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Description

(1) The nanoISA-TAB-Nano investigation file leverages the ISA-TAB investigation file, and it allows for the description of the primary investigation and associated studies including assays and protocols.   An investigation can have one or more studies.   For example, an investigation titled “Dendrimer-Based MRI Contrast Agents” may have two studies titled as “Characterizing the Size of Dendrimer based MRI Contrast Agents” and “Determining the cytotoxicity property of  of Dendrimer based MRI Contrast Agents in porcine proximal tubule cells” Each study can have one or more assays depending on the endpoint measured and the technique used.   For example, a cytoxicity study may be conducted using an MTT assay and a LDH release assay.   While a size characterization study can include two types of assays based on the technique used – one using DLS and the other using AFM.

(2) The ISA-TAB specification provides flexibility in representing the level of granularity in information associated with a study; however, the level of granularity should factor in the effective representation of assays and protocols in conformance with the specification.   For example, a study focusing on “Size Characterizations” will have multiple size measurements (for example, Z-average size, hydrodynamic size) and may involve the use of multiple techniques (for example, size by DLS, size by AFM).   These can be represented effectively in the ISA-TAB file structure that nanoISA-TAB-Nano uses. 

(3) The investigation file provides descriptive information about studies including design descriptors, publications, factors, assays, protocols, and contacts.   This descriptive information lays the foundation for other nanoISA-TAB-Nano files.   For example, TABLE 1 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 (e.g.for example, temperature, solvent medium) used in the study and their associated units of measurement (if the factors are quantitative).   The values of these factors (for example, PBS, 25 Celsius) are specified either in the study or the assay file.

File Format

The nanoISA-TAB-Nano investigation file leverages the ISA-TAB file format, which is a vertical-based spreadsheet format with row headers in the first column, as shown in TABLE 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

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

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 PUBLICATIONS
• INVESTIGATION CONTACTS
• MATERIAL
• STUDY
  • STUDY DESIGN DESCRIPTORS
  • STUDY PUBLICATIONS
  • STUDY FACTORS
  • STUDY ASSAYS
  • STUDY PROTOCOLS
  • STUDY CONTACTS

ISA-TAB-Nano Extensions--- ISA-TAB-Nano Nano-TAB Extensions--- Nano-TAB 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 nanoISA-TAB-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 nanoISA-TAB-Nano files.   The source could be an ontology or a controlled vocabulary. The source name is the full name or the acronym of the ontology/controlled vocabulary. This is a required field if the term source name is referenced in any of the nanoISA-TAB-Nano files. 

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 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 below:includes concepts from ISA-TAB and extensions made in support of ISA-TAB-Nano:

Investigation IdentifierInvestigation identifier--- 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 diseaseSubmission 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 Disease---Disease(s) that are the subject of an investigation, if applicable. ISA-TAB-Nano introduced this concept to Disease(s) that are the subject of an investigation, if applicable.  This concept is introduced in nano-TAB 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 nano-TAB. 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 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 nano-TAB. 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 OutcomeInvestigation outcome---A textual description of the outcome(s) of description summarizing the conclusion of an investigation.   This concept is introduced in nano-TAB 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 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.

ISA-TAB-Nano 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 Investigation person fax---The fax number of a person who is the point of contact for the investigation. 

Investigation person addressPerson First Name---The mailing address first name of a person who is the point of contact for the investigation. 

Investigation person affiliationPerson Mid Initials---The name of the organization to which the middle initial(s) of a person who is the point of contact belongsfor the investigation. 

Investigation person rolePerson Email---The term which classifies the role(s) performed by email address of a person who is the point of contact for the investigation.

Investigation person role term accession numberPerson Phone--- Identification The telephone 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.

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 (i.e., 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.

Study

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 nano-TAB 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 nano-TAB 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 nano-TAB

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 nano-TAB.

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

Study file name---The name of the nano-TAB 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 nano-TAB 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 (e.g. 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 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 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.

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 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.

Material

This section allows for the 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:

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. 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 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. (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 is selected. This name should match one of the names entered in the 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 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 Publication Status.

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

Study

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Factors

This section The STUDY PUBLICATIONS section allows for the identification of articles (published) factors associated with the study. TABLE 10 shows an An example of the STUDY PUBLICATIONS section along with example dataFACTORS section is in the Investigation File Example page. This section uses seven has four concepts taken from ISA-TAB concepts.

Study pubmed IDFactor Name---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 (i.e., 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 nano-TAB. 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 (e.g., 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 nano-TAB 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 nano-TAB.

Study assay measurement name term source REF--- The name which identifies the source from where the term for study assay measurement name is selected. This concept is taken from ISA-TAB.

Study assay measurement unit--- The standard of measurement used to express the value of a dimensional quantity obtained from the assay.  This concept is introduced in nano-TAB to identify the unit associated with a measurement.

Study assay measurement unit term accession number--- Identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value for study measurement unit.  This concept is introduced in nano-TAB to identify the source from where the unit of a measurement is selected and referenced in the study or assay files.

Study assay measurement unit term source REF--- The name which identifies the source from where the term for study assay measurement unit is selected.  This concept is introduced in nano-TAB to identify the source from where the unit of a measurement is selected and referenced in the study or assay files.

Study assay measurement statistic--- The types of statistical measures reported in the assay data (e.g., mean, standard deviation, etc.).  This concept is introduced in nano-TAB.

Study assay measurement statistic term accession number--- Identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value for study assay measurement statistic.  This concept is introduced in nano-TAB.

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

Study assay file name--- Name of the nano-TAB 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 3 concepts are introduced in nano-TAB and are indicated in the definitions below:

Study factor name---The name of one independent variable (factor) manipulated by the experimentalist with the intention to affect the subject of study (i.e. 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.   

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 or a controlled vocabulary, if the term is entered as a value for Study Factor Type.

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

Study 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 NumberStudy 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 Assay Measurement Type.

Study factor name term source Assay Measurement Type Term Source REF---The name which identifies the source from where the term for study factor name 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 factor unitAssay Technology Type---The standard of measurement used to express the value of a quantitative and dimensional factor.  This concept is introduced in nano-TAB to identify the unit of every quantitative factor.type of technology (technique or method) used for the assay measurement (for example, Dynamic light scattering).

Study Assay Technology Type Term Accession NumberStudy factor unit term accession number---Identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value for study factor unit.  This concept is introduced in nano-TAB to identify the source from where the unit  of a factor is selected and referenced in the study or assay files. Study Assay Technology Type.

Study Assay Technology Type Term Source Study factor unit term source REF---The name which identifies the source from where the term for study factor unit Study Assay Technology Type is selected.   This name should match one of the names entered in the term source name field. This concept is introduced in nano-TAB to identify the source from where the unit of a factor is selected and referenced in the study or assay files.

Study factor type---A term used for the classification of factors associated with the study (e.g. 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. 

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

Study Assay Measurement Name 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

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 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 nano-TAB (indicated in the defintion).

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

Study protocol type---The term used to classify the protocol (e.g., 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 nano-TAB, 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 nano-TAB files.

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

, 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 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 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 NameStudy protocol parameter name--- A semicolon-delimited (";") list of parameter names used as an identifier in the nano-TAB Study or Assay files.  A protocol parameter is a constant associated with a protocol, which is not varied as part of an experiment.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 NumberStudy protocol parameter name term accession number--- Identification number of a term selected seleced from an ontology or a controlled vocabulary, if the term is entered as a value for the study protocol parameter name Study Protocol Component Type.

Study protocol parameter name term source Protocol Components Type 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 parameter unit--- The standard of measurement used to express the value of a quantitative and dimensional parameter.  This concept is introduced in nano-TAB to identify the unit of a parameter.

Study protocol parameter unit term accession number--- Identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value study protocol parameter unit.  This concept is introduced in nano-TAB to identify the source from where the unit of a parameter is selected and referenced in the study or assay files.

Study protocol parameter unit term source REF--- The name which identifies the source from where the term for study protocol parameter unit is selected. This concept is introduced in nano-TAB to identify the source from where the unit of a parameter is selected and referenced in the study or assay files.

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

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

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 component 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 the study protocol component type Study Person Role.

Study protocol component 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 Example
• Investigation File Template
• Investigation File Glossary