December Community Call - Lung
Presenters:
Martijn Nawijn - Pathology & Medical Biology, GRIAC Research Institute, University Medical Center Groningen
Lisa Sikkema - Fabian Theis lab, Helmholtz Centre Munich
Slides:
- Overview of the HCA-Lung initiative - Martijn Nawijn
- Lung Data structure, analysis, pipelines, and metadata details - Lisa Sikkema
Video recording:
Summary
Key learnings
- Many groups working on lung across Europe and US, different aspects - development, disease, adult lung, mouse lung
- Some groups collect extended annotation towards location of the sample within the organ (Pascal Barbry)
- Fabian Theis’ lab - effort to understand variation - both normal and abnormal - by integration of many different datasets - based on the provided metadata
- The more metadata the better to identify batch effects
Needs from the community
- Align metadata within the Lung community
- Integrate different data within the Lung community
- Determine what metadata is needed for the imaging data - FISH
- Documenting location of origin of the sample
- Basic demographic data, clinical/smoking data, etc
- Use of ontologies to ensure interoperability
- Collect as much metadata as possible to enable batch effect correction
Ideas for how to action
- Organ specialists to collaborate with ontology experts to review existing ontologies, suggest addition of new ones
- Collect additional metadata (clinical data) - this is helpful for batch correction
- Provide guidelines, document best practices for depicting the location of origin of sample
- Find out a way to link overview images of the sample to the data submission to the HCA
- Expand HCA metadata to support imaging experiments