Study

1.1.1.1       Description

The Study file provides a mapping between the samples, materials, and processing events associated with a study.  Samples can be biological materials (e.g. cell line, animal), nanomaterials, or small molecules.  For physico-chemical characterizations of nanomaterials, the sample is the nanomaterial.  For in vitro and in vivo characterizations, the sample is the biological specimen (cell line, animal, etc.).  The nanomaterial applied to the sample is considered a Study Factor along with other factors that vary in the experiment (e.g. dose).  The Study file is required as it functions as the primary mapping between the samples and the study.  For studies involving nanomaterials, the Material file is references as a qualifier and allows for a detailed description of the composition and characteristics of the nanomaterial.

1.1.1.2       File Format

The ISA-TAB file format leverages a horizontal based spreadsheet format with column headers and row values.  An example subset of this format is provided below.  Please note, concepts specified within the bracket “[]” are variable depending on the type of sample.

1.1.1.3       nano-TAB Extensions

In nanotechnology, both the material and specimen can function as the primary subject of the study and as such, nano-TAB re-defined the concept of a sample to include both biological specimens and materials.  To accommodate additional metadata needed to effectively describe the material sample, a Material file was introduced.

To accommodate the nano-TAB changes, references to the sample were renamed and are identified as follows:

1.1.1       STUDY

An example of the STUDY section of the spreadsheet is provided in Exhibit 4.5 along with example data.

Exhibit 4.5 Example STUDY Section

Definitions for concepts in the STUDY section are provided below.

Study Identifier - Name used as an identifier for the study.

Study Title - Name used as a title for the study.

Study Description – Text description of the study.

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

Study 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.

Study 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.

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

Study Submission Date - Date the study was initiated in the format YYYY-MM-DD.

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

Study File Name - References the name of the Study file(s).

Study File URI - URI of the study file location.  If a URI is not provided, the file should be included as an attachment to submitted nano-TAB files. Note: This term is a nano-TAB extension.

Study File Version - The version number (e.g. 1.0) of the file. Note: This term is a nano-TAB extension.

Study File Description - Text description providing additional information on the file. Note: This term is a nano-TAB extension.

1.1.2       STUDY DESIGN DESCRIPTORS

An example of the STUDY DESIGN DESCRIPTORS section of the spreadsheet is provided in Exhibit 4.6 along with example data.

Exhibit 4.6 Example STUDY DESIGN DESCRIPTORS Section

Definitions for concepts in the STUDY DESIGN DESCRIPTORS section are provided below.

Study Design Type - The classification of the study based on the overall study design (e.g. comparison study).

Study Design Type Term Accession Number - Identification number of the term that is selected from an ontology or a controlled vocabulary, and is entered as a value for the file Type. Note: This term is a nano-TAB extension.

Study Design Type Term Source REF - Name of the ontology or the controlled vocabulary from which a term is selected as a value for the file Type. Note: This term is a nano-TAB extension.

1.1.3       STUDY PUBLICATIONS

An example of the STUDY PUBLICATION section of the spreadsheet is provided in Exhibit 4.7 along with example data.

Exhibit 4.7 Example STUDY PUBLICATIONS Section

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

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

Study Publication DOI - Publication Document Object Identifier.

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

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

Study Publication Status - The status of the publication.

Study 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.

Study 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       STUDY FACTORS

An example of the STUDY FACTORS section of the spreadsheet is provided in Exhibit 4.8 along with example data.

Exhibit 4.8 Example STUDY FACTORS Section

Definitions for concepts in the STUDY FACTORS section are provided below.

Study Factor Name - An independent variable manipulated by the experimentalist with the intention to affect biological systems in a way (i.e. Stressor).

Study Factor Type - The classification of factors associated with the study (e.g. condition).

Study Factor Type Term Accession Number – Identification number of a term selected from an ontology or a controlled vocabulary, and entered as a value for the Study Factor.

Study Factor Type Term Source REF - Name of the ontology or controlled vocabulary from which a term is selected and entered as a value for the Study Factor.

1.1.5       STUDY ASSAYS

An example of the STUDY ASSAYS section of the spreadsheet is provided in Exhibit 4.9 along with example data.

Exhibit 4.9 Example STUDY ASSAYS Section

Definitions for concepts in the STUDY ASSAYS section are provided below.

Study Assay Measurement Type - The endpoint (measurement value) of the assay.

Study Assay Measurement Type Term Accession Number - Identification number of a term selected from an ontology or a controlled vocabulary, and entered as a value for the Assay Measurement Type.

Study Assay Measurement Type Term Source REF – Name of the ontology or controlled vocabulary from which a term is selected and entered as a value for the Assay Measurement Type .

Study Assay Technology Platform - The manufacturer and platform name of the instruments used in the study.

Study Assay file Name - The name of the assay file(s) associated with the study.

1.1.6       STUDY PROTOCOLS

An example of the STUDY PROTOCOLS section of the spreadsheet is provided in Exhibit 4.10 along with example data.

Exhibit 4.10 Example STUDY PROTOCOLS Section

Definitions for concepts in the STUDY PROTOCOLS section are provided below.

Study Protocol Name - The name of the protocol used within the study and referenced in the sample and assay files. The formal plan of an experiment or research activity, including the objective, rationale, design, materials and methods for the conduct of the study; intervention description, and method of data analysis.

Study Protocol Type - The classification of the protocol associated with the study.

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

Study Protocol Type Term Source REF – Name of the ontology or controlled vocabulary from which a term is selected and entered as a value for the Protocol Type.

Study Protocol Description - Free-text description of the protocol.

Study Protocol URI - External pointer to the protocol document.

Study Protocol Parameters Name - List of parameter names associated with the protocol separated by semicolons.  A protocol parameter is a constant associated with a protocol that is not varied as part of the experiment.

Study Protocol Parameters Name Term Accession - Identification number of a term selected from an ontology or a controlled vocabulary, and entered as a value for the Parameters Name.

Study Protocol Parameters Name Term Source REF - Name of the ontology or controlled vocabulary from which a term is selected and entered as a value for the Parameters Name.

Study Protocol Components Name - List of component names associated with the protocol separated by semicolons.  Components include instruments, software, and reagent names associated with a protocol.

Study Protocol Components Type - Classification of protocol components such as instrument, software, and reagent.

Study Protocol Components Type Term Accession - Identification number of a term selected from an ontology or a controlled vocabulary, and entered as a value for the Protocol Components Type.

Study Protocol Components Type Term Source REF - Name of the ontology or controlled vocabulary from which a term is selected and entered as a value for the Protocol Components Type.

1.1.7       STUDY CONTACTS

An example of the STUDY CONTACTS section of the spreadsheet is provided in Exhibit 4.11 along with example data.

Exhibit 4.11 Example STUDY CONTACTS Section

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

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

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

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

Study Person Email - Email address of the point of contact

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

Study Person Fax - Fax number of the point of contact.

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

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

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

Study 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.

Study 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.

1.2       Study file

The Study file is a horizontally oriented spreadsheet.  The file supports the following types of information:

s  the source name and sample name

s  the characteristics of the sample including material type and provider

s  references to the protocol and associated protocol parameters

s  study factors and other study fields

Specific concepts often leveraged in the Study file are provided below.

Source Name – The starting material before applying a protocol to obtain the sample.

Sample Name - The unique identification name of the material used as the subject of the study.  For nanotechnology physico-chemical characterizations, the sample is the nanomaterial and is referenced by the material identifier.  For in vitro and in vivo characterizations, the biological specimen is the primary subject of the study and is referenced by the specimen name.

Material Type - The type of sample such as biospecimen, nanomaterial, or small molecule.

Characteristics [] - Descriptive information about a biological specimen.  Characteristic concepts are variable and described in brackets.  Note: Characteristics associated with a material (nanomaterial, small molecule) are specified in the Material file.

Characteristics [organism] - Refers to the taxon of the biological sample.

Characteristics [cell type] - Refers to the distinct form of a cell of the biological sample.

Protocol Ref - The name of the protocol used to prepare the sample.

Parameter Value [] - Concepts associated with a sample preparation protocol that are not varied in the experiment.  Parameters concepts are variable and described in brackets. 

Parameter Value [medium] - Refers to the substance in which the sample is transmitted.

Factor Value [] - An independent variable manipulated by the experimentalist with the intention to affect biological systems (i.e. stressor). Factor concepts are variable and described in brackets.

Factor Value [nanomaterial] – The material identifier of the nanomaterial applied to the biospecimen.  Often followed by Factor Value [dose].

Material File Reference - Represents the name of the Material file which provides detailed information on the nanomaterial or small molecule