tmtk - TranSMART data curation toolkit

Author:Jochem Bijlard Source Code:https://github.com/thehyve/tmtk/ Generated:Jul 31, 2020 License:GPLv3 Version:0.5.8

Philosophy

A toolkit for ETL curation for the tranSMART data warehouse for translational research.

The TranSMART curation toolkit (tmtk) aims to provide a language and set of classes for describing data to be uploaded to tranSMART. The toolkit can be used to edit and validate studies prior to loading them with transmart-batch.

Functionality currently available:

• create a transmart-batch ready study from clinical data files.
• load an existing study and validate its contents.
• edit the transmart concept tree in The Arborist graphical editor.
• create chromosomal region annotation files.
• map HGNC gene symbols to corresponding Entrez gene IDs using mygene.info.

Note

tmtk is a python3 package meant to be run in Jupyter notebooks. Results for other setups may vary.

Basic Usage

Step 1: Opening a notebook

First open a Jupyter Notebook, open a shell and change directory to some place where your data is. Then start the notebook server:

cd /path/to/studies/
jupyter notebook

This should open your browser to Jupyters file browser, create a new notebook for here.

Step 2: Using tmtk

# First import the toolkit into your environment
import tmtk

# Then create a <tmtk.Study> object by pointing to study.params of a transmart-batch study
study = tmtk.Study('~/studies/a_tm_batch_ready_study/study.params')
# Or, by using the study wizard on a directory with correctly structured, clinical data files.
# (Visit the transmart-batch documentation to find out what is expected.)
study = tmtk.wizard.create_study('~/studies/dir_with_some_clinical_data_files/')

Now we have loaded the study as a tmtk.Study object we have some interesting functions available:

# Check whether transmart-batch will find any issues with the way your study is setup
study.validate_all()

# Graphically manipulate the concept tree in this study by using The Arborist
study.call_boris()

Contents

• Changelog
• User examples
  • Create study from clinical data.
  • TranSMART Arborist
  • Using transmart-batch from Jupyter
• Data formats overview
  • Study folder format
  • Clinical Data
  • Metadata tags and description
  • High dimensional and Omics datatypes
  • Backout
• API Description
  • Study class
  • Params classes
  • Clinical classes
  • Annotations
  • High Dimensional data
  • Metadata Tags
  • Utilities
  • Toolbox package
  • The Arborist
• Data templates
  • Create study templates

Contributors

• Wibo Pipping
• Stefan Payrable
• Ward Weistra