The reporter annotation for microarrays is typically available as a file used by the array spotter. These files come in a number of formats, the most common of which is the GAL ("GenePix Array List") file. For submission to MIAMExpress this file needs to be converted into the ADF format, which can be used to provide array annotation in a MIAME-compliant format.
To create an ADF file you will need to convert the spotter output file from its original layout (for instance, Block - Column - Row format) into the ADF (MetaColumn - MetaRow - Column - Row) layout. We have provided a conversion tool to help you do this.
In addition to reformatting your file, the converter also provides you with an opportunity to batch-query the BioMart system. In this way you can extend the annotation of your array to cover many biological sequence annotation databases (For example, adding annotation from Ensembl, InterPro, and OMIM).
There are three steps to creating a valid ADF file:
When you visit the converter web page, you will be greeted by the following form:
To create the initial ADF, simply specify:
Please note: It is possible to use the converter even if your species or sequence database identifier type are not in the pull-down menus. The conversion of the coordinate columns will still take place; the only difference is that the link to BioMart will not be generated, and you can skip merging the ADF with the BioMart annotation.
The values in the screenshot above would be used for this example GAL file: MouseOligoSpotter.gal. Clicking the "Convert to ADF" button will take you to the results page:
Here you can retrieve your reformatted ADF by selecting the "Chip layout in ADF format" link. You should save this file for further processing. You can also check that the correct column of sequence identifiers has been selected from the results web page.
Finally, when you are satisfied, clicking on the "BioMart ADF compatible annotation" link will query BioMart with the sequence identifiers you have selected, and should generate output similar to the image below. This file should also be saved to disk.
Please note: If your spotter output file cannot be converted using this web form, contact the curation team at arraysubs@ebi.ac.uk stating the errors which you encountered.
You should now have two files saved to disk: the partially completed ADF, and the BioMart output file. These files need to be merged on the common column you indicated on the original converter submission page. We have provided a short Perl script to help you do this: adf_biomart_merge.pl. This script may be downloaded and invoked using this command-line syntax:
perl adf_biomart_merge.pl -a <ADF file> -b <BioMart file> -c <ADF column containing shared identifiers>
The script will generate a new file containing the merged ADF and BioMart annotation. This merged file should be used for subsequent steps.
To annotate your array to the MIAME standard, you will need to add further columns to your ADF. These columns should contain information on the type of biosequence used (e.g. cDNA_clone) and the way in which the reporters were used (e.g., experimental versus control). Full documentation on the requirements for MIAMExpress submission are here: ADF help notes.
Once you have completed your ADF, you should validate it using our ADF checker web page. This will check your ADF for the correct format and annotation.
Once you have a valid ADF you will be able to submit it to MIAMExpress. For help with this, please see the MIAMExpress array help notes.