Suppr超能文献

基因本体论的词汇属性。

The lexical properties of the gene ontology.

作者信息

McCray Alexa T, Browne Allen C, Bodenreider Olivier

机构信息

LHNCBC, National Library of Medicine, Bethesda, MD, USA.

出版信息

Proc AMIA Symp. 2002:504-8.

Abstract

The Gene Ontology (GO) is a construct developed for the purpose of annotating molecular information about genes and their products. The ontology is a shared resource developed by the GO Consortium, a group of scientists who work on a variety of model organisms. In this paper we investigate the nature of the strings found in the Gene Ontology and evaluate them for their usefulness in natural language processing (NLP). We extend previous work that identified a set of properties that reliably identifies natural language phrases in the Unified Medical Language System (UMLS). The results indicate that a large percentage (79%) of GO terms are potentially useful for NLP applications. Some 35% of the GO terms were found in a corpus derived from the MEDLINE bibliographic database, and 27% of the terms were found in the current edition of the UMLS.

摘要

基因本体论(Gene Ontology,GO)是为注释有关基因及其产物的分子信息而开发的一种构建体。该本体论是由基因本体论联盟(GO Consortium)开发的共享资源,该联盟由一群致力于各种模式生物研究的科学家组成。在本文中,我们研究了基因本体论中发现的字符串的性质,并评估它们在自然语言处理(NLP)中的有用性。我们扩展了先前的工作,该工作确定了一组能够可靠识别统一医学语言系统(UMLS)中自然语言短语的属性。结果表明,很大比例(79%)的GO术语可能对NLP应用有用。约35%的GO术语出现在源自MEDLINE文献数据库的语料库中,27%的术语出现在UMLS的当前版本中。

相似文献

3
Development and evaluation of RapTAT: a machine learning system for concept mapping of phrases from medical narratives.
J Biomed Inform. 2014 Apr;48:54-65. doi: 10.1016/j.jbi.2013.11.008. Epub 2013 Dec 4.
4
MedLexSp - a medical lexicon for Spanish medical natural language processing.
J Biomed Semantics. 2023 Feb 2;14(1):2. doi: 10.1186/s13326-022-00281-5.
6
Collecting specialty-related medical terms: Development and evaluation of a resource for Spanish.
BMC Med Inform Decis Mak. 2021 May 4;21(1):145. doi: 10.1186/s12911-021-01495-w.
7
Unified Medical Language System term occurrences in clinical notes: a large-scale corpus analysis.
J Am Med Inform Assoc. 2012 Jun;19(e1):e149-56. doi: 10.1136/amiajnl-2011-000744. Epub 2012 Apr 4.
9
Translating the Foundational Model of Anatomy into French using knowledge-based and lexical methods.
BMC Med Inform Decis Mak. 2011 Oct 26;11:65. doi: 10.1186/1472-6947-11-65.
10
Mapping the gene ontology into the unified medical language system.
Comp Funct Genomics. 2004;5(4):354-61. doi: 10.1002/cfg.407.

引用本文的文献

2
How to link ontologies and protein-protein interactions to literature: text-mining approaches and the BioCreative experience.
Database (Oxford). 2012 Mar 21;2012:bas017. doi: 10.1093/database/bas017. Print 2012.
3
War of ontology worlds: mathematics, computer code, or Esperanto?
PLoS Comput Biol. 2011 Sep;7(9):e1002191. doi: 10.1371/journal.pcbi.1002191. Epub 2011 Sep 29.
4
Translational systems genomics: ontology and imaging.
Summit Transl Bioinform. 2009 Mar 1;2009:21-5.
5
Rewriting and suppressing UMLS terms for improved biomedical term identification.
J Biomed Semantics. 2010 Mar 31;1(1):5. doi: 10.1186/2041-1480-1-5.
6
Mapping the gene ontology into the unified medical language system.
Comp Funct Genomics. 2004;5(4):354-61. doi: 10.1002/cfg.407.
7
Interface terminologies: facilitating direct entry of clinical data into electronic health record systems.
J Am Med Inform Assoc. 2006 May-Jun;13(3):277-88. doi: 10.1197/jamia.M1957. Epub 2006 Feb 24.
8
Mining protein function from text using term-based support vector machines.
BMC Bioinformatics. 2005;6 Suppl 1(Suppl 1):S22. doi: 10.1186/1471-2105-6-S1-S22. Epub 2005 May 24.
9
A sentence sliding window approach to extract protein annotations from biomedical articles.
BMC Bioinformatics. 2005;6 Suppl 1(Suppl 1):S19. doi: 10.1186/1471-2105-6-S1-S19. Epub 2005 May 24.
10
The compositional structure of Gene Ontology terms.
Pac Symp Biocomput. 2004:214-25. doi: 10.1142/9789812704856_0021.

本文引用的文献

2
Saccharomyces Genome Database (SGD) provides secondary gene annotation using the Gene Ontology (GO).
Nucleic Acids Res. 2002 Jan 1;30(1):69-72. doi: 10.1093/nar/30.1.69.
3
Creating the gene ontology resource: design and implementation.
Genome Res. 2001 Aug;11(8):1425-33. doi: 10.1101/gr.180801.
4
Ontology-based knowledge representation for bioinformatics.
Brief Bioinform. 2000 Nov;1(4):398-414. doi: 10.1093/bib/1.4.398.
5
A knowledge model for analysis and simulation of regulatory networks.
Bioinformatics. 2000 Dec;16(12):1120-8. doi: 10.1093/bioinformatics/16.12.1120.
6
How knowledge drives understanding--matching medical ontologies with the needs of medical language processing.
Artif Intell Med. 1999 Jan;15(1):25-51. doi: 10.1016/s0933-3657(98)00044-x.
7
The nature of lexical knowledge.
Methods Inf Med. 1998 Nov;37(4-5):353-60.

文献AI研究员

20分钟写一篇综述,助力文献阅读效率提升50倍。

立即体验

用中文搜PubMed

大模型驱动的PubMed中文搜索引擎

马上搜索

文档翻译

学术文献翻译模型,支持多种主流文档格式。

立即体验