Download Info-PubMed

Info-PubMed
User Guide
University of Tokyo, JAPAN
NaCTeM, UK
Info-PubMed
(1) Info-PubMed provides information from Medline
on protein-protein interactions.
(2) Given the name of a gene or protein, it shows a
list of the names of other genes/proteins which
co-occur in sentences from Medline, along with
the frequency of co-occurrence.
(3)Co-occurrence of two proteins/genes in the
same sentence does not imply that they interact.
Use of Information Extraction techniques allows
Info-Pubmed to identify a set of sentences which
clearly indicate that the interaction exists.
Step 1
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Go to the InfoPubMed website
https://www-tsujii.is.s.u-tokyo.ac.jp/info-pubmed/
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You will see the screen in the next slide.
The red ‘Read Me’ window shows an explanation of the window that
the cursor is currently in. Moving the cursor over each window will
allow you to read the explanations of the ‘Trash’, ‘Interaction Viewer’,
‘Content Viewer’, ‘Gene Searcher’ and ‘My Folder’ windows.
You can move a window by positioning the cursor in the coloured
bar at the top of the window and pressing the left mouse button.
Step 2
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In the ‘Gene Searcher’ window, enter the
name of a gene or protein that you are
interested in.
For example, if you are interested in Raf1, type “raf1” in
the ‘Gene Searcher’ and press the ‘Search’ button. You
will see a list of genes whose description in our
dictionary contains “raf1”.
Gene/Gene Products
Your are interested in
Search Button
Notes
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The dictionary in Info-PubMed (GENIA dictionary) has 200,000 gene/protein names.
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The ‘Gene Searcher’ identifies genes whose descriptions contain the given string. If
the string is the name of protein, it probably appears in the field of ‘product’ in the
dictionary. The field ‘product’ refers to gene products, most of which are proteins.
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Other fields in a dictionary entry are ‘symbol’, ‘name’, and ‘synonym’.
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By clicking the field button in the ‘Gene Searcher’ window, you can view a list of
available fields and also restrict the fields that will be searched.
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Boxes in the leftmost column are GeneBoxes. You can drag them to other windows,
such as ‘Interaction Viewer’, ‘Content Viewer’, ‘Trash’, and ‘My Folder’.
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GeneBox is indicated as “GENE” in the leftmost position in the box. The different
colour indicates genes in different species.
By clicking this button,
you can restrict spieces.
By clicking this button,
you can restrict search fields
Fields
GeneBoxes
Step 3
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Move the windows and, if necessary, adjust their sizes so that you
can see the ‘Gene Searcher’ and ‘Interaction Viewer’ on your
screen.
Drag one of the GeneBoxes from the ‘Gene Searcher’ to the
‘Interaction Viewer’.
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–
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•
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to drag a GeneBox, position the cursor on the box and press the left
mouse button.
You will see a list of genes/proteins which co-occur in the same
sentences as the gene/proteins you moved to the window, along
with co-occurrence frequency.
The GeneBox in the leftmost column is the one you have moved
to ‘Interaction Viewer’.
The GeneBoxes in the second column correspond to
gene/proteins which co-occur in the same sentences, followed by
the boxes in the third column, InteractionBoxes.
Drag this GeneBox to the
Interaction Viewer
The GeneBox (RAF1) you dragged into InteractionView
Genes/Proteins that
interact with RAF1
InteractionBoxes
Notes
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An InteractionBox is indicated in the leftmost
position in the box as Interaction.
In an InteractionBox, two figures are followed
by the names of the two gene/protein which
co-occur in the same sentences.
The first figure is the number of sentences in
Medline which are judged to express direct
interaction of the two gene/proteins.
The second figure is the number of sentences
in which the two genes/proteins co-occur.
Step 4
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Drag an InteractionBox to ‘ContentViewer’ to see the
content of the box.
An InteractionBox is a set of SentenceBoxes.
A SentenceBox corresponds to a sentence in Medline
in which the two gene/proteins co-occur.
A SentenceBox indicates whether the co-occurrence in
the sentence is direct evidence of interaction or not.
If it is judged as direct evidence of interaction, it is
indicated as Interaction. Otherwise, it is indicated as
Co-occurrence.
Drag this InteractionBox
to ContentViewer
SentenceBox
Property which means the co-occurrence
In the sentence is a direct evidence of interaction
Property which means the co-occurrence
In the sentence is a mere co-occurrence
Step 5
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You can drag GeneBoxes,
InteractionBoxes or SentenceBoxes to
‘My Folder’ in order to keep them for later
use.
A set of programs for manipulating the
boxes in ‘My Folder’, including one which
draws a network based on the
InteractionBoxes in ‘My Folder’, will be
provided in near future..