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- 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.
- 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.