Introduction

In contrast to the PubMed interface where results are organized based on articles, Chilibot directly presents the key information user is seeking, i.e. sentences containing both of the terms. These sentences are organized into different relationship types based on linguistic analysis of the text.

In addition, Chilibot is especially suited to batch process large number of terms (e.g. microarray results). The relationships are summarized into as a graph, with links to sentences describing the relationships, as well as the terms themselves.

Many advanced options are available, including color coding the terms, editing the synonyms (e.g. gene/protein names), and context restricted search. It also automatically suggests new hypotheses based on information in the literature. Therefore, we recommend using Chilibot whenever you are searching relationships from PubMed (i.e. putting two keywords in the PubMed search box). Some examples of "two term search" to rapidly retrieve information include:

	 BDNF & TRKB  (what is the relationship between these two proteins?)
	 BDNF & apoptosis (What is the relationship between a protein and a keyword?) 
	 BDNF & hippacampus (Is BDNF expressed in the hippocampus?)
	 BDNF & phosphorelation 
	 BDNF & polymorphism
 

The following more advanced example queries the pairwise relationships among ten genes, and that for each of the gene with 3 keywords (note the special keyword SECONDLIST), with user supplied additional synonyms. This example uses the pairwise search function to do a two-list search. We have provided a simpler interface for two-list search for begining users.

	 BDNF
	 TRKB
	 TRKC
	 CHRNA7
	 PSD95
	 CREB
	 HPRT
	 ARC
	 NUR77
	 SECONDLIST
	 APOPTOSIS (programed cell death; PCD)
	 Hippocampus
	 STEM CELLS
 

Registration

User input

Accepted terms

Color coding the nodes

Example:
BDNF	0.4
TRKB	1.3
APOPTOSIS 1.0

Numbers > 1 correspond to varying shades of green, while numbers between 0 and 1 correspond to different shade of red. Only folds (i.e. positive numbers) are allowed. Negative numbers, usually log(FoldChange), can be converted into folds by taking its antilog.

Customizing synonyms

	 APOPTOSIS (programed cell death; PCD)
 

Types of search

Two term search

One list pairwise search

Pairwise queries are exhaustive searches of all possible relationships between any two terms in a list.

Two-list search

Chilibot defaults to conduct pair-wise queries. Sometimes, users are interested in one-to-many type of relationships. For example, a user wants to find the relationship between one term (e.g. polymorphism) and a list of genes. The interaction between the genes are non-relevant. The two lists search is a variant of the pairwise search in that it accepts two lists. Terms in the first list will be pairwisely searched against each other. List one terms also is searched against each term in list 2. However, terms in list 2 are not searched against each other. This can be done using the two list search boxes. Alternatively, you can use the pairwise search box, just separate your two lists with the special keyword 'SECONDLIST' (example).

Context restriction

For example, we want to know if the polymorphism of a list of gene is associated with a particular disease. We can then do a two list search (context = disease name; list 1= polymorphism; list2=list of genes). Of course, you can also include phosphorelation, glycosylation, etc in your list. (see examples here and here)

This can be achieved by provide a few keywords in the 'context keyword' box. Chilibot then ignores abstracts that do not contain these keywords. If multiple keywords are provided, please connect them with Boolean operators.

Modulation

Working with the results

Basic navigation

Re-graphing

Generating hypotheses

Editing the synonyms

Names with less than three letters are particularly prone to errors. Thus, we flagged some of them with "!". These flagged names are excluded from the query by default. You can include them in the query by deleting the exclamation mark.

Deleting relationships

Automating your searches

#!/usr/local/bin/perl use LWP::Simple qw(get); # Provide your email address so that you receive a notification when a query is done (if more than 6 terms are queried). my $email="me\@my.domain"; #my $sessionName="testing"; # session name is optional my $terms="apoptosis\ncreb\nbdnf\n"; &searchChilibot ($email, $sessionName, $terms); sub searchChilibot{ my $email=shift; my $sessionName=shift; my $terms=shift; my $url="http://www.chilibot.net/cgi-bin/chilibot/chilibot.cgi?email=$email&IN=t&list=$terms&name=$sessionName"; print "Waiting for Chilibot response (may take a while) ..\n"; my $response=get ($url); if ( $response=~m|Done!.+?<a href=(.+index\.html)|){ print "search is done: http://www.chilibot.net$1\n"; } if ($response=~m|<div *class=\"warning\">(.*)</div>|){ print "error:$1\n"; } }

Publication

Chen H and Sharp BM.Content-rich biological network constructed by mining PubMed abstracts. BMC Bioinformatics. 2004 Oct 8;5:147 [Full text]

Cited in: