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Biomedical Text Processing and HVP/INSIGHT

Efficient LSDB Curation with More Effective Automatic Search and Text Mining Tools Nicola Stokes, Lawrence Cavedon, Justin Zobel, Tim Smith. Query. Biomedical Text Processing and HVP/INSIGHT . Collection of Journal Papers. Search Engine. Text Mining. Indexing. Entity Identification. +.

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Biomedical Text Processing and HVP/INSIGHT

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  1. Efficient LSDB Curation with More Effective Automatic Search and Text Mining ToolsNicola Stokes, Lawrence Cavedon, Justin Zobel, Tim Smith

  2. Query Biomedical Text Processing and HVP/INSIGHT Collection of Journal Papers Search Engine Text Mining Indexing Entity Identification + Index Ranked List Relationship Identification Querying Facts LSDB

  3. What makes searching the literature difficult? • Terminology Variation: • Lexical Variation: Sec61alpha, Sec61a, “Sec61 alpha”, “Sec61 a” • Synonymy:MLH1 has the following synonyms FCC2; COCA2; HNPCC; hMLH1; HNPCC2; MGC5172 • Most popular search engines haven’t caught up with the idea that we are now in the genomic era.

  4. What makes searching the literature difficult?

  5. What makes searching the literature difficult? • Also problems with mutation nomenclature • Sample search scenario • PMS2 c.23+10G>T • PMS2 IVS1+10 • PMS2 IVS1 • PMS2 polymorphism IVS1 • PMS2 polymorphism • Solution – Query Expansion • We need your queries! http://asterix.csse.unimelb.edu.au/~ymh/bioproxy/

  6. Query Biomedical Text Processing and HVP/INSIGHT Collection of Journal Papers Search Engine Text Mining Indexing Entity Identification + Index Ranked Documents Relationship Identification Querying Facts LSDB

  7. Text Mining • Text Mining is the processing of extracting information from unstructured text. • Applications – finding functional relationships between gene, discovering protein-protein interactions, interpret microarray experiments, associate genes with phenotypes • Use machine learning techniques to find patterns and rules A combined <experiment_type: immunoprecipitation/ western blot analysis> was used to study the affect of <gene: MSH6> mutations on the <gene: MSH2>- <gene:MSH6> interaction.

  8. Query Biomedical Text Processing and HVP/INSIGHT Collection of Journal Papers Search Engine Text Mining Indexing Entity Identification + Index Ranked Documents Relationship Identification Querying Facts LSDB

  9. Questions?

  10. Using MeSH and Entrez Gene for Expansion PRNP [Homo sapiens]: prion protein; ASCR, CD230, CJD, GSS, MGC26679, PRIP, PrP, PrP27-30, PrP33-35C, PrPc, CD230 antigen; major prion protein; prion protein; prion protein PrP; prion-related protein What is the role of PrnP in mad cow disease? Entrez Gene entry for PrnP: MeSH Entry entry for Mad Cow Disease: Bovine Spongiform Encephalopathy; BSE; BSEs; Bovine Spongiform Encephalitis

  11. Using MeSH and Entrez Gene for Expansion What is the role of PrnP in mad cow disease? Transmissible spongiform encephalopathies(TSEs) are a group of fatal, neurodegenerative disorders characterized by the accumulation of an abnormal (aberrantly folded) isoform of a cellular host protein (PrPC), denominated prion protein (PrPSc). Ovine and caprine scrapie, bovine spongiform encephalopathy(BSE) and human variant Creutzfeldt-Jakob disease (vCJD) are all caused by this infectious agent.

  12. TREC Genomics 2007 Task What DRUGS have been tested in animal models of Alzheimer's disease? We show that Ibuprofen suppresses plaque pathology and inflammation in a mouse model for Alzheimer's Disease. ….chemical compounds that show promise in reducing amyloid formation or reducing tau phosphorylation in AD, include inhibitors of β-secretase or γ-secretase; agents that reduce fibrillinogenesis of the amyloid peptide; and inhibitors of glycogen synthase kinase-3 (GSK-3). These compounds have only been tested in mouse models….

  13. TREC Genomics Track • Aim of TREC: to support the information needs of researchers involved in Functional Genomics. • Aim of Biomedical Researcher: Discover new functional relationships between genes/proteins, with the aim of identifying new drug targets or disease treatments. • Collected sample queries – generate 5 query templates: What is the role of a gene(s) in a particular disease? What is the role of HMG and HMGB1 in hepatitis?

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