基于本体的科学摘要交互式信息提取
Ontology-based interactive information extraction from scientific abstracts.
作者信息
Milward David, Bjäreland Marcus, Hayes William, Maxwell Michelle, Oberg Lisa, Tilford Nick, Thomas James, Hale Roger, Knight Sylvia, Barnes Julie
机构信息
Linguamatics Ltd, St. John's Innovation Centre, Cambridge CB4 0WS, UK.
出版信息
Comp Funct Genomics. 2005;6(1-2):67-71. doi: 10.1002/cfg.456.
Abstract
Over recent years, there has been a growing interest in extracting information automatically or semi-automatically from the scientific literature. This paper describes a novel ontology-based interactive information extraction (OBIIE) framework and a specific OBIIE system. We describe how this system enables life scientists to make ad hoc queries similar to using a standard search engine, but where the results are obtained in a database format similar to a pre-programmed information extraction engine. We present a case study in which the system was evaluated for extracting co-factors from EMBASE and MEDLINE.
摘要
近年来，人们对从科学文献中自动或半自动提取信息的兴趣与日俱增。本文描述了一种新颖的基于本体的交互式信息提取（OBIIE）框架以及一个特定的OBIIE系统。我们阐述了该系统如何使生命科学家能够进行类似于使用标准搜索引擎的临时查询，但结果是以类似于预编程信息提取引擎的数据库格式获得的。我们展示了一个案例研究，其中对该系统从EMBASE和MEDLINE中提取辅助因子进行了评估。
相似文献
1
Ontology-based interactive information extraction from scientific abstracts.基于本体的科学摘要交互式信息提取
Comp Funct Genomics. 2005;6(1-2):67-71. doi: 10.1002/cfg.456.
2
Textpresso: an ontology-based information retrieval and extraction system for biological literature.Textpresso：一个基于本体的生物文献信息检索与提取系统。
PLoS Biol. 2004 Nov;2(11):e309. doi: 10.1371/journal.pbio.0020309. Epub 2004 Sep 21.
3
G-Bean: an ontology-graph based web tool for biomedical literature retrieval.G-Bean：基于本体图的生物医学文献检索网络工具。
BMC Bioinformatics. 2014;15 Suppl 12(Suppl 12):S1. doi: 10.1186/1471-2105-15-S12-S1. Epub 2014 Nov 6.
4
Text mining tools for extracting information about microbial biodiversity in food.用于从食品中提取微生物生物多样性信息的文本挖掘工具。
Food Microbiol. 2019 Aug;81:63-75. doi: 10.1016/j.fm.2018.04.011. Epub 2018 Apr 21.
5
Replicating medication trend studies using ad hoc information extraction in a clinical data warehouse.利用临床数据仓库中的特定信息提取来复制药物趋势研究。
BMC Med Inform Decis Mak. 2019 Jan 18;19(1):15. doi: 10.1186/s12911-018-0729-0.
6
Ontology-centric integration and navigation of the dengue literature.以本体为中心的登革热文献整合与导航
J Biomed Inform. 2008 Oct;41(5):806-15. doi: 10.1016/j.jbi.2008.04.004. Epub 2008 May 5.
7
Ad Hoc Information Extraction for Clinical Data Warehouses.临床数据仓库的临时信息提取
Methods Inf Med. 2018 May;57(1):e22-e29. doi: 10.3414/ME17-02-0010. Epub 2018 May 25.
8
Automatic sorting of toxicological information into the IUCLID (International Uniform Chemical Information Database) endpoint-categories making use of the semantic search engine Go3R.利用语义搜索引擎Go3R将毒理学信息自动分类到IUCLID（国际统一化学信息数据库）端点类别中。
Toxicol In Vitro. 2014 Jun;28(4):571-87. doi: 10.1016/j.tiv.2013.12.011. Epub 2014 Jan 2.
9
Information content in Medline record fields.医学在线数据库（Medline）记录字段中的信息内容。
Int J Med Inform. 2004 Jun 30;73(6):515-27. doi: 10.1016/j.ijmedinf.2004.02.008.
10
MedScan, a natural language processing engine for MEDLINE abstracts.MedScan，一款用于医学在线数据库摘要的自然语言处理引擎。
Bioinformatics. 2003 Sep 1;19(13):1699-706. doi: 10.1093/bioinformatics/btg207.
引用本文的文献
1
Developing Clinical Risk Prediction Models for Worsening Heart Failure Events and Death by Left Ventricular Ejection Fraction.基于左心室射血分数开发心力衰竭恶化事件和死亡的临床风险预测模型。
J Am Heart Assoc. 2023 Oct 3;12(19):e029736. doi: 10.1161/JAHA.122.029736. Epub 2023 Sep 30.
2
CSL-Tox: an open-source analytical framework for the comparison of short-term and long-term toxicity end points and assessing the need of chronic studies in drug development.CSL-Tox：一个用于比较短期和长期毒性终点以及评估药物开发中慢性研究必要性的开源分析框架。
Sci Rep. 2023 Sep 8;13(1):14865. doi: 10.1038/s41598-023-41899-4.
3
Breast arterial calcification is associated with incident atrial fibrillation among older but not younger post-menopausal women.在绝经后老年女性而非年轻女性中，乳腺动脉钙化与新发房颤相关。
Eur Heart J Open. 2023 Feb 28;3(2):oead017. doi: 10.1093/ehjopen/oead017. eCollection 2023 Mar.
4
Leveraging an Informatics Approach to Identify an Unmet Clinical Need for / Testing Among Patients With Ovarian Cancer.利用信息学方法识别卵巢癌患者未满足的临床需求/检测需求。
JCO Clin Cancer Inform. 2022 Sep;6:e2200034. doi: 10.1200/CCI.22.00034.
5
Automatically identifying opioid use disorder in non-cancer patients on chronic opioid therapy.自动识别慢性阿片类药物治疗的非癌症患者中的阿片类药物使用障碍。
Health Informatics J. 2022 Apr-Jun;28(2):14604582221107808. doi: 10.1177/14604582221107808.
6
A Natural Language Processing-Based Approach for Identifying Hospitalizations for Worsening Heart Failure Within an Integrated Health Care Delivery System.基于自然语言处理的方法在集成医疗服务系统中识别心力衰竭恶化的住院情况。
JAMA Netw Open. 2021 Nov 1;4(11):e2135152. doi: 10.1001/jamanetworkopen.2021.35152.
7
Nd:YAG capsulotomy incidence associated with five different single-piece monofocal intraocular lenses: a 3-year Spanish real-world evidence study of 8293 eyes.5 种不同单焦点人工晶状体与 Nd:YAG 后囊膜切开术发生率的相关性：8293 只眼 3 年西班牙真实世界证据研究。
Eye (Lond). 2022 Nov;36(11):2205-2210. doi: 10.1038/s41433-021-01828-z. Epub 2021 Nov 11.
8
A Patient-Centered Conceptual Model of Symptoms and Their Impact in Early Parkinson's Disease: A Qualitative Study.以患者为中心的早期帕金森病症状及其影响的概念模型：一项定性研究。
J Parkinsons Dis. 2022;12(1):137-151. doi: 10.3233/JPD-202457.
9
Target Adverse Event Profiles for Predictive Safety in the Postmarket Setting.目标不良事件特征在上市后环境下的预测安全性。
Clin Pharmacol Ther. 2021 May;109(5):1232-1243. doi: 10.1002/cpt.2074. Epub 2020 Nov 7.
10
Implementation and comparison of two text mining methods with a standard pharmacovigilance method for signal detection of medication errors.实施并比较两种文本挖掘方法与一种标准药物警戒方法，用于检测药物错误信号。
BMC Med Inform Decis Mak. 2020 May 24;20(1):94. doi: 10.1186/s12911-020-1097-0.
本文引用的文献
1
Computer-assisted generation of a protein-interaction database for nuclear receptors.用于核受体的蛋白质相互作用数据库的计算机辅助生成
Mol Endocrinol. 2003 Aug;17(8):1555-67. doi: 10.1210/me.2002-0424. Epub 2003 May 8.
2
A literature network of human genes for high-throughput analysis of gene expression.用于基因表达高通量分析的人类基因文献网络。
Nat Genet. 2001 May;28(1):21-8. doi: 10.1038/ng0501-21.
3
Identifying the Interaction between Genes and Gene Products Based on Frequently Seen Verbs in Medline Abstracts.
Genome Inform Ser Workshop Genome Inform. 1998;9:62-71.
4
Automatic extraction of protein interactions from scientific abstracts.
Pac Symp Biocomput. 2000:541-52. doi: 10.1142/9789814447331_0051.
Zotero 插件