Module detail: Checker.pm

NAME

ArrayExpress::MAGETAB::Checker - MAGE-TAB experiment checking.

SYNOPSIS

 use ArrayExpress::MAGETAB::Checker;
 
 my $checker = ArrayExpress::MAGETAB::Checker->new({
     idf => $magetab_idf,
 });
 
 $checker->check();

DESCRIPTION

This module provides the basic operations needed for checking a MAGE-TAB document and associated data files.

OPTIONS

The following options must be used in addition to those provided by the parent class (see the ArrayExpress::Curator::ExperimentChecker manpage):

idf

The MAGE-TAB IDF filename to be checked.

TESTS

The following tests are performed by this module, with output printed to the error and/or report logs:

IDF Contents

Checks that at least one of each of the following items are present in the IDF, warning the user if any are missing:

 Experimental Factor
 Contact
 Publication
 Protocol
 SDRF

Experiment info

Warns the user if any of the following pieces of experiment annotation are missing:

 Experiment Design
 Release Date
 Title
 Description

Term Sources

Checks all instances of Term Source REFs, and warns the user if an undeclared Term Source Name has been used. Also notifies the user if a Term Source declared in the IDF has not been used in the SDRF.

Experimental Factors

Checks all SDRF Factor Value columns, and warns the user if an undeclared Experimental Factor Name has been used. Also notifies the user if a Experimental Factor declared in the IDF has not been used in the SDRF.

Undeclared Experimental Factors

Checks all material characteristics against the factors described by the document, alerting the user if any such characteristics vary during the experiment without having been declared as an experimental factor.

Source Characteristics

Checks that each Source material has at least some annotation. This is not, however, a full test of MIAME compliance.

PubMed ID

Warns the user if a non-numeric PubMed ID has been entered.

Submission and release dates

Warns the user if experiment or release dates are in an incorrect format.

Submitter

Checks that a submitter contact has been provided, and that their last name and email address have both been included in the IDF.

Protocols

Checks that all protocols referenced in the Hybridization spreadsheet section are declared in the Protocol section (and vice versa).

Protocol description length

Warns if any of the protocol texts seem too brief.

Protocol usage

Checks that a protocol has been attached to each step of the experiment (biomaterial treatments, hybridization, scanning and normalization).

Parameters

Checks that all parameters referenced in the Hybridization spreadsheet section are declared in the Protocol section (and vice versa).

Files

Confirms that each data file is associated with an array design (i.e., Array Design REF or Array Design File), and at least one experimental factor value.

Experiment Design Graph

Creates the links between sample, extract, labeled extract and hybridization, and writes a biomaterials log file listing the numbers of each. If the Graphviz software is installed (http://www.graphviz.org) then the script will use the 'dot' program to produce a PNG format graph showing how the various components relate to each other.

Tim Rayner (rayner@ebi.ac.uk), ArrayExpress team, EBI, 2007.

Acknowledgements go to the ArrayExpress curation team for feature requests, bug reports and other valuable comments.