Textpresso: an ontology-based information retrieval and extraction system for biological literature.
Textpresso: an ontology-based information retrieval and extraction system for biological literature.
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DOI：
10.1371/journal.pbio.0020309
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发表时间：
2004-11
期刊：
影响因子：
9.8
通讯作者：
Sternberg PW
中科院分区：
文献类型：
--
作者：
Müller HM;Kenny EE;Sternberg PW
我们已经开发了一个新的文本挖掘系统，用于科学文献，其功能远远超出了简单的关键字搜索引擎。Textpresso的两个主要元素是将科学文章全文分成单个句子的集合，以及实现可以搜索文章和单个句子数据库的术语类别。类别是生物概念的类别（例如，基因、等位基因、细胞或细胞群、表型等）以及涉及两个对象的类（例如，协会、法规等）或描述一个（例如，生物过程等）。它们一起形成了一个对象和概念类型的目录，称为本体论。在用术语填充该本体之后，对整个文章和摘要语料库进行标记以识别这些类别的术语。目前的本体包括33个术语类别。搜索引擎使用户能够在句子或文档中搜索这些标签和/或关键字中的一个或组合，并且由于本体允许查询词义，因此可以制定语义查询。全文访问将生物数据类型的召回率从45%提高到95%。特定生物事实的提取，如基因-基因相互作用，可以通过本体显著加速，Textbooks自动执行几乎与专家策展人一样好地识别句子;在搜索两个唯一命名的基因和一个相互作用术语时，本体使搜索效率提高了3倍。Textbooks目前专注于秀丽隐杆线虫文献，有3，800篇全文文章和16，000篇摘要。本体的词典包含14，500个条目，每个条目包括特定单词或短语的所有版本，并且它包括基因本体数据库的所有类别。文本库是一个有用的策展工具，也是研究人员的搜索引擎，可以很容易地扩展到其他生物体特定的文本语料库。可通过http://www.textpresso.org或http://www.wormbase.org上的WormBase访问TextData。随着网上全文科学论文的日益增多，TextData等新工具将有助于从研究文献中提取信息和知识
We have developed Textpresso, a new text-mining system for scientific literature whose capabilities go far beyond those of a simple keyword search engine. Textpresso's two major elements are a collection of the full text of scientific articles split into individual sentences, and the implementation of categories of terms for which a database of articles and individual sentences can be searched. The categories are classes of biological concepts (e.g., gene, allele, cell or cell group, phenotype, etc.) and classes that relate two objects (e.g., association, regulation, etc.) or describe one (e.g., biological process, etc.). Together they form a catalog of types of objects and concepts called an ontology. After this ontology is populated with terms, the whole corpus of articles and abstracts is marked up to identify terms of these categories. The current ontology comprises 33 categories of terms. A search engine enables the user to search for one or a combination of these tags and/or keywords within a sentence or document, and as the ontology allows word meaning to be queried, it is possible to formulate semantic queries. Full text access increases recall of biological data types from 45% to 95%. Extraction of particular biological facts, such as gene-gene interactions, can be accelerated significantly by ontologies, with Textpresso automatically performing nearly as well as expert curators to identify sentences; in searches for two uniquely named genes and an interaction term, the ontology confers a 3-fold increase of search efficiency. Textpresso currently focuses on Caenorhabditis elegans literature, with 3,800 full text articles and 16,000 abstracts. The lexicon of the ontology contains 14,500 entries, each of which includes all versions of a specific word or phrase, and it includes all categories of the Gene Ontology database. Textpresso is a useful curation tool, as well as search engine for researchers, and can readily be extended to other organism-specific corpora of text. Textpresso can be accessed at http://www.textpresso.org or via WormBase at http://www.wormbase.org. With the increasing availability of full-text scientific papers online, new tools, such as Textpresso, will help to extract information and knowledge from research literature
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影响因子：
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