Incorporate status quo specification details

[HLWeil]

The way tools handle the ARC has gradually grown beyond the current ISA and ARC specifications. I composed a list of status-quo differences in the tools and the current state of the specification. These should be discussed and implemented into the ARC-specification:

Changes to ISA-Tab

• Xlsx vs txt files

• Investigation file keys:

  • Investigation PubMed ID changed to Investigation Publication PubMed ID
  • Study PubMed ID changed to Study Publication PubMed ID
  • [BUG] investigation file deviates from ISA ARCCommander#107

• Metadata sheets

  • Assay files now contain a metadata sheet with the assay section from the study section and an additional performers section
  • Study files now contain a metadata sheet with only the top-level study section
  • Sheetnames: isa_study, isa_assay and isa_investigation

• Annotation table process separation

  • Process separation in ISA-Tab is marked using the Protocol REF column. Now, instead this separation is done by having different sheets
  • Annotation table sheet names correspond to isa-json process names
  • Annotation Table headers:
    • Space between category and name was introduced
      • e.g. Characteristics [Organism] vs Characteristics[Organism]
    • Ontological Annotation of headers:
      • E.g. Term Source REF (PATO:0000146) vs only Term Source REF
    • Added Component columns
    • Characteristic instead of Characteristics
    • Factor instead of Factor Value
    • Parameter isntead of Parameter Value
    • Entity headers now specify whether it’s Input or Output:
      • E.g. Input [Source Name] and Output [Sample Name]

Further Specifications

• Paths

  • Based on arc root
  • Or relative to reference path:
    • Data file paths in assay files: assays/<assayName>/dataset
    • Data file paths in study files: studies/<studyName>/resources
    • Assay file name in metadata section: assays
    • Study file name in metadata section: studies

Parsing behaviour

• Processes are parsed in a different way compared to ISA-API

  • In ISA-API, the input and output of the resulting process can be interpreted like in a chemical formula. All inputs map interchangeably to all outputs.
  • Currently in ARCtrl, the table logic is continued in the results isa_process.json. The n-th input maps to the n-th output in the lists