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MAPPBuilder

Overview

MAPPBuilder is an accessory application for GenMAPP. Given a list of gene IDs, MAPPBuilder automatically creates a MAPP file (.mapp) containing those genes, that can be viewed and modified with the GenMAPP Program. A MAPP generated from MAPPBuilder will not contain any graphics from the Drafting Toolbar except for gene objects and the label. Other tools can be added to the MAPP after it is created with MAPPBuilder.

A typical MAPP created by MAPPBuilder might look like this:

Input File Format

In order for MAPPBuilder to accurately import your gene list into a GenMAPP MAPP file, your input file must be in the proper format. MAPPBuilder imports files that are in a tab-delimited text format (.txt), which is typically exported by spreadsheet or database programs (e.g., Microsoft Excel). The format of your file should be as follows:

GeneID SystemCode Label Head Remarks MAPPName
100011 L 100011   hyperlink MAPP1
2DMB_MOUSE S 2DMB_MOUSE     MAPP1
106983 L 106983     MAPP1
Q8BG74 S Q8BG74     MAPP1
MGI:101775 M MGI:101775     MAPP1
MGI:101802 M MGI:101802   hyperlink MAPP1
107116 L 107116     MAPP1

The first row must contain the column headings GeneID, SystemCode, Label, Head, Remarks, and MAPPName. The spelling of these headings must be exactly like this and they must be in this exact order. Subsequent rows contain information about the genes or labels that you want to appear on the MAPP. To add genes to your MAPP fill in the fields as follows:

GeneID – The gene identifier from one of the GenMAPP accepted gene ID systems. The gene ID is the link between the gene object on the MAPP and information in the Gene Database and data in your ExpressionDataset. This field must contain an ID for each gene added to a MAPP. Gene identifiers of the type Other must be 30 characters or fewer. Commas, quotes (single or double), or the dollar sign may not be used as an Other gene identifier. Other non-alphanumeric characters are allowed. Click here for formatting examples for the various gene ID types accepted by GenMAPP.

SystemCode – The type of gene identifier in the GeneID field. This field must be filled in for each gene added to a MAPP.

Label – The label is the text you wish to appear within the gene box on the MAPP. We suggest that you use the gene symbol approved by the model organism database for each species to facilitate communication of MAPPs between researchers. Double quotes and the dollar sign may not be used in a label. This field will be truncated beyond 50 characters. If this field is left blank, the word “Gene” will appear in the gene box.

Head – The Backpage heading is the first line or title of the Backpage. If you leave this field blank, it will default to the gene label.

Remarks – Text entered here will appear on the Backpage for that gene below the annotation for that gene from the Gene Database. Double quotes and the dollar sign may not be used in this field. Any valid web address beginning with http:// or www will be displayed as a valid hyperlink. This field can be left blank.

MAPPName – This is the filename for the MAPP and the title that will appear on the MAPP. This field must be filled in for each gene added to a MAPP. Several MAPPs can be built from the same input file by entering different MAPPNames for different genes. When MAPPBuilder encounters a new MAPPName in the same file, a new MAPP is started. Genes (and labels) that belong to the same MAPP should be in contiguous rows in the input file. Be sure that you do not use the same MAPPName twice for two different contiguous lists of genes, or the second occurrence of the MAPPName will create a MAPP file that overwrites the first.

The maximum number of genes (or labels) that MAPPBuilder will add to the same MAPP is 300. If there are more than 300 genes (or labels) that belong to the same MAPPName, MAPPBuilder will create a second file with the same name with the number 2 appended to it (e.g. Filename 2).

MAPP Names of more than 50 characters will be truncated to 50 in the MAPP title but not the filename.

Adding a label on a MAPP

In addition to gene objects, MAPPBuilder will also allow you to add a text label in between two genes on a MAPP. To add a label in a list of genes, fill in the fields as follows:

GeneID – Leave blank to place a text label on a MAPP.

SystemCode – To add a label, enter the word Label.

Label – This is the text of the label. Double quotes and the dollar sign may not be used.

Head – Leave blank to place a text label on a MAPP.

Remarks – Leave blank to place a text label on a MAPP.

MAPPName – This is the filename for the MAPP and the title that will appear on the MAPP. This field must be filled in for each label added to a MAPP. The same rules apply as described for genes above.

When you have finished formatting your file, save it as a tab-delimited text file (.txt).

Creating MAPP Files with MAPPBuilder

To run MAPPBuilder, proceed as follows:

  1. From the GenMAPP Drafting Board window, choose the menu item Tools > MAPPBuilder. The MAPPBuilder window will open. Select the input file you wish to use to make a MAPP by clicking on the Select File button. Choose the file in the Open window that appears and click OK.

  2. Select the destination folder for your new MAPPs. This defaults to C:\GenMAPP 2 Data\MAPPs, but you can browse to any folder by clicking on the Select Destination Folder button.

  3. MAPPBuilder looks in the Gene Database for the gene IDs in your input file. If a gene ID is not found in the Gene Database, you have the option of allowing MAPPBuilder to add the gene ID to the Other category of the Gene Database. Checking the box enables this feature. If you leave the box unchecked, MAPPBuilder will add any gene IDs not found to an Exception File called Filename.EX.txt in the same folder as the input file.

  1. Fill out the MAPP Information fields. These fields will be the same for each MAPP generated from the same input file.

Author – Enter the name(s) of the individuals that created the MAPP using 50 characters or fewer.

Maintained by – Enter the name(s) of the individuals that are currently responsible for the content of the MAPP, if different than the Author. This field must be 50 characters or fewer.

E-mail – Enter the e-mail address for the person who is willing to be contacted about the MAPP, the “corresponding author.” This is usually the e-mail address of a person listed in the Author or Maintained by fields. This field must be 50 characters or fewer.

Remarks – Enter any remarks or explanations for this particular MAPP. For example, you may wish to list a reference for the MAPP or information about nomenclature or symbols used in the MAPP here. This field must be 50 characters or fewer.

Copyright – If you wish to copyright your MAPP, GenMAPP will display on the MAPP the Copyright and © next to the year and entity you supply in this field. For example, if you fill in 2003, Whizbang Labs, the Information Area on the MAPP will display Copyright © 2003, Whizbang Labs. This field must be 50 characters or fewer.

Notes – Text entered in the Notes field will not appear on the MAPP, but will be available through the MAPP Information window. The amount of text this field can hold is unlimited. If you run out of room in any of the other fields, this is a good place to put the full information.

Note: the MAPP Information Area also has a Last modified date field. MAPPBuilder automatically fills in this field with the date the MAPP is created.

  1. When you have selected the input file, the destination folder, and filled in the MAPP Information fields, you can start the MAPP-building process by clicking on the Make MAPPs button at the bottom of the window. When MAPPBuilder has finished, the MAPPs can be found in the destination folder. At this time you make more MAPPs by changing your selections for input file, destination folder, and/or MAPP Information. Once you have finished making MAPPs, exit MAPPBuilder by choosing File > Close or by clicking on the close button in the title bar.

Errors During MAPP Creation

If MAPPBuilder finds lines in the input file that cannot be imported due to formatting errors or gene IDs that cannot found in your Gene Database, it returns an error for each of those lines. The erroneous lines can be found in the exception file, which will be named Filename.EX.txt, and will be stored in the same folder as your input file.

Some examples of conversion errors are:

Once you have made corrections to the input file based on the exception file, you can import it to MAPPBuilder again.