9. Annotate ISA studies and assays

Describe the sample-to-data flow using ISA

• the ./assays/<assayName>/isa.assay.xlsx should relate to the ./assays//protocols

  • Add a sheet with the same name as the file for each protocol file; e.g. ./assays/<assayName>/protocols/plant-growth.md --> ./assays/<assayName>/isa.assay.xlsx:plant-growth.md
  • Link the protocol file name (e.g. plant-growth.md) in the respective Protocol REF column

• all files stored in a folder ./assays/<assayName>/dataset should be linked in an Output building block of the ./assays/<assayName>/isa.assay.xlsx

  • Use Output [Raw Data File] to link raw data generated by a machine, measuring device, etc.
  • Use Output [Derived Data File] to link data produced by a computational workflow, script, software
  • 💡 Note that an assay can produce
    • samples from samples: e.g. Input [Sample Name] leaf samples -> Output [Sample Name] RNA extract samples
    • data from samples: e.g. Input [Sample Name] cDNA libraries -> Output [Raw Data File] qRT-PCR results
    • data from data: e.g. Input [Raw Data File] qRT-PCR results -> Output [Derived Data File] Plot of relative gene expression

• use Sample/Material/Data nodes (Input [ ] / Output[ ]) ...

  • ... to link between processes (sheets) within one study/assay
  • ... to link across multiple studies and / or assays

The final result (across all isa.*.xlsx sheets) should be a gapless connection from isa.study.xlsx-sheets through isa.assay.xlsx-sheets representing the flow through the various Input/Output nodes of sample/material --> through processes/protocols --> to Input/Output nodes of sample/material/raw data/derived data. So that any file stored in a ./assays/<assayName>/dataset can be traced back along the chain of processes to the original sample in the lab.