Faculty Bibliography

Integration of disparate biomedical terminologies is becoming increasingly important as links between biological science and clinical medicine grow. Mapping concepts in the Gene Ontology (GO) to the UMLS may help further this integration and allow for more efficient information exchange among researchers. Using a gold standard of GO term--UMLS concept mappings provided by the NCI, we examined the performance of various published and combined mapping techniques, in order to maximize precision and recall. We found that for the previously published techniques precision varied between (0.61-0.95), and recall varied from (0.65-0.90), whereas for the hybrid techniques, precision varied between (0.66-0.97), and recall from (0.59-0.93). Our study reveals the benefits of using mapping techniques that incorporate domain knowledge, and provides a basis for future approaches to mapping between distinct biomedical vocabularies

A major purpose of biomedical terminologies is to provide uniform concept representation, allowing for improved methods of analysis of biomedical information. While this goal is being realized in bioinformatics, with the emergence of the Gene Ontology as a standard, there is still no real standard for the representation of clinical concepts. As discoveries in biology and clinical medicine move from parallel to intersecting paths, standardized representation will become more important. A large portion of significant data, however, is mainly represented as free text, upon which conducting computer-based inferencing is nearly impossible. In order to test our hypothesis that existing biomedical terminologies, specifically the UMLS Metathesaurus and SNOMED CT, could be used as templates to implement semantic and logical relationships over free text data that is important both clinically and biologically, we chose to analyze OMIM (Online Mendelian Inheritance in Man). After finding OMIM entries' conceptual equivalents in each respective terminology, we extracted the semantic relationships that were present and evaluated a subset of them for semantic, logical, and biological legitimacy. Our study reveals the possibility of putting the knowledge present in biomedical terminologies to its intended use, with potentially clinically significant consequences

We developed the Guideline Execution by Semantic Decomposition of Representation (GESDOR) model to share guidelines encoded in different formats at the execution level. For this purpose, we extracted a set of generalized guideline execution tasks from the existing guideline representation models. We then created the mappings between specific guideline representation models and the set of the common guideline execution tasks. Finally, we developed a generic task-scheduling model to harmonize the existing approaches to guideline task scheduling. The evaluation has shown that the GESDOR model can be used for the effective execution of guidelines encoded in different formats, and thus realizes guideline sharing at the execution level

Ofri reviews Sloan-Kettering by Abba Kovner and translated by Eddie Levenston

Fifty-two heroin addicts were inducted onto buprenorphine under the care of psychiatric residents in a setting modeled on office practice. Subjects were maintained on a protocol of six weeks of 16 mg daily dosing, then tapered to zero dose up to week 16, and maintained on placebo through week 18. Of 44 subjects who continued after the first induction dose, 11 terminated during maintenance, 17 during taper; and 16 while on zero dose. Twice weekly urine toxicologies showed significant successive declines in samples positive for heroin use across these three periods: 70%, 41%, and 20%, respectively. Among historical variables, only prior AA attendance distinguished subjects who achieved zero dose from those who did not. A comparison with recent studies suggests that relatively inexperienced office-based physicians can maintain patients on buprenorphine at a level comparable to that reported for research clinic settings, but with comparable rates of heroin abstinence. These findings are discussed in light of potential options for office-based opioid maintenance