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analysis_data Initial code commit Nov 27, 2016
bktree @ 825b7cd Added BK-Tree submodule to repo Dec 21, 2016
map_sra_to_ontology
setup_map_sra_to_ontology Added missing file cellline_to_disease_implied_terms.json May 18, 2018
website Update website. New pages. Polished May 5, 2017
.gitmodules Added BK-Tree submodule to repo Dec 21, 2016
README.md Update README.md Dec 13, 2017
run_pipeline.py run_pipeline.py accepts list of key-val pairs Jun 2, 2017

README.md

MetaSRA: normalized human sample-specific metadata for the Sequence Read Archive

This repository contains the code implementing the pipeline used to construct the MetaSRA database described in our publication: https://doi.org/10.1093/bioinformatics/btx334.

This pipeline re-annotates key-value descriptions of biological samples using biomedical ontologies.

The MetaSRA can be searched and downloaded from: http://metasra.biostat.wisc.edu/

Dependencies

This project requires the following Python libraries:

Setup

In order to run the pipeline, a few external resources must be downloaded and configured. First, set up the PYTHONPATH environment variable to point to the directory containing the map_sra_to_ontology directory as well as to the bktree directory. Then, to set up the pipeline, run the following commands:

cd ./setup_map_sra_to_ontology
./setup.sh

This script will download the latest ontology OBO files, the SPECIALIST Lexicon files, and configure the ontologies to work with the pipeline.

Usage

The pipeline can be run on a set of sample-specific key-value pairs using the run_pipeline.py script. This script is used as follows:

python run_pipeline.py <input key-value pairs JSON file>

The script accepts as input a JSON file storing a list of sets of key-value pairs. For example, the pipeline will accept a file with the following content:

[
  {   
    "ID": "P352_141",
    "age": "48",
    "bmi": "24",
    "gender": "female",
    "source_name": "vastus lateralis muscle_female",
    "tissue": "vastus lateralis muscle"
  },
  {   
    "ID": "P352_141",
    "age": "29",
    "bmi": "30",
    "gender": "male",
    "source_name": "vastus lateralis muscle_female",
    "tissue": "vastus lateralis muscle"
  }
 ]