Biomedical Ontology and Tools for Database Curation

生物医学本体论和数据库管理工具

• 批准号: 6885487
• 负责人: Colleen Elizabeth Crangle
• 金额: $ 9.93万
• 依托单位: CONVERSPEECH, LLC
• 依托单位国家: 美国
• 财政年份: 2005
• 资助国家: 美国
• 起止时间: 2005-03-11 至 2006-09-30
• 项目状态: 已结题
• 来源: https://reporter.nih.gov/project-details/6885487
• 关键词: computer program /software; computer system design /evaluation; fungal genetics; information retrieval; information system analysis; molecular biology information system; yeasts

DESCRIPTION (provided by applicant): This proposal describes a new tool for text data mining-a biomedical language ontology and integrated natural-language-processing methods. Our long-term goal is to provide resources for biomedical knowledge discovery from text. Our immediate goal is to provide a knowledge discovery tool for the curation of organism databases such as the Genome Database (SGD). The proposed research not only serves the research needs of the SGD community, it also helps the broader biomedical community exploit the strengths of the comparative approach to biological research. The hypothesis of this proposal is that knowledge discovery from biomedical text requires a knowledge base that integrates both genomic and linguistic information. This hypothesis is based on two observations: (a) the language of biomedicine, like all natural language, is complex in structure and morphology (the basic units of meaning) and poses problems of synonymy (several terms having the same meaning), polysemy (a term having more than one meaning), hypernymy (one term being more general than another), hyponymy (one term being more specific than another), denotation (what a term refers to in contrast to what it means), and denotation and description (different ways of referring to the same thing); and (b) important biomedical knowledge sources, such as the Gene Ontology (GO), are expressed in natural language. The specific aims of the proposed project are to: 1. Extend an existing biomedical language ontology to include genomic and linguistic data from SGD; 2. Use this ontology to discover, in full-text articles made available by SGD, information about the molecular function of yeast gene products that can be inferred from direct experimental assays; 3. Evaluate the effectiveness of the new tool and methods by comparing its results to those of the SGD curators for gene products that have GO functional annotations with evidence code IDA (Inferred from Direct Assay).

描述（由申请人提供）：该提案描述了一种用于文本数据挖掘的新工具-生物医学语言本体和集成的自然语言处理方法。我们的长期目标是为从文本中发现生物医学知识提供资源。我们的近期目标是提供一个知识发现工具，用于管理生物数据库，如基因组数据库（SGD）。拟议的研究不仅服务于SGD社区的研究需求，它还有助于更广泛的生物医学界利用生物研究比较方法的优势。该建议的假设是，从生物医学文本中发现知识需要一个整合了基因组信息和语言信息的知识库。这一假设基于两个观察结果：（a）生物医学语言与所有自然语言一样，在结构和形态上都很复杂（意义的基本单位），并提出了同义问题（几个术语具有相同的含义），一词多义（一个词有一个以上的意思），上位（一个术语比另一个术语更一般），上下义关系（一个术语比另一个术语更具体），外延（一个术语所指的是什么，与它的意思相反），以及外延和描述（指同一事物的不同方式）;以及（B）重要的生物医学知识源，例如基因本体（GO），以自然语言表达。拟议项目的具体目标是：1.扩展现有的生物医学语言本体，以包括来自SGD的基因组和语言数据; 2.使用此本体发现，在SGD提供的全文文章中，可以从直接实验测定中推断出有关酵母基因产物分子功能的信息; 3.通过将其结果与SGD策展人的结果进行比较，评估新工具和方法的有效性，这些基因产品具有GO功能注释，证据代码为IDA（从直接测定推断）。