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A tool for categorizing Gene Ontology into subgraphs of user-defined emergent concepts
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README.rst

GOcats

https://raw.githubusercontent.com/MoseleyBioinformaticsLab/GOcats/master/doc/_static/images/GOcats_logo.png

GOcats is an Open Biomedical Ontology (OBO) parser and categorizing utility--currently specialized for the Gene Ontology (GO)--which can help scientists interpret large-scale experimental results by organizing redundant and highly- specific annotations into customizable, biologically-relevant concept categories. Concept subgraphs are defined by lists of keywords created by the user.

Full API documentation, userguide, and tutorial can be found on readthedocs

Currently, the GOcats package can be used to:
  • Create subgraphs of GO which each represent a user-specified concept.
  • Map specific, or fine-grained, GO terms in a Gene Annotation File (GAF) to an arbitrary number of concept categories.
  • Explore the Gene Ontology graph within a Python interpreter.

Citation

Please cite the GitHub repository until our manuscript is accepted for publication: https://github.com/MoseleyBioinformaticsLab/GOcats.git

Installation

GOcats runs under Python 3.4+ and is available through python3-pip. Install via pip or clone the git repo and install the following dependencies and you are ready to go!

Install on Linux

Pip installation

Dependencies should be automatically installed using this method. It is strongly recommended that you install with this method. .. code:: bash

pip3 install gocats

GitHub Package installation

Make sure you have git installed:

cd ~/
git clone https://github.com/MoseleyBioinformaticsLab/GOcats.git

Dependencies

GOcats requires the following Python libraries:

  • docopt for creating the :mod:`gocats` command-line interface.
  • jsonpickle for saving Python objects in a JSON serializable form and outputting to a file.

To install dependencies manually:

pip3 install docopt
pip3 install jsonpickle

Install on Windows

Windows version not yet available; sorry about that.

Quickstart

For instructions on how to format your keyword list and advanced argument usage, consult the tutorial, guide, and API

Subgraphs can be created from the command line.

python3 -m gocats create_subgraphs /path_to_ontology_file ~/GOcats/gocats/exampledata/examplecategories.csv ~/Output --supergraph_namespace=cellular_component --subgraph_namespace=cellular_component --output_termlist

Mapping files can be found in the output directory:

  • GC_content_mapping.json_pickle # A python dictionary with category-defining GO terms as keys and a list of all subgraph contents as values.
  • GC_id_mapping.json_pickle # A python dictionary with every GO term of the specified namespace as keys and a list of category root terms as values.

GAF mappings can also be made from the command line:

python3 -m gocats categorize_dataset YOUR_GAF.goa YOUR_OUTPUT_DIRECTORY/GC_id_mapping.json_pickle YOUR_OUTPUT_DIRECTORY MAPPED_DATASET_NAME.goa

License

Made available under the terms of The Clear BSD License. See full license in LICENSE.

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