Investigation

1.1.1.1       Description

The ISA-TAB Investigation file allows for the description of the primary investigation and associated studies including assays and protocols.  For example, an investigation title may be “Dendrimer-Based MRI Contrast Agents” and associated studies may be “Characterizing the Size of Dendrimer based MRI Contrast Agents” and “Determining the Hemolytic Properties of Dendrimer based MRI Contrast Agents”. 

The ISA-TAB specification provides flexibility in representing the level of granularity 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 assay measurements (e.g. Z-Average Size, Hydrodynamic Size) and may involve the use of multiple protocols (e.g. Size by DLS, Size by AFFM).  These can be represented effectively in the ISA-TAB file structure.  A study focusing on “Physico-Chemical Characterizations” would have numerous and diverse assay measurements (e.g. Size, Molecular Weight, Surface, etc.) and protocols and it may be challenging to represent and group the assay measurements and protocols associated with each characterization type.

Studies within the Investigation file provide descriptive information about the study including design descriptors, publications, factors, assays, protocols, and contacts.  This descriptive information lays the foundation for other ISA-TAB files.  For example, the Study Factors section of the Investigation file provides details of the factors (e.g. media solvent, temperature) used in the study.  The value of these factors (e.g. PBS, 25 Celsius) is then specified in the Assay file.

1.1.1.2       File Format

The Investigation file format leverages a vertical based spreadsheet format with columns representing multiple values.  In the example subset of the Investigation file below, column A indicates the field names and columns B and C are field values.

1.1.1.3       nano-TAB Extensions

In support of nano-TAB, the following extensions and constraints were applied to the ISA-TAB Investigation file and are further described in Section 4.

1.1       Investigation file

The Investigation file is a vertically oriented spreadsheet containing tab delimited column values.  The Investigation file consists of the following sections as defined by ISA-TAB:

s  ONTOLOGY SOURCE REFERENCE

s  INVESTIGATION

s  INVESTIGATION PUBLICATION

s  INVESTIGATION CONTACTS

s  STUDY

º   STUDY DESIGN DESCRIPTORS

º   STUDY PUBLICATIONS

º   STUDY FACTORS

º   STUDY ASSAYS

º   STUDY PROTOCOLS

º   STUDY CONTACTS

An investigation can contain multiple studies. As such the entire study section is typically repeated.

1.1.1       ONTOLOGY SOURCE REFERENCE

An example of the ONTOLOGY SOURCE REFERENCE section of the spreadsheet is provided in Exhibit 4.1 along with example data.

Exhibit 4.1 Example ONTOLOGY SOURCE REFERENCE section

Definitions for concepts in the ONTOLOGY SOURCE REFERENCE section are provided below.

Term Source Name - List of ontologies containing terms referenced in the nano-TAB files.

Term Source file - The URI of the ontology.

Term Source Version - Version for each ontology referenced in the nano-TAB files.

Term Source Description - Description of each ontology referenced in the nano-TAB files.

1.1.2       INVESTIGATION

An example of the INVESTIGATION section of the spreadsheet is provided in Exhibit 4.2 along with example data.

Exhibit 4.2 Example INVESTIGATION Section

Definitions for concepts in the INVESTIGATION section are provided below.

Investigation Identifier - Name used as an identifier for the investigation.

Investigation Title - Name used as a title for the investigation.

Investigation Description – Text description of the investigation.

Investigation Disease - Disease(s) that are the subject of the investigation, if applicable.  Note: This term is a nano-TAB extension.

Investigation Disease Term Accession Number – Identification number of a term selected from an ontology or a controlled vocabulary, and entered as a value for the Disease. Note: This term is a nano-TAB extension.

Investigation Disease Term Source REF - Name of the ontology or controlled vocabulary from which a term is selected and entered as a value for the Disease. Note: This term is a nano-TAB extension.

Investigation Outcome - Text description of the outcome of the investigation. Note: This term is a nano-TAB extension.

Investigation Submission Date - Date the investigation was initiated in the format YYYY-MM-DD.

Investigation Public Release Date - Date the investigation was published or made publically available in the format YYYY-MM-DD.

1.1.3       INVESTIGATION PUBLICATIONS

An example of the INVESTIGATION PUBLICATION section of the spreadsheet is provided in Exhibit 4.3 along with example data.

Exhibit 4.3 Example INVESTIGATION PUBLICATIONS Section

Definitions for concepts in the INVESTIGATION PUBLICATIONS section are provided below.

Investigation PubMed ID - Identifier of the publication in the PubMed publication source.

Investigation Publication DOI - Publication Document Object Identifier.

Investigation Publication Author List - List of authors separated by semi-colons.

Investigation Publication Title - Name used as a title for the publication.

Investigation Publication Status - The status of the publication.

Investigation Publication Status Term Accession Number - Identification number of a term selected from an ontology or a controlled vocabulary, and entered as a value for the Publication Status.

Investigation Publication Status Term Source REF - Name of the ontology or controlled vocabulary from which a term is selected and entered as a value for the Publication Status.

1.1.4       INVESTIGATION CONTACTS

An example of the INVESTIGATION CONTACTS section of the spreadsheet is provided in Exhibit 4.4 along with example data.

Exhibit 4.4 Example INVESTIGATION CONTACTS Section

Definitions for concepts in the INVESTIGATION CONTACTS section are provided below.

Investigation Person Last Name - Last name of the point of contact.

Investigation Person First Name - First name of the point of contact.

Investigation Person Mid Initials – Middle Initials of the point of contact.

Investigation Person Email - Email address of the point of contact

Investigation Person Phone - Phone number of the point of contact.

Inv Investigation Person Fax - Fax number of the point of contact.

Investigation Person Address - Mailing address of the point of contact.

Investigation Person Affiliation - Organization in which the point of contact belongs.

Investigation Person Roles - Role of the point of contact in the investigation.

Investigation Person Roles Term Accession Number - Identification number of a term selected from an ontology or a controlled vocabulary, and entered as a value for Person Roles.

Investigation Person Roles Term Source REF - Name of the ontology or controlled vocabulary from which a term is selected and entered as a value for Person Roles.