Text mining

Krallinger M, Valencia A. Text-mining and information-retrieval services for molecular biology. Genome Biol 2005 6 224. 

Text mining is the bread-and-butter method used by researchers on a daily basis [31, 32]. If you ask researchers what they really want from information management, you might be surprised how often they wish for a science Google to mine for data. As beautiful and simple as this paradigm sounds. 

Krallinger M, Erhardt RA, Valencia A. Text-mining approaches in molecular biology and biomedicine. Drug Disc Today 2005 10 439-45. 

Gieger C, Deneke H, Pluck J. The future of text mining in genome-based clinical research. Biosilico 2003 1 97-102. 

As set forth above, terms are identified from free text and database records by text mining. The terms are then associated with relevant concepts, which... 

Extraction and tagging using text mining techniques... 

Example on Psoriasis. The term psoriasis was identified by our text mining tools in a document or record. Table 31.3 depicts the corresponding knowledge that we extracted from our thesaurus and ontology to feed the UltraLink. 

Example on Myeloblastic Leukemia. The term myeloblastic leukemia can be easily identified in a document or record by text mining. 

The KSP and, therefore, also the UltraLink are deployed within Novartis and are in daily use. We intend to further extend the abilities of the Ultra-Link. To achieve this objective we will concentrate our activities on text mining, ontological engineering, formal reasoning, enhancement of metaknowledge, and, finally, machine learning approaches. 

Text-Mining as a Novel Virtual Screening Tool. 113... 

TMVS Text-mining based virtual screening... 

To a computer scientist, VS is nothing but another text mining, only the bits and bytes stored that contain molecular information adopt a format quite different from natural language and without adequate warning cannot be quickly interpreted. It is not that modem day text does not contain text that is not natural language, but that they are adequately flagged and do not stop the NLP software. For example,... 

Tanabe L et al. MedMiner an internet text-mining tool for biomedical information, with application to gene expression profiling. BioTechniques 1999 27 1210-1217. 

Textome body of scientific literature accessible to text mining... 

This is the realm of in silica simulations, text mining, database management, classic in silica qualitative SAR modeling and physiology modeling. 

Shtatland,T.,Guettier,D.,Kossodo,M.,Pivo-varov, M. and Weissleder, R. (2007) PepBank - A Database of Peptides Based on Sequence Text Mining and Public Peptide Data Sources. BMC Bioinform, 8, 280. 

The bottom line is that in the hands of creative, experienced researchers, text mining of the literature or literature-based discovery can only serve to increase the opportunities within drug discovery and enhance life science research. Turning the ironic proverbial phrase around to read an hour in the library saves a month in the lab would be a more advisable approach. 

The conversion of chemical names and identihers into appropriate chemical structure representations offers the ideal path for chemists and organizations to mine chemical information. Because chemical names are not unique and a multitude of labels can map to a single chemical entity, the facile conversion of alphanumeric text identihers to a connection table representation enables superior data capture, representation, indexing, and mining. The industry s need to mine more information from both the historical corpus as well as new sources is obvious, and a number of researchers have initiated research into the domain of chemical identiher text mining and conversion. Multiple efforts have been made in the held of bioinformatics research,8 and, while interesting as a parallel, in this chapter we will focus the efforts to extract and convert identihers related to chemical entities rather than, for example, genes, enzymes, or proteins. 

Proceedings of the First International Workshop on Text Mining in Bioinformatics (TMBio), Arlington, VA. BMC Bioinformatics, 2007, 8. Available at http //www.biomed central.com/1471-2105/8 issue=S9 (accessed December 25, 2007). 

The National Center for Text Mining, United Kingdom http //www.nactem.ac.uk/soft ware.php software=namedentity (accessed December 16, 2007). 

Diverse text mining approaches have been successfully applied to the scientific literature in biology and medicine. The situation is less well developed for the chemical literature because of the focus on compound structures rather than text. The advent of optical structure recognition offers the promise that mining the chemical literature will be even more successful than it is in these other fields of scientific endeavor. 

Likewise, an automated approach to link chemical and biological information based on text mining will profit largely from being able to normalize textual entities and to map them to nonredundant referential entries in databases. 

---