# geoCancerPrognosticDatasetsRetriever GEO Cancer Prognostic Datasets Retriever is a bioinformatics tool for cancer prognostic dataset retrieval from the GEO website. ## Summary

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.

## Installation geoCancerPrognosticDatasetsRetriever can be used on any Linux or macOS machines. To run the program, you need to have the following programs installed on your computer:

By default, Perl is installed on all Linux or macOS operating systems. Likewise, 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: ```diff perl Makefile.PL make make install ``` On Linux Ubuntu, you might need to run the last command as a superuser (`sudo make install`) and to manually install the libfile-homedir-perl package (`sudo apt-get install -y libfile-homedir-perl`), if not already installed in your Perl 5 configuration. CPAN install: ```diff cpanm App::geoCancerPrognosticDatasetsRetriever ``` To uninstall: ```diff cpanm --uninstall App::geoCancerPrognosticDatasetsRetriever ``` ## 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. ## Execution instructions Run geoCancerPrognosticDatasetsRetriever with the following command: ```diff geoCancerPrognosticDatasetsRetriever -d "CANCER_TYPE" -p "PLATFORMS_CODES" ``` An example command using "bladder cancer" as a query: ```diff geoCancerPrognosticDatasetsRetriever -d "bladder cancer" -p "GPL570 GPL97 GPL96" ``` The input and output files of geoCancerPrognosticDatasetsRetriever will be found in the `~/geoCancerPrognosticDatasetsRetriever_files/data/` and `~/geoCancerPrognosticDatasetsRetriever_files/results/` directories, respectively.

Help information can be read by typing the following command:

```diff geoCancerPrognosticDatasetsRetriever -h ```

This command will print the following instructions:

```diff 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 ``` ## 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). ## Contact

geoCancerPrognosticDatasetsRetriever was developed by:
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