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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 the following table shows a subset of the Investigation File, which is the study factors section of the investigation file. This section provides the names of factors (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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The ISA-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 1the following table. The fields are divided into sections. Therefore, the field values in the investigation file are entered in column order. For instance, in TABLE 1the following table, Column A indicates the field names and Columns B and C contain the field values.

TABLE 1 Example Subset of the Investigation File Format

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ISA-TAB-Nano Extensions--- ISA-TAB-Nano extends the ISA-TAB Investigation File specification by introducing new fields. All fields are defined below The following sections define all fields.

Ontology Source Reference

This section is used to record records information about ontologies containing the terms referenced in the ISA-TAB-Nano  files. TABLE 1 on the  The Investigation File Example page 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 of a term is selected and referenced used 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.

T erm Source File--- A file name or a URI of the source named in the term source name 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 Term Source File has a value.

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

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This section allows for the description of the investigation. An example of the INVESTIGATION section is in TABLE 2 on the Investigation File Example page. The INVESTIGATION section uses nine concepts and includes concepts from ISA-TAB and extensions made in support of ISA-TAB-Nano:

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Investigation Description---A textual description of the investigation.

Investigation Dubmission Submission Date---The date on which the investigation was reported to a repository (format: YYYY-MM-DD).

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Investigation Disease---Disease(s) that are the subject of an investigation, if applicable. This concept is introduced in ISA-TAB-Nano to introduced this concept to identify the disease(s) related to the subject of the investigation. (ISA-TAB Extension for ISA-TAB-Nano)

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 Investigation Disease. ISA-TAB-Nano to introduced this concept to identify the term accession number for the disease. (ISA-TAB Extension for ISA-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 Term Source Name field. This concept is introduced in ISA-TAB-Nano to introduced this concept to identify the term source ref for the disease. (ISA-TAB Extension for ISA-TAB-Nano)

Investigation Outcome---A textual description summarizing the conclusion of an investigation. This concept is introduced in ISA-TAB-Nano to introduced this concept to identify the outcome of the investigation. (ISA-TAB Extension for ISA-TAB-Nano)

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This section allows for the identification of articles (published) associated with the investigation. An example of the INVESTIGATION PUBLICATIONS section is in TABLE 3 on the Investigation File Example page. There are seven ISA-TAB concepts used in this section:

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Investigation Publication Status Term Accession Number---The identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value for investigation publication status Investigation Publication Status.

Investigation Publication Status Term Source REF---The name which identifies the source from where the term for investigation publication status Investigation Publication Status is selected. This name should match one of the names entered in the term source name Term Source Name field.

Investigation Contacts

This section allows for the identification of the point(s) of contact for the investigation. An example of the INVESTIGATION CONTACTS section is in TABLE 4 on the Investigation File Example pageExample page. There are 11 ISA-TAB concepts used as field names: An example of the INVESTIGATION CONTACTS section is in TABLE 4 on the Investigation File Example page. There are 11 ISA-TAB concepts used as field names:Investigation Person

Investigation Person Last Name---The last name of a person who is the point of contact for the investigation.

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Investigation Person Roles 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.

Investigation Person Roles 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 Investigation Person Role.

Material

This section allows for the identification of materials used in the investigation and associated studies.  There are 2 two concepts used in the MATERIAL section.  An  An example of the MATERIAL section is in TABLE 5 on the Investigation File Example page. The MATERIAL section is introduced in ISA-TAB-Nano introduced the MATERIAL section. These  These concepts are described below:

Material File Name---The name of the ISA-TAB-Nano Material File, which lists information about the composition and characteristics of the nanomaterials or other small molecules. There can be only one file per cell. This concept is introduced in ISA-TAB-Nano to introduced this concept to identify the name of the Material File. (ISA-TAB Extension for ISA-TAB-Nano) 

Material Source Name---The name of the nanomaterial or small molecule associated with the Material File. There can be only one Material Source Name per column. This concept is introduced in ISA-TAB-Nano to introduced this concept to identify source name of the material. (ISA-TAB Extension for ISA-TAB-Nano)

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This section allows for the description of one or more studies conducted as part of an investigation. An example of the STUDY section is in TABLE 6 on the Investigation File Example page. There are 11 concepts used in the STUDY section, seven of which are taken from ISA-TAB and four are introduced in were added by ISA-TAB-Nano. 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.

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

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 diseaseStudy Disease. (ISA-TAB Extension for ISA-TAB-Nano)

Study Disease Term Source REF---The name which identifies the source from where the term for study disease Study Disease is selected. This name should match one of the names entered in the term source name Term Source Name field. (ISA-TAB Extension for ISA-TAB-Nano)

Study Outcome---A textual description about the outcome(s) of the study. This concept is introduced in ISA-TAB-Nano to introduced this concept to provide a summary or conclusion of a study. (ISA-TAB Extension for ISA-TAB-Nano)

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This section allows for the identification of design type of the study. An example of the STUDY DESIGN DESCRIPTORS section is in TABLE 7 on the Investigation File Example page. There are 3 three 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 (for example, comparison study). The term can be free-text or taken from a controlled vocabulary/ontology.

Study Design 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 design type Study Design Type.

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

Study Publications

This section allows for the identification of articles (published) associated with the study. An example of the STUDY PUBLICATIONS section is in TABLE 8 on the Investigation File Example page. . This section uses seven ISA-TAB concepts.

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Study Publication Status Term Accession Number---The identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value for study publication status Study Publication Status.

Study Publication Status Term Source REF---The name which identifies the source from where the term for study publications status Study Publications Status is selected. This name should match one of the names entered in the term source name Term Source Name.

Study Factors

This section allows for the identification of factors associated with the study. An example of the STUDY FACTORS section is in TABLE 9 on the Investigation File Example page. This section has four concepts taken from ISA-TAB.

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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.

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

Study Assays

This 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. An example of the STUDY ASSAYS section is in TABLE 10 on the Investigation File Example page. The STUDY ASSAYS section has 11 concepts. Out of these, 8  eight concepts are taken from ISA-TAB. The remaining concepts are introduced in ISA-ISA-TAB-Nano introduced the remaining concepts.

Study Assay Measurement Type---A term to qualify the endpoint, or what is being measured.

Study Assay Measurement Type 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 assay measurement type Study Assay Measurement Type.

Study Assay Measurement Type Term Source REF---The name which identifies the source from where the term for study assay measurement type is Study Assay Measurement Type  is selected. This name should match one of the names entered in the term source name Term Source Name field.

Study Assay Technology Type---The type of technology (technique or method) used for the assay measurement (for example, Dynamic light scattering).

Study Assay Technology 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 assay technology type Study Assay Technology Type.

Study Assay Technology Type Term Source REF---The name which identifies the source from where the term for study assay technology type Study Assay Technology Type is selected. This name should match one of the names entered in the term source name Term Source Name field.

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

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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 Study Assay Measurement Name. (ISA-TAB Extension for ISA-TAB-Nano)

Study Assay Measurement Name Term Source REF--- The name which identifies the source from where the term for study assay measurement name Study Assay Measurement Name is selected. (ISA-TAB Extension for ISA-TAB-Nano)

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This 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. An example of the STUDY PROTOCOLS section is in TABLE 11 on the Investigation File Example page. There are 14 concepts in this section taken from ISA-TAB.

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Study Protocol 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 protocol type Study 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 study protocol type Study Protocol Type.

Study Protocol Description---A textual description of the protocol.

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Study Protocol Parameters 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 experimentan intrinsic experimental condition that may be varied or constant.

Study Protocol Parameters 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 the study protocol parameter name Study Protocol Parameter Name.

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

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

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Study Protocol Components Type Term Accession Number--- Identification number of a term seleced from an ontology or a controlled vocabulary, if the term is entered as a value for the study protocol component type Study Protocol Component Type.

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

Study Contacts

This section allows the identification of the point of contact for a study. An example of the STUDY CONTACTS section is in TABLE 12 on the Investigation File Example page. The STUDY CONTACTS section has 11 ISA-TAB concepts.

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Study Person Roles 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 person role Study Person Role.

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

Files

The Investigation File Examples, Template, and Glossary are listed here.following pages provide the investigation file examples, template, and glossary:

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