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The ISA-TAB-Nano 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  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.

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 ISA-TAB-Nano uses. 

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 ISA-TAB-Nano 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.for example, 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.

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TABLE1 Example Subset of the Investigation File Format

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

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This section is used to define the vocabulary source from which a term is selected and referenced in the ISA-TAB-Nano files.   TABLE 3 shows an example of the ONTOLOGY SOURCE REFERENCE section along with example data. This section uses four ISA-TAB concepts:

Term source name---The name of the source from where a term is selected and referenced in the ISA-TAB-Nano 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 ISA-TAB-Nano files. 

Term source file--- A file name or a URI of the source named in the term source name field. 

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.  

Term source description---Text description to disambiguate resources when homologous acronyms are used.

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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 ISA-TAB-Nano to identify the disease(s) related to the subject of the investigation

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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 ISA-TAB-Nano.

Investigation outcome---A textual description of the outcome(s) of an investigation.   This concept is introduced in ISA-TAB-Nano 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.

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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 5 along with example data. There are 11 ISA-TAB concepts used as field names:

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.

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

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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.

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The STUDY section allows for the description of one or more studies conducted as part of an investigation. TABLE 7 shows an example of the STUDY section along with example data. There are 11 concepts used in the STUDY section, seven of which are taken from ISA-TAB and four are introduced in ISA-TAB-Nano and are indicated as such in the definition.   These concepts are described below:

Study identifier---A unique identifier used for the study.   It is either a temporary identifier supplied by users or one generated by a repository or other database. 

Study title---A concise phrase used to encapsulate the purpose and goal of the study.

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Study public release date---The date on which the study is publicly released or published (format: YYYY-MM-DD). 

Study description---A textual description of the study, with components such as objectives or goals.

Study disease---Disease(s) that are the subject of the study, if applicable.   This concept is introduced in ISA-TAB-Nano to identify the disease(s) related to the study.

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

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Study file name---The name of the ISA-TAB-Nano study file, which lists information about the biological specimens (cells, tissues, organs, animal model, body fluids), nanoparticles  small ;small organic molecules, and other types of samples assayed in a study.   There can be only one file name per cell.

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The STUDY DESIGN DESCRIPTORS section allows for the identification of design type of the study. TABLE 8 shows an example of the STUDY DESIGN DESCRIPTORS section along with example data. There are 3 concepts used in the STUDY DESCRIPTORS section.   These concepts are taken from ISA-TAB. 

Study design type---A term describing the classification of the study based on the overall study (experimental) design (e.g. for example, comparison study).   The term can be free-text or taken from a controlled vocabulary/ontology.

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Study design type term source REF---The name which identifies the source from where the term for study design type is selected.   This name should match one of the names entered in the term source name field.

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The STUDY CONTACTS section allows the identification of the point of contact for a study.   An example of the STUDY CONTACTS section is shown in TABLE 9 along with example data. The STUDY CONTACTS section has 11 ISA-TAB concepts. 

Study person last name---The last name of a person who is the point of contact for the study.

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Study person role term source REF--- The name which identifies the source from where the term for study person role is selected.   This name should match one of the names entered in the term source name field.

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Study publication title---A concise phrase used as a title for the publication associated with the study. 

Study publication status---A term describing the status of a publication (i.e.that is, submitted, in preparation, published), associated with the study.

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

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The STUDY ASSAYS section allows for the identification of type of measurement and the type of technology used for the measurement in an assay that is part of a study.   TABLE 11 shows an example of the STUDY ASSAYS section along with example data. The STUDY ASSAYS section has 17 concepts.   Out of these, 8 concepts are taken from ISA-TAB. The remaining concepts are introduced in ISA-TAB-Nano. The source is indicated in the definition below

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Study assay measurement type term source REF---The name which identifies the source from where the term for study assay measurement type is selected.   This name should match one of the names entered in the term source name field. This concept is taken from ISA-TAB.

Study assay technology type---The type of technology (technique or method) used for the assay measurement (e.g.for example, Dynamic light scattering). This concept is taken from ISA-TAB.

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Study assay technology type term source REF---The name which identifies the source from where the term for study assay technology type is selected.   This name should match one of the names entered in the term source name field. This concept is taken from ISA-TAB.

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Study assay measurement name---A semicolon-delimited list of names of quantities whose values are the outputs of an assay measurement.   This concept is introduced in ISA-TAB-Nano to define the variables measured as output of an assay.

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Study assay file name--- Name of the ISA-TAB-Nano Assay file corresponding to the study assay.   This is a required field. There can be only one assay file name per cell. This concept is taken from ISA-TAB.

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The STUDY FACTORS section allows for the identification of factors associated with the study.   TABLE 12 shows an example of the STUDY FACTORS section along with example data. This section has nine concepts.   Out of these, 6 concepts are taken from ISA-TAB. The other 3 three concepts are introduced in ISA-TAB-Nano and are indicated in the definitions below:

Study factor name---The name of one independent variable (factor) manipulated by the experimentalist with the intention to affect the subject of study (i.e. that is, Stressor).   This is a required field, if there are factors in an assay study. Only one factor name is allowed per cell.   The value of a factor is given either in the study or in the assay file.   

Study factor name term accession number---Identification number of the term selected from an ontology or a controlled vocabulary, if the term is entered as a value for study factor name.

Study factor name term source REF---The name which identifies the source from where the term for study factor name is selected.    This name should match one of the names entered in the term source name field.

Study factor type---A term used for the classification of factors associated with the study (e.g. for example, condition). This is a required field if there are factors in an assay study. More than one term is allowed per cell; multiple terms are separated by semicolons. 

Study factor type 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 study factor type.

Study factor type term source REF---The name which identifies the source from where the term for study factor type is selected.   This name should match one of the names entered in the term source name field. 

Study Protocols

The STUDY PROTOCOLS section allows for the identification of the type of protocols, and the parameters and components of a protocol used in a study.   A protocol describes 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.   TABLE 13 shows an example of the STUDY PROTOCOLS section along with example data. There are 17 concepts in this section; 14 concepts are taken from ISA-TAB and the other three concepts are introduced in ISA-TAB-Nano (indicated in the defintion).

Study protocol name---The name of the protocols used within a study and will be referenced in the ISA-TAB-Nano Study or Assay files. 

Study protocol type---The term used to classify the protocol (e.g.for example, synthesis, assay, etc.).

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Study protocol URI---Pointer to protocol documents or resources external to ISA-TAB-Nano, which can be accessed by their Uniform Resource Identifier (URI).   If URI is not available, enter the protocol document file name and make the protocol document available along with ISA-TAB-Nano files.

Study protocol version---A semicolon-delimited (";") list of parameter names used as an identifier in the ISA-TAB-Nano Study or Assay files .  A protocol parameter is a constant associated with a protocol, which is not varied as part of an experiment.

Study protocol parameter name---A semicolon-delimited (";") list of parameter names used as an identifier in the ISA-TAB-Nano Study or Assay files.   A protocol parameter is a constant associated with a protocol, which is not varied as part of an experiment.

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Study protocol parameter name term source REF---The name which identifies the source from where the term for study protocol parameter name.   This name should match one of the names entered in the term source name field.

Study protocol component name--- A semicolon-delimited (";") list of names identifying the components of a protocol.   Component names include instrument names, software names, and reagent names.

Study protocol component type--- The term to classify the protocol component, e.g.for example, instrument, software, and reagent.

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Study protocol component type term source REF--- The name which identifies the source from where the term for study protocol component type is selected.   This name should match one of the names entered in the term source name field.

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