NDLI: METSP: A Maximum-Entropy Classifier Based Text Mining Tool for Transporter-Substrate Identification with Semistructured Text

Content Provider	PubMed Central
Author	Zhao, Min Chen, Yanming Qu, Dacheng Qu, Hong
Copyright Year	2015
Abstract	The substrates of a transporter are not only useful for inferring function of the transporter, but also important to discover compound-compound interaction and to reconstruct metabolic pathway. Though plenty of data has been accumulated with the developing of new technologies such as in vitro transporter assays, the search for substrates of transporters is far from complete. In this article, we introduce METSP, a maximum-entropy classifier devoted to retrieve transporter-substrate pairs (TSPs) from semistructured text. Based on the high quality annotation from UniProt, METSP achieves high precision and recall in cross-validation experiments. When METSP is applied to 182,829 human transporter annotation sentences in UniProt, it identifies 3942 sentences with transporter and compound information. Finally, 1547 confidential human TSPs are identified for further manual curation, among which 58.37% pairs with novel substrates not annotated in public transporter databases. METSP is the first efficient tool to extract TSPs from semistructured annotation text in UniProt. This tool can help to determine the precise substrates and drugs of transporters, thus facilitating drug-target prediction, metabolic network reconstruction, and literature classification.
Related Links	http://dx.doi.org/10.1155/2015/254838
Starting Page	254838
File Format	PDF
ISSN	23146133
e-ISSN	23146141
Journal	BioMed Research International
Volume Number	2015
Language	English
Publisher	Hindawi Publishing Corporation
Publisher Date	2015-01-01
Access Restriction	Open
Rights Holder	Hindawi Publishing Corporation
Subject Keyword	Research in Higher Education
Content Type	Text
Resource Type	Article
Subject	Immunology and Microbiology Medicine Biochemistry, Genetics and Molecular Biology

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METSP: A Maximum-Entropy Classifier Based Text Mining Tool for Transporter-Substrate Identification with Semistructured Text

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METSP: A Maximum-Entropy Classifier Based Text Mining Tool for Transporter-Substrate Identification with Semistructured Text