Diabetes related genes expressed in pancreas Version 1
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This notebook shows how to integrate genomic and image data resources. This notebook looks at the question Which diabetes related genes are expressed in the pancreas?
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.
We use the intermine API and the IDR API
The notebook can be launched in My Binder
Inputs
Parameters needed to configure the workflow:
- TISSUE = "Pancreas"
- DISEASE = "diabetes"
Ouputs
- List of genes found using HumanMine
- List of images from IDR for one of the gene found
Version History
Version 1 (earliest) Created 23rd Nov 2021 at 11:28 by Jean-Marie Burel
Deleted humanmine_v2.ipynb
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Created: 23rd Nov 2021 at 11:28
Last updated: 23rd Nov 2021 at 11:46
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https://orcid.org/0000-0002-1789-1861
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Software and data format standards for management of microscopy image data. Joint project between international private and public research
Space: Independent Teams
Public web page: https://www.openmicroscopy.org/
Creator: Jean-Marie Burel
Submitter: Jean-Marie Burel
External LinkCollection of workflows exploring data in the Image Data Resource (IDR).
