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Daniel Rico , PhD. drico@cnio.es

Course on Functional Analysis. ::: i nformation H iperlinked O ver P roteins - iHOP -. Madrid, February 16th, 2010. Daniel Rico , PhD. drico@cnio.es. Bioinformatics Unit CNIO. ::: Introduction. i nformation h iperlinked Over p roteins - iHOP -. User-Friendly Text mining tool

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Daniel Rico , PhD. drico@cnio.es

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  1. Course on Functional Analysis ::: information Hiperlinked Over Proteins - iHOP - Madrid, February 16th, 2010. Daniel Rico, PhD. drico@cnio.es Bioinformatics Unit CNIO

  2. :::Introduction. information hiperlinked Over proteins - iHOP - User-Friendly Text mining tool Searches into PubMed abstracts Uses genes and proteins ashyperlinks between sentences and abstracts. iHOP converts PubMed information into one navigable resource. 80.000 different genes H. sapiens, M. musculus, D. melanogaster…more than 1500 organisms A Gene Network for Navigating the Literature. Hoffmann, R., Valencia, A. Nature Genetics 36, 664 (2004)

  3. :::Main Window. information hiperlinked Over proteins - iHOP - http://www.ihop-net.org/

  4. ::: Help. information hiperlinked Over proteins - iHOP -

  5. Results options :::Searching genes. information hiperlinked Over proteins - iHOP -

  6. Open Abstract Open Abstract High Impact Journal Add this Sentence to Gene Model Main gene Associated genes Relevant Biomedical terms Compounds Colour legend :::Results options. Defining Information for this Gene

  7. Interaction experimental evidence etc. Use the Filter and options menu to include or exclude specific experimental data sets. :::Results options. Interaction Information for this Gene This view contains all sentences found in the literature for the main gene of a page (gene A) and other genes (gene B).

  8. :::Results options. information hiperlinked Over proteins - iHOP - Most Recent Information for this Gene Minimal Information for this Gene No literature info

  9. :::Gene model. information hiperlinked Over proteins - iHOP - Gene model is a interactive graph where you can add interesting sentences and interactions.

  10. :::iHOP Confidence Value. information hiperlinked Over proteins - iHOP - The synomnym ambiguity limitation Many gene or protein synonyms are ambiguous, thus one and the same synonym is often used for different genes. Even human experts can have difficulties to resolve such ambiguities and automatic systems, like iHOP, will therefore always exhibit certain errors. The iHOP confidence value Although no definite solution for the problem of synonym ambiguity is in sight, it is possible to put an automatically derived confidence value to specific gene references. This iHOP confidence value is illustrated through the colour intensity of a star The absence of a star does not mean that a certain term could not be a gene, but simply that supporting evidence is not available.

  11. ::: End Points . . .

  12. ::: GEPAS mirror at CNIO. http://gepasmirror.bioinfo.cnio.es/gepas/

  13. ::: AKS2 Next course Edition :::

  14. Thanks !! ggomez@cnio.es

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