Constructing a molecular interaction network for thyroid cancer via large-scale text mining of gene and pathway events

被引:6
作者
Wu, Chengkun [1 ]
Schwartz, Jean-Marc [2 ]
Brabant, Georg [3 ,4 ]
Peng, Shao-Liang [1 ]
Nenadic, Goran [5 ,6 ,7 ]
机构
[1] Natl Univ Def Technol, Sch Comp Sci, Changsha 410073, Hunan, Peoples R China
[2] Univ Manchester, Fac Life Sci, Manchester M13 9PT, Lancs, England
[3] Univ Manchester, Christie Hosp, Dept Endocrinol, Manchester M20 4BX, Lancs, England
[4] Med Univ Lubeck, Med Clin 1, Expt & Clin Endocrinol, D-23538 Lubeck, Germany
[5] Manchester Inst Biotechnol, 131 Princess St, Manchester M1 7DN, Lancs, England
[6] Univ Manchester, Sch Comp Sci, Manchester M13 9PL, Lancs, England
[7] Hlth E Res Ctr HeRC, Farr Inst Hlth Informat Res, Manchester M13 9PL, Lancs, England
关键词
IDENTIFICATION; NORMALIZATION; EXTRACTION; BIOLOGY; SYSTEM;
D O I
10.1186/1752-0509-9-S6-S5
中图分类号
Q [生物科学];
学科分类号
07 ; 0710 ; 09 ;
摘要
Background: Biomedical studies need assistance from automated tools and easily accessible data to address the problem of the rapidly accumulating literature. Text-mining tools and curated databases have been developed to address such needs and they can be applied to improve the understanding of molecular pathogenesis of complex diseases like thyroid cancer. Results: We have developed a system, PWTEES, which extracts pathway interactions from the literature utilizing an existing event extraction tool (TEES) and pathway named entity recognition (PathNER). We then applied the system on a thyroid cancer corpus and systematically extracted molecular interactions involving either genes or pathways. With the extracted information, we constructed a molecular interaction network taking genes and pathways as nodes. Using curated pathway information and network topological analyses, we highlight key genes and pathways involved in thyroid carcinogenesis. Conclusions: Mining events involving genes and pathways from the literature and integrating curated pathway knowledge can help improve the understanding of molecular interactions of complex diseases. The system developed for this study can be applied in studies other than thyroid cancer. The source code is freely available online at https://github.com/chengkun-wu/PWTEES.
引用
收藏
页数:10
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