This repository includes an XSD model for representing transcriptomics data to retain interoperability and computable meaning and an XML instance of the transcriptomics de-identified data for a patient from The Cancer Genome Atlas (TCGA). The assumption behind the proposed model is that the model represents a transcriptomics result for one patient, one sample, is performed on one sequencing platform and analyzed by one analysis platform. However, variable number of genes reporting is accommodated.
- XSD files the proposed model in XSD model schema.
- geneExpressionTestSchema_V5.xsd is the original XSD schema showing the elements. A complete description of the elements can be found at Model_element_description
- Gene Expression Lab Report_Template_V7.xsd is the schema for mapped openEHR templates
- XML files are the instances using the schema.
- Sample GE XML_Small.xml: XML instance containing a subset of gene expression from the TCGA patient sample for validation against our XSD schema.
- Sample GE XML_Large.xml.: Gene expression instance containing entire data from the TCGA patient sample for validation against our XSD schema.
- Clone this repository to your local drive
- In terminal type: git clone https://github.com/mumtahena/Transcriptomics_data_model or
- You may use "Clone in Desktop" or "Download ZIP" buttons on the right side panel to download the repository.
- Use an XML editor such as oXygen to view and validate the XSD models and XML model instances
- Guilherme Del Fiol, MD, PhD
- Bret Heale, PhD
- Aly Khalifa
- Mumtahena Rahman, PharmD
For any questions, please email Moom Rahman Roosan [roosan@chapman.edu]