Biomedical subjects

Alexander Nikitin

Publications and source records attributed to Alexander Nikitin.

3 recordsLinked to original sources

PubMed2006

Automatic pathway building in biological association networks.

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.

Databases, Bibliographic↗

PubMed2004

Extracting human protein interactions from MEDLINE using a full-sentence parser.

MOTIVATION: The living cell is a complex machine that depends on the proper functioning of its numerous parts, including proteins. Understanding protein functions and how they modify and regulate each other is the next great challenge for life-sciences researchers. The collective knowledge about protein functions and pathways is scattered throughout numerous publications in scientific journals. Bringing the relevant information together becomes a bottleneck in a research and discovery process. The volume of such information grows exponentially, which renders manual curation impractical. As a viable alternative, automated literature processing tools could be employed to extract and organize biological data into a knowledge base, making it amenable to computational analysis and data mining. RESULTS: We present MedScan, a completely automated natural language processing-based information extraction system. We have used MedScan to extract 2976 interactions between human proteins from MEDLINE abstracts dated after 1988. The precision of the extracted information was found to be 91%. Comparison with the existing protein interaction databases BIND and DIP revealed that 96% of extracted information is novel. The recall rate of MedScan was found to be 21%. Additional experiments with MedScan suggest that MEDLINE is a unique source of diverse protein function information, which can be extracted in a completely automated way with a reasonably high precision. Further directions of the MedScan technology improvement are discussed. AVAILABILITY: MedScan is available for commercial licensing from Ariadne Genomics, Inc.

Abstracting and Indexing↗

PubMed2003

Pathway studio--the analysis and navigation of molecular networks.

SUMMARY: PathwayAssist is a software application developed for navigation and analysis of biological pathways, gene regulation networks and protein interaction maps. It comes with the built-in natural language processing module MedScan and the comprehensive database describing more than 100 000 events of regulation, interaction and modification between proteins, cell processes and small molecules. AVAILABILITY: PathwayAssist is available for commercial licensing from Ariadne Genomics, Inc. The light version with limited functionality will be available for free for academic users at www.ariadnegenomics.com/downloads/.

Database Management Systems↗