Converter

The Converter program works with MAPPs and Expression Datasets, and performs three principal functions:

• Conversion of GenMAPP version 1 files to a format that is compatible with GenMAPP version 2.0, a critical step since version 1 files will not work in version 2.0.
• Conversion of gene IDs on MAPPs from previous versions of GenMAPP, including GenBank and UniProt, to more specific ones. Converter works with both version 1.0 and version 2.0 files. If you download a new version of a Gene Database, you can use Converter to attempt to convert any leftover GenBank IDs in your version 2.0 MAPPs to more specific IDs if those relationships exist in the updated Gene Database.
• Switching gene IDs on MAPPs from one gene ID system to another system supported by GenMAPP.

Converting Between Program Versions

From the main Drafting Board menus, select Tools > Converter. Be sure that the Gene Database and the species represented there are correct. If not, click the Gene Database button and select the desired Gene Database from the dialog that appears.

Select Convert from previous version.

Choose whether you are converting MAPPs or Expression Datasets.

If you select Entire folder, Converter converts all the MAPPs or Expression Datasets within that folder. Check Include Subfolders to convert an entire folder branch.

Under Source, choose the actual files you want to convert, that is the .gex or .mapp files. If you have chosen Entire folder the source will be a folder. Source files are always copied, not replaced. The original file is prefixed with V1_. For example, if you convert MyMAPP.mapp, the original is renamed V1_MyMAPP.mapp and the converted file is MyMAPP.mapp.

Under Destination, choose desired location of the converted files. If you checked Include Subfolders, the source subfolder names are used to fill out the branches under the destination folder.

To complete the conversion, click on the Go button.

Conversion of Gene IDs on MAPPs from previous versions of GenMAPP

Since the number of existing GenBank IDs is so large, Gene Databases for some species, such as human and mouse, cannot include GenBank IDs. GenMAPP.org provides specialized conversion databases for mouse and human, labeled Converter, for example, Hs-Converter_20040411.gdb. (To download these databases, see Adding Gene Databases.) In addition to file format conversion, there are two options that will simultaneously switch the gene IDs while switching the file format:

Convert GenBank switches GenBank IDs to more specific IDs. For mouse data, the conversion will be to MGI and for human the conversion will be to UniProt. If no ID conversion can be made to those two systems for a particular gene, the gene identifier will be translated into Entrez Gene, UniProt (for mouse), or UniGene, in that order of priority.

Convert UniProt converts UniProt IDs to Entrez Gene or UniGene, for human data. For mouse data, the Converter first tries to find MGI IDs, before searching for Entrez Gene and Unigene.

If Converter finds more than one ID (of any kind) for a particular gene, all of them are shown on the MAPP tiled (offset) one on top of another. Delete all those that do not apply. You may have to reposition the remaining gene on the MAPP.

Conversion Log File

Once the conversion process is finished, Converter creates a log file in the destination folder, with the name inputfilename.log. For example, if the input file is Mm_Glycolysis and Gluconeogenesis.mapp, the log file is named Mm_Glycolysis and Gluconeogenesis.log. This file is in tab-delimited text format to be easily viewable in a spreadsheet program such as Excel. It has information on how the individual gene identifiers in the input files were converted. The log file is organized as follows:

We recommend that you review this file to identify potential problems in the conversion process. For example, you should check which gene IDs were not converted.

Switching Between Gene ID Systems

From the main Drafting Board window menus, select Tools > Converter. Be sure that the Gene Database and the species represented there are correct. If not, click the Gene Database button and select the desired Gene Database from the dialog that appears. To bring up the gene switcher interface, click the Switch Gene ID system button.

To protect the integrity of gene expression data, it is only possible to switch gene ID systems for MAPPs.

If you select Entire folder, Converter converts all the MAPPs within that folder. Check Include Subfolders to convert an entire folder branch.

Under Source, choose the actual .mapp files you want to convert. If you have chosen Entire folder the source will be a folder. Source files are always copied, not replaced. The original file is prefixed with Old_. For example, if you convert MyMAPP.mapp, the original is renamed Old_MyMAPP.mapp and the converted file is MyMAPP.mapp.

Under Destination, choose desired location of the converted files. If you checked Include Subfolders, the source subfolder names are used to fill out the branches under the destination folder.

In the Switch From field, select the gene ID system or systems in the MAPPs that you wish to convert from. To select multiple systems, hold down the Ctrl key as you click.

In the Switch To field, select the gene ID system you wish to convert the genes to. You may choose only one system from the list. Once you select a gene ID system in the Switch To field, some gene ID systems listed in the Switch From field may be put within brackets. This indicates that no link between those systems and the chosen Switch To system exists in the database, so therefore that particular conversion cannot be made.

The Select All and Deselect All buttons selects and deselects all gene ID systems in the Switch From field.

To complete the conversion, click on the Go button.

Gene ID System Switch Log File

Once the conversion process is finished, Converter creates a log file in the destination folder, with the name inputfilename.log. For example, if the input file is Mm_TGF_Beta_Signaling_Pathway.mapp, the log file is named Mm_TGF_Beta_Signaling_Pathway.log. This file is in tab-delimited text format to be easily viewable in a spreadsheet program such as Excel. It has information on which genes identifiers in the input files that were converted. The log file is organized as follows: