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Description

The study file provides a mapping between the samples (biospecimens and material samples) and processing events (occurs whenever a protocol is applied) associated with a study.   It is also used to provide provides values for the parameters and factors associated with an assay of the sample. In nanoISA-TAB-Nano, factors can be either entered in the study file or in the assay file.   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, and so forth).   The nanomaterial applied to a biospecimen in an in-vitro or in-vivo assay is considered as a study factor along with other factors that vary in the experiment (for example, dose).   The study file is required as it functions as the primary mapping file between the samples and the assay.   For studies involving nanomaterials (also applies to small molecules), the material file allows for a detailed description of the composition and characteristics of the nanomaterial, and the nanoISA-TAB-Nano material file name is referenced as a qualifier for the source sample (nanomaterial) in the study file.

File Format

The nanoISA-TAB-Nano study file leverages the ISA-TAB file format, which is a horizontal-based spreadsheet format with column headers in the first row.  An  The following table provides an example subset of this format is provided in TABLE  14. 

TABLE 14: Example Subset of the Study File Format

Fields

Nano-TAB extends the ISA-TAB specification for the study file by redefining the concept of a sample and adding a new field called MATERIAL FILE to reference the material files that contain description of the material samples.

Please note, the concept specified within the bracket “\[ \]” is a  variable depending on the type of sample. According to the ISA-TAB  specification, the Study file has different types of fields called  nodes, attributes of nodes, qualifiers of nodes’ attributes, and other  valid fields.  [TABLES 15 and 16 |ICR:Study File Examples]on the Study Files Examples page provide additional examples of files using these different types of fields.

Nodes

_Source Name_\---The unique identification name of the source from where the sample is derived.  Source names can be qualified using the following column attributes: _characteristic_ \[ \], _material type_, _material file_, _provider_, and _comment_.

The concept specified within the bracket “[ ]” is a variable depending on the type of sample. According to the ISA-TAB specification, the Study file has different types of fields called nodes, attributes of nodes, qualifiers of nodes’ attributes, and other valid fields. The tables on the Study File Example page provide additional examples of files using these different types of fields.

Nodes

Source Name---The unique identification name of the source from where the sample is derived. (1) If the sample assayed is a biological specimen, its source is the starting biological material from which the sample was derived after the application of a protocol. The name of the source typically refers to the cell line or animal number for biological specimens.  (2) If the sample assayed is a material that is nanoparticle sample or some chemical substance not derived from a biological sourcematerial, then the corresponding source name should refer to the starting sample that was modified by a protocol for the assay.   In this case, the source name should match the value recorded for material source identifier in the corresponding nano-TAB material file.Source names can be qualified using the following column attributes: Characteristics [ ], Material Type, Provider, and Comment.

Sample Name Wiki Markup_Sample Name_\---The unique identification name of the sample. The sample is obtained after the application of a protocol .  Sample names can be qualified using the following column attributes: _characteristic_ \[ \], _material type_, _material file_, and _comment_ Characteristics [ ], Material Type, Provider, and Comment.

Attributes of Study Nodes

One or more attributes are can be used to provide more information about a study node. The different node attributes are described below:

Material typeType---An attribute for the source name or sample name (e.g. Source Name or Sample Name (for example, biospecimen, nanoparticle sample, small molecule etc.).   The term can be a free-text description or taken from an ontology or a controlled vocabulary.   If it is the latter, then the following qualifiers are used:   term accession number and term source Term Accession Number and Term Source REF.

Wiki Markup_Characteristic \[ \]_\Characteristics [ ]---An attribute for _source name_ and _sample name_.  The term for each characteristic \[ \] attribute is written within brackets (e.g., Characteristic \[organism\], Characteristic \[cell type\], etc.).Material File---The name of the nano-TAB material file that contains detailed descriptions of the source sample. This column is not applicable for biospecimens.for Source Name and Sample Name. The term for each characteristics [ ] attribute is written within brackets (for example, Characteristics [organism], Characteristics [cell type], etc.).

Provider---An attribute for source name Source Name, which refers to the name of the person or the vendor providing the source sample.

Attributes of processing events for study nodes--- One or more attributes are can be used to describe a step in the preparation of a sample.

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Performer---The name of the person who carried out the protocol.

Wiki Markup_Date_\---The calendar day on which the protocol was carried out.   The date format should be in YYYY-MM-DD.   If there are other dates to be recorded (e.g., the date when a sample was received from a (for example, the date when a sample was received from a vendor), one should create a _comment \[ \]_ column and specify the type of date within the square brackets (e.g., Comment \[date received\]). Comment [ ] column and specify the type of date within the square brackets (such as Comment [date received]).

Parameter Value [<parameter name]---Value of a parameter, which may be invariant, when applying a protocol. The parameter name is written within brackets and must match the term used as value for the Study Protocol Parameter Name in the ISA-TAB-Nano investigation Wiki Markup_Parameter value \[<parameter term\]_\---Value of a parameter, which is kept constant, when applying a protocol.&nbsp; The parameter term is written within brackets and must match the term used as value for the _study protocol parameter name_ in the nano-TAB investigation file.

Qualifiers for Study Nodes’ Attributes

Each node attribute may be qualified using the following concepts, if applicable.

Wiki Markup_Unit_\---The standard of measurement used if the values for _characteristic_ \[ \], _parameter value \[ \]_ or _factor value \[ \]_ columns are quantitative and dimensional. If the term for _unit_ is taken from an ontology/controlled vocabulary, then its _term accession number_ and the _term source REF_ should be defined in the nano-TAB investigation file.for Characteristic [ ], Parameter Value [ ] or Factor Value [ ] columns are quantitative and dimensional. If the term for Unit is from an ontology/controlled vocabulary, then its Term Accession Number and the Term Source REF should be defined in the ISA-TAB-Nano Study File.

Term Accession Number---Identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value in Source Name, Material Type, Characteristics [ ], Parameter Value [ ], Unit or Factor Value [ ] Wiki Markup_Term Accession Number_\---Identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value in _source name_, _material type,_ _characteristic \[ \]_, _parameter value \[ \]_, _unit_ or _factor value \[ \]_ columns.

Term Source REF---The name which identifies the source from where a term is selected and entered in nanoISA-TAB-Nano study files.   This name should match one of the names entered in the term source name Term Source Name field in the nanoISA-TAB investigation -Nano Investigation file.

Other study fields

Wiki Markup_Factor Value \ [<factor name>\]_\---The value of an independent experimental variable manipulated by the experimentalist investigator with the intention to affect the subject of study (i.e. (such as stressor). Factor terms names are given in brackets, and must be defined in the nanoISA-TAB -Nano investigation file in the STUDY FACTORS section.

Wiki Markup_Comment \ [ \ ]_\---Any comment that provides additional information, which is added only when no other appropriate field exists.exists. Comment fields should be attached to the closest node or the closest field.

Files

The following pages provide the study file examples, template, and glossary:

• Study File Examples
• Study File Template
• Study File GlosssaryGlossary