Page History

...

TABLE1 Example Subset of the Investigation File Format

...

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

The STUDY section allows MATERIAL 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 identification of materials used in the investigation and associated studies.  There are 2 concepts used in the STUDY section, seven of which are taken from ISA-TAB and four are introduced in ISA-TAB-MATERIAL section. The MATERIAL section is introduced in ISA-TAB-Nano. These concepts are described below:

Study identifierMaterial File Name---A unique identifier used for the study. It is either a temporary identifier supplied by users or one generated by a repository or other database.

Study title---A concise phrase used to encapsulate the purpose and goal of the study.

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

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

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

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.

Material Source Name---A name of the nanomaterial or small molecule associated with the Material File. There can be only one Material Source Name per column.

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 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.

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

Study file name---The name of the ISA-TAB-Nano study file, which lists information about the biological specimens (cells, tissues, organs, animal model, body fluids), nanoparticles; small organic molecules, and other types of samples assayed in a study. There can be only one file name per cell.

Study file description---A textual description which provides additional information on the ISA-TAB-Nano study file.

Study Design Descriptors

The STUDY DESIGN DESCRIPTORS section allows for the identification of design type of the study. TABLE 8 shows an example of the STUDY DESIGN DESCRIPTORS section along with example data. There are 3 concepts used in the STUDY DESCRIPTORS section. These concepts are taken from ISA-TAB.

Study design type---A term describing the classification of the study based on the overall study (experimental) design (for example, comparison study). The term can be free-text or taken from a controlled vocabulary/ontology.

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 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.

, 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. 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 Design Descriptors

The STUDY DESIGN DESCRIPTORS section allows for the identification of design type of the study. TABLE 8 shows an example of the STUDY DESIGN DESCRIPTORS section along with example data. There are 3 concepts used in the STUDY DESCRIPTORS section. These concepts are taken from ISA-TAB.

Study Design Type---A term describing the classification of the study based on the overall study (experimental) design (for example, comparison study). The term can be free-text or taken from a controlled vocabulary/ontology.

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

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

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

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

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

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

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

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

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

Study

...

Factors

The STUDY PUBLICATIONS FACTORS section allows for the identification of articles (published) associated factors associated with the study. TABLE 1012 shows an example of the STUDY PUBLICATIONS FACTORS section along with example data. 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 (that is, submitted, in preparation, published), associated with the study.

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, 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 statusfactor type.

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

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 11 concepts. Out of these, 8  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 typeAssay 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 NumberStudy 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 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 typeAssay 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 NumberStudy 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 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 platformTechnology Platform---The manufacturer and platform name of the instruments used in the study assay. This concept is taken from ISA-TAB.

Study assay measurement nameAssay 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 NumberStudy 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 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 nameAssay File Name--- Name of the ISA-TAB-Nano Assay file corresponding to the study assay. This is a required field. There can be only one assay file name per cell. This concept is taken from ISA-TAB.

Study

...

Protocols

The STUDY FACTORS PROTOCOLS section allows for the identification of factors associated with the study. TABLE 12 shows an example of the STUDY FACTORS 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. This section has nine concepts. Out of these, 6 concepts are There are 14 concepts in this section taken from ISA-TAB. The other three concepts are introduced in ISA-TAB-Nano and are indicated in the definitions below:

Study Protocol NameStudy 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.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 NumberStudy factor name term accession number--- Identification number of the a term selected from an ontology or a controlled vocabulary, if the term is entered as a value for study factor name.protocol type

Study factor name term source Protocol Type 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.

Name of the ontology or controlled vocabulary from which a term is selected and entered as a value for study protocol type.

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

Study Protocol URI---Pointer to protocol documents or resources external to ISA-TAB-Nano, which can be accessed by their Uniform Resource Identifier (URI). If URI is not available, enter the protocol document file name and make the protocol document available along with ISA-TAB-Nano files.

Study Protocol Version---An identifier for the version to ensure protocol tracking.

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

Study Protocol Parameters Name Term Accession 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 the study factor typeprotocol parameter name.

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

Study Protocols

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

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

Study protocol type---The term used to classify the protocol (for example, synthesis, assay, etc.).

Study protocol type term accession number--- Identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value for study protocol type

Study protocol type term source REF---Name of the ontology or controlled vocabulary from which a term is selected and entered as a value for study protocol type.

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

Study protocol URI---Pointer to protocol documents or resources external to ISA-TAB-Nano, which can be accessed by their Uniform Resource Identifier (URI). If URI is not available, enter the protocol document file name and make the protocol document available along with ISA-TAB-Nano files.

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

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

Study protocol parameters name term accession number---Identification number of a term selected from an ontology or a controlled vocabulary, if the term is entered as a value for the study protocol parameter name.

Study protocol parameters name term source REF---The name which identifies the source from where the term for study protocol parameter name. This name should match one of the names entered in the term source name field.

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

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

for study protocol parameter name. This name should match one of the names entered in the term source name field.

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

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

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

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

Study Contacts

The STUDY CONTACTS section allows the identification of the point of contact for a study. An example of the STUDY CONTACTS section is shown in TABLE 9 along with example data. The STUDY CONTACTS section has 11 ISA-TAB concepts.

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

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

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

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

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

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

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

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

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

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

Study protocol components type term source Person Roles Term Source REF--- The name which identifies the source from where the term for study protocol component typeperson role is selected. This name should match one of the names entered in the term source name field.

...