Biomedical Ontology and Tools for Database Curation

描述(由申请人提供)：本提案描述了一种新的文本数据挖掘工具--生物医学语言本体和综合自然语言处理方法。我们的长期目标是从文本中为生物医学知识发现提供资源。我们的近期目标是为生物体数据库的管理提供一个知识发现工具，如基因组数据库(SGD)。拟议的研究不仅满足了SGD社区的研究需求，还帮助更广泛的生物医学界利用生物研究的比较方法的优势。这一建议的假设是，从生物医学文本中发现知识需要一个整合了基因组和语言信息的知识库。这一假设基于两个观察：(A)生物医学语言和所有自然语言一样，在结构和形态上(基本的意义单位)是复杂的，并存在同义(几个术语具有相同的含义)、多义(一个术语具有多个含义)、上指(一个术语比另一个术语更普遍)、下义(一个术语比另一个术语更具体)、外延(一个术语与其含义相反)、外延和描述(指同一事物的不同方式)的问题；以及(B)重要的生物医学知识来源，如基因本体论(GO)，以自然语言表示。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.使用该本体在SGD提供的全文文章中发现关于酵母基因产品的分子功能的信息，这些信息可以从直接的实验分析中推断出来；3.通过将其结果与SGD策展人的结果进行比较来评估新工具和方法的有效性，这些基因产品具有使用证据代码IDA(从直接分析推断)的GO功能注释。

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).