A MAPP Set is a collection of MAPPs in HTML format presentable in an internet browser. You can use GenMAPP to create a MAPP Set from a folder of MAPPs, including subfolders, if you wish. Your MAPP set may display an Expression Dataset with any number of Color Sets represented. You may switch between Color Sets at will on the individual MAPPs in the MAPP Set; GenMAPP creates separate HTML pages for each Color Set and a clickable list of Color Sets at the top of each MAPP. This allows for easy, almost instantaneous comparison of Color Sets in a browser without the need to use the GenMAPP program for viewing.
MAPPs in sets have preformed Backpages, also in HTML format, with links for the gene objects to which they refer. If you click on a gene, the Backpage opens. The Backpage contains annotations from the Gene Database and hyperlinks to the public databases from which the information was derived. If the MAPP was colored with an Expression Dataset, the expression data will also appear on the Backpage. You must, of course, have a functioning web connection to use the hyperlinks.
GenMAPP creates two types of gene indexes, the MAPP Index and the Gene Index. The MAPP Index is a web page containing a listing of the MAPPs in the set. The name of each MAPP is an active hyperlink that allows the user to jump immediately to that MAPP. The Gene Index is saved in two formats: one is formatted as a web page and one is a tab-delimited text file. Both contain a listing of all the genes in the MAPP Set and indicating on which MAPPs they appear. Live hyperlinks to each MAPP are included in the web-formatted Gene Index.
From the main Drafting Board window, left-click the File menu, choose Export and then MAPP Set. You will be presented with a MAPP Set window from which you may select your MAPP Set parameters.
The MAPP Source is the folder where your collection of MAPPs that you wish to create MAPP Sets for resides. You may choose to Include subfolders of the root folder you specify. In the example above, if Include subfolders is not checked, your set will include only those MAPPs in the Mm_Contributed_20050630 folder. With Include subfolders checked, your set will include not only those MAPPs but any MAPPs in the listed subfolders as well as subfolders of those subfolders and so forth.
The HTML destination is where the set of HTML-format MAPPs are
saved. If you Include subfolders in your source, GenMAPP will create
the same subfolders in your destination for those MAPPs. You may create a new
folder under your highlighted folder by clicking the
icon. All
hyperlinks in the MAPP Set are relative to the destination folder. In other
words, you can move that folder and its subfolders anywhere, your web site, for
example, and the links will still be valid.
You may Choose Expression Dataset for your MAPPs. If you already have an Expression Dataset open in the Drafting Board window, it will appear in the MAPP Sets window. You may change it by left-clicking the Choose Expression Dataset button.
When you have an Expression Dataset specified, you will be presented with a list of Color Sets. You may choose to include All Color Sets or None by left-clicking the appropriate button. You may also choose a single Color Set by left-clicking it in the list, or multiple ones by holding down the Ctrl key as you left-click.
If multiple Color Sets are chosen for export, GenMAPP will create separate views for each Color Set, as well as summary view for all Color Sets. This summary view is similar to viewing multiple Color Sets on MAPPs, where gene boxes on the MAPP will be partitioned into colored stripes, each representing a Color Set. There will be no gene value exported for the summary view.
For all MAPP Set exports, a blank MAPP will also be exported in addition to the selected Color Set.
If you check Overwrite existing files without asking, GenMAPP will replace any files it finds in the folders of the same name without confirmation. You would probably choose this option if you were recreating a MAPP Set.
The Create Set button will start the process when you have made all your choices.
Many people will use these MAPP Sets for posting on web sites. Some web servers have problems with certain characters in file and folder names so GenMAPP changes doubtful characters to underscores. For example, the source folder GenMAPP.org MAPPs will be the destination folder GenMAPP.org_MAPPs because space is one of those doubtful characters.
Clicking Cancel during MAPP Set creation immediately stops the export process.
| Note: MAPP Sets can be created only if all the MAPPs in the folder
tree are from the current GenMAPP version. If your source folder contains MAPPs
from an earlier version of GenMAPP, the MAPP Set process will inform you of
that, remind
you to convert all the MAPPs to the current version.
Remember that all the MAPPs in the folder tree must be in the current version. If you choose to convert to the same folders in which the old MAPPs reside, you will have to manually delete the old-version (V1_) MAPP copies. |
GenMAPP creates two types of gene indexes, the MAPP Index and the Gene Index. All index files appear in the root destination folder, C:\GenMAPP 2 Data\Exports in the example above, or in a subfolder you created. The names of the indexes are the name of the root source folder with an underscore prepended and index type following. For example, for the MAPP Index the filename would be _MAPPIndex_Mm_Contributed_20050630.htm, and for the Gene Index the filename would be _GeneIndex_Mm_Contributed_20050630.txt. The underscore ensures that the index remains at the beginning or end of the folder listing, depending on your computer's sort order.
The MAPP Index file is an organized listing of the MAPPs in the MAPP Set in HTML format, for example, _MAPPIndex_Mm_MAPPArchive_20040218.htm. When you open this in a browser (typically double-click on the file) you can click on a MAPP title to open that MAPP. With most browsers, if you hold the Shift key while clicking, the MAPP will open in a separate browser window, leaving your index in the first.
The organization of the MAPP Index is identical to the folder hierarchy from the MAPP Set source folder. The index shows you each folder and subfolder and the MAPPs within each.
In order to keep the full functionality of the MAPP Set, you cannot change the name of the index file.
The second type of index contains all the genes represented in the MAPPs in the set and on which MAPP they appear. This index is saved in two copies, one as a tab-delimited text file, and the other as a HTML-formatted file. Below is an example of what a tab-delimited Gene Index file might look like in Excel:
| Type | Gene ID | Gene Label | MAPP | Other IDs |
| L | 13542 | Dvl1 | cellular_process-GenMAPP/Mm_Wnt_Signaling/Mm_Wnt_Signaling_0.htm | [M]MGI:94941 [S]P51141 [S]DVL1_MOUSE [U]Mm.3400 |
| L | 13543 | Dvl2 | cellular_process-GenMAPP/Mm_Wnt_Signaling/Mm_Wnt_Signaling_0.htm | [M]MGI:106613 [S]Q60838 [S]DVL2_MOUSE [U]Mm.5114 |
| L | 13544 | Dvl3 | cellular_process-GenMAPP/Mm_Wnt_Signaling/Mm_Wnt_Signaling_0.htm | [M]MGI:108100 [S]Q61062 [S]DVL3_MOUSE [U]Mm.247259 |
This index lists the Gene ID Type (see the Gene Database for codes and their Gene ID Types), the Gene ID, and the label of the gene object on the MAPP. It also shows the relative path of the MAPP within the MAPP set, in other words, the subfolder and MAPP file name where the gene appears. It is ordered by Gene Type and Gene ID.
A final column shows other possible identifiers for the gene in the form ID Type|ID. For example L|13542 is the Entrez Gene ID for the gene.
The HTML-formatted version of the Gene Index is organized similarly, but has a live link to the MAPP for each gene, rather than the MAPP path.
MAPP Sets are organized so that you can easily use the entire MAPP Set or a single folder or even a single MAPP within the set. Each MAPP has its own folder that contains the HTML pages for the different Color Set renditions of the MAPP itself and a _Support folder for all the graphics and Backpages for those MAPPs.
The MAPP Set index files are common to the entire MAPP Set. To extract a fully indexed MAPP Set from of the subfolder, you would have to recreate the set using the subfolder as the root HTML Destination.
MAPP Sets are often generated for sending to collaborators or for posting on a web site. GenMAPP facilitates this by making all links within the MAPP Set relative to the root destination folder. When you move or copy the MAPP Set from its original location, open the root destination folder and copy all the files and folders within it to the new location.
For example, if your destination folder was a folder named MAPP Set under Exports and you generated a MAPP Set from the Mm_Contributed_20050630 that included subfolders cellular_process-GenMAPP, metabolic_process-GenMAPP, molecular_function-GenMAPP and physiological_process-GenMAPP, the MAPP Set folder would have those subfolders. Highlight everything in the MAPP Set folder and copy or move it to the new location. Don't forget the index files.
From the new location you may now call up the index (_MAPPIndex_Mm_Contributed_20050630.htm in the example) by either double-clicking on it in Windows or linking to it in a web site. You can now click on the MAPP you want to view.