Creating an IDF

The IDF (Investigation Description Format) file is used to give an overview of the experiment, including the experimental variables (factors) used, protocols, quality control strategy, publication information and contact details. An example of an IDF document is given below:


IDF

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IDF tags

The IDF component of a MAGE-TAB document consists of a set of unique tags attached to their corresponding values in a simple tab-delimited text format. For example, "Experiment Description" should be followed by a free-text description of the experiment. Most of the following fields can be used with more than one value, so that (for example) multiple protocols, persons, experimental factors etc. can be defined in a single IDF file. In these cases, the different "objects" are separated by tabs (e.g in the image above notice the "Experimental Factor Name" tag has three corresponding values 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 (";").


IDF

I want to create a MAGE-TAB file


A full description of every valid IDF tag is given below

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 Experimental Factor Ontology. The study design class is particularly useful here.

Experimental Design Term Source REF

The source of the Experimental Design terms; his must reference one of the Term Source Names defined in the IDF file.

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). The actual values of these variables will be listed in the SDRF file, in "Factor Value [<factor name>]" columns.

Experimental Factor Type

A term describing the type of each experimental factor. These terms will usually come from the Experimental Factor Ontology.

Experimental Factor Term Source REF

The source of the Experimental Factor Type terms; this must reference one of the Term Source Names defined in the IDF file.

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. This tag is mandatory for sequencing submissions.

Person Roles

The role(s) performed by each person. Typically these terms should come from the Experimental Factor Ontology. See for example the list of organization role terms. If more than one role is needed per person, the roles should be given as a semicolon (;) delimited list.

Person Roles Term Source REF

The source of the Person Roles terms; his must reference one of the Term Source Names defined in the IDF file.

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 Experimental Factor Ontology. See for example the list of qc_type terms.

Quality Control Term Source REF

The source of the Quality Control Type terms; his must reference one of the Term Source Names defined in the IDF file.

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 Experimental Factor Ontology. See for example the list of replicate terms.

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.

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.

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.

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. You can ask us to change this later. 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).

Publication Status Term Source REF

The source of the Publication Status terms; his must reference one of the Term Source Names defined in the IDF file.

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. The text should clearly explain what you did in your experiment - this will help the curation team to check and process your MAGE-TAB document.

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.

Protocol Type

The type of the protocol, taken from a controlled vocabulary. Typically this term should come from the Experimental Factor Ontology . See for example the list of protocol terms.

Protocol Description

A free-text description of the protocol. This text is included in a single tab-delimited field.

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 (;).

parameters

Protocol Hardware

The hardware used by the protocol. This tag is mandatory for nucleic acid sequencing protocols.

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.

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. In the IDF file is an (optional) list of sources from which controlled vocabulary terms may have been used elsewhere in the MAGE-TAB document. These term sources may be fully-fledged ontologies like the Experimental Factor Ontology, databases providing queryable accession numbers (e.g. ArrayExpress), or simply a file defining terms for local users. These so-called "Term Sources" are defined in the IDF and may be used throughout the MAGE-TAB. If they are not used, then all controlled vocabulary terms are assumed to be user-defined. This name will be used in all corresponding "Term Source REF" fields.


term source usage

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 Comment[AdditionalFile:TXT].

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