Download iHOP - Bioinformatics Unit

Course on Functional Analysis
::: information Hiperlinked Over Proteins - iHOP Madrid, February 16th, 2010.
Daniel Rico, PhD.
[email protected]
Bioinformatics Unit
CNIO
::: Introduction.
information hiperlinked Over proteins - iHOP -
User-Friendly Text mining tool
Searches into PubMed abstracts
Uses genes and proteins as hyperlinks between sentences and abs
iHOP converts PubMed information into one navigable resource.
80.000 different genes
H. sapiens, M. musculus, D. melanogaster…more than 1500 organ
A Gene Network for Navigating the Literature.
Hoffmann, R., Valencia, A.
Nature Genetics 36, 664 (2004)
::: Main Window.
information hiperlinked Over proteins - iHOP -
http://www.ihop-net.org/
::: Help.
information hiperlinked Over proteins - iHOP -
::: Searching genes.
information hiperlinked Over proteins - iHOP -
Results
options
::: Results options.
Defining Information for this Gene
Open Abstract
Open Abstract
High Impact Journal
Colour
legend
Main gene
Associated genes
Relevant Biomedical terms
Compounds
Add this Sentence
to Gene Model
::: 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).
Interaction
experimental
evidence
etc.
Use the Filter and options menu to include
or exclude specific experimental data sets
::: Results options.
information hiperlinked Over proteins - iHOP -
Most Recent Information for this Gene
Minimal Information for this Gene
No literature info
::: Gene model.
information hiperlinked Over proteins - iHOP -
Gene model is a interactive
graph where you can add
interesting sentences and
interactions.
::: 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 gene
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 automatical
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.
::: End Points . . .
::: GEPAS mirror at CNIO.
http://gepasmirror.bioinfo.cnio.es/gepas/
::: AKS2
Next course
Edition :::
Thanks !!
[email protected]