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---------------------------------------------------------------------------------------------------------------------------------------Investigation File Exemplar

Description

(1) The nano-TAB investigation file leverages the ISA-TAB investigation file, and it allows for the description of the primary investigation and associated studies including assays and protocols.  An investigation can have one or more studies.  For example, an investigation titled “Dendrimer-Based MRI Contrast Agents” may have two studies titled as “Characterizing the Size of Dendrimer based MRI Contrast Agents” and “Determining the cytotoxicity property of  Dendrimer based MRI Contrast Agents in porcine proximal tubule cells” Each study can have one or more assays depending on the endpoint measured and the technique used.  For example, a cytoxicity study may be conducted using an MTT assay and a LDH release assay.  While a size characterization study can include two types of assays based on the technique used – one using DLS and the other using AFM.

(2) The ISA-TAB specification provides flexibility in representing the level of granularity in information associated with a study; however, the level of granularity should factor in the effective representation of assays and protocols in conformance with the specification.  For example, a study focusing on “Size Characterizations” will have multiple size measurements (for example, Z-average size, hydrodynamic size) and may involve the use of multiple techniques (for example, size by DLS, size by AFM).  These can be represented effectively in the ISA-TAB file structure that nano-TAB uses. 

(3) The investigation file provides descriptive information about studies including design descriptors, publications, factors, assays, protocols, and contacts.  This descriptive information lays the foundation for other nano-TAB files.  For example, TABLE 1 shows a subset of the Investigation File, which is the study factors section of the investigation file.  This section provides the names of factors (e.g., temperature, solvent medium) used in the study and their associated units of measurement (if the factors are quantitative).  The values of these factors (for example, PBS, 25 Celsius) are specified either in the study or the assay file.

File Format

The nano-TAB investigation file leverages the ISA-TAB file format, which is a vertical-based spreadsheet format with row headers in the first column, as shown in TABLE 1. The fields are divided into sections. Therefore, the field values in the investigation file are entered in column order. For instance, in TABLE 1, Column A indicates the field names and Columns B and C contain the field values.

TABLE1 Example Subset of the Investigation File Format

A

B

C

STUDY FACTORS



Study Factor Name

temperature

solvent medium

Study Factor Name Term Accession Number

PATO_0000146

NPO_1855

Study Factor Name Term Source REF

PATO

NPO

Study Factor Unit

celsius


Study Factor Unit Term Accession Number

UO_0000027


Study Factor Unit Term Source REF

UO


Study Factor Type

condition

condition

Study Factor Type Term Accession Number



Study Factor Type Term Source REF



Nano-TAB Extensions--- Nano-TAB extends the ISA-TAB Investigation File specification by introducing new fields, which are listed in TABLE 2.

TABLE 2 Extensions and Constraints Applied to the ISA-TAB Investigation File in Support of Nano-TAB

Section

Field

Change

Field Status (if applicable)

INVESTIGATION

Investigation disease

Addition

Required

INVESTIGATION

Investigation disease term accession number

Addition

Required

INVESTIGATION

Investigation disease term source REF

Addition

Required

INVESTIGATION

Investigation outcome

Addition

Optional

STUDY

Study disease

Addition

Required

STUDY

Study disease term accession number

Addition

Required

STUDY

Study disease term source REF

Addition

Required

STUDY

Study outcome

Addition

Optional

STUDY ASSAYS

Study assay measurement name

Addition

Required

STUDY ASSAYS

Study assay measurement name term accession number

Addition

Required

STUDY ASSAYS

Study assay measurement name term source REF

Addition

Required

STUDY ASSAYS

Study assay measurement unit

Addition

Required

STUDY ASSAYS

Study assay measurement unit term accession number

Addition

Required

STUDY ASSAYS

Study assay measurement unit term source REF

Addition

Required

STUDY ASSAYS

Study assay measurement statistic

Addition

Required

STUDY ASSAYS

Study assay measurement statistic term accession number

Addition

Required

STUDY ASSAYS

Study assay measurement statistic term source REF

Addition

Required

STUDY FACTORS

Study factor unit

Addition

Required

STUDY FACTORS

Study factor unit term accession  number

Addition

Required

STUDY FACTORS

Study factor unit term source REF.

Addition

Required

STUDY PROTOCOLS

Study protocol parameter unit

Addition

Required

STUDY PROTOCOLS

Study protocol parameter unit term accession number

Addition

Required

STUDY PROTOCOLS

Study protocol parameter unit term source REF

Addition

Required

Investigation Example Files

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