sparc-fair-codeathon / hubmap-link Goto Github PK

Catalog and visualize ontology overlaps between HuBMAP and SPARC’s reference and sample data.

Sub-tasks:

• #4
• #5
• #6
• #7
• #8
• #9

1. Use the latest CCF Release v1.1 heart GLBs: Female and Male -- Ignore the VH_M/F_blod_vasculature_of_heart scene nodes
2. Load the source GLB and the fitted/generated GLB and ensure that they are sufficiently overlapping/fitted when loading into Blender
3. Update markdown documentation on how to generate these
4. Setup PR with the updated organs and documentation for Bruce to integrate

1. Map the RUI locations here to SPARC scaffold registrations
2. Ensure the code to do this is sufficiently reusable (does not need to be perfect yet)
3. Document usage (markdown) and code
4. Setup PR with code, documentation, and mapped registrations for Bruce to take from there

• The routes are a little sub-optimal, so clean them up to be more obvious
• Clean up some API code duplication/messiness
• Document the routes in the README.md

Epicardium - the visceral layer of serous pericardium comprised of mesothelial cells, fat, connective tissues, and nerves.

outer surface of myocardium - The outermost 2-D surface of the myocardium where it meets the other tissue types in the heart wall.

outer surface of myocardium of left ventricle - The outermost 2-D surface of the myocardium of the left ventricle where it meets the other tissue types in the heart wall.

outer surface of myocardium of right ventricle - The outermost 2-D surface of the myocardium of the right ventricle where it meets the other tissue types in the heart wall.

endocardium of myocardium of left atrium - The innermost 2-D surface of the myocardium at organ scale, touching the lumen of the left atrium, treating endocardium thickness as negligible or as part of myocardium.

endocardium of myocardium of right atrium - The innermost 2-D surface of the myocardium at organ scale, touching lumen of the right atrium, treating endocardium thickness as negligible or as part of myocardium.

endocardium of myocardium of left ventricle - The innermost 2-D surface of the myocardium at organ scale, touching lumen of the left ventricle, treating endocardium thickness as negligible or as part of myocardium.

endocardium of myocardium of right ventricle - The innermost 2-D surface of the myocardium at organ scale, touching lumen of the right ventricle, treating endocardium thickness as negligible or as part of myocardium.

luminal surface of left pulmonary vein - The innermost surface of the left pulmonary vein.

Synonym: tunica intima of left pulmonary vein

luminal surface of middle pulmonary vein - The innermost surface of the middle pulmonary vein.

Synonym: tunica intima of middle pulmonary vein

luminal surface of right pulmonary vein - The innermost surface of the right pulmonary vein.

Synonym: tunica intima of right pulmonary vein

luminal surface of inferior vena cava - The innermost surface of the inferior vena cava.

Synonym: tunica intima of inferior vena cava

luminal surface of superior vena cava - The innermost surface of the superior vena cava.

Synonym: tunica intima of superior vena cava

luminal surface of aorta - The 2-D surface of the aorta in contact with blood.

luminal surface of root of aorta - The 2-D surface of the aortic valve/root in contact with blood, subset of "luminal surface of aorta".

luminal surface of pulmonary trunk - The 2-D surface of the pulmonary trunk in contact with blood.

luminal surface of root of pulmonary trunk - The 2-D surface of the pulmonary valve/root in contact with blood, subset of "luminal surface of pulmonary trunk"

1. Given #27 take the generated SPARC scaffold registrations and map them back as CCF registrations
2. Ensure the code to do this is sufficiently reusable (does not need to be perfect yet)
3. Document usage (markdown) and code
4. Setup PR with code, documentation, and mapped registrations for Bruce to take from there

Assign roles for each team member and document in the README.md

1. Convert and add the documentation gathered here as a markdown document to capture the evolving SOP
2. Setup PR with documentation for Bruce to integrate

Document our workflow and why, outlining what the problem is and how you think you will solve it in graphic form (max five (5) powerpoint slides) and place it in the root of the repo and link from README.md.

1. Generate a GLB per frame of animation for each of the CCF heart GLBs: Female and Male
2. Load the source GLB and the keyframe GLB and ensure that they are sufficiently overlapping/fitted when loading into Blender
3. Add markdown documentation on how to generate these
4. Setup PR with the GLB keyframes and documentations for Bruce to take from there

• Use compodoc and sonarcloud to measure coverage
• Update all code with tests and documentation to get us to >80% coverage

Some open questions about our project to resolve sooner than later

• What technology stack(s) to use?
  Sam: I think the simplest way to go will be to implement this as a pure static client-side browser app unless the volume of data or processing proves to be intractable.

• Should processing be on the fly or run periodically?
  Sam: Unless query/transfer/processing overhead proves an issue, I favor on-the-fly.

• Do we need a server (beyond static file hosting via GitHub Pages)?
  Sam: Ideally not.

What else? (feel free to add to this issue)

Map and Visualize sample data in HuBMAP and SPARC 3D reference systems

Sub-tasks:

• #10
• #11
• #12
• #13
• #14
• #15

SPARC data is currently placed relative to the skin as we do not have all the scaffolds converted and do not currently have a way to find their placement within the scaffold.