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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



 Fields

The field names in an investigation file are organized vertically in the first column.  These fields are divided into 11 sections as defined by ISA-TAB. These sections are:

  • ONTOLOGY SOURCE REFERENCE
  • INVESTIGATION
  • INVESTIGATION CONTACTS
  • INVESTIGATION PUBLICATION
  • STUDY
    • STUDY DESIGN DESCRIPTORS
    • STUDY CONTACTS
    • STUDY PUBLICATIONS
    • STUDY ASSAYS
    • STUDY FACTORS
    • STUDY PROTOCOLS

Ontology Source Reference

This section is used to define the vocabulary source from which a term is selected and referenced in the nano-TAB files.  TABLE 2 shows an example of the ONTOLOGY SOURCE REFERENCE section along with example data.

The ONTOLOGY SOURCE REFERENCE section uses the four concepts described below:

Term source name---The name of the source from where a term is selected and referenced in the nano-TAB files.  The source could be an ontology or a controlled vocabulary. The source name is the full name or the acronym of the ontology/controlled vocabulary. This is a required field if the term source name is referenced in any of the nano-TAB files.  This concept is taken from ISA-TAB.

Term source file--- A file name or a URI of the source named in the term source name field.  This concept is taken from ISA-TAB.

Term source version---version number of the vocabulary source file.  This is a required field if the field for term source file has a value.   This concept is taken from ISA-TAB.

Term source description---Text description to disambiguate resources when homologous acronyms are used.  This concept is taken from ISA-TAB.

Investigation

This section is used to describe an investigation. An example of the INVESTIGATION section is in TABLE 3 along with example data.

The INVESTIGATION section uses the nine concepts described below:

Investigation identifier--- A locally unique identifier or an accession number provided by a repository.  This concept is taken from ISA-TAB.

Investigation title---A concise phrase used as a title for the investigation.  This concept is adapted from ISA-TAB.

Investigation description---A textual description of the investigation.  This concept is taken from ISA-TAB.

Investigation disease---Disease(s) that are the subject of an investigation, if applicable.  This concept is introduced in nano-TAB to identify the disease(s) related to the subject of the investigation

Investigation disease term accession number---Identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value for investigation disease. This concept is introduced in nano-TAB.

Investigation disease term source REF--- The name which identifies the source from where the term for investigation disease is selected. This name should match one of the names entered in the term source name field.  This concept is introduced in nano-TAB.

Investigation outcome---A textual description of the outcome(s) of an investigation.  This concept is introduced in nano-TAB to provide a brief summary or conclusion of an investigation

Investigation submission date---The date on which the investigation was reported to a repository (format: YYYY-MM-DD).  This concept is taken from ISA-TAB.

Investigation public release date---The date on which the investigation is publicly released or published (format: YYYY-MM-DD).  This concept is taken from ISA-TAB.

Investigation Contacts

The INVESTIGATION CONTACTS section allows for the identification of the point(s) of contact for an investigation.  An example of the INVESTIGATION CONTACTS section of the spreadsheet is in TABLE 2 along with example data.

There are 11 concepts used as field names in the INVESTIGATION CONTACTS section.  These concepts are taken from ISA-TAB and are described below:

Investigation person last name---The last name of a person who is the point of contact for the investigation. 

Investigation person first name---The first name of a person who is the point of contact for the investigation. 

Investigation person middle initials---The middle initial(s) of a person who is the point of contact for the investigation.

Investigation person email---The email address of a person who is the point of contact for the investigation. 

Investigation person phone---The telephone number of a person who is the point of contact for the investigation.

Investigation person fax---The fax number of a person who is the point of contact for the investigation. 

Investigation person address---The mailing address of a person who is the point of contact for the investigation. 

Investigation person affiliation--- The name of the organization to which the point of contact belongs. 

Investigation person role--- The term which classifies the role(s) performed by person who is the point of contact for the investigation.

Investigation person role term accession number--- Identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value for investigation person role

Investigation person role term source REF--- Name of the ontology or controlled vocabulary from which a term is selected and entered as a value for investigation person role.

investigation Publications

The INVESTIGATION PUBLICATIONS section allows for the identification of articles (published) associated with the investigation. TABLE 3 shows an example of the INVESTIGATION PUBLICATIONS section along with example data.

There are 7 concepts used in the INVESTIGATION PUBLICATIONS section.  These concepts are taken from ISA-TAB and are described below:

Investigation pubmed ID---PubMed identifier of the publication associated with the investigation.

Investigation publication DOI---A Digital Object Identifier (DOI) of the publication associated with the investigation.

Investigation publication author list---A semicolon-delimited (";") list of authors of a publication associated with the investigation.

Investigation publication title---A concise phrase used as a title for the publication associated with the investigation.

Investigation publication status---A term describing the status of a publication (i.e., submitted, in preparation, published).

Investigation publication status term accession number---The identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value for investigation publication status.

Investigation publication status term source REF---The name which identifies the source from where the term for investigation publication status is selected.  This name should match one of the names entered in the term source name field.

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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