Developing a manually annotated clinical document corpus to identify phenotypic information for inflammatory bowel disease

<p>Abstract</p> <p>Background</p> <p>Natural Language Processing (NLP) systems can be used for specific Information Extraction (IE) tasks such as extracting phenotypic data from the electronic medical record (EMR). These data are useful for translational research and are often found only in free text clinical notes. A key required step for IE is the manual annotation of clinical corpora and the creation of a reference standard for (1) training and validation tasks and (2) to focus and clarify NLP system requirements. These tasks are time consuming, expensive, and require considerable effort on the part of human reviewers.</p> <p>Methods</p> <p>Using a set of clinical documents from the VA EMR for a particular use case of interest we identify specific challenges and present several opportunities for annotation tasks. We demonstrate specific methods using an open source annotation tool, a customized annotation schema, and a corpus of clinical documents for patients known to have a diagnosis of Inflammatory Bowel Disease (IBD). We report clinician annotator agreement at the document, concept, and concept attribute level. We estimate concept yield in terms of annotated concepts within specific note sections and document types.</p> <p>Results</p> <p>Annotator agreement at the document level for documents that contained concepts of interest for IBD using estimated Kappa statistic (95% CI) was very high at 0.87 (0.82, 0.93). At the concept level, F-measure ranged from 0.61 to 0.83. However, agreement varied greatly at the specific concept attribute level. For this particular use case (IBD), clinical documents producing the highest concept yield per document included GI clinic notes and primary care notes. Within the various types of notes, the highest concept yield was in sections representing patient assessment and history of presenting illness. Ancillary service documents and family history and plan note sections produced the lowest concept yield.</p> <p>Conclusion</p> <p>Challenges include defining and building appropriate annotation schemas, adequately training clinician annotators, and determining the appropriate level of information to be annotated. Opportunities include narrowing the focus of information extraction to use case specific note types and sections, especially in cases where NLP systems will be used to extract information from large repositories of electronic clinical note documents.</p

Efeito da Energia, Relação Energia: Proteína e Fase de Crescimento Sobre o Desempenho e Composição de Carcaça de Frangos de Corte Effect of Energy, Energy: Protein Ratio and Growing Phase on The Performance and Carcass Composition of Broilers

Dois experimentos (EXP) avaliaram os efeitos da redução de proteína bruta (PB) em dietas com alta (A) (3.200kcal EM/kg) e baixa (B) (2.900kcal EM/kg) energia, sobre o desempenho e composição de carcaças de frangos de corte machos. Os níveis de PB foram reduzidos para obter as relações energia: proteína (E:PB) 139, 146, 153 e 160 (kcal/%) para as dietas iniciais (EXP 1), e 160, 167, 174 e 181(kcal/%) para as dietas de crescimento (EXP 2), em ambos os níveis de energia, mantendo constantes os níveis de MET+CIS e LIS. Todas as aves receberam uma mesma dieta antes (EXP 2) ou após (EXP 1) o fornecimento das dietas experimentais. O fornecimento das dietas A proporcionou melhor desempenho, no entanto resultou em maior deposição de gordura nas carcaças. No EXP 1, as aves alimentadas com as dietas B apresentaram ganho de peso (GP) similar àquelas alimentadas com as dietas A no período total (1 a 42 dias), porém melhor conversão calórica (CC) (kcal/kg) (p<0,01). Foi observada também melhor CC, com relação E:PB 139. Menores níveis de PB dietética resultaram, algumas vezes, em um menor GP, porém sempre foi verificada uma pior CC nas relações mais amplas E:PB. Em ambos os Experimentos (EXP), o maior nível de energia e a redução da PB dietética melhoraram a utilização da PB consumida.<br>Two experiments (EXP) were carried out to investigate the effects of crude protein (CP) levels reduction in high-energy (H) (3.200kcal ME/kg) and low-energy (L) (2.900kcal ME/kg) diets, on the performance and carcass composition of male broiler chickens. The CP levels were decreased to meet the following energy: protein (E:PB) ratios: 139, 146, 153 and 160 (kcal/%) for starter diets (EXP 1) and 160, 167, 174 and 181 (kcal/%) for grower diets (EXP 2), in both energy levels, keeping MET + CIS and LYS levels at the same concentration. All birds received a same diet before (EXP 2) or after (EXP 1) feeding the experimental diets. Feeding H diets resulted in better performance, but also in higher carcass fat deposition. In EXP 1, birds fed with L diets during the starter period had similar body weight gain (BWG), in the total period (1 to 42 days), than those H diets, however with better caloric conversion (kcal/kg) (CC). Also, the best CC was obtained with E:PB of 139. Lower BWG, sometimes occurred with lower levels of dietary CP, but in all experiments the CC was decreased with wider E:PB ration. In both EXP, protein utilization was improved with higher levels of dietary energy and with lower levels of dietary CP