Use Public Resources to answer a biological question
Version 1

Workflow Type: Jupyter
Stable

Learning Objectives

  • How to access genomic resource via its Python API
  • How to access image resource via its Python API
  • Relate image data to genomic data

Diabetes related genes expressed in pancreas

This notebook looks at the question Which diabetes related genes are expressed in the pancreas? Tissue and disease can be modified.

Steps:

  • Query humanmine.org, an integrated database of Homo sapiens genomic data using the intermine API to find the genes.
  • Using the list of found genes, search in the Image Data Resource (IDR) for images linked to the genes, tissue and disease.
  • Analyse the images found.

Launch

This notebook uses the environment.yml file.

See Setup.

Version History

Version 1 (earliest) Created 1st Jun 2023 at 11:14 by Jean-Marie Burel

Initial commit


Frozen Version-1 3f91976
help Creators and Submitter
Creators
Submitter
Discussion Channel
Citation
Burel, J.-M., & Walczysko, P. (2023). Use Public Resources to answer a biological question. WorkflowHub. https://doi.org/10.48546/WORKFLOWHUB.WORKFLOW.494.1
Activity

Views: 2162

Created: 1st Jun 2023 at 11:14

Last updated: 1st Jun 2023 at 11:18

help Attributions

None

help Collections
Total size: 3.83 MB
Powered by
(v.1.14.1)
Copyright © 2008 - 2023 The University of Manchester and HITS gGmbH