CEUR workshop proceedings最新文献_第4页

Qualitative causal analyses of biosimulation models. 生物模拟模型的定性因果分析。

CEUR workshop proceedings Pub Date : 2016-08-01 Epub Date: 2016-11-29

Maxwell L Neal, John H Gennari, Daniel L Cook

{"title":"Qualitative causal analyses of biosimulation models.","authors":"Maxwell L Neal, John H Gennari, Daniel L Cook","doi":"","DOIUrl":"","url":null,"abstract":"We describe an approach for performing qualitative, systems-level causal analyses on biosimulation models that leverages semantics-based modeling formats, formal ontology, and automated inference. The approach allows users to quickly investigate how a qualitative perturbation to an element within a model's network (an increment or decrement) propagates throughout the modeled system. To support such analyses, we must interpret and annotate the semantics of the models, including both the physical properties modeled and the dependencies that relate them. We build from prior work understanding the semantics of biological properties, but here, we focus on the semantics for dependencies, which provide the critical knowledge necessary for causal analysis of biosimulation models. We describe augmentations to the Ontology of Physics for Biology, via OWL axioms and SWRL rules, and demonstrate that a reasoner can then infer how an annotated model's physical properties influence each other in a qualitative sense. Our goal is to provide researchers with a tool that helps bring the systems-level network dynamics of biosimulation models into perspective, thus facilitating model development, testing, and application.","PeriodicalId":72554,"journal":{"name":"CEUR workshop proceedings","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5551042/pdf/nihms890699.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"35315735","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

OOSTT: a Resource for Analyzing the Organizational Structures of Trauma Centers and Trauma Systems. OOSTT：分析创伤中心和创伤系统组织结构的资源。

CEUR workshop proceedings Pub Date : 2016-08-01

Joseph Utecht, John Judkins, J Neil Otte, Terra Colvin, Nicholas Rogers, Robert Rose, Maria Alvi, Amanda Hicks, Jane Ball, Stephen M Bowman, Robert T Maxson, Rosemary Nabaweesi, Rohit Pradhan, Nels D Sanddal, M Eduard Tudoreanu, Robert J Winchell, Mathias Brochhausen

{"title":"OOSTT: a Resource for Analyzing the Organizational Structures of Trauma Centers and Trauma Systems.","authors":"Joseph Utecht, John Judkins, J Neil Otte, Terra Colvin, Nicholas Rogers, Robert Rose, Maria Alvi, Amanda Hicks, Jane Ball, Stephen M Bowman, Robert T Maxson, Rosemary Nabaweesi, Rohit Pradhan, Nels D Sanddal, M Eduard Tudoreanu, Robert J Winchell, Mathias Brochhausen","doi":"","DOIUrl":"","url":null,"abstract":"Organizational structures of healthcare organizations has increasingly become a focus of medical research. In the CAFÉ project we aim to provide a web-service enabling ontology-driven comparison of the organizational characteristics of trauma centers and trauma systems. Trauma remains one of the biggest challenges to healthcare systems worldwide. Research has demonstrated that coordinated efforts like trauma systems and trauma centers are key components of addressing this challenge. Evaluation and comparison of these organizations is essential. However, this research challenge is frequently compounded by the lack of a shared terminology and the lack of effective information technology solutions for assessing and comparing these organizations. In this paper we present the Ontology of Organizational Structures of Trauma systems and Trauma centers (OOSTT) that provides the ontological foundation to CAFÉ's web-based questionnaire infrastructure. We present the usage of the ontology in relation to the questionnaire and provide the methods that were used to create the ontology.","PeriodicalId":72554,"journal":{"name":"CEUR workshop proceedings","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2016-08-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5312685/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140195269","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Measurement Error and Causal Discovery. 测量误差和因果发现。

CEUR workshop proceedings Pub Date : 2016-06-01 Epub Date: 2017-02-08

Richard Scheines, Joseph Ramsey

引用次数: 0

Investigating Term Reuse and Overlap in Biomedical Ontologies. 研究生物医学本体中的术语重用和重叠。

CEUR workshop proceedings Pub Date : 2015-07-01 Epub Date: 2015-11-18

Maulik R Kamdar, Tania Tudorache, Mark A Musen

引用次数: 0

A Database Framework for Classifier Engineering. 分类器工程的数据库框架。

CEUR workshop proceedings Pub Date : 2015-05-01 Epub Date: 2015-06-11

Benny Kimelfeld, Christopher Ré

引用次数: 0

Intelligence Level Performance Standards Research for Autonomous Vehicles. 自动驾驶汽车智能水平性能标准研究。

CEUR workshop proceedings Pub Date : 2015-01-01

Roger B Bostelman, Tsai H Hong, Elena Messina

引用次数: 0

Towards a foundational representation of potential drug-drug interaction knowledge. 对潜在的药物-药物相互作用知识的基础表示。

CEUR workshop proceedings Pub Date : 2014-10-01

Mathias Brochhausen, Jodi Schneider, Daniel Malone, Philip E Empey, William R Hogan, Richard D Boyce

引用次数: 0

Virtual Fly Brain - Using OWL to support the mapping and genetic dissection of the Drosophila brain. 虚拟蝇脑 - 使用 OWL 支持果蝇大脑的绘图和遗传解剖。

CEUR workshop proceedings Pub Date : 2014-10-01

David Osumi-Sutherland, Marta Costa, Robert Court, Cahir J O'Kane

引用次数: 0

Human Development Domain of the Ontology of Craniofacial Development and Malformation. 颅面发育和畸形本体的人类发展领域。

CEUR workshop proceedings Pub Date : 2013-07-01

Jose Lv Mejino, Ravensara S Travillian, Timothy C Cox, Linda G Shapiro, James F Brinkley

{"title":"Human Development Domain of the Ontology of Craniofacial Development and Malformation.","authors":"Jose Lv Mejino, Ravensara S Travillian, Timothy C Cox, Linda G Shapiro, James F Brinkley","doi":"","DOIUrl":"","url":null,"abstract":"In this paper we describe an ontological scheme for representing anatomical entities undergoing morphological transformation and changes in phenotype during prenatal development. This is a proposed component of the Anatomical Transformation Abstraction (ATA) of the Foundational Model of Anatomy (FMA) Ontology that was created to provide an ontological framework for capturing knowledge about human development from the zygote to postnatal life. It is designed to initially describe the structural properties of the anatomical entities that participate in human development and then enhance their description with developmental properties, such as temporal attributes and developmental processes. This approach facilitates the correlation and integration of the classical but static representation of embryology with the evolving novel concepts of developmental biology, which primarily deals with the experimental data on the mechanisms of embryogenesis and organogenesis. This is important for describing and understanding the underlying processes involved in structural malformations. In this study we focused on the development of the lips and the palate in conjunction with our work on the pathogenesis and classification of cleft lip and palate (CL/P) in the FaceBase program. Our aim here is to create the Craniofacial Human Development Ontology (CHDO) to support the Ontology of Craniofacial Development and Malformation (OCDM), which provides the infrastructure for integrating multiple and disparate craniofacial data generated by FaceBase researchers.","PeriodicalId":72554,"journal":{"name":"CEUR workshop proceedings","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5331931/pdf/nihms711379.pdf","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"34783867","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Towards a Consistent and Scientifically Accurate Drug Ontology. 实现一致且科学准确的药物本体论。

CEUR workshop proceedings Pub Date : 2013-01-01

William R Hogan, Josh Hanna, Eric Joseph, Mathias Brochhausen

{"title":"Towards a Consistent and Scientifically Accurate Drug Ontology.","authors":"William R Hogan, Josh Hanna, Eric Joseph, Mathias Brochhausen","doi":"","DOIUrl":"","url":null,"abstract":"Our use case for comparative effectiveness research requires an ontology of drugs that enables querying National Drug Codes (NDCs) by active ingredient, mechanism of action, physiological effect, and therapeutic class of the drug products they represent. We conducted an ontological analysis of drugs from the realist perspective, and evaluated existing drug terminology, ontology, and database artifacts from (1) the technical perspective, (2) the perspective of pharmacology and medical science (3) the perspective of description logic semantics (if they were available in Web Ontology Language or OWL), and (4) the perspective of our realism-based analysis of the domain. No existing resource was sufficient. Therefore, we built the Drug Ontology (DrOn) in OWL, which we populated with NDCs and other classes from RxNorm using only content created by the National Library of Medicine. We also built an application that uses DrOn to query for NDCs as outlined above, available at: http://ingarden.uams.edu/ingredients. The application uses an OWL-based description logic reasoner to execute end-user queries. DrOn is available at http://code.google.com/p/dr-on.","PeriodicalId":72554,"journal":{"name":"CEUR workshop proceedings","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"2013-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5111807/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141285544","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0