Proteomics Module

This module enables the collection of proteomics patient data using the cptac Python package to collect mRNA data for one of six available cancer types. This module includes the following:

File name	Description
getAllDatasets.py	This script is run within the Docker build process to get all datasets into the Python environment. Obsolete after Aug 2023 change to cptac package.
protDataSetsCLI.py	This script is the primary tool to pull a specific cancer data type
Dockerfile	This file contains the two scripts above and the cptac Python package
prot-data-cwl-tool.cwl	This is a CWL tool to run the Docker image with the command line tool

To run

There are three ways to get proteomics data, depending on your environment. Each one should output a file.tsv in your local directory

If you have Python and cptac installed

Simply run the command

python getAllDatasets.py
python protDataSetsCLI.py --cancerType=brca

If you have Docker installed

Then you can run the command via the docker interactive mode

docker build . -t prot-module
docker run --volume $PWD:/tmp -ti prot-module python /bin/protDataSetsCLI.py --cancerType=brca

If you have Docker and a CWL engine

Here we have an example using the cwl-tool engine, but this should run any other engine as well.

cwl-tool prot-data-cwl-tool.cwl --cancerType brca

If using alongside another CWL implementation (like toil-cwl-runner or arvados-cwl-runner), you can install then run with cwltool:

pip install cwltool
cwltool prot-data-cwl-tool.cwl --cancerType brca

Cancer types

Dataset name	Description	Data reuse status	Publication link
Brca	breast cancer	no restrictions	https://pubmed.ncbi.nlm.nih.gov/33212010/
Ccrcc	clear cell renal cell carcinoma (kidney)	no restrictions	https://pubmed.ncbi.nlm.nih.gov/31675502/
Colon	colorectal cancer	no restrictions	https://pubmed.ncbi.nlm.nih.gov/31031003/
Endometrial	endometrial carcinoma (uterine)	no restrictions	https://pubmed.ncbi.nlm.nih.gov/32059776/
Gbm	glioblastoma	no restrictions	https://pubmed.ncbi.nlm.nih.gov/33577785/
Hnscc	head and neck squamous cell carcinoma	no restrictions	https://pubmed.ncbi.nlm.nih.gov/33417831/
**Lscc	lung squamous cell carcinoma	password access only	unpublished**
Luad	lung adenocarcinoma	no restrictions	https://pubmed.ncbi.nlm.nih.gov/32649874/
Ovarian	high grade serous ovarian cancer	no restrictions	https://pubmed.ncbi.nlm.nih.gov/27372738/
**Pdac	pancreatic ductal adenocarcinoma	password access only	unpublished**