发布求助
文献互助 智能选刊 最新文献

Summit on translational bioinformatics最新文献

筛选
英文 中文
Adoption and Adaptation of caGrid for CTSA. 网格在CTSA中的应用与适应。
Summit on translational bioinformatics Pub Date : 2009-03-01
Shannon Hastings, Scott Oster, Stephen Langella, Calixto Melean, Tara Borlawsky, Rakesh Dhavel, Philip Payne
{"title":"Adoption and Adaptation of caGrid for CTSA.","authors":"Shannon Hastings,&nbsp;Scott Oster,&nbsp;Stephen Langella,&nbsp;Calixto Melean,&nbsp;Tara Borlawsky,&nbsp;Rakesh Dhavel,&nbsp;Philip Payne","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>The field of informatics has been going through a rapid change over the past decade. New technologies such as grid computing[1-5] and knowledge anchored data, combined with major funding and growing community thrusts aimed at creating a richer multi-institutional research and clinical environment such as caBIG™[6-8] (Cancer Bioinformatics Grid), BIRN[9] (Bioinformatics Research Network), and CTSA(Clinical and Translational Science Awards) have lead to new ways to bring together information across institutional boundaries. This had lead to service oriented architectures based developments in creating semantically interoperable data and analytical services to increase speed, efficiency, and outcome of clinical and research efforts spanning the fields of medicine. The TRIAD (Translational Informatics and Data Management Grid) System, which will be used as the middleware system enabling the OSU CTSA to create a scalable, secure, and knowledge anchored data sharing environment, will adopt and adapt the caGrid infrastructure designed for the caBIG™ program.</p>","PeriodicalId":89276,"journal":{"name":"Summit on translational bioinformatics","volume":"2009 ","pages":"44-8"},"PeriodicalIF":0.0,"publicationDate":"2009-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041578/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29694058","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
Integration of Neuroimaging and Microarray Datasets through Mapping and Model-Theoretic Semantic Decomposition of Unstructured Phenotypes. 通过非结构化表型的映射和模型理论语义分解整合神经成像和微阵列数据集。
Summit on translational bioinformatics Pub Date : 2009-03-01
Spiro P Pantazatos, Jianrong Li, Paul Pavlidis, Yves A Lussier
{"title":"Integration of Neuroimaging and Microarray Datasets through Mapping and Model-Theoretic Semantic Decomposition of Unstructured Phenotypes.","authors":"Spiro P Pantazatos,&nbsp;Jianrong Li,&nbsp;Paul Pavlidis,&nbsp;Yves A Lussier","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>An approach towards heterogeneous neuroscience dataset integration is proposed that uses Natural Language Processing (NLP) and a knowledgebased phenotype organizer system (PhenOS) to link ontology-anchored terms to underlying data from each database, and then maps these terms based on a computable model of disease (SNOMED CT®). The approach was implemented using sample datasets from fMRIDC, GEO and Neuronames and allowed for complex queries such as \"List all disorders with a finding site of brain region X, and then find the semantically related references in all participating databases based on the ontological model of the disease or its anatomical and morphological attributes\". Precision of the NLP-derived coding of the unstructured phenotypes in each datasets was 88% (n=50), and precision of the semantic mapping between these terms across datasets was 98% (n=100). To our knowledge, this is the first example of the use of both semantic decomposition of disease relationships and hierarchical information found in ontologies to integrate heterogeneous phenotypes across clinical and molecular datasets.</p>","PeriodicalId":89276,"journal":{"name":"Summit on translational bioinformatics","volume":"2009 ","pages":"85-9"},"PeriodicalIF":0.0,"publicationDate":"2009-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041585/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29694502","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
Integrating Clinical Data into the i2b2 Repository. 将临床数据集成到i2b2存储库中。
Summit on translational bioinformatics Pub Date : 2009-03-01
Aaron Abend, Dan Housman, Bruce Johnson
{"title":"Integrating Clinical Data into the i2b2 Repository.","authors":"Aaron Abend,&nbsp;Dan Housman,&nbsp;Bruce Johnson","doi":"","DOIUrl":"","url":null,"abstract":"","PeriodicalId":89276,"journal":{"name":"Summit on translational bioinformatics","volume":"2009 ","pages":"1-5"},"PeriodicalIF":0.0,"publicationDate":"2009-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041580/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29694632","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
Consistent visualizations of changing knowledge. 对不断变化的知识进行一致的可视化。
Summit on translational bioinformatics Pub Date : 2009-03-01
Hannah J Tipney, Ronald P Schuyler, Lawrence Hunter
{"title":"Consistent visualizations of changing knowledge.","authors":"Hannah J Tipney,&nbsp;Ronald P Schuyler,&nbsp;Lawrence Hunter","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Networks are increasingly used in biology to represent complex data in uncomplicated symbolic form. However, as biological knowledge is continually evolving, so must those networks representing this knowledge. Capturing and presenting this type of knowledge change over time is particularly challenging due to the intimate manner in which researchers customize those networks they come into contact with. The effective visualization of this knowledge is important as it creates insight into complex systems and stimulates hypothesis generation and biological discovery. Here we highlight how the retention of user customizations, and the collection and visualization of knowledge associated provenance supports effective and productive network exploration. We also present an extension of the Hanalyzer system, ReOrient, which supports network exploration and analysis in the presence of knowledge change.</p>","PeriodicalId":89276,"journal":{"name":"Summit on translational bioinformatics","volume":"2009 ","pages":"129-32"},"PeriodicalIF":0.0,"publicationDate":"2009-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041575/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29693830","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
A Controlled Vocabulary to Represent Sonographic Features of the Thyroid and its application in a Bayesian Network to Predict Thyroid Nodule Malignancy. 表达甲状腺声像图特征的控制词汇及其在贝叶斯网络中预测甲状腺结节恶性肿瘤的应用。
Summit on translational bioinformatics Pub Date : 2009-03-01
Yueyi I Liu, Aya Kamaya, Terry S Desser, Daniel L Rubin
{"title":"A Controlled Vocabulary to Represent Sonographic Features of the Thyroid and its application in a Bayesian Network to Predict Thyroid Nodule Malignancy.","authors":"Yueyi I Liu,&nbsp;Aya Kamaya,&nbsp;Terry S Desser,&nbsp;Daniel L Rubin","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>It is challenging to distinguish benign from malignant thyroid nodules on high resolution ultrasound. Many ultrasound features have been studied individually as predictors for thyroid malignancy, none with a high degree of accuracy, and there is no consistent vocabulary used to describe the features. Our hypothesis is that a standard vocabulary will advance accuracy. We performed a systemic literature review and identified all the sonographic features that have been well studied in thyroid cancers. We built a controlled vocabulary for describing sonographic features and to enable us to unify data in the literature on the predictive power of each feature. We used this terminology to build a Bayesian network to predict thyroid malignancy. Our Bayesian network performed similar to or slightly better than experienced radiologists. Controlled terminology for describing thyroid radiology findings could be useful to characterize thyroid nodules and could enable decision support applications.</p>","PeriodicalId":89276,"journal":{"name":"Summit on translational bioinformatics","volume":"2009 ","pages":"68-72"},"PeriodicalIF":0.0,"publicationDate":"2009-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041558/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29694499","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
A semantic image annotation model to enable integrative translational research. 一种语义图像标注模型，支持综合翻译研究。
Summit on translational bioinformatics Pub Date : 2009-03-01
Daniel L Rubin, Pattanasak Mongkolwat, David S Channin
{"title":"A semantic image annotation model to enable integrative translational research.","authors":"Daniel L Rubin,&nbsp;Pattanasak Mongkolwat,&nbsp;David S Channin","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Integrating and relating images with clinical and molecular data is a crucial activity in translational research, but challenging because the information in images is not explicit in standard computer-accessible formats. We have developed an ontology-based representation of the semantic contents of radiology images called AIM (Annotation and Image Markup). AIM specifies the quantitative and qualitative content that researchers extract from images. The AIM ontology enables semantic image annotation and markup, specifying the entities and relations necessary to describe images. AIM annotations, represented as instances in the ontology, enable key use cases for images in translational research such as disease status assessment, query, and inter-observer variation analysis. AIM will enable ontology-based query and mining of images, and integration of images with data in other ontology-annotated bioinformatics databases. Our ultimate goal is to enable researchers to link images with related scientific data so they can learn the biological and physiological significance of the image content.</p>","PeriodicalId":89276,"journal":{"name":"Summit on translational bioinformatics","volume":"2009 ","pages":"106-10"},"PeriodicalIF":0.0,"publicationDate":"2009-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041574/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29694506","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
Integrating automated workflows, human intelligence and collaboration. 集成自动化工作流、人工智能和协作。
Summit on translational bioinformatics Pub Date : 2009-03-01
Barbara Mirel, Felix Eichinger, Viji Nair, Matthias Kretzler
{"title":"Integrating automated workflows, human intelligence and collaboration.","authors":"Barbara Mirel,&nbsp;Felix Eichinger,&nbsp;Viji Nair,&nbsp;Matthias Kretzler","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Many methods and tools have evolved for microarray analysis such as single probe evaluation, promoter module modeling and pathway analysis. Little is known, however, about optimizing this flow of analysis for the flexible reasoning biomedical researchers need for hypothesizing about disease mechanisms. In developing and implementing a workflow, we found that workflows are not complete or valuable unless automation is well-integrated with human intelligence. We present our workflow for the translational problem of classifying new sub-types of renal diseases. Using our workflow as an example, we explain opportunities and limitations in achieving this necessary integration and propose approaches to guide such integration for the next great frontier-facilitating exploratory analysis of candidate genes.</p>","PeriodicalId":89276,"journal":{"name":"Summit on translational bioinformatics","volume":"2009 ","pages":"79-83"},"PeriodicalIF":0.0,"publicationDate":"2009-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041562/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29694501","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
Analysis of AML Genes in Dysregulated Molecular Networks. AML基因在失调分子网络中的分析。
Summit on translational bioinformatics Pub Date : 2009-03-01
Eunjung Lee, Hyunchul Jung, Predrag Radivojac, Jong-Won Kim, Doheon Lee
{"title":"Analysis of AML Genes in Dysregulated Molecular Networks.","authors":"Eunjung Lee,&nbsp;Hyunchul Jung,&nbsp;Predrag Radivojac,&nbsp;Jong-Won Kim,&nbsp;Doheon Lee","doi":"","DOIUrl":"","url":null,"abstract":"<p><strong>Background: </strong>Identifying disease causing genes and understanding their molecular mechanisms are essential to developing effective therapeutics. Thus, several computational methods have been proposed to prioritize candidate disease genes by integrating different data types, including sequence information, biomedical literature, and pathway information. Recently, molecular interaction networks have been incorporated to predict disease genes, but most of those methods do not utilize invaluable disease-specific information available in mRNA expression profiles of patient samples.</p><p><strong>Results: </strong>Through the integration of protein-protein interaction networks and gene expression profiles of acute myeloid leukemia (AML) patients, we identified subnetworks of interacting proteins dysregulated in AML and characterized known mutation genes causally implicated to AML embedded in the subnetworks. The analysis shows that the set of extracted subnetworks is a reservoir rich in AML genes reflecting key leukemogenic processes such as myeloid differentiation,</p><p><strong>Conclusion: </strong>We showed that the integrative approach both utilizing gene expression profiles and molecular networks could identify AML causing genes most of which were not detectable with gene expression analysis alone due to their minor changes in mRNA.</p>","PeriodicalId":89276,"journal":{"name":"Summit on translational bioinformatics","volume":"2009 ","pages":"1-18"},"PeriodicalIF":0.0,"publicationDate":"2009-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041561/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29694635","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 potential for automated question answering in the context of genomic medicine: An assessment of existing resources and properties of answers. 基因组医学背景下自动问答的潜力:对现有资源和答案属性的评估。
Summit on translational bioinformatics Pub Date : 2009-03-01
Casey Lynnette Overby, Peter Tarczy-Hornoch, Dina Demner-Fushman
{"title":"The potential for automated question answering in the context of genomic medicine: An assessment of existing resources and properties of answers.","authors":"Casey Lynnette Overby,&nbsp;Peter Tarczy-Hornoch,&nbsp;Dina Demner-Fushman","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Knowledge gained in studies of genetic disorders is reported in a growing body of biomedical literature containing reports of genetic variation in individuals that map to medical conditions and/or response to therapy. These scientific discoveries need to be translated into practical applications to optimize patient care. Translating research into practice can be facilitated by supplying clinicians with research evidence. We assessed the role of existing tools in extracting answers to translational research questions in the area of genomic medicine. We: evaluate the coverage of translational research terms in the Unified Medical Language Systems (UMLS) Metathesaurus; determine where answers are most often found in full-text articles; and determine common answer patterns. Findings suggest that we will be able to leverage the UMLS in development of natural language processing algorithms for automated extraction of answers to translational research questions from biomedical text in the area of genomic medicine.</p>","PeriodicalId":89276,"journal":{"name":"Summit on translational bioinformatics","volume":"2009 ","pages":"1-25"},"PeriodicalIF":0.0,"publicationDate":"2009-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041571/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29693649","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
Toward an ontological treatment of disease and diagnosis. 朝向疾病的本体论治疗和诊断。
Summit on translational bioinformatics Pub Date : 2009-03-01
Richard H Scheuermann, Werner Ceusters, Barry Smith
{"title":"Toward an ontological treatment of disease and diagnosis.","authors":"Richard H Scheuermann,&nbsp;Werner Ceusters,&nbsp;Barry Smith","doi":"","DOIUrl":"","url":null,"abstract":"<p><p>Many existing biomedical vocabulary standards rest on incomplete, inconsistent or confused accounts of basic terms pertaining to diseases, diagnoses, and clinical phenotypes. Here we outline what we believe to be a logically and biologically coherent framework for the representation of such entities and of the relations between them. We defend a view of disease as involving in every case some physical basis within the organism that bears a disposition toward the execution of pathological processes. We present our view in the form of a list of terms and definitions designed to provide a consistent starting point for the representation of both disease and diagnosis in information systems in the future.</p>","PeriodicalId":89276,"journal":{"name":"Summit on translational bioinformatics","volume":"2009 ","pages":"116-20"},"PeriodicalIF":0.0,"publicationDate":"2009-03-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3041577/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"29693828","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
首页 上一页 下一页 尾页
0
×
引用
GB/T 7714-2015
复制
MLA
复制
APA
复制
导出至
BibTeX EndNote RefMan NoteFirst NoteExpress
×
提示
您的信息不完整，为了账户安全，请先补充。
现在去补充
×
提示
您因"违规操作"
具体请查看互助需知
我知道了
×
提示
现在去查看 取消
×
提示
确定
请完成安全验证×
相关产品
×
本文献相关产品
联系我们：info@booksci.cn Book学术提供免费学术资源搜索服务，方便国内外学者检索中英文文献。致力于提供最便捷和优质的服务体验。 Copyright © 2023 布克学术 All rights reserved.
京ICP备2023020795号-1
ghs 京公网安备 11010802042870号
Book学术文献互助
Book学术文献互助群
群 号：481959085
Book学术官方微信