KNOWLEDGE BASED BIOLOGICAL MODELING INFORMATION SYSTEM

基于知识的生物建模信息系统

• 批准号: 2797084
• 负责人: G. OVERTON
• 金额: $ 37.54万
• 依托单位: UNIVERSITY OF PENNSYLVANIA
• 依托单位国家: 美国
• 财政年份: 1991
• 资助国家: 美国
• 起止时间: 1991-09-30 至 2000-09-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/2797084
• 关键词: artificial intelligence; cell differentiation; computer assisted sequence analysis; computer system design /evaluation; data collection methodology /evaluation; erythropoiesis; gene expression; genetic regulatory element; information retrieval; information system analysis; information systems; nucleic acid sequence; vocabulary development for information system

DESCRIPTION (Taken from the application abstract): Gene expression databases will take on growing importance as the complexities of development and differentiation, and normal versus diseased states are studied in greater detail. Vast amounts of sequence data are now available for the study of gene expression, along with an anticipated surge in high-throughput data on differential gene expression. Much of the key information remains in the primary literature inaccessible for computational analysis. The goal of the proposed project is to provide in a single integrated system, the information management, analysis, and visualization tools containing these data sources. Such a system requires the representation of gene expression encompassing spatial, temporal and quantitative dimensions; the collection and encoding of information from online resources and the primary literature; the integration of analysis methodologies tailored to the study of gene expression; and the availability of interfaces able to query and visualize the data in human comprehensible form. The prototype system, EpoDB, focuses on erythropoiesis, but will generalize to the study of gene expression along any pathway of differentiation. This research will enhance and extend the existing information management technology through integration of a declarative constraint language into the representation language, development of an integrity constraint system to facilitate synchronization with external databases, and implementation of a query language and optimizer. Schemas and controlled vocabularies will be tailored to represent DNA and chromosomal features relating to gene regulation, temporal events describing expression levels during development and differentiation, and descriptions of gene control processes, pathways and networks. The foundation for EpoDB will be extracted from online resources (GenBank, TRANSFAC, MedLine, etc.), restructured and analyzed to remove errors. Data relevant to gene expression during erythropoiesis will be entered from the literature by trained annotators. Improved versions of data entry editing tools will be developed to improve quality control, ease of annotation, and allow annotation by external users through Web interfaces. Incorporated into EpoDB will also be results of data analysis such as transcriptional regulatory patterns discovered by statistical techniques, by pattern matching techniques, and by classification hierarchies of genes and patterns. EpoDB will be accessible through query interfaces and visualization tools built for the WWW using the evolving bioTk system. Data and the system tools will be distributed on a regular basis.

描述（取自应用程序摘要）：基因表达 随着发展的复杂性，数据库将越来越重要 和分化以及正常状态与患病状态的研究 更大的细节。 现在可以使用大量序列数据 基因表达的研究，以及预期的高通量激增 有关差异基因表达的数据。 许多关键信息仍然存在 在主要文献中无法访问计算分析。 目标 拟议的项目是在单个集成系统中提供 信息管理，分析和可视化工具包含这些 数据源。 这样的系统需要代表基因表达 包括空间，时间和定量维度；收藏 以及从在线资源和主要资源中编码信息 文学;为研究量身定制的分析方法的整合 基因表达；以及能够查询的接口的可用性和 以人类可理解形式可视化数据。 原型系统， EPODB，重点关注红细胞生成，但将概括为基因的研究 沿任何分化途径的表达。 这项研究将增强 并通过 将声明性约束语言整合到表示形式中 语言，制定完整性约束系统以促进 与外部数据库同步，并实现查询 语言和优化器。 模式和受控词汇将是 量身定制以表示与基因有关的DNA和染色体特征 调节，描述发育过程中表达水平的时间事件 和分化以及基因控制过程的描述，途径 和网络。 EPODB的基础将从在线中提取 资源（GenBank，Transfac，Medline等），对 删除错误。 与促红细胞生成期间基因表达相关的数据将 可以通过训练有素的注释者从文学中输入。 改进版本的 数据输入编辑工具将被开发以改善质量控制，轻松 注释，允许外部用户通过Web注释 接口。 并入EPODB也将是数据分析的结果 例如统计发现的转录调节模式 通过图案匹配技术和分类技术的技术 基因和模式的层次结构。 EPODB将通过查询访问 使用不断发展的界面和可视化工具为www构建 Biotk系统。 数据和系统工具将在常规上分发 基础。

项目成果

A relational schema for both array-based and SAGE gene expression experiments.

基于阵列和 SAGE 基因表达实验的关系模式。

• DOI: 10.1093/bioinformatics/17.4.300
• 发表时间: 2001
• 期刊: Bioinformatics (Oxford, England)
• 作者: Stoeckert,C;Pizarro,A;Manduchi,E;Gibson,M;Brunk,B;Crabtree,J;Schug,J;Shen-Orr,S;Overton,GC
• 通讯作者: Overton,GC

QGB: a system for querying sequence database fields and features.

QGB：用于查询序列数据库字段和特征的系统。

• DOI: 10.1089/cmb.1994.1.3
• 发表时间: 1994
• 期刊: Journal of computational biology : a journal of computational molecular cell biology
• 作者: Overton,GC;Aaronson,JS;Haas,J;Adams,J
• 通讯作者: Adams,J

SORTEZ: a relational translator for NCBI's ASN.1 database.

SORTEZ：NCBI 的 ASN.1 数据库的关系翻译器。

• DOI: 10.1093/bioinformatics/10.4.369
• 发表时间: 1994
• 期刊: Computer applications in the biosciences : CABIOS
• 作者: Hart,KW;Searls,DB;Overton,GC
• 通讯作者: Overton,GC

Integrated databases and computer systems for studying eukaryotic gene expression.

用于研究真核基因表达的集成数据库和计算机系统。

• DOI: 10.1093/bioinformatics/15.7.669
• 发表时间: 1999
• 期刊: Bioinformatics (Oxford, England)
• 作者: Kolchanov,NA;Ponomarenko,MP;Frolov,AS;Ananko,EA;Kolpakov,FA;Ignatieva,EV;Podkolodnaya,OA;Goryachkovskaya,TN;Stepanenko,IL;Merkulova,TI;Babenko,VV;Ponomarenko,YV;Kochetov,AV;Podkolodny,NL;Vorobiev,DV;Lavryushev,
• 通讯作者: Lavryushev,

EpoDB: a database of genes expressed during vertebrate erythropoiesis.

EpoDB：脊椎动物红细胞生成过程中表达的基因数据库。

• DOI: 10.1093/nar/26.1.288
• 发表时间: 1998
• 期刊: Nucleic acids research
• 影响因子: 14.9
• 作者: Salas,F;Haas,J;Brunk,B;StoeckertJr,CJ;Overton,GC
• 通讯作者: Overton,GC