aortic VTI), Doppler velocity index (DVI). At rest MxPG and MnPG were 29.2 ± 7.1 and 16.6 ± 5.8mmHg, respectively; EOA and EOAi resulted 1.14 ± 0.3 cm(2) and 0.76 ± 0.2 cm(2)/m(2); DVI was normal (0.50 ± 0.1). At follow-up LVM and LVMi decreased significantly from pre-operative value of 258 ± 43g and 157.4 ± 27.7g/m(2) to 191 ± 23.8g and 114.5 ± 10.6g/m(2), respectively. DSE increased significantly HR, CO, EF, MxGP (up to 83.4 ± 2 1.9mmHg), MnPG (up to 43.2 ± 12.7mmHg). EOA, EOAi, DVI increased insignificantly (from baseline up to 1.2 ± 0.4 cm(2), 0.75 ± 0.3cm(2)/m(2) and 0.48 ± 0.1 respectively). Two patients developed significant intraventricular gradients. CONCLUSION: These data show that SJMR 17-mm prostheses can be safely implanted in aortic position in relatively aged patients, offering a satisfactory hemodynamic performance at rest and under DSE, with full utilization of its available orifice, suggesting that a possible mild prosthesis-patient mismatch is not an issue of clinical relevance when this small prosthesis is used. Rest and Dobutamine stress echocardiography is a useful and effective means for evaluating prosthesis hemodynamics and for monitoring the expected LVH regression

Towards the Adaptive Semantic Web

In this paper we show how personalization techniques from the area of adaptive hypermedia can be achieved in the semantic web. Our approac

How to reason with OWL in a logic programming system.

Logic programming has always been a major ontology modeling paradigm, and is frequently being used in large research projects and industrial applications, e.g., by means of the F-Logic reasoning engine OntoBroker or the TRIPLE query, inference, and transformation language and system. At the same time, the Web Ontology Language OWL has been recommended by the W3Cfor modeling ontologies for the web. Naturally, it is desirable to investigate the interoperability between both paradigms. In this paper, we do so by studying an expressive fragement of OWL DL for which reasoning can be reduced to the evaluation of Horn logic programs. Building on the KAON 2 algorithms for transforming OWL DL into disjunctive Datalog, we give a detailed account of how and to what extent OWL DL can be employed in standard logic programming systems. En route, we derive a novel, simplified characterization of the supported fragment of OWL DL. © 2006 IEEE