General Help On Searching

The Soybean Breeders Toolbox (SBT) is designed to present data which will be of interest to both soybean genetic researchers as well as soybean breeders. This data is presented both textually and graphically. Since soybean research is actively being conducted by laboratories around the world it should be considered a "work in progress". Consider the SBT as a community resource and if you notice an inconsistency or error please bring it to our attention. Your contributions will be publically recognised.

The SBT is divided into two distinct areas, Maps and text data. The "Search database" function is designed to allow queries to begin with a text query. This function of the main SBT window is designed to accept both specific and general searches based on a text entry. If you have a specific query it can be entered in this pane. If you are not familiar with the data types in the SBT, wild card searches are available. To see a listing of all data types click on the pull-down menue in the search pane. If you select a data type and click the "Go" button a listing of all items of that data type is returned. If the list is extensive, it will be returned as an alphabetical list starting with items that begin with a number in there name. You can click on any blue letter or number in the navigation pane to display items starting with that symbol.

General browsing of the data contained in the SBT can be initiated using a graphical display of individual genetic maps by clicking on the "Map Collection" link. Clicking on this link displays a listing of all the genetic maps contained in the Toolbox. Clicking on any Map Collection name will cause each the map names of each linkage group identified in the experiment to be displayed. By selecting a particular map it will be possible to see what molecular markers or Quantitative Traits (QTLs) have been mapped to that linkage group. Periodically, a "Composite" genetic map is summarized from all mapping data contianed in our database where there are correspondences in common. These map collections are identified with the word "Composite" followed immediately with the year that it was assembled. Thus GmComposite2003 represents the composite of all mapping data in the year 2003.

Map Collection Help

Each map collection represents the data derived from published mapping experiments. Data from these papers are transferred by SoyBase curitorial staff to computer files for presentation by CMap. Each map collection identifier begins "Gm" followed by a descriptor of the type of data used for the mapping experiment. Map data can be accessed in two ways. First, you can view data associated with a particular map collection, by entering its identifier in the "Search database" input box. Choose "Map Collection" from the "All Categories" pulldown box then click the "Go" button to the immediate right of the text input box. A new window will open containing data associated with the map collection including a link to a reference for the original article describing the experiment.

If you are unfamiliar with the genetic maps of soybean, you could also browse a list of map collections by clicking the "Map Collection" link on the main page. Clicking this link will cause a new pane to appear containing all genetic maps available in the Toolbox. Selecting one of the map collection names will cause a new pane to appear that lists the names of the maps of each indivdiual linkage group produced in the experiment.

Map Help

To view a map from a particular Map Collection click on the map name of the linkage group listed in the pane or window. A new page will appear containing the a map of the selected linkage group.

Maps and map collections are generated from individual mapping experiments. Data from published experiments are transferred by SoyBase staff to computer files for presentation by CMap. CMap is a product of the Generic Model Organism Database project (GMOD).

CMap Tutorial

A CMap tutorial as well as general CMap help is available as a link at the top of each CMap display. Each linkage group is ordered into a display similar to a chromosome idiograph. Molecular markers are indicated on the map by black type next to the vertical bar representing a linkage group. A Centimorgan scale is presented on the left side of the linkage group. QTL intervals are indicated by colored lines bounded by diamond shapes at each end. These are presented to the extreme right side of the linkage group map. The QTLs are color coded by arbitrary types. A legend for the features presented in a CMap display is located at the bottom of each map. The marker names, QTL intervals and names are all "clickable" and will return genetic data associated with feature selected.

Note: Many featured items on the CMap display are clickable even though they do not cause the cursor to change when you mouse-over them. So when in doubt about a feature in the CMap display, try clicking on it to see if it is active.

To compare a "reference" map to other maps, use the "Map Options" function of CMap located below the map legend. You can add maps for comparison to the "reference map" (the one you originally selected) to the left or right of the reference map using this function. Click on the "Add Maps Left/Right" link. A new pane will be displayed. To add a map choose the "Add Map Set" pull-down menu. A list of all map collections will be displayed. Choose a map collection to pick an individual linkage group map from. When selected a list of all linkage groups from the chosen map collection that HAVE A FEATURE IN COMMON will be displayed. If a map in the chosen map collection does not have a feature in common with the reference map, IT WILL NOT BE DISPLAYED IN THE LIST. Thus you will only have access to maps that have a "correspondence" to the reference map. Once a map has been chosen, click the "Add Maps" button on the pane to re-build the display with the comparative map. This procedure can be repeated with any number of maps. Note that the more comparative maps displayed, the slower the page will be to re-build. There are many more functions available to the user in CMap. For a full description, please click the "Tutorial" link found at the top of each CMap display.

Locus Help

Information about specific loci can be obtained by typing the name of a locus into the text input box of the "Search database" function of the main SBT window and selecting "locus" from the "All Categories" pull-down menu then clicking the "Go" button. If you are not sure of the entire locus name, wildcard searches are permitted. To substitue any character at a single position in a locus name use the "?" character. For example, "A878_?" would return "A878_1", "A878_2" and "A878_3". It would not return "A878_10" or higher. To match multiple positions with any character use the "*" symbol. For example searching on "Satt4*" returns 98 hits, Satt400 - Satt499. When a locus is selected a new window opens displaying the data for the record. Links within a document are indicated by a blue color.

General querying of the loci mapped in soybean can also be displayed by clincking the "Locus" link on the main page.

QTL Help

QTL information can be obtained directly by searching on a particular QTL identifier using the "Search database" function. If you know the name of a particular QTL you can simply enter it in the "Search database" text entry box, select "QTL" from the "All Categories" pull-down menue and clicking on the "Go" button. You can also access QTL information from CMap displays by clicking on a QTL identifier pictured in the CMap display. The data returned from a QTL query will contain text and occasionally graphic information. Any text in blue is a link to more information

A list of all QTLs in the Toolbox can also be obtained by clicking on the "QTL" link on the Toolbox main page.

Pathology Help

The "Pathology" data type contains a description of the symptoms (pathology) caused by an organism in soybean. A list of "Pathology" identifiers can be obtained by clicking on the "Pathology" link on the Toolbox main page. If you want information on a particular pathology, its identifier can be entered in the "Search database" text box and choosing "Pathology" from the "All Categories" pull-down menu.

Disease Help

The "Disease" data type contains a description of soybean diseases, the causitive agent and other data about the disease. A list of the diseases contained in the Toolbox can be obtained by clicking on the "Disease" link on the home page. If you know the name of a particular soybean disease, you can get the data by entering the disease name in the "Search database" text box and choosing "Disease" from the "All Categories" pull-down menu and then clicking on the "Go" button.