New Features

• Modified the ISA-TAB-Nano 1.2 version where needed and provided ISA-TAB-Nano Guidelines - Draft to address user comments. Modifications and guidelines include:
• General
  • Standardized the approach for handling metadata that is not applicable. This includes providing reasons for information that is missing in ISA-TAB-Nano columns or rows. (See guidelines on Providing Reasons for Missing Values) (Challenge #4)
  • Documented the convention for using a URI to represent Ontology Term Accession Numbers (See guidelines for Referencing Ontology Terms)  (Challenge #9)
• Investigation File
  • Commented on the definition of an investigation for the purpose of collecting data from literature (See guidelines on Organizing Investigations and Studies) (Challenge #13)
• Material File
  • Provided more clarity with examples in documentation in regards to how nominal particle characteristics which refer to chemical composition (and other chemical composition information such as component "Material Chemical Name" values) vs. experimental are recorded (See guidelines on Support for Nominal Particle Characteristics vs. Experimental) (Challenge #2)
  • Documented how to handle "purity" and "impurities" (See guidelines on Support for Nominal Particle Characteristics vs. Experimental) (Challenge #2)
  • Documented approaches to linking multiple external files to a Material File (See guidelines on Linking Multiple External Files)  (Challenge #6)
  • Updated the description of the comments to indicate that comments can be placed anywhere in the Material File. Modified the Material File template to add Comment [] after the Sample Name and Protocol REF field as an example. (See guidelines on Support for Comments) (Challenge #8)
  • Removed not applicable columns in the Material File template and reflected the distinction between Source Name and Sample Name "Characteristics []" in the template by adding a characteristics column after the Sample Name column in addition to after the Source Name column. (See guidelines on Support for Sample Characteristics) (Challenge #8)
• Assay File
  • Made the Measurement Value an attribute off of the assay name node (See guidelines on Measurement Value as an Attribute off of the Assay Node) and updates to the Assay File page (Additional Challenge #1)

  • Standardized the approach for recording data specified in ranges (Discussion still in progress, this will be moved to a future release; see guidelines on Standard Approach for Recording Data Specified in Ranges) (Challenge #3)

  • Clarified the definitions for Parameter Value and Factor Value (See guidelines on Definitions for Parameter Value and Factor Value) (Challenge #10)

Fixes

• Assay File
  • Made the Measurement Value an attribute off of the assay name node (See guidelines on Measurement Value as an Attribute off of the Assay Node) (Additional Challenge #1)

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