This page provides detailed help on the Investigation Design Format (IDF), and lists all the available tags for use in MAGE-TAB IDF documents. For an overview of the MAGE-TAB submission process, and examples of both IDF and SDRF, please see these submission help notes and MAGE-TAB overview. For more detail on the MAGE-TAB format, please see the MAGE-TAB specification.

Most of the following fields can be used with more than one value, so that (for example) multiple Protocols, Persons, Experimental Factors and Term Sources can be defined in a single IDF file. In these cases, the different "objects" are separated by tabs. Those fields which can contain only one value are indicated below. In some cases (Person Roles, Protocol Parameters) it is possible to have multiple values within a given "object". For example, one person may have many roles. In such cases the multiple roles should be separated by semicolons (";").

MAGE-TAB documents may optionally include information on the sources of any controlled terms used, providing users with the ability to link to ontologies, databases or other sources of controlled vocabularies to describe their experiment. These so-called "Term Sources" are defined in the IDF and may be used throughout the document. If they are not used, then all controlled vocabulary terms are assumed to be user-defined.

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Investigation Title
The overall title of the investigation. This tag can only have one value.

Experimental Design
The experiment design types which are applicable to this study. Typically these terms should come from the MGED Ontology. The ExperimentDesignType subclasses are particularly useful here. See for example the list of BiologicalProperty terms available. Controlled vocabulary term.

Experimental Design Term Source REF
The source of the Experimental Design terms; this must reference one of the Term Source Names defined elsewhere in the IDF file (see below).

Experimental Design Term Accession Number
The accession number for this term, taken from the indicated Term Source.

Experimental Factor Name
A user-defined name for each experimental factor studied by the experiment. These experimental factors represent the variables within the investigation (e.g. growth condition, genotype, organism part, disease state). The actual values of these variables will be listed in the SDRF file, in "Factor Value [<factor name>]" colummns. Used as an identifier within the MAGE-TAB document.

Experimental Factor Type
A term describing the type of each experimental factor. These terms will usually come from the MGED Ontology. The ExperimentalFactorCategory subclasses are particularly useful here. See for example the list of BioMaterialCharacteristicCategory terms available. Controlled vocabulary term.

Experimental Factor Term Source REF
The source of the Experimental Factor Type terms; this must reference one of the Term Source Names defined elsewhere in the IDF file (see below).

Experimental Factor Term Accession Number
The accession number for this term, taken from the indicated Term Source.

Person Last Name
The last name of each person associated with the experiment.

Person First Name
The first name of each person associated with the experiment.

Person Mid Initials
The middle initials of each person associated with the experiment.

Person Email
The email address of each person associated with the experiment.

Person Phone
The telephone number of each person associated with the experiment.

Person Fax
The Fax number of each person associated with the experiment.

Person Address
The street address of each person associated with the experiment.

Person Affiliation
The organization affiliation for each person associated with the experiment.

Person Roles
The role(s) performed by each person. Typically these terms should come from the MGED Ontology. See for example the list of Roles terms. If more than one role is needed per person, the roles should be given as a semicolon (";") delimited list, for example: "submitter;data_coder;investigator". Controlled vocabulary term.

Person Roles Term Source REF
The source of the Person Roles terms; this must reference one of the Term Source Names defined elsewhere in the IDF file (see below).

Person Roles Term Accession Number
The accession number for this term, taken from the indicated Term Source.

Quality Control Type
The quality control procedures used. Typically these terms should come from the MGED Ontology. See for example the list of QualityControlDescriptionType terms. Controlled vocabulary term.

Quality Control Term Source REF
The source of the Quality Control Type terms; this must reference one of the Term Source Names defined elsewhere in the IDF file (see below).

Quality Control Term Accession Number
The accession number for this term, taken from the indicated Term Source.

Replicate Type
The replicate strategies used. Typically these terms should come from the MGED Ontology. See for example the list of ReplicateDescriptionType terms. Controlled vocabulary term.

Replicate Term Source REF
The source of the Replicate Type terms; this must reference one of the Term Source Names defined elsewhere in the IDF file (see below).

Replicate Term Accession Number
The accession number for this term, taken from the indicated Term Source.

Normalization Type
The normalization strategies used. Typically these terms should come from the MGED Ontology. See for example the list of NormalizationDescriptionType terms. Controlled vocabulary term.

Normalization Term Source REF
The source of the Normalization Type terms; this must reference one of the Term Source Names defined elsewhere in the IDF file (see below).

Normalization Term Accession Number
The accession number for this term, taken from the indicated Term Source.

Date of Experiment
The date on which the experiment was performed. This tag can only have one value.

Public Release Date
The date on which the experimental data will be/was released. This tag can only have one value.

PubMed ID
The PubMed IDs of the publication(s) associated with this investigation (where available).

Publication DOI
A Digital Object Identifier (DOI) for each publication (where available).

Publication Author List
The list of authors associated with each publication.

Publication Title
The title of each publication.

Publication Status
A term describing the status of each publication (e.g. "submitted", "in preparation", "published"). Controlled vocabulary term.

Publication Status Term Source REF
The source of the Publication Status terms; this must reference one of the Term Source Names defined elsewhere in the IDF file (see below).

Publication Status Term Accession Number
The accession number for this term, taken from the indicated Term Source.

Experiment Description
A short paragraph describing the experiment as free-text. This tag can only have one value.

Protocol Name
The names of the protocols used within the MAGE-TAB document. These will be referenced in the SDRF in the "Protocol REF" columns. Used as an identifier within the MAGE-TAB document.

Protocol Type
The type of the protocol, taken from a controlled vocabulary. Typically this term should come from the MGED Ontology. See for example the list of ExperimentalProtocolType terms. Controlled vocabulary term.

Protocol Description
A free-text description of the protocol. This text is included in a single tab-delimited field. If you wish to include tab or newline characters as part of this text, you must enclose the whole text within double quotes (").

Protocol Parameters
A semicolon-delimited list of parameter names; these names are used in the SDRF file (as "Parameter Value [<parameter name>]" headings) to list the values used for each protocol parameter. If more than one parameter was used for a given protocol, they should be separated with semicolons (";"). Used as an identifier within the MAGE-TAB document.

Protocol Hardware
The hardware used by the protocol.

Protocol Software
The software used by the protocol.

Protocol Contact
The name and contact details to be used for enquiries concerning the protocol.

Protocol Term Source REF
The source of the Protocol Type terms; this must reference one of the Term Source Names defined elsewhere in the IDF file (see below). Examples: MGED ontology, OBI.

Protocol Term Accession Number
The accession number for this term, taken from the indicated Term Source.

SDRF File
The name(s) of the SDRF file(s) accompanying this IDF file.

Term Source Name
The names of the Term Sources (ontologies or databases) used within the MAGE-TAB document. This name will be used in all corresponding "Term Source REF" fields. Examples: MGED Ontology, NCI MetaThesaurus, ArrayExpress. Used as an identifier within the MAGE-TAB document.

Term Source File
A filename or valid URI at which the Term Source may be accessed.

Term Source Version
The version of the Term Source used throughout the MAGE-TAB document.

Comment[<user-defined tag>]
A user-defined value which is associated with the investigation. For example, ArrayExpress uses "Comment [ArrayExpressSubmissionDate]" to record the date of submission to the database; alternatively, tags such as "Comment [Goal]" might be used to indicate the purpose behind an investigation.

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