BioContrasts: extracting and exploiting protein-protein contrastive relations from biomedical literature
BioContrasts: extracting and exploiting protein-protein contrastive relations from biomedical literature
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DOI：
10.1093/bioinformatics/btk016
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发表时间：
2006-03-01
期刊：
影响因子：
5.8
通讯作者：
Ng, SK
中科院分区：
文献类型：
--
作者：
Kim, JJ;Zhang, Z;Ng, SK
动机：对比是学习过程和探索未知的有用的概念工具。例如，蛋白质之间的对比信息可以揭示两种蛋白质之间的相似性，差异和关系，从而为更好地理解蛋白质提供宝贵的见解。生物医学文献中发现了此类对比信息。然而，目前还没有报道的尝试，在目前的生物医学文本挖掘工作，系统地提取和提出这样有用的对比信息从文献exploitation.Results：我们的BioContrasts系统提取蛋白质-蛋白质对比信息从MEDLINE摘要，并提出了一个网络应用程序开发的生物学家的信息。对比信息在文本摘要中被识别为“A但不是B”等对比否定模式。从250万篇MEDLINE摘要中成功提取了799169对对比表达。使用对比蛋白质名称与Swiss-Prot条目的基础，我们能够在Swiss-Prot蛋白质条目之间产生41471个对比。这些对比信息通过一个用户友好的交互式门户网站呈现，可用于生物途径的改进等应用。可用性：BioContrast可在http://biocontrasts.i2r.a-star.edu.sg上访问。它也反映在http://biocontrasts.biopathway.orgSupplementary信息：补充材料可在生物信息学在线。联系：skng@i2r.a-star.edu.sg; park@cs.kaist.ac.kr。
Motivation: Contrasts are useful conceptual vehicles for learning processes and exploratory research of the unknown. For example, contrastive information between proteins can reveal what similarities, divergences and relations there are of the two proteins, leading to invaluable insights for better understanding about the proteins. Such contrastive information are found to be reported in the biomedical literature. However, there have been no reported attempts in current biomedical text mining work that systematically extract and present such useful contrastive information from the literature for exploitation.Results: Our BioContrasts system extracts protein-protein contrastive information from MEDLINE abstracts and presents the information to biologists in a web-application for exploitation. Contrastive information are identified in the text abstracts with contrastive negation patterns such as 'A but not B'. A total of 799 169 pairs of contrastive expressions were successfully extracted from 2.5 million MEDLINE abstracts. Using grounding of contrastive protein names to Swiss-Prot entries, we were able to produce 41 471 pieces of contrasts between Swiss-Prot protein entries. These contrastive pieces of information are then presented via a user-friendly interactive web portal that can be exploited for applications such as the refinement of biological pathways.Availability: BioContrasts can be accessed at http://biocontrasts.i2r.a-star.edu.sg. It is also mirrored at http://biocontrasts.biopathway.orgSupplementary information: Supplementary materials are available at Bioinformatics online.Contact: skng@i2r.a-star.edu.sg; park@cs.kaist.ac.kr.