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Description

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 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.

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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.

TABLE1 Example Subset of the Investigation File Format

Fields

Fields

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

• ONTOLOGY SOURCE REFERENCE
• INVESTIGATION
• INVESTIGATION PUBLICATIONS
• INVESTIGATION CONTACTSINVESTIGATION PUBLICATION
• MATERIAL
• STUDY
  • STUDY DESIGN DESCRIPTORS
  • STUDY CONTACTSPUBLICATIONS
  • STUDY PUBLICATIONSFACTORS
  • STUDY ASSAYS
  • STUDY FACTORSPROTOCOLS
  • STUDY PROTOCOLSCONTACTS

ISA-TAB-Nano Extensions--- ISA-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. The following sections define all fields.

Ontology Source Reference

This section is used to define the vocabulary source from which a term is selected and records information about ontologies containing the terms referenced in the ISA-TAB-Nano Nano  files. TABLE 3 shows  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 nameSource 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 fileSource File--- A file name or a URI of the source named in the term source name Term Source Name field.

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

Investigation

This section is used to describe an allows for the description of the investigation. An  An example of the INVESTIGATION section is in TABLE 4 along with example datathe Investigation File Example page. The INVESTIGATION section uses nine concepts and the source is indicated in the definition belowincludes concepts from ISA-TAB and extensions made in support of ISA-TAB-Nano:

Investigation identifierIdentifier--- A locally unique identifier or an accession number provided by a repository. This concept is taken from ISA-TAB.

Investigation titleTitle---A concise phrase used as a title for the investigation. This concept is adapted from ISA-TAB.

Investigation descriptionDescription---A textual description of the investigation. This concept is taken from ISA-TAB.

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

Investigation Public Release Date---The date on which the investigation is publicly released or published (format: YYYY-MM-DD).

Investigation DiseaseInvestigation 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 NumberInvestigation 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 for Investigation Disease. ISA-TAB-Nano introduced this concept to identify the term accession number for the disease. (ISA-TAB Extension for ISA-TAB-Nano.)

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

Investigation outcomeOutcome---A textual description of the outcome(s) of description summarizing the conclusion 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.

Investigation Contacts

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 mid 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.

introduced this concept to identify the outcome of the investigation. (ISA-TAB Extension for ISA-TAB-Nano)

Investigation Publications

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

Investigation Pubmed ID---PubMed identifier of the publication associated with the investigation.

Investigation Publication DOI---A Digital Object Identifier (DOI) of the publication associated with the investigation.

Investigation Publication Author List---A semicolon-delimited (";") list of authors of a publication associated with the investigation.

Investigation Publication Title---A concise phrase used as a title for the publication associated with the investigation.

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

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 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.

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 the Investigation File Example page. There are 11 ISA-TAB concepts used as field names:

Investigation Person Last Name---The last name of a Investigation person roles--- The term which classifies the role(s) performed by person who is the point of contact for the investigation.

Investigation person roles term accession numberPerson First Name--- 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 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 Publications

The INVESTIGATION PUBLICATIONS section allows for the identification of articles (published) associated with the investigation. TABLE 6 shows an example of the INVESTIGATION PUBLICATIONS section along with example data. There are seven ISA-TAB concepts used in this section:

Investigation pubmed ID---PubMed identifier of the publication associated with the investigation.

Investigation publication DOI---A Digital Object Identifier (DOI) of the publication associated with the investigation.

Investigation publication author list---A semicolon-delimited (";") list of authors of a publication associated with the investigation.

Investigation publication title---A concise phrase used as a title for the publication associated with the investigation.

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

The first name of a person who is the point of contact for the investigation.

Investigation Person Mid 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 Roles--- The term which classifies the role(s) performed by person who is the point of contact for the investigation.

Investigation Person Roles Term Accession Number--- Identification 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 Person Role.

Investigation publication status term source Person Roles 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.

Study

Name of the ontology or controlled vocabulary from which a term is selected and entered as a value for Investigation Person Role.

Material

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

Study identifierMaterial File Name---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.

Study submission date---The date on which the study is submitted to an archive (format: YYYY-MM-DD).

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.

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 ISA-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 ISA-TAB-Nano.

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

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 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 ISA-TAB-Nano study file.

Study Design Descriptors

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 (for example, comparison study). The term can be free-text or taken from a controlled vocabulary/ontology.

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. ISA-TAB-Nano 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. ISA-TAB-Nano introduced this concept to identify source name of the material. (ISA-TAB Extension for ISA-TAB-Nano)

Study

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 the Investigation File Example page. There are 11 concepts used in the STUDY section, seven of which are from ISA-TAB and four were added by ISA-TAB-Nano. 

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.

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

Study Submission Date---The date on which the study is submitted to an archive (format: YYYY-MM-DD).

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

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

Study Disease Term Accession NumberStudy 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 Disease. (ISA-TAB Extension for ISA-TAB-Nano)

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

Study Contacts

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.

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

Study person mid initials---The middle initial(s) of a person who is the point of contact for the study.

Study person email---The email address of a person who is the point of contact for the study.

Study person phone---The telephone number of a person who is the point of contact for the study.

Study person fax--- The fax number of a person who is the point of contact for the study

Study person address--- The mailing number of a person who is the point of contact for the study

Study person affiliation--- The name of the organization to which the point of contact belongs.

Study person roles--- The term which classifies the role(s) performed by person who is the point of contact for the study.

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 roles 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.

Study Publications

The STUDY PUBLICATIONS section allows for the identification of articles (published) associated with the study. TABLE 10 shows an example of the STUDY PUBLICATIONS section along with example data. This section uses seven ISA-TAB concepts.

Study pubmed ID---PubMed identifier of the publication associated with the study.

Study publication DOI---A Digital Object Identifier (DOI) of the publication associated with the study.

Study publication author list---A semicolon-delimited (";") list of authors of a publication associated with the study.

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 (that is, submitted, in preparation, published), associated with the study.

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 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.

Study Assays

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

Study assay measurement type---A term to qualify the endpoint, or what is being measured. This concept is taken from ISA-TAB.

Term Source Name field. (ISA-TAB Extension for ISA-TAB-Nano)

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

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 organic molecules, and other types of samples assayed in a study. There can be only one file name per cell.

Study Design Descriptors

This section allows for the identification of design type of the study. An example of the STUDY DESIGN DESCRIPTORS section is in the Investigation File Example page. There are three concepts used in the STUDY DESCRIPTORS section. These concepts are 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 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.

Study Publications

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

Study Pubmed ID---PubMed identifier of the publication associated with the study.

Study Publication DOI---A Digital Object Identifier (DOI) of the publication associated with the study.

Study Publication Author List---A semicolon-delimited (";") list of authors of a publication associated with the study.

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 (that is, submitted, in preparation, published), associated with the study.

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 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.

Study Factors

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

Study Factor Name---The name of one independent variable (factor) manipulated by the experimentalist with the intention to affect the subject of study (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 Type---A term used for the classification of factors associated with the study (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 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. This concept is taken from ISA-TAB Study Factor Type.

Study assay measurement type term source Factor Type Term Source REF---The name which identifies the source from where the term for study assay measurement type is Study Factor 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 (for example, Dynamic light scattering). This concept is taken from ISA-TAB.

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. This concept is taken from ISA-TAB.

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 the Investigation File Example page. The STUDY ASSAYS section has 11 concepts. Out of these, eight concepts are from ISA-TAB. 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 Term Source REF---The name which identifies the source from where the term for Study Assay Measurement Type  is selected. This 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 Term Source Name field.

Study technology platformAssay Technology Type---The manufacturer and platform name of the instruments used in the study assay. This concept is taken from ISA-TAB.

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.

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 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 is selected. This concept is taken from ISA-TAB.

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.

Study Factors

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 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 (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 (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.

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 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.

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

Study Assay Measurement Name---A semicolon-delimited list of names of quantities whose values are the outputs of an assay measurement. (ISA-TAB Extension for ISA-TAB-Nano)

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. (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 is selected. (ISA-TAB Extension for ISA-TAB-Nano)

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.

Study Protocols

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 the Investigation File Example page. There are 14 concepts in this section taken from ISA-TAB.

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 (for example, synthesis, assay, etc.).

Study Protocol Type Term Accession Number--- Identification number of a term selected from 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 Protocol Type

Study Protocol Type Term Source 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 (for example, synthesis, assay, etc.).

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 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 description---A textual description of the protocol.

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---An identifier for the version to ensure protocol tracking.

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 experiment.

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 parameters 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 components 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 components type--- The term to classify the protocol component, for example, instrument, software, and reagent.

Name of the ontology or controlled vocabulary from which a term is selected and entered as a value for Study Protocol Type.

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

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---An identifier for the version to ensure protocol tracking.

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 an 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 Parameters 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 Components 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 Components Type--- The term to classify the protocol component, for example, instrument, software, and reagent.

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 Components 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.

Study Contacts

This section allows the identification of the point of contact for a study. An example of the STUDY CONTACTS section is in the Investigation File Example page. 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.

Study Person First Name---The first name of a person who is the point of contact for the study.

Study Person Mid Initials---The middle initial(s) of a person who is the point of contact for the study.

Study Person Email---The email address of a person who is the point of contact for the study.

Study Person Phone---The telephone number of a person who is the point of contact for the study.

Study Person Fax--- The fax number of a person who is the point of contact for the study

Study Person address--- The mailing number of a person who is the point of contact for the study

Study Person Affiliation--- The name of the organization to which the point of contact belongs.

Study Person Roles--- The term which classifies the role(s) performed by person who is the point of contact for the study.

Study Person Roles Term Accession NumberStudy protocol components type term accession number--- Identification number of a term seleced selected from an ontology or a controlled vocabulary, if the term is entered as a value for the study protocol component type Study Person Role.

Study protocol components type term source Person Roles Term Source REF--- The name which identifies the source from where the term for study protocol component type 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 following pages provide the investigation file examples, template, and glossary:

• Investigation File ExamplesExample
• Investigation File Template
• Investigation File Glossary