Building an Ontology for Identity Resolution in Healthcare and Public Health

Integration of disparate information from electronic health records, clinical data warehouses, birth certificate registries and other public health information systems offers great potential for clinical care, public health practice, and research. Such integration, however, depends on correctly matching patient-specific records using demographic identifiers. Without standards for these identifiers, record linkage is complicated by issues of structural and semantic heterogeneity.Objectives: Our objectives were to develop and validate an ontology to: 1) identify components of identity and events subsequent to birth that result in creation, change, or sharing of identity information; 2) develop an ontology to facilitate data integration from multiple healthcare and public health sources; and 3) validate the ontology’s ability to model identity-changing events over time.Methods: We interviewed domain experts in area hospitals and public health programs and developed process models describing the creation and transmission of identity information among various organizations for activities subsequent to a birth event. We searched for existing relevant ontologies. We validated the content of our ontology with simulated identity information conforming to scenarios identified in our process models.Results: We chose the Simple Event Model (SEM) to describe events in early childhood and integrated the Clinical Element Model (CEM) for demographic information. We demonstrated the ability of the combined SEM-CEM ontology to model identity events over time.Conclusion: The use of an ontology can overcome issues of semantic and syntactic heterogeneity to facilitate record linkage.     

在本体中如何表达对象特征的运算框架

本体的对象特征（ObjectProperty，OP）的运算语境在《生物医学知识整合论》一书中被称为“概念的语境变量框架”（FrameofContextualVariableofConcept，FCVC），简称为对象特征的“运算框架”（ComputingFrame，CF）。当用Prot6g6建立本体时，一般只能根据对象特征的数学特征加以定义，这些数学特征包括定义域，值域，反关系，是否为函数，是否具有对称性，反对称性，自返性和传递性等，因而事实上用传统的Protege方法是无法表达CF的。根据这类定义，计算机和应用程序是无法理解和处理一个OP的运算语境，因而只能对由该OP驱动的相应的断言“一知半解”。探索的一种新方法引入一种新型的认知和操作类0bjectPropertyEntityConcept—OPEC作为0P的对应体，并放置于实体类树结构中：借助这种新型类，就能利用Protege对实体类的强大的定义功能（与对0P类的定义功能相比较而言）对相应的OP的CF作定义，从而使计算机和应用程序获得阅读和理解0P的运算语境的机会，并进而对由该0P驱动的断言获得更深的理解。     

Nosology,ontology and promiscuous realism

Medics may consider worrying about their metaphysics and ontology to be a waste of time. I will argue here that this is not the case. Promiscuous realism is a metaphysical position which holds that multiple, equally valid, classification schemes should be applied to objects (such as patients) to capture different aspects of their complex and heterogeneous nature. As medics at the bedside may need to capture different aspects of their patients' problems, they may need to use multiple classification schemes (multiple nosologies), and thus consider adopting a different metaphysics to the one commonly in use.     

Oro‐facial pain and temporomandibular disorders classification systems: A critical appraisal and future directions

It is a difficult undertaking to design a classification system for any disease entity, let alone for oro‐facial pain (OFP) and more specifically for temporomandibular disorders (TMD). A further complication of this task is that both physical and psychosocial variables must be included. To augment this process, a two‐step systematic review, adhering to PRISMA guidelines, of the classification systems published during the last 20 years for OFP and TMD was performed. The first search step identified 190 potential citations which ultimately resulted in only 17 articles being included for in‐depth analysis and review. The second step resulted in only 5 articles being selected for inclusion in this review. Five additional articles and four classification guidelines/criteria were also included due to expansion of the search criteria. Thus, in total, 14 documents comprising articles and guidelines/criteria (8 proposals of classification systems for OFP; 6 for TMD) were selected for inclusion in the systematic review. For each, a discussion as to their advantages, strengths and limitations was provided. Suggestions regarding the future direction for improving the classification process with the use of ontological principles rather than taxonomy are discussed. Furthermore, the potential for expanding the scope of axes included in existing classification systems, to include genetic, epigenetic and neurobiological variables, is explored. It is therefore recommended that future classification system proposals be based on combined approaches aiming to provide archetypal treatment‐oriented classifications.     

溃疡性结肠炎差异表达基因及中药预测的生物信息学分析

通过生物信息学技术分析比较溃疡性结肠炎(UC)患者与健康人的基因芯片数据,初步筛选UC的差异表达基因,进而预测治疗UC的潜在中药药物。从基因表达数据库(GEO)下载GSE36807基因芯片,使用R语言分析得到上调和下调的差异表达基因,通过String数据库、Cytoscape软件及其插件分析得到差异表达基因的核心基因,对核心基因进行基因本体及京都基因与基因组百科全书分析,通过核心基因与医学本体信息检索平台(Coremine Medical)相互映射,筛选治疗UC的中药。筛选出648个差异表达基因,包括251个下调基因和397个上调基因。上调差异表达基因共得出15个核心基因,包括CXCL8,IL1B,MMP9,CXCL1,CXCL10,CXCL9,CXCL2,CXCL5,TIMP1,CXCL11,STAT1,LCN2,IL1RN,MMP1,IDO1;其生物过程与通路主要富集在白细胞介素、趋化因子配体和细胞因子、趋化因子介导的信号通路,与炎症反应、防御反应、细胞趋化性、分泌颗粒、IL17信号通路、Toll样受体信号通路、NOD样受体信号通路、TNF信号通路等密切相关。治疗UC的潜在中药药物有姜黄、黄连、黄芩、石斛、地榆、黄柏、白及、苍术等。差异表达基因和核心基因的分析促进了对UC发病机制的理解,该研究为UC中药干预的新药开发提供了潜在基因靶标与研发思路。     

中医方剂本体构建过程中的概念形式化研究

目的:探索方剂学领域相关概念的形式化,为方剂知识语义查询提供支持。方法:以中医方剂学本体研究为基础,以本体描述语言OWL为基本工具进行概念形式化,同时引入Manchester OWL Syntax简化概念形式化的复杂程度。结果:形成一套较为有效的概念形式化方法,并在方剂本体开发过程中应用。结论:中医概念形式化能够促进领域知识的语义查询和推理。     

Causation in evidence‐based medicine: in reply to Strand and Parkkinen

Strand and Parkkinen criticize our dispositional account of causation in evidence‐based medicine for failing to provide a proper epistemology of causal knowledge. In particular, they claim that we do not explain how causal inferences should be drawn. In response, we point out that dispositionalism does indeed have an account of the epistemology of causation, including counterfactual dependence, intervention, prediction and clinical decision. Furthermore, we argue that this is an epistemology that fits better with the known fallibility of even our best‐informed predictions. Predictions are made on the basis that causes dispose or tend towards their effects, rather than guarantee them. The ontology of causation remains a valuable study for, among other reasons, it tells us that powers do not always combine additively. This counts against the monocausality that is tested by randomized controlled trials.     

Gene profiles of a human bronchial epithelial cell line after in vitro exposure to respiratory (non-)sensitizing chemicals: Identification of discriminating genetic markers and pathway analysis

Respiratory sensitization is a concern for occupational and environmental health in consumer product development. Despite international regulatory requirements there is no established protocol for the identification of chemical respiratory sensitizers. New tests should be based on mechanistic understanding and should be preferentially restricted to in vitro assays. The major goal of this study was to investigate the alterations in gene expression of human bronchial epithelial (BEAS-2B) cells after exposure to respiratory sensitizers and respiratory non-sensitizing chemicals, and to identify genes that are able to discriminate between both groups of chemicals. BEAS-2B cells were exposed during 6, 10, and 24 h to the respiratory sensitizers ammonium hexachloroplatinate IV, hexamethylene diisocyanate, and trimellitic anhydride, the irritants acrolein and methyl salicylate, and the skin sensitizer 1-chloro-2,4-dinitrobenzene. Overall changes in gene expression were evaluated using Agilent Whole Human Genome 4× 44K oligonucleotide arrays. Fisher Linear Discriminant Analysis was used to obtain a ranking of genes that reflects their potential to discriminate between respiratory sensitizing and respiratory non-sensitizing chemicals. The 10 most discriminative genes were BC042064, A_24_P229834, DOCK11, THC2544911, DLGAP4, NINJ1, PFKM, FLJ10986, IL28RA, and CASP9. Based on the differentially expressed genes, pathway analysis was used to identify possible underlying mechanisms of respiratory sensitization. We demonstrated that in bronchial epithelial cells the canonical PTEN signaling pathway is probably the most specific pathway in the context of respiratory sensitization. Results are indicative that the BEAS-2B cell line can be used as an alternative cell model to screen chemical compounds for their respiratory sensitizing potential.     

A New Coding System for Metabolic Disorders Demonstrates Gaps in the International Disease Classifications ICD‐10 and SNOMED‐CT,Which Can Be Barriers to Genotype–Phenotype Data Sharing

Data sharing is essential for a better understanding of genetic disorders. Good phenotype coding plays a key role in this process. Unfortunately, the two most widely used coding systems in medicine, ICD‐10 and SNOMED‐CT, lack information necessary for the detailed classification and annotation of rare and genetic disorders. This prevents the optimal registration of such patients in databases and thus data‐sharing efforts. To improve care and to facilitate research for patients with metabolic disorders, we developed a new coding system for metabolic diseases with a dedicated group of clinical specialists. Next, we compared the resulting codes with those in ICD and SNOMED‐CT. No matches were found in 76% of cases in ICD‐10 and in 54% in SNOMED‐CT. We conclude that there are sizable gaps in the SNOMED‐CT and ICD coding systems for metabolic disorders. There may be similar gaps for other classes of rare and genetic disorders. We have demonstrated that expert groups can help in addressing such coding issues. Our coding system has been made available to the ICD and SNOMED‐CT organizations as well as to the Orphanet and HPO organizations for further public application and updates will be published online ( www.ddrmd.nl and www.cineas.org ).