Exploring datasets by gene and organ

[tsliaw]

Need:
Combine WGS data with global transcriptomic profiling using RNA-seq to look for functional dysregulation of a few genes.

User Scenario:

• Navigates to portal and searches by “Biosample” and filters by Anatomy for “blood” and “venous blood”
• Filters list to only look at WGS and RNA-seq assays
• Explore datasets to target gene(s) of interest relevant to datasets of those assays
• Exports list of files that belong to those datasets that can be used to actually obtain these files or request access to them

UI Features to Achieve Use Case:

• [x] Ability to search and filter datasets by samples
• [x] Ability to search and filter datasets by assay types
• [ ] Ability to search datasets by gene/gene expression
• [ ] Ability to filter datasets found by above search (gene search) by data types or samples [combined/continuous searches]
• [ ] Ability to export list of files that belongs to datasets found

Source: Evaluation of CFDE use cases and relevancy to HuBMAP

[tsliaw]

Current Status:

• Datasets can be filtered by samples.
• Datasets can be filtered by assay types.
• M&C query interface is in beta testing for searching datasets by gene of interest and gene expression . Filtering those results by datasets is in mockups, but harder to do in the beta version.
• Exportation in m&c query currently not supported.