| |
Automatic pathway building in biological association networks
- 作者:Anton Yuryev (1)
Zufar Mulyukov (1) Ekaterina Kotelnikova (1) Sergei Maslov (1) Sergei Egorov (1) Alexander Nikitin (1) Nikolai Daraselia (1) Ilya Mazo (1)
- 刊名:BMC Bioinformatics
- 出版年:2006
- 出版时间:December 2006
- 年:2006
- 卷:7
- 期:1
- 全文大小:1349KB
- 参考文献:1. ass="a-plus-plus">Ariadne Genomics Inc. download center[<a href="http://www.ariadnegenomics.com/downloads/dltracking.php?id=20&prod=rn" class="a-plus-plus">http://www.ariadnegenomics.com/downloads/dltracking.php?id=20&prod=rna>]
2. Daraselia N, Egorov S, Yazhuk A, Novichkova S, Yuryev A, Mazo I: ass="a-plus-plus">Extracting Protein Function Information from MEDLINE Using a Full-Sentence Parser. / Proceeding of the Second European Workshop on Data Mining and Text Mining for Bioinformatics 2004, 11鈥?8. 3. Weeber M, Vos R, Klein H, De Jong-Van Den Berg LT, Aronson AR, Molema G: ass="a-plus-plus">Generating hypotheses by discovering implicit associations in the literature: a case report of a search for new potential therapeutic uses for thalidomide. / J Am Med Inform Assoc 2003, ass="a-plus-plus">10:252鈥?59. <a class="external" href="http://dx.doi.org/10.1197/jamia.M1158">CrossRefa> 4. Wren JD, Garner HR: ass="a-plus-plus">Shared relationship analysis: ranking set cohesion and commonalities within a literature-derived relationship network. / Bioinformatics 2004, ass="a-plus-plus">20:191鈥?98. <a class="external" href="http://dx.doi.org/10.1093/bioinformatics/btg390">CrossRefa> 5. Ono T, Hishigaki H, Tanigami A, Takagi T: ass="a-plus-plus">Automated extraction of information on protein 鈥?protein interactions from the biological literature. / Bioinformatics 2001, ass="a-plus-plus">17:155鈥?61. <a class="external" href="http://dx.doi.org/10.1093/bioinformatics/17.2.155">CrossRefa> 6. Sekimizu T, Park HS, Tsujii J: ass="a-plus-plus">Identifying the interaction between genes and gene products based on frequently seen verbs in MEDLINE abstracts. / Genome informatics 1998, ass="a-plus-plus">9:62鈥?1. 7. Santos C, Eggle D, States DJ: ass="a-plus-plus">Wnt pathway curation using automated natural language processing: combining statistical methods with partial and full parse for knowledge extraction. / Bioinformatics 2005, ass="a-plus-plus">8:1653鈥?658. 8. Novichkova S, Egorov S, Daraselia N: ass="a-plus-plus">MedScan, a natural language processing engine for MEDLINE abstracts. / Bioinformatics 2003, ass="a-plus-plus">19:1699鈥?706. <a class="external" href="http://dx.doi.org/10.1093/bioinformatics/btg207">CrossRefa> 9. Daraselia N, Yuryev A, Egorov S, Novichkova S, Nikitin A, Mazo I: ass="a-plus-plus">Extracting human protein interactions from MEDLINE using a full-sentence parser. / Bioinformatics 2004, ass="a-plus-plus">20:604鈥?11. <a class="external" href="http://dx.doi.org/10.1093/bioinformatics/btg452">CrossRefa> 10. Marshall B, Su H, McDonald D, Eggers S, Chen H: ass="a-plus-plus">Aggregating Automatically Extracted Regulatory Pathway Relations. / IEEE 鈥?Transactions on Information Technology in Biomedicine 2004. TITB-00165鈥?004 11. Ideker T, Ozier O, Schwikowski B, Siegel AF: ass="a-plus-plus">Discovering regulatory and signaling circuits in molecular interaction networks. / Bioinformatics 2002, ass="a-plus-plus">18:S233鈥?0. 12. ass="a-plus-plus">Gene Ontology[<a href="http://www.geneontology.org" class="a-plus-plus">http://www.geneontology.orga>] 13. Ispolatov I, Yuryev A, Mazo I, Maslov S: ass="a-plus-plus">Binding properties and evolution of homodimers in protein-protein interaction networks. / Nucleic Acids Res 2005, ass="a-plus-plus">33:3629鈥?635. <a class="external" href="http://dx.doi.org/10.1093/nar/gki678">CrossRefa> 14. Sivachenko AY, Yuryev A, Daraselia N, Mazo I: ass="a-plus-plus">Identifying Local Gene Expression Patterns in Biomolecular Networks. [<a href="http://conferences.computer.org/bioinformatics/CSB2005/PDF2/073_sivachenkoa_expression.pdf" class="a-plus-plus">http://conferences.computer.org/bioinformatics/CSB2005/PDF2/073_sivachenkoa_expression.pdfa>] / 2005 IEEE Computational Systems Bioinformatics Conference Stanford, California Aug. 8鈥?1; 2005 15. Sivachenko A, Yuryev A, Daraselia N, Mazo : ass="a-plus-plus">Bayesian framework for integration of microarray data and binary gene-to-gene regulatory relationships. / Annual Meeting of the International Society for Computational Biology (ISCB'2005) Detroit, Michigan June 25鈥?9; 2005 16. Su AI, Wiltshire T, Batalov S, Lapp H, Ching KA, Block D, Zhang J, Soden R, Hayakawa M, Kreiman G, Cooke MP, Walker JR, Hogenesch JB: ass="a-plus-plus">A gene atlas of the mouse and human protein-encoding transcriptomes. [<a href="http://www.ncbi.nlm.nih.gov/geo/gds/gds_browse.cgi?gds=596" class="a-plus-plus">http://www.ncbi.nlm.nih.gov/geo/gds/gds_browse.cgi?gds=596a>] / Proc Natl Acad Sci U S A 2004, ass="a-plus-plus">101:6062鈥?067. <a class="external" href="http://dx.doi.org/10.1073/pnas.0400782101">CrossRefa> 17. Dunne A, O'Neill LA: ass="a-plus-plus">The interleukin-1 receptor/Toll-like receptor superfamily: signal transduction during inflammation and host defense. / Sci STKE 2003, ass="a-plus-plus">171:re3.
- 作者单位:Anton Yuryev (1)
Zufar Mulyukov (1) Ekaterina Kotelnikova (1) Sergei Maslov (1) Sergei Egorov (1) Alexander Nikitin (1) Nikolai Daraselia (1) Ilya Mazo (1)
1. Ariadne Genomics Inc, 9700 Great Seneca Hwy, Suite 113, Rockville, MD, 20850, USA
- ISSN:1471-2105
文摘
Background Scientific literature is a source of the most reliable and comprehensive knowledge about molecular interaction networks. Formalization of this knowledge is necessary for computational analysis and is achieved by automatic fact extraction using various text-mining algorithms. Most of these techniques suffer from high false positive rates and redundancy of the extracted information. The extracted facts form a large network with no pathways defined. Results We describe the methodology for automatic curation of Biological Association Networks (BANs) derived by a natural language processing technology called Medscan. The curated data is used for automatic pathway reconstruction. The algorithm for the reconstruction of signaling pathways is also described and validated by comparison with manually curated pathways and tissue-specific gene expression profiles. Conclusion Biological Association Networks extracted by MedScan technology contain sufficient information for constructing thousands of mammalian signaling pathways for multiple tissues. The automatically curated MedScan data is adequate for automatic generation of good quality signaling networks. The automatically generated Regulome pathways and manually curated pathways used for their validation are available free in the ResNetCore database from Ariadne Genomics, Inc. [1]. The pathways can be viewed and analyzed through the use of a free demo version of PathwayStudio software. The Medscan technology is also available for evaluation using the free demo version of PathwayStudio software.
| |
NGLC 2004-2010.National Geological Library of China All Rights Reserved.
Add:29 Xueyuan Rd,Haidian District,Beijing,PRC. Mail Add: 8324 mailbox 100083
For exchange or info please contact us via email.
| |