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Description
(1) The nanoISA-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 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.
(2) 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 nanoISA-TAB-Nano uses.
(3) 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 nanoISA-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., 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.
File Format
The nanoISA-TAB-Nano investigation file leverages the ISA-TAB file format, which is a vertical-based spreadsheet format with row headers in the first column, as shown in TABLE 1. The fields are divided into sections. Therefore, the field values in the investigation file are entered in column order. For instance, in TABLE 1, Column A indicates the field names and Columns B and C contain the field values.
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- ONTOLOGY SOURCE REFERENCE
- INVESTIGATION
- INVESTIGATION CONTACTS
- INVESTIGATION PUBLICATION
- STUDY
- STUDY DESIGN DESCRIPTORS
- STUDY CONTACTS
- STUDY PUBLICATIONS
- STUDY ASSAYS
- STUDY FACTORS
- STUDY PROTOCOLS
NanoISA-TAB-Nano Extensions--- NanoISA-TAB-Nano extends the ISA-TAB Investigation File specification by introducing new fields, which are listed in TABLE 2 on the Investigation File Example Page. All fields are defined below.
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This section is used to define the vocabulary source from which a term is selected and referenced in the nanoISA-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 nanoISA-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 nanoISA-TAB-Nano files.
Term source file--- A file name or a URI of the source named in the term source name field.
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Investigation disease---Disease(s) that are the subject of an investigation, if applicable. This concept is introduced in nanoISA-TAB-Nano to identify the disease(s) related to the subject of the investigation
Investigation disease 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 disease. This concept is introduced in nanoISA-TAB-Nano.
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 nanoISA-TAB-Nano.
Investigation outcome---A textual description of the outcome(s) of an investigation. This concept is introduced in nanoISA-TAB-Nano to provide a brief summary or conclusion of an investigation
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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 nanoISA-TAB-Nano and are indicated as such in the definition. These concepts are described below:
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Study disease---Disease(s) that are the subject of the study, if applicable. This concept is introduced in nanoISA-TAB-Nano to identify the disease(s) related to the study.
Study disease 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 disease. This concept is introduced in nanoISA-TAB-Nano
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 is introduced in nanoISA-TAB-Nano.
Study outcome---A textual description about the outcome(s) of the study. This concept is introduced in nanoISA-TAB-Nano to provide a summary or conclusion of a study.
Study file name---The name of the nanoISA-TAB-Nano study file, which lists information about the biological specimens (cells, tissues, organs, animal model, body fluids), nanoparticles small organic molecules, and other types of samples assayed in a study. There can be only one file name per cell.
Study file description---A textual description which provides additional information on the nanoISA-TAB-Nano study file.
Study Design Descriptors
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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 nanoISA-TAB-Nano. The source is indicated in the definition below
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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 nanoISA-TAB-Nano to define the variables measured as output of an assay.
Study assay measurement name 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 assay measurement name. . This concept is introduced in nanoISA-TAB-Nano.
Study assay measurement name term source REF--- The name which identifies the source from where the term for study assay measurement name is selected. This concept is taken from ISA-TAB.
Study assay measurement unit--- The standard of measurement used to express the value of a dimensional quantity obtained from the assay. This concept is introduced in nanoISA-TAB-Nano to identify the unit associated with a measurement.
Study assay measurement unit 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 measurement unit. This concept is introduced in nanoISA-TAB-Nano to identify the source from where the unit of a measurement is selected and referenced in the study or assay files.
Study assay measurement unit term source REF--- The name which identifies the source from where the term for study assay measurement unit is selected. This concept is introduced in nanoISA-TAB-Nano to identify the source from where the unit of a measurement is selected and referenced in the study or assay files.
Study assay measurement statistic--- The types of statistical measures reported in the assay data (e.g., mean, standard deviation, etc.). This concept is introduced in nanoISA-TAB-Nano.
Study assay measurement statistic 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 assay measurement statistic. This concept is introduced in nanoISA-TAB-Nano.
Study assay measurement statistic term source REF--- The name which identifies the source from where the term for study assay measurement statistic 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 file name--- Name of the nanoISA-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 concepts are introduced in nanoISA-TAB-Nano and are indicated in the definitions below:
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Study factor unit---The standard of measurement used to express the value of a quantitative and dimensional factor. This concept is introduced in nanoISA-TAB-Nano to identify the unit of every quantitative factor.
Study factor unit 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 unit. This concept is introduced in nanoISA-TAB-Nano to identify the source from where the unit of a factor is selected and referenced in the study or assay files.
Study factor unit term source REF---The name which identifies the source from where the term for study factor unit is selected. This name should match one of the names entered in the term source name field. This concept is introduced in nanoISA-TAB-Nano to identify the source from where the unit of a factor is selected and referenced in the study or assay files.
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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 nanoISA-TAB-Nano (indicated in the defintion).
Study protocol name---The name of the protocols used within a study and will be referenced in the nanoISA-TAB-Nano Study or Assay files.
Study protocol type---The term used to classify the protocol (e.g., synthesis, assay, etc.).
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Study protocol URI---Pointer to protocol documents or resources external to nanoISA-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 nanoISA-TAB-Nano files.
Study protocol version---A semicolon-delimited (";") list of parameter names used as an identifier in the nanoISA-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 nanoISA-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 unit--- The standard of measurement used to express the value of a quantitative and dimensional parameter. This concept is introduced in nanoISA-TAB-Nano to identify the unit of a parameter.
Study protocol parameter unit term accession number--- Identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value study protocol parameter unit. This concept is introduced in nanoISA-TAB-Nano to identify the source from where the unit of a parameter is selected and referenced in the study or assay files.
Study protocol parameter unit term source REF--- The name which identifies the source from where the term for study protocol parameter unit is selected. This concept is introduced in nanoISA-TAB-Nano to identify the source from where the unit of a parameter is selected and referenced in the study or assay files.
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