Modified the ISA-TAB-Nano 1.0 version to address user comments. Modifications include:
Addition of a MATERIAL section in the ISA-TAB Investigation File to reference the Material File Name and Material Source Name. Removal of Material File in the Study File.
Removal of a separate field in the ISA-TAB Assay File to capture Statistics. Users should reference the Statistic in the Measurement Value parameter name in brackets (e.g. Measurement Value [Mean (diameter)]”).
Enforced the following business rule:
If the assay is a physico-chemical characterization, there should be no study factors of Study Factor Type nanoparticle sample
If the assay is a biological assay (in vitro, in vivo), the Study Factor Name and type must be of nanoparticle sample if the assay is applying a nanoparticle sample to a biological system.
Fixes
Fixed ISA-TAB-Nano Investigation File examples to use a prefix for Term Accession Number and Term Source REF in the Investigation File per the ISA-TAB specification (not required for other ISA-TAB files)
Fixed ISA-TAB-Nano Study File examples to follow the appropriate ISA-TAB ordering requirements
In the Study File, order Protocol REF and associated parameters immediately after Source Name and associated attributes and before Sample Name and Factor Values
Fixed ISA-TAB-Nano Assay File examples to follow the appropriate ISA-TAB ordering requirements
In the Assay File, order Protocol REF to be included after Sample Name
Fixed ISA-TAB-Nano Assay File examples to remove the Source Name. Only the Sample Name should be referenced in the Assay File.
Known Issues and Workarounds
Currently, ISA-TAB does not support Study Grant Number and Study Funding Agency as standard fields in the Investigation Files. These fields can be added in a comments field.
Grouping of assays is subjective to the particular study. Recommend grouping of assays that use the same sample under one study.
For studies involving insertion of tumor cells into mice and the application of a nanoparticle as a treatment, the tumor cells should be parameter values and the nanoparticle should be factor values.