Summit on translational bioinformatics最新文献_第3页

Ontology mapping and data discovery for the translational investigator. 翻译研究者的本体映射和数据发现。

Summit on translational bioinformatics Pub Date : 2010-03-01

Rob Wynden, Mark G Weiner, Ida Sim, Davera Gabriel, Marco Casale, Simona Carini, Shannon Hastings, David Ervin, Samson Tu, John H Gennari, Nick Anderson, Ketty Mobed, Prakash Lakshminarayanan, Maggie Massary, Russ J Cucina

引用次数: 0

Social network analysis of an online melanoma discussion group. 一个在线黑色素瘤讨论组的社交网络分析。

Summit on translational bioinformatics Pub Date : 2010-03-01

Kathleen T Durant, Alexa T McCray, Charles Safran

引用次数: 0

Representing multi-database study schemas for reusability. 表示多数据库研究模式以实现可重用性。

Summit on translational bioinformatics Pub Date : 2010-03-01

Judith R Logan, Scott Britell, Lois M L Delcambre, Vandana Kapoor, J Gabriel Buckmaster

引用次数: 0

Composite patient reports: a laboratory informatics perspective and pilot project for personalized medicine and translational research. 综合病人报告:个性化医疗和转化研究的实验室信息学视角和试点项目。

Summit on translational bioinformatics Pub Date : 2009-03-01

Adi V Gundlapalli, Julio C Delgado, Brian R Jackson, Guido J Tricot, Harry R Hill

{"title":"Composite patient reports: a laboratory informatics perspective and pilot project for personalized medicine and translational research.","authors":"Adi V Gundlapalli, Julio C Delgado, Brian R Jackson, Guido J Tricot, Harry R Hill","doi":"","DOIUrl":"","url":null,"abstract":"Clinical laboratories are a strong and integral partner in personalized health care. Laboratory information systems hold a vast amount of data representing human phenotypes, genotypes, biomarkers, progression of disease and response to therapy. These structured and unstructured free text data are critical for patient care and a resource for personalized medicine and translational research. Laboratory data are integrated into many electronic medical records that provide \"summary reports\" and \"trending\" to visualize longitudinal patient data. However, these generic reports are not sufficient to manage complex sub-specialty patients. There is an urgent need for end-user driven composite reports for the care of such patients. Using multiple myeloma as a model, this pilot was performed to assess the needs of stakeholders and create a customized report. This laboratory informatics solution is delivered at the point of care through the hospital EMR. Future work will involve further integration with hospital systems to promote clinical decision support and translational research.","PeriodicalId":89276,"journal":{"name":"Summit on translational bioinformatics","volume":"2009 ","pages":"39-43"},"PeriodicalIF":0.0,"publicationDate":"2009-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041581/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29694057","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

Conceptual dissonance: evaluating the efficacy of natural language processing techniques for validating translational knowledge constructs. 概念失调:评估自然语言处理技术对翻译知识建构的有效性。

Summit on translational bioinformatics Pub Date : 2009-03-01

Philip R O Payne, Alan Kwok, Rakesh Dhaval, Tara B Borlawsky

{"title":"Conceptual dissonance: evaluating the efficacy of natural language processing techniques for validating translational knowledge constructs.","authors":"Philip R O Payne, Alan Kwok, Rakesh Dhaval, Tara B Borlawsky","doi":"","DOIUrl":"","url":null,"abstract":"The conduct of large-scale translational studies presents significant challenges related to the storage, management and analysis of integrative data sets. Ideally, the application of methodologies such as conceptual knowledge discovery in databases (CKDD) provides a means for moving beyond intuitive hypothesis discovery and testing in such data sets, and towards the high-throughput generation and evaluation of knowledge-anchored relationships between complex bio-molecular and phenotypic variables. However, the induction of such high-throughput hypotheses is non-trivial, and requires correspondingly high-throughput validation methodologies. In this manuscript, we describe an evaluation of the efficacy of a natural language processing-based approach to validating such hypotheses. As part of this evaluation, we will examine a phenomenon that we have labeled as \"Conceptual Dissonance\" in which conceptual knowledge derived from two or more sources of comparable scope and granularity cannot be readily integrated or compared using conventional methods and automated tools.","PeriodicalId":89276,"journal":{"name":"Summit on translational bioinformatics","volume":"2009 ","pages":"95-9"},"PeriodicalIF":0.0,"publicationDate":"2009-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041552/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29694504","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

Agent-based modeling supporting the migration of registry systems to grid based architectures. 基于代理的建模支持注册系统向基于网格的架构迁移。

Summit on translational bioinformatics Pub Date : 2009-03-01

Martin E Cryer, Lewis Frey

{"title":"Agent-based modeling supporting the migration of registry systems to grid based architectures.","authors":"Martin E Cryer, Lewis Frey","doi":"","DOIUrl":"","url":null,"abstract":"With the increasing age and cost of operation of the existing NCI SEER platform core technologies, such essential resources in the fight against cancer as these will eventually have to be migrated to Grid based systems. In order to model this migration, a simulation is proposed based upon an agent modeling technology. This modeling technique allows for simulation of complex and distributed services provided by a large scale Grid computing platform such as the caBIG(™) project's caGRID. In order to investigate such a migration to a Grid based platform technology, this paper proposes using agent-based modeling simulations to predict the performance of current and Grid configurations of the NCI SEER system integrated with the existing translational opportunities afforded by caGRID. The model illustrates how the use of Grid technology can potentially improve system response time as systems under test are scaled. In modeling SEER nodes accessing multiple registry silos, we show that the performance of SEER applications re-implemented in a Grid native manner exhibits a nearly constant user response time with increasing numbers of distributed registry silos, compared with the current application architecture which exhibits a linear increase in response time for increasing numbers of silos.","PeriodicalId":89276,"journal":{"name":"Summit on translational bioinformatics","volume":"2009 ","pages":"26-30"},"PeriodicalIF":0.0,"publicationDate":"2009-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041565/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29694055","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

The open biomedical annotator. 开放的生物医学注释器。

Summit on translational bioinformatics Pub Date : 2009-03-01

Clement Jonquet, Nigam H Shah, Mark A Musen

引用次数: 0

Ontology based clinical query extraction. 基于本体的临床查询提取。

Summit on translational bioinformatics Pub Date : 2009-03-01

Pinar Wennerberg, Manuel Möller, Paul Buitelaar, Sonja Zillner

引用次数: 0

Natural language query in the biochemistry and molecular biology domains based on cognition search™. 基于认知搜索的生物化学和分子生物学领域的自然语言查询。

Summit on translational bioinformatics Pub Date : 2009-03-01

Elizabeth J Goldsmith, Saurabh Mendiratta, Radha Akella, Kathleen Dahlgren

{"title":"Natural language query in the biochemistry and molecular biology domains based on cognition search™.","authors":"Elizabeth J Goldsmith, Saurabh Mendiratta, Radha Akella, Kathleen Dahlgren","doi":"","DOIUrl":"","url":null,"abstract":"Motivation: With the increasing volume of scientific papers and heterogeneous nomenclature in the biomedical literature, it is apparent that an improvement over standard pattern matching available in existing search engines is required. Cognition Search Information Retrieval (CSIR) is a natural language processing (NLP) technology that possesses a large dictionary (lexicon) and large semantic databases, such that search can be based on meaning. Encoded synonymy, ontological relationships, phrases, and seeds for word sense disambiguation offer significant improvement over pattern matching. Thus, the CSIR has the right architecture to form the basis for a scientific search engine.Result: Here we have augmented CSIR to improve access to the MEDLINE database of scientific abstracts. New biochemical, molecular biological and medical language and acronyms were introduced from curated web-based sources. The resulting system was used to interpret MEDLINE abstracts. Meaning-based search of MEDLINE abstracts yields high precision (estimated at >90%), and high recall (estimated at >90%), where synonym, ontology, phrases and sense seeds have been encoded. The present implementation can be found at http://MEDLINE.cognition.com.Contact: Elizabeth.goldsmith@UTsouthwestern.edu Kathleen.dahlgren@cognition.com.","PeriodicalId":89276,"journal":{"name":"Summit on translational bioinformatics","volume":"2009 ","pages":"32-7"},"PeriodicalIF":0.0,"publicationDate":"2009-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041583/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29694056","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

Evaluation of cardiovascular risk assessment models with respect to the clinical interpretation of atherosclerosis in a different type II diabetes cohort. 评价心血管风险评估模型与不同II型糖尿病队列动脉粥样硬化的临床解释

Summit on translational bioinformatics Pub Date : 2009-03-01

L W C Chan, Y Sun

引用次数: 0