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{scrollbar:icons=false} h1. {page-info:title} {panel:title=Contents of this Page} {toc:minLevel=2} {panel} {panel:title=Additional Information} * [Investigation File Examples\|Investigation File Examples] * [Investigation File Template\|ISA-TAB-Nano^i_xxxx.xls] * [Investigation File Glossary\|ISA-TAB-Nano^InvestigationFileTermGlossary.xls] {panel} h2. 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. 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 (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. h2. File Format 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 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. TABLE1 Example Subset of the Investigation File Format \|\| A \|\| B \|\| C \|\| \| STUDY FACTORS \| n/a \\ \| n/a \\ \| \| Study Factor Name \| temperature \| solvent medium \| \| Study Factor Name Term Accession Number \| PATO_0000146 \| NPO_1855 \| \| Study Factor Name Term Source REF \| PATO \| NPO \| \| Study Factor Type \| condition \| condition \| \| Study Factor Type Term Accession Number \| none \\ \| none \\ \| \| Study Factor Type Term Source REF \| none \\ \| none \\ \| h2. Fields 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 CONTACTS * INVESTIGATION PUBLICATION * STUDY STUDY DESIGN DESCRIPTORS STUDY CONTACTS STUDY PUBLICATIONS STUDY ASSAYS STUDY FACTORS STUDY PROTOCOLS ISA-TAB-Nano Extensions--\- ISA-TAB-Nano extends the ISA-TAB Investigation File specification by introducing new fields, which are listed in [TABLE 2\|ICR:Investigation File Examples] on the Investigation File Example Page. All fields are defined below. h3. Ontology Source Reference 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\|ICR:Investigation File Examples] 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. _T{_}{_}erm 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. h3. Investigation This section is used to describe an investigation. An example of the INVESTIGATION section is in [TABLE 4\|ICR:Investigation File Examples] along with example data. The INVESTIGATION section uses nine concepts and the source is indicated in the definition below: _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 _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 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_ 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. h3. 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\|ICR:Investigation File Examples] 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_. h3. Investigation Publications The INVESTIGATION PUBLICATIONS section allows for the identification of articles (published) associated with the investigation. [TABLE 6 \|ICR:Investigation File Examples]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). _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. h3. Study The STUDY section allows for the description of one or more studies conducted as part of an investigation. [TABLE 7\|ICR:Investigation File Examples] 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. _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. h3. Study Design Descriptors The STUDY DESIGN DESCRIPTORS section allows for the identification of design type of the study. [TABLE 8\|ICR:Investigation File Examples] 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. _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. h3. 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 \|ICR:Investigation File Examples]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 middle 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 role_\--\- The term which classify the role(s) performed by person who is the point of contact for the study. _Study 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 _study person role_. _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. h3. Study Publications The STUDY PUBLICATIONS section allows for the identification of articles (published) associated with the study. [TABLE 10\|ICR:Investigation File Examples] 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_. h3. 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 \|ICR:Investigation File Examples]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. _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 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 (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. _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. _Study technology platform_\---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. h3. Study Factors The STUDY FACTORS section allows for the identification of factors associated with the study. [TABLE 12\|ICR:Investigation File Examples] 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. _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. h3. _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\|ICR:Investigation File Examples] 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_\---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. _Study protocol parameter 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 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, for example, instrument, software, and reagent. _Study protocol component type term accession_ number--\- Identification number of a term select[ISA-TAB-Nano^InvestigationFileTermGlossary.xls]ed 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 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. * [Investigation File Examples\|Investigation File Examples] * [Investigation File Template\|ISA-TAB-Nano^i_xxxx.xls] * [Investigation File Glossary\|ISA-TAB-Nano^InvestigationFileTermGlossary.xls]

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h1. {page-info:title}
{panel:title=Contents of this Page}
{toc:minLevel=2}
{panel}
{panel:title=Additional Information}
* [Investigation File Examples|Investigation File Examples]
* [Investigation File Template|ISA-TAB-Nano^i_xxxx.xls]
* [Investigation File Glossary|ISA-TAB-Nano^InvestigationFileTermGlossary.xls]
{panel}

h2. 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.

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 (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.

h2. File Format

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 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.

TABLE1 Example Subset of the Investigation File Format
|| A || B || C ||
| STUDY FACTORS | n/a \\ | n/a \\ |
| Study Factor Name | temperature | solvent medium |
| Study Factor Name Term Accession Number | PATO_0000146 | NPO_1855 |
| Study Factor Name Term Source REF | PATO | NPO |
| Study Factor Type | condition | condition |
| Study Factor Type Term Accession Number | none \\ | none \\ |
| Study Factor Type Term Source REF | none \\ | none \\ |

h2. Fields

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 CONTACTS
* INVESTIGATION PUBLICATION
* STUDY
** STUDY DESIGN DESCRIPTORS
** STUDY CONTACTS
** STUDY PUBLICATIONS
** STUDY ASSAYS
** STUDY FACTORS
** STUDY PROTOCOLS

ISA-TAB-Nano Extensions--\- ISA-TAB-Nano extends the ISA-TAB Investigation File specification by introducing new fields, which are listed in [TABLE 2|ICR:Investigation File Examples] on the Investigation File Example Page. All fields are defined below.

h3. Ontology Source Reference

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|ICR:Investigation File Examples] 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.

_T{_}{_}erm 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.

h3. Investigation

This section is used to describe an investigation. An example of the INVESTIGATION section is in [TABLE 4|ICR:Investigation File Examples] along with example data. The INVESTIGATION section uses nine concepts and the source is indicated in the definition below:

_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

_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 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_ 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.

h3. 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|ICR:Investigation File Examples] 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_.

h3. Investigation Publications

The INVESTIGATION PUBLICATIONS section allows for the identification of articles (published) associated with the investigation. [TABLE 6 |ICR:Investigation File Examples]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).

_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.

h3. Study

The STUDY section allows for the description of one or more studies conducted as part of an investigation. [TABLE 7|ICR:Investigation File Examples] 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.

_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.

h3. Study Design Descriptors

The STUDY DESIGN DESCRIPTORS section allows for the identification of design type of the study. [TABLE 8|ICR:Investigation File Examples] 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.

_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.

h3. 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 |ICR:Investigation File Examples]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 middle 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 role_\--\- The term which classify the role(s) performed by person who is the point of contact for the study.

_Study 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 _study person role_.

_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.

h3. Study Publications

The STUDY PUBLICATIONS section allows for the identification of articles (published) associated with the study. [TABLE 10|ICR:Investigation File Examples] 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_.

h3. 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 |ICR:Investigation File Examples]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.

_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 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 (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.

_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.

_Study technology platform_\---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.

h3. Study Factors

The STUDY FACTORS section allows for the identification of factors associated with the study. [TABLE 12|ICR:Investigation File Examples] 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.

_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.

h3. _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|ICR:Investigation File Examples] 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_\---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.

_Study protocol parameter 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 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, for example, instrument, software, and reagent.

_Study protocol component type term accession_ number--\- Identification number of a term select[ISA-TAB-Nano^InvestigationFileTermGlossary.xls]ed 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 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.

* [Investigation File Examples|Investigation File Examples]
* [Investigation File Template|ISA-TAB-Nano^i_xxxx.xls]
* [Investigation File Glossary|ISA-TAB-Nano^InvestigationFileTermGlossary.xls]

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