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This section is used to define the vocabulary source from which a term is selected and referenced in the nano-TAB files.  TABLE 3 shows an example of the ONTOLOGY SOURCE REFERENCE section along with example data. This section uses the four ISA-TAB concepts:

Term source name---The name of the source from where a term is selected and referenced in the nano-TAB 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 nano-TAB files.  This concept is taken from ISA-TAB. 

Term source file--- A file name or a URI of the source named in the term source name field.  This concept is taken from ISA-TAB.

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.   This concept is taken from ISA-TAB. 

Term source description---Text description to disambiguate resources when homologous acronyms are used.  This concept is taken from ISA-TAB.

Investigation

This section is used to describe an investigation. An example of the INVESTIGATION section is in TABLE 4 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.

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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.

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.

Study Publications

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

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

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

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

Study publication title---A concise phrase used as a title for the publication associated with the study. 

Study publication status---A term describing the status of a publication (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.   

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 unit---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.

Study factor unit term accession number---Identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value for study factor unit.  This concept is introduced in 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 unit term source REF---The name which identifies the source from where the term for study factor unit is selected.  This name should match one of the names entered in the term source name field. This concept is introduced in 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. 

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 Protocols

The STUDY PROTOCOLS section allows for the identification of the type of protocols, and the parameters and components of a protocol used in a study.  A protocol describes the formal plan of an experiment or research activity, including the objective, rationale, design, materials and methods for the conduct of the study; intervention description, and method of data analysis.  TABLE 13 shows an example of the STUDY PROTOCOLS section along with example data. There are 17 concepts in this section; 14 concepts are taken from ISA-TAB and the other three concepts are introduced in 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.

Study 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.

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 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 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 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.

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