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New Features

• Modified the ISA-TAB-Nano 1.0 1 version to address user comments. Modifications include:
• Addition of a MATERIAL section in the ISA-TAB Investigation File to reference Removed the Material Linkage column from 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:
  1. If the assay is a physico-chemical characterization, there should be no study factors of Study Factor Type nanoparticle sample 
  2. 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.

• . The Material Constituent column identifies the materials that are linked if the Material Linkage Type is specified.
• Modified the Material Linkage Type descrption to indicate that if the linkage type is an entrapment or encapsulation, the Material Type column can specify whether the constituent is entrapped or encapsulated.
• Rephrased Material File instructions as follows:  "Materials of different chemical composition or physical characteristics should be described in separate Material files."
• Enhanced the definition of material Characteristics to indicate that nominal particle characteristics (or vendor supplied) should be included in the Material File as characteristics. Experimentally determined characteristics should be included in the Assay File.  

Fixes

• Fixed Material File glossary, template, and examples to reflect the above modifications

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.

Version History

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Version	Release Date
ISA-TAB-Nano 1.2	March 2014
ISA-TAB-Nano 1.1	June 2013
ISA-TAB-Nano 1.0	August 2012

 

 

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