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=head1 NAME

GeoCancerPrognosticDatasetsRetriever - GEO Cancer Prognostic Datasets Retriever is a bioinformatics tool for cancer prognostic dataset retrieval from the GEO website.

=head1 SYNOPSIS

    Usage: geoCancerPrognosticDatasetsRetriever -d "CANCER_TYPE" -p "PLATFORMS_CODES"

An example command using "bladder cancer" as a query: 

    geoCancerPrognosticDatasetsRetriever -d "bladder cancer" -p "GPL570 GPL97 GPL96"

The input and output files of geoCancerPrognosticDatasetsRetriever will be found in the `/data/` and `/results/` directories, respectively.

=head1 DESCRIPTION

Gene Expression Omnibus (GEO) Cancer Prognostic Datasets Retriever is a bioinformatics tool for cancer prognostic dataset retrieval from the GEO database. It requires a GeoDatasets input file listing all GSE dataset entries for a specific cancer (for example, bladder cancer), obtained as a download from the GEO database. This bioinformatics tool functions by applying two heuristic filters to examine individual GSE dataset entries listed in a GEO DataSets input file. The Prognostic Text filter flags for prognostic keywords (ex. "prognosis" or "survival") used by clinical scientists and present in the title/abstract entries of a GSE dataset. If found, this tool retrieves those flagged datasets. Next, the second filter (Prognostic Signature filter) filters these datasets further by applying prognostic signature pattern matching (Perl regular expression signatures) to identify if the GSE dataset is a likely prognostic dataset.

=head1 INSTALLATION

geoCancerPrognosticDatasetsRetriever can be used on any Linux or macOS machines. To run the program, you need to have the cURL program (version 7.68.0 or later) installed on your computer.

By default, cURL is installed on all macOS versions. cURL may not be installed on Linux and would need to be manually installed through a Linux distribution’s software centre. It will be installed automatically on Linux Ubuntu by geoCancerPrognosticDatasetsRetriever.

Manual install:

    $ perl Makefile.PL
    $ make
    $ make install

=head1 DATA FILE

The required input file is a GEO DataSets file obtainable as a download  from GEO DataSets, upon querying for any particular cancer (for example, bladder cancer) in geoCancerPrognosticDatasetsRetriever.

=head1 HELP

Help information can be read by typing the following command: 

    geoCancerPrognosticDatasetsRetriever -h

This command will print the following instructions:

Usage: geoCancerPrognosticDatasetsRetriever -h

Mandatory arguments:

    CANCER_TYPE           type of the cancer as query search term
    PLATFORM_CODES        list of GPL platform codes

    Optional arguments:
    -h                    show help message and exit

=head1 AUTHOR

Abbas Alameer (Bioinformatics and Molecular Modelling Group, Kuwait University), in collaboration with Davide Chicco (University of Toronto)

For information, please contact Abbas Alameer at abbas.alameer(AT)ku.edu.kw

=head1 COPYRIGHT AND LICENSE

Copyright 2021 by Abbas Alameer, Kuwait University

This program is free software; you can redistribute it and/or modify
it under the terms of the GNU General Public License, version 2 (GPLv2).


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