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MedMiner Home	Chip Specific Search	Chip Independent Search	Upload Your Own Chip	Disclaimer
Tutorial	View List of Filter Terms	Download MedMiner Paper	Credits	Feedback

The MedMiner filters will extract and organize relevant sentences in the literature based on a gene, gene-gene or gene-drug query. This tool combines the GeneCards and PubMed search engines with user input and automated server-side scripts in an integrated text filtering system.

To try out this tool, click the "Chip Specific Search" link above.

"MedMiner: an Internet Text-Mining Tool for Biomedical Information, with Application to Gene Expression Profiling," L. Tanabe, U. Scherf, L. H. Smith, J. K. Lee, L. Hunter and J. N. Weinstein, BioTechniques 27:1210-1217.

The default gene set is the list of OncoChip Genes represented in the NCI/DCS Human OncoGene set.

The search term entered will be sent as a query to the GeneCards server. The GeneCards search engine will process the query and return GeneCards which have a matching field. The returned gene names will be searched against the gene names on the chip and highlight them. A comma-delimited list of id numbers alone is provided, suitable for entry into local analysis programs. For example, one can generate a dendogram of genes related to the given pathway.

The gene synonym search terms are used to search the list of gene synonyms. A radio button list of genes is shown on a new web page. From there, two particular genes are chosen and the synonyms are shown on a new web page. Any number of gene/disorder synonyms can be chosen and new terms can be entered in a text entry box. The PubMed search is conducted using a Boolean expression based on the synonyms chosen.

The drug synonym search term is used to search a list of DTP/NCI drug synonyms. A radio button list of drugs is shown on a new web page. From there, one particular drug is chosen from the list and these synonyms are shown on a new web page. Any number of drug synonyms can be chosen and new terms can be entered in a text entry box. The PubMed search is conducted using a Boolean expression based on the synonyms chosen.

At the top of the page, a link is provided to download all the abstracts. A listing of relevant abstracts and sentences follows with a link to each single complete abstract. Currently, relevance is determined by empirical means, related to cancer. At the end of the page, a summary is shown which shows the number of relevant abstracts and sentences extracted.