Category Cross-Omics>Data/Text Mining Systems/Tools

Abstract Chilibot is specialized search software for the PubMed literature database. It is designed to rapidly identify relationships between genes, proteins, or any keywords that the user might be interested in.

In contrast to the PubMed interface where results are organized based on articles, Chilibot directly presents the key information the user is seeking, i.e. sentences containing both of the input terms.

These sentences are organized into different relationship types based on the linguistic analysis of the text.

In addition, Chilibot is especially suited to batch processing a large number of terms (e.g. microarray results). The relationships are summarized into 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, the manufacturer recommends using Chilibot whenever you are searching relationships from PubMed [i.e. putting two (2) keywords into the PubMed search box].

Products features/capabilities include:

User input --

Accepted terms - Chilibot accept two (2) types of terms:

a) Gene / protein symbols - Due to the large number of synonyms for gene / proteins, the best option is the official symbol for each model organism. Other symbols work as well but you may find less information.

b) Keywords - You can use any keyword(s) but be aware that short acronyms may have many different meanings. To avoid ambiguity, you can provide the acronym as well as the full name.

Color coding the nodes - The default node color is cyan. You can change that by adding a number to each term.


Numbers > 1 correspond to varying shades of green, while numbers between 0 and 1 correspond to different shades of red. Only folds (i.e. positive numbers) are allowed.

Negative numbers, usually log(Fold Change), can be converted into folds by taking its antilog.

Customizing synonyms - You can provide synonyms of your own for Chilibot to use. All synonyms are combined using Boolean "OR" before querying PubMed. To supply synonyms, insert them in parenthesis after the term but in the same line. You can also use ';' to separate different synonyms.

Types of searches --

Two term search - This is the simplest form of the Chilibot search. It retrieves sentences describing the relationship between two (2) terms.

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 is 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 pair wisely searched against each other. List one terms are also 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'.

Context restriction - Chilibot defaults to search the entire PubMed for relationships. However, users may wish to restrict the search to a subset of PubMed to increase the relevance of the results.

This can be achieved by providing 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 - "Modulate" or "Modulation" are special keywords in Chilibot. When they are used, Chilibot searches for words such as 'inhibition', 'stimulation', 'increase', 'reduce', etc. that is indicative of regulatory relationships.

This is very useful if you are interested in finding genes or proteins that have a regulatory relationship with your keyword (or protein) but you don't know what they are.

Working with the results --

Basic navigation - The results are presented to the user as a 'summary graph', with square boxes representing the queried terms and lines between the boxes representing the relationships.

There is an icon (circles or rhomboids) in the middle of each line, representing the different kind of relationships. Clicking on the boxes will open a portal site for the represented term. Clicking on the circles/rhomboids will bring up sentences describing the relationships.

Re-graphing - The manufacturer provides several methods for the user to re-organize the graph, including selectively excluding some less significant relationship types.

Users can also generate sub-network graphs focused on one selected node and all its connections. Other available options include more complicated sub-network graphs and different graph layout algorithms.

Generating hypotheses - The process of generating a hypothesis is based on the results that a particular node (A) has No direct relationship with node C. But A is directly connected to at least one other node(s) (e.g. B), which directly connects to C. The system then hypothesize that A-C has a relationship.

To generate hypotheses for any term, click on the node in any graph to bring up the portal page of that node. Then, click on the 'TERM might be related to ...' button.

Editing the synonyms - The optimal use of synonyms is critical to the overall performance of Chilibot. Chilibot provides a list of synonyms that are collected from several genomic/proteomic databases.

Nomenclatures are semi-manually curated before being compiled into a larger database but they may Not fit your needs. Thus, all synonyms are provided to the user before the queries are conducted and they can be edited at that time.

Automating your searches --

The current version of Chilibot is compatible with limited scripting functionality.

System Requirements

The Chilibot main program is not available for download. Due to user requests, we have made the synonym database used in Chilibot available, without fee, for academic use only.


Manufacturer Web Site Chilibot

Price Contact manufacturer.

G6G Abstract Number 20255

G6G Manufacturer Number 102858