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Module detail: Validate.pm |
ArrayExpress::Curator::Validate - a module used by expt_check.pl
use ArrayExpress::Curator::Validate;
my $checker = ArrayExpress::Curator::Validate->new({
spreadsheet_filename => $tab2mage_file,
});
$checker->check();
This module provides a set of subroutines used by the experiment checker script to confirm the MIAME metadata supplied in a Tab2MAGE spreadsheet.
The following options must be used in addition to those provided by the parent class (see the ArrayExpress::Curator::ExperimentChecker manpage):
spreadsheet_filenameThe Tab2MAGE spreadsheet to check.
The following tests are performed by this module, with output printed to the error and/or report filehandles:
Confirms that each hybridization is associated with an array design (i.e., ArrayExpress accession number), and at least one experimental factor value.
Checks that each BioSource has at least some annotation. This is not, however, a full test of MIAME compliance.
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.
Checks that all protocols referenced in the Hybridization spreadsheet section are declared in the Protocol section (and vice versa).
Confirms that all declared protocols in the Protocol section have accession numbers.
Warns if any of the protocol texts seem too brief.
Checks that a protocol has been attached to each step of the experiment (biomaterial treatments, hybridization, scanning and normalization).
Checks that all parameters referenced in the Hybridization spreadsheet section are declared in the Protocol section (and vice versa).
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.
Warns the user if the specified publication journal name is not in the included list of standard Entrez journal abbreviations.
Warns the user if a non-numeric PubMed ID has been entered.
Warns the user if submission and/or release dates have not been specified.
Checks that both submitter name and email have been provided.
Tim Rayner (rayner@ebi.ac.uk), ArrayExpress team, EBI, 2005.
Acknowledgements go to the ArrayExpress curation team for feature requests, bug reports and other valuable comments.