Carnival Papers

[augustearth]

Carnival Papers 1 and 2

Paper 1

JOSS paper advertising Carnival to the public.

Requirements

• Well documented code
• Basic clinical model
• An example app that demonstrates relevant functionality
• Documentation on how to build an app from scratch
• Read from CSV, relational

Paper 2

Scientifically focussed paper. How does one do semantic integration with ontologies and Carnival.

• Carnival clinical model
• Not a toy example
• Pull from real public data
• Intersection with OBO (OBI, OBIB, DO, etc.)
• Generate RDF
• Show path for extension to other ontologies/domains

Requirements

• Create a Carnival-clinical extension
• Demonstrate how Carnival might be used to answer a real question without solving one. Combining technology and science can be problematic because it becomes unclear where to publish, who are suitable reviewers, and who would use the technology.
• Include an OMOP data set
• Include a REDCap data set
• Genomics? Perhaps the next paper...
• Ontologies? RDF? Shackle?
• Make meaningful use of OBO ontologies. Subsumption heirarchies, all patients diagnosed with lung cancer. Tie together disparate elements of graph eg. this assay has output on glucose levels. Lab panels output an array of results, linking to ontology terms would be helpful.
• Links and constraints between property graph elements and OBO ontologies
• Do we want to generate an RDF triple store?!?! It would be useful to run triples through tools like Shackle. Useful as a data interchange format?
• Show how use of ontologies enforces semantic standards for data integration

Paper 3

Apply the above to a real study ie. lung cancer.