Hua Xu

..This study sought to develop natural-language-processing algorithms to extract drug-dose information from clinical text, and to assess the capabilities of such tools to automate the data-extraction process for pharmacogenetic studies...

..Further analysis demonstrated that the improvement by the TCRS method was mainly from additionally detected rare senses, thus indicating its usefulness for building more complete sense inventories of clinical abbreviations...

..Our evaluation using a 10-fold cross validation showed that the PCFG parser dramatically improved parsing performance when compared to the CFG parser...

..5%, 93.9%, and 96.0% respectively. We then applied MedEx unchanged to outpatient clinic visit notes. It performed similarly with F-measures over 90% on a set of 25 clinic visit notes...

..To develop methods for building corpus-specific sense inventories of abbreviations occurring in clinical documents...

..8% (precision 98.8% and recall of 91.2%). When a voting scheme was used to combine output from various ML classifiers, the system achieved the highest F-measure of 95.7%...

..Further investigations must validate extension of NLP approaches for other types of CRC screening applications...

..Our results showed that the customized module achieved significantly higher F-measures at all levels of classification (i.e., sentence, document, patient) compared to the direct application of the cTAKES module to the Vanderbilt data...

..Existing knowledge sources, such as Entrez Gene and the MEDLINE database, contain information concerning the characteristics of a particular gene that could be used to disambiguate gene symbols...

..996 for document level concept identification, and 0.93 for patient level case detection...

..Electronic health record (EHR) systems linked to biobanks may allow for pharmacogenomic analysis, but they have not yet been used for this purpose...

..In this paper, we introduce another classification approach based on words of the concept strings and compare it to the contextual syntactic approach...

..This project was part of the 2010 Center of Informatics for Integrating Biology and the Bedside/Veterans Affairs (VA) natural-language-processing challenge...

..We applied the framework to determine patient warfarin exposure at hospital admissions and achieved 87% precision, 79% recall, and an area under the receiver-operator characteristic curve of 0.93...

..54 and recall of 0.654 was achieved by the top prediction; precision of 0.64 and recall of 0.769 was achieved by the top 2 predictions. Error analysis revealed problems in the current method, and provided insight into future improvements...

..This task required accurate recognition of medication name, dosage, mode, frequency, duration, and reason for drug administration...

..This study suggested that accurate identification of clinical abbreviations is a challenging task and that more advanced abbreviation recognition modules might improve existing clinical NLP systems...

..Accurate prediction of potential ADRs is required in the entire life cycle of a drug, including early stages of drug design, different phases of clinical trials, and post-marketing surveillance...

..74 (95% CI: [.70-.76]) and 0.70 (95% CI [.63-.76]), respectively. We adapt a JAVA viewer known as PGviewer for the simultaneous visualization of images with NLP extracted information...

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..Thus, there is a need to explicitly address the factors and to systematically quantify their effects on performance...

..For example, to achieve an AUC of 0.79, the random sampling method used 32 samples, while our best active learning algorithm required only 12 samples, a reduction of 62.5% in manual annotation effort...

..When reusable data are needed from notes, providers can use structured documentation or rely on post-hoc text processing to produce structured data, as appropriate...

..04%). We conclude that such corpus-based methods are effective for generating semantic lexicons, which may improve named entity recognition tasks and may aid in augmenting synonymy within existing terminologies...

..The importance of other drug absorption, distribution, metabolism, and elimination (ADME) gene variants has not been well characterized...

..The system detected completed colonoscopies with recall and precision of 0.93 and 0.92. The system was superior to a query of colonoscopy billing codes to determine screening status...

..To facilitate search and identification of gene-associated clinical trials by potential participants and clinicians, it is important to develop automated methods to identify genetic information from narrative trial documents...

..875 on the same test set, indicating that integrating sense frequency information with local context is effective for clinical abbreviation disambiguation...

..The evaluation outcome showed that the extended NLP system had a sensitivity of 90.6% and a precision of 91.6%. Results indicated that this system performed satisfactorily for capturing information for the cancer research project...

..It included six sessions, a tutorial - Introduction to Proteome Informatics, a workshop - Next Generation Sequencing, and a poster session. The selected papers in this Supplement issue represent the genomic focus in ICIBM 2012...

..Such methods may prove useful for future curriculum evaluations and revisions...

..The priority score reflects the average of all the scores given by the full committee after a thorough discussion. ..

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..The informatics approach will be validated on EMRs from two major hospitals to demonstrate its generalizability. Epidemiological findings from our study will be compared to reported findings for validation. ..