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Description
The Study study file provides a mapping between the samples, materials, samples (biospecimens and material samples) and processing events (occurs whenever a protocol is applied) associated with a study. Samples can be biological materials (e.g. cell line, animal), nanomaterials, or small molecules. . It also provides values for the parameters and factors associated with an assay of the sample. In ISA-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, etc.and so forth). The nanomaterial applied to the sample a biospecimen in an in-vitro or in-vivo assay is considered as a Study Factor study factor along with other factors that vary in the experiment (e.g. for example, dose). The Study study file is required as it functions as the primary mapping file between the samples and the studyassay. For studies involving nanomaterials (also applies to small molecules), the Material file is references as a qualifier and material file allows for a detailed description of the composition and characteristics of the nanomaterial, and the ISA-TAB-Nano material file name is referenced as a qualifier for the source sample (nanomaterial) in the study file.
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File Format
unmigratedThe ISA-wiki-markupThe TAB-Nano study file leverages 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. \\
<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="43fe1be9-0b81-4e77-86b3-5ea67975932e"><ac:plain-text-body><![CDATA[ | Source Name | Sample Name | Material Type | Characteristics [organism] | Characteristics [cell type] | ]]></ac:plain-text-body></ac:structured-macro> |
PK1cell | PK1cell-low-0h | biospecimen | Suis Scrofa | LLC-PK1 | ||
PK1cell | PK1cell-low-0h | biospecimen | Suis Scrofa | LLC-PK1 |
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:
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Field
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Change
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Description
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Field Status
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Source Name
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Re-defined concept
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Required
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Sample Name
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Support material samples
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The sample name typically referenced biological materials. The sample name can also reference the material identifier
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Required
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Material File Reference
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Addition
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Represents the name of the Material file which provides detailed information on the nanomaterial or small molecule
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Required for nanotechnology studies
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<ac:structured-macro ac:name="unmigrated-wiki-markup" ac:schema-version="1" ac:macro-id="d7a5af36-a256-4f23-94e4-844a342178e0"><ac:plain-text-body><![CDATA[
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Factor Value[nanomaterial]
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Addition of [nanomaterial]
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References the material identifier of the nanomaterial that is applied to the biological specimen for in vitro and in vivo characterizations. The
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Required for nanotechnology in vitro and in vivo characterizations
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]]></ac:plain-text-body></ac:structured-macro>
format, which is a horizontal-based spreadsheet format with column headers in the first row. The following table provides an example subset of this format.
Example Subset of the Study File Format
A | B | C |
|---|---|---|
Source Name | Material Type | Characteristic[cell type] |
LLC-PK1 | biospecimen | porcine proximal tubule cells |
LLC-PK1 | biospecimen | porcine proximal tubule cells |
Fields
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. 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. If the sample assayed is a nanoparticle sample or some chemical substance not derived from a biological material, then the corresponding source name should refer to the starting sample that was modified by a protocol for the assay. Source names can be qualified using the following column attributes: Characteristics [ ], Material Type, Provider, and Comment.
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: Characteristics [ ], Material Type, Provider, and Comment.
Attributes of Study Nodes
One or more attributes can be used to provide more information about a study node. The different node attributes are described below:
Material Type---An attribute for the 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 REF.
Characteristics [ ]---An attribute 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, 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 can be used to describe a step in the preparation of a sample.
Protocol REF---The name of the protocol used to prepare the sample. This name should match a value for the field study protocol name in the investigation file (within the study protocols section).
Performer---The name of the person who carried out the protocol.
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 (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 (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 file.
Qualifiers for Study Nodes’ Attributes
Each node attribute may be qualified using the following concepts, if applicable.
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 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--
1.1.1 STUDY
An example of the STUDY section of the spreadsheet is provided in Exhibit 4.5 along with example data.
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A
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B
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C
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STUDY
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Study Identifier
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NCL200612A
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Study Title
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Physical Chemical Characterization
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Study Description
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Dynamic light scattering (DLS) technique was used to measure the hydrodynamic size of this dendritic nanomaterial. The effects of sample concentration, buffer, and temperature on the hydrodynamic size (stability) also were measured. Purity was analyzed by HPLC and Capillary Electrophoresis.
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Study Disease
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Study Disease Term Accession Number
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Study Disease Term Source REF
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Study Outcome
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Study Submission Date
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2006-12-01
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Study Public Release Date
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2006-12-01
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Study File Name
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s_Size.txt
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Study File URI
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Study File Version
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Study File Description
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.
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A
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B
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C
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STUDY DESIGN DESCRIPTORS
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Study Design Type
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comparison
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Study Design Type Term Accession Number
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Study Design Type Term Source REF
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.
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A
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B
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C
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STUDY PUBLICATIONS
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Study PubMed ID
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18095846
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Study Publication DOI
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10.2217/17435889.2.6.789
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Study Publication Author List
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Hall JB; Dobrovolskaia MA; Patri AK; McNeil SE
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Study Publication Title
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Characterization of nanoparticles for therapeutics
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Study Publication Status
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peer reviewed
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Study Publication Status Term Accession Number
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Study Publication Status Term Source REF
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NPO
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.
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A
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B
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C
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STUDY FACTORS
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Study Factor Name
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Temperature
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Media solvent
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Study Factor Type
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condition
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condition
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Study Factor Type Term Accession Number
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Study Factor Type Term Source REF
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NPO
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NPO
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.
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A
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B
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C
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STUDY ASSAYS
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Study Assay Measurement Type
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size
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Study Assay Measurement Type Term Accession Number
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Study Assay Measurement Type Term Source REF
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NPO
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Study Assay Technology Platform
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Dynamic Light Scattering
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Study Assay file Name
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a_size_DLS.txt
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.
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A
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B
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C
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STUDY PROTOCOLS
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Study Protocol Name
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Measuring the Size of Nanoparticles in Aqueous Media Using Batch-Mode Dynamic Light Scattering
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Study Protocol Type
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Size
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Study Protocol Type Term Accession Number
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Study Protocol Type Term Source REF
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NPO
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Study Protocol Description
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Hydrodynamic Size/Size Distribution via Dynamic Light Scattering (DLS)
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Study Protocol URI
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Study Protocol Version
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1.00
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Study Protocol Parameters Name
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pH of solution;NaCl concentration
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Study Protocol Parameters Name Term Accession Number
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Study Protocol Parameters Name Term Source REF
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NPO
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Study Protocol Components Name
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Malvern DLS
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Study Protocol Components Type
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Instrument
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Study Protocol Components Type Name Term Accession Number
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Study Protocol Components Type Name Term Source REF
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NPO
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.
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A
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B
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C
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STUDY CONTACTS
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Study Person Last Name
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patri
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Study Person First Name
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anil
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Study Person Mid Initials
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Study Person Email
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patria@mail.nih.gov
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Study Person Phone
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3018465237
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Study Person Fax
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Study Person Address
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MSC 1050 Boyles Street, Frederick, MD 21702
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Study Person Affiliation
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Nanotechnology Characterization Laboratory
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Study Person Roles
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investigator
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Study Person Roles Term Accession Number
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Study Person Roles Term Source REF
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MO
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.
| Wiki Markup |
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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. |
| Wiki Markup |
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Characteristics \[organism\] - Refers to the taxon of the biological sample. |
| Wiki Markup |
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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.
| Wiki Markup |
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Parameter Value \[\] - Concepts associated with a sample preparation protocol that are not varied in the experiment. Parameters concepts are variable and described in brackets. |
| Wiki Markup |
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Parameter Value \[medium\] - Refers to the substance in which the sample is transmitted. |
| Wiki Markup |
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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. |
| Wiki Markup |
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Factor Value \[nanomaterial\] -- The material identifier of the nanomaterial applied to the biospecimen. Often followed by Factor Value \[dose\]. |
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if the term is entered as a value in Source Name, Material Type, Characteristics [ ], 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 ISA-TAB-Nano study files. This name should match one of the names entered in the Term Source Name field in the ISA-TAB-Nano Investigation file.
Other study fields
Factor Value [<factor name>]---The value of an experimental variable manipulated by the investigator with the intention to affect the subject of study (such as stressor). Factor names are given in brackets, and must be defined in the ISA-TAB-Nano investigation file in the STUDY FACTORS section.
Comment [ ]---Any comment that provides additional information, which is added only when no other appropriate field 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:
