• Documentation

Gramene Maps and CMap Database Help Document

A. Maps Concepts

B. Searching/Browsing

C. Comparing and Customizing Maps

D. Other Help

Maps Concepts

A. Maps and Map Sets

In Maps, a map is a linear array of interconnected features. This could represent a single linkage group in the case of a genetic map, or a single contig for physical maps. Related maps are grouped into map sets. Generally, these are the result of a particular study, such as the set of linkage groups produced by a genetic mapping study. For more information about the map sets contained in the database, visit the Map Set Info page.

B. Reference and Comparative Maps

In Maps, you can use the CMap tool to compare maps. (For more information on CMap see http://www.gmod.org/cmap.) To set up a comparison, first select a reference map set, then a reference map. This serves as the basis for any comparisons that will be made. Once the reference map image has been rendered, select one or two comparative maps. These comparative maps may be added to both the left and the right of the reference map. Additional maps may be added for as long as valid comparisons are available.

C. Features and Feature Types

Any item that is positioned on a map is called a feature. The position may be either a point or an interval. Different feature types are displayed on the map image and represented by different shapes (such as horizontal tick marks [for points], line intervals, boxes, arrows, etc.) or different colors, and will be identified on the map legend. For more information on any feature, click on it to view the corresponding feature detail page. Features are frequently mapped markers from the Markers module, and the feature detail will link to the marker data in the Markers module.

D. Correspondences

The lines that connect features on one map to features on another map denote correspondences. These correspondences are assigned either automatically (based on feature name) or manually by the data curator to designate features on different maps that are equivalent in some manner. Different colors represent different correspondence types, and will be identified on the map legend.

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Map search/browse options

1. Maps

This page is used to view and compare maps.
• Map searches will result in your map being displayed in the CMap Viewer. Options for changing your views and for comparing maps will be discussed in the next section.
1. Select a species from the drop-down list. Oryza sativa is the default, unless you have previously visited the page, whereby you will open to the last species you searched. If you change species you will need to click "Change Species". Only map sets from this species will be displayed in the next drop-down list. Note that selecting a new reference species when in the middle of a search will reset all other map options.
2. Select a reference map set from the drop-down list, and click on "Show Selected Set's Maps". For descriptions of all the map sets, see the Map Sets link in the Maps menu above, Info page. You must select a reference map set before any of the other options become available. Note that selecting a new reference map set part way through a search will reset all other map options.
   • The Gramene Annotated Nipponbare Sequence map (formerly the Gramene IRGSP Assembly) is specifically created as an ideal reference map because all maps in CMap have a reference to this map, and this allows you to compare maps that don't have direct correlations with each other.
3. Select a reference map from the drop-down list that appears after you select a reference map set. (You must first select a reference map set before this option becomes available.) The list is limited to maps that are part of the selected map set. Choosing a reference map allows other options to become available.
• If only one map is selected from the reference maps list, a start and stop can be specified for the map.
• If you don't want to accept the default settings for this map you may select how each feature type will be displayed, if at all. Choose to ignore, display or display only those features that have correspondences displayed. The "Other" value tells Maps how to handle feature types that are not on the current maps but may be on comparative maps added later. These can be changed at any time by using the "Feature Options".
4. Click on "Draw Maps".
• Your selection is immediately rendered as a map image. By default, the entire length of the map is displayed. This first map is called the "reference map". To learn about your map options, see section #1 under "Viewing and Comparing Maps".
• Any maps you may add to either side will be referred to as "comparative maps" . See the next section on "Comparing Maps". (See section #2 under "Viewing and Comparing Maps".)

2. Map Search

• The Map Search page allows searching for a map based on species, map set, and map name (if known). For searching multiple maps by name, separate them with whitespace or commas.The results give you information about the maps, such as the Map Name, Number of related maps, Number of related maps per unit, Number of correspondences, start, stop, and numbers of each feature type on the map. This information is sortable.
• If you want to search maps with a minimum number of correspondences to other maps, use the Map Search method, which is conducted similarly to the above search, but in fewer steps.

3. Feature Search

• Type in one or more names or accession ID's in the "Feature Names" box, separating them with whitespace or commas. Names with multiple words should be enclosed with "double quotes". Use "*" or "%" as wildcards.
• Optionally filter by one or more species, and by one or more feature types. By default, both the feature name and alternate name fields will be searched, but this may be restricted to one or the other.
• Results are sortable by clicking on hyperlinked column headers, and features link to the map set, CMap, and feature detail. Click on "View on Map" to see the map with the feature highlighted.
Feature Details - The feature details page lists what is known about a feature and its correspondences.
• Feature Name - The name of the feature. This is the text that is displayed as the feature label in the map image.
• Aliases - Synonyms, aliases, or other names by which a feature may be known.
  • The feature alias details page shows the alias for a given feature name along with any defined attributes and cross-references.
• Acc ID -Unique accession ID.
• Feature Type - The type of a feature.
  • The feature type detail page describes the feature display on a map and give a feature type description. For an overview of all possible feature types, see feature types.
• Map - Map on which this feature may be found.
  • Map Details - Viewing Map Details will open the map with the feature highligted on the map. Below the map and the CMap options you will find the Map Details and Map Features.
• Start - The start position of a feature.
• Stop - The stop position of a feature. No entry ("NULL") means that the feature is a point.
• Cross-References and Attributes - Any links to external databases or the feature information available in the Markers database.
• Correspondences - This table lists all the corresponding features from other maps associated with the feature. Click on the feature's name to view the feature details page for the corresponding feature. "View On Map" takes you to the appropriate map with the corresponding feature highlighted. "Comparative View" also takes you to the Map Viewer, but with both the original reference map and the corresponding map being compared.
  • The Correspondence detail page provides details about a correspondence between two features in Maps. At the top, the features are listed along with their maps, positions and feature types. There are links present to take you to the details on the map sets, maps, or the features themselves. Also present are any attributes and cross-references which have been defined by the curators. Below it you will see all the evidence supporting the correspondence along with a link to the details on each evidence.

4. Matrix

The matrix will show the number of correlations between the selected reference map(s) and all maps in CMap.
1. Select your reference set options - these maps will be compared to all the maps in CMap. It is recommended to limit your reference map(s) to at least a species and/or map type or your results will be overwhelmingly large. For example, if you are looking for rice QTL maps with correlations other species, select map typs "QTL" and species "Rice".
   • Select "Use Colors" and the results will (or should be) be color-coded by number of correspondences.
   • Select "hide empty rows" to omit those mapsets with "0" correlations
2. Click Submit
   • In its initial view, the matrix shows the number of correspondences between pairs of map sets. Selected reference maps will be listed down the right hand side of the page, and across the top of the matrix will list the maps in CMap organized by map type and then species.
   • The table will display the total number of correlations between each map set.There are two numbers. The first number is the number of correlations, the second number is the number of maps that contain these correlations.
3. Click on a number in a cell to view a more detailed comparison between a specific pair of map sets, broken down by map.
4. Click on a number in a cell to go to the map viewer showing a comparison of the two maps.

5. Browse by:

a. Map Sets - lists all maps in CMap, organized by species. This page displays the full and abbreviated names of the map set. (For more information on what constitutes a map set, see the Section A above.) Also shown are the species, map type, map units, any remarks the curator has added, and the listing of the maps in the set if the maps are allowed to act as reference maps. Optionally you may restrict the list by species and/or map type. These link to Map Set and Map details, Matrix, and map viewer.

b. Feature Types. This page displays each feature type's name, shape, color and description. These link to search results for each feature type, from which you sort results by column, or link to the map set and map viewer, and returns you to the Feature Search (see above).

c. Map Types. Map types give Accession ID, map unit, and brief map type and map legend descriptions. Additionally, each map type is flagged as to whether or not it is considered by the curators as a "relational only" map, meaning that maps of this type can only be viewed in relation to some reference map. (You will not be able to select these as a reference map). Links from here lead to a map type search - putting you back to Map Set information (see above, "a".)

d. Species - Groups map sets by species type and map type. Links to map set data and info (for accessing the map viewer), as well as the matrix (for exploring correlations with other maps.)

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Viewing Maps and Customizing Maps

1. Viewing Maps in CMap

Get a map using one of the search or browse options above (ie see Map search/browse options -->Maps)
• At the top of the image is a box indicating the species and map set name.
• Below that, but above the map is the map name and number of features [in brackets].
• Clicking on the map name and/or feature number will open the map details below your map (the same as "?" below.)
• In addition to this information, the box at the top of the page and the area above the map will offer some or all of the following controls (each surrounded by a box):
  • [ i ]: View the map set information
  • [ ? ]: View the map details page for the map. For the reference map it will open below the map, for a comparative map it will take you to a new page.
  • [ X ]: Delete the map set from the viewer (does not apply to the original reference map, this will be found only on any comparative maps you have added)
  • [ x ]: Delete the map from the viewer (does not apply to the original reference map, this will be found only on any comparative maps you have added)
  • [ L ]: Limit this slot to only this map - In the instance where you may have simultaneously selected multiple maps from a mapset, these maps will appear in the same "slot" or panel of maps. Clicking the "L" will delete all the other maps in that slot (panel).
  • [ F ]: Flip the map - Sometimes when there are a lot of cross-overs, it may be helpful to flip one of the maps for a better view.
  • [ UF ]: Unflip the map - Found only on maps that have been flipped. Click this to return it to it's original position.
  • [ M ]: View the Matrix for this map. - Open the matrix to let you see all the maps in Gramene that have correlations to this map. This may help you to select a comparative map.
  • [ N ]: Create a new map viewer - Lets you start from the beginning, using the selected map as the reference map.
• The vertical scale bar indicates positions along the length of the map. The distance measure (e.g., cM) being used, when appropriate, is printed at the bottom of the scale bar. Features are drawn at appropriate positions. A legend defining the color and the various feature types shown on the map is printed at the bottom of the image. Click on a feature label to view the feature details page for that feature.
• Note that not every feature may be labeled. The drawing algorithm will try to fit as many labels as it can, until there is no more available space. To see more labels, you may wish to increase the image size or decrease the font size. You may also specify "Start" and "End" positions to zoom in to a particular region on the reference map.
• If two or more maps are being compared, each map will be drawn in a separate slot/panel. Adjacent maps will have correspondence lines that connect corresponding features. The color of the line depends on the type of correspondence, indicated in the legend at the bottom of the map image.
• In the lower-right-hand corner is a watermark indicating the version of CMap used to draw the map. This is also hyperlinked to the CMap homepage, www.gmod.org/cmap.

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2. Customizing and Comparing Maps

Once you have a map in the map viewer there are many options for customizing the view as well as comparing the map to other maps in CMap.
Underneath the map are four buttons as follows:
• Save Link - Maps cannot be bookmarked, but links may be created using the "Save Link" button on the map viewer page. SEE Saved Links help below
• Dotplot needs explanation
• eliminate Orphans - Remove comparison maps that don't have correspondences to a reference map. needs explanation - when do you use this? are you saying that any maps you add to a comparison map also have to have correspondences to the reference map? And that even if a map has a correspondence to a reference map it will not be displayed as an option unless it also has a correspondence to the reference map? can you uneliminate them?
• New Reference Maps - Click to to begin a new reference map selection from the beginning (see "Maps", above.)

a. Map Options Menu (compare maps)

This is where you can add comparative maps to your reference map. Each Map set with one or more maps displayed on the image is represented in this table. The reference map set is shaded a different color than the comparative maps. The individual maps from each mapset are also displayed unless there are a large number in the slot/panel.
• Add Maps Left/Add Maps Right - Click on these to add comparative maps to either/both side(s). A new menu will open in a grey box.
  1. Min. Correspondences - Optionally, Indicate an integer value of the minimum number of correspondences that a map must have to another map in order to be displayed. Click "Refresh Menu" if you have changed this number.
  2. Compare Maps (Left and Right) - From the drop down selection, select the map set from which you would like to use a map for comparison. The number in brackets indicates the number of maps within the map set that meet your minimum correspondences filter to your current reference map.
  3. Select one or more of the maps to add to the viewer. Only maps which have some correspondence to the neighboring map are listed. The number of correspondences is shown in square brackets. The default is to compare all the maps of the mapset, but you may select a single map for comparison, or select multiple maps by pressing the "CTRL" button as you make your selections.
  4. Stack - If you select two or more comparison maps, use this selection to compile them into one maps. needs explanation - why would a user want to do this?The number associated with the "stack", when viewed, simply refers to the position of that map set from the reference map. Maps on the left will be negative numbers, maps on the right will be positive.
  5. Click "Add Maps" to draw your comparison map.
• After your comparative map has been added, you may continue to add maps for as long as there are comparisons to be made (repeat previous steps). Each map will be compared to it's adjacent map.
• An important purpose of the reference map is to be able to compare two maps that have correlations to the reference map, but not to each other. This is the purposed of the Gramene Annotated Nipponbare map - all the features that are on maps in CMap have been put onto this map. Using the Gramene Annotated map allows you to compare two maps without correlations by loading one map on the right and one map on the left.
• You may also edit some other map options as follows:
  • Min. Correspondences - Once a comparative map has been added, this box will reflect the number you entered above when adding the map. If this number is changed, be sure to redraw map. This may be used when you have multiple maps from a map set as comparative maps, and you decide to increase the minimum number of correspondences, then maps with fewer correspondences will be dropped. HOWEVER, this does not work in reverse - if you decrease the minimum correspondences, it will not increase the number of maps from that mapset that are displayed - in this case you should delete the map set and add it again with the new minimum number of correspondences.
  • Align Vertically - This option is available only for the reference set. If there are multiple reference maps, you can choose to have them side by side or stacked vertically. Click "redraw".
  • Stack - you can stack or unstack maps here. See explanation in step #4 above.
  • Start/Stop - Each individual map has this option. It dictates the start and stop can be specified for the map.
  • Magnification - Each individual map has this option. It dictates the magnification of this map compared to it's original size.
  • Flip - Each individual map has this option. It dictates if this map is flipped. This option can also be accessed from the map, itself, and is useful when the correlational lines cross over each other.

b. Feature Options Menu (Customize what is displayed on the map.)

• Highlight Features - Enter features to highlight them on the map. Separate multiple features with commas or spaces. If you wish to highlight a feature that has spaces in its name, then enclose the feature name in double quotes.
• Feature Types - Select how each feature type will be handled. Choose to ignore or not display a feature type, display a feature type, or display that feature type only when it has correspondences to the comparison map. The "Other" value tells Maps how to handle feature types that are not on the current maps but may appear on future comparative maps.
• Show Labels - Select which class of feature labels to show on the map.
  • None: Show no labels.
  • Landmarks: Show labels of features designated as landmarks or those with correspondences.
  • All: Show all labels that will fit in the image.
• Collapse Overlapping Features - Allows you to collapse spanning features of the same type which occupy the exact same coordinates as other features.

c. Correspondence Options (Customize the comparisons between the maps)

• Include Correspondence Types - Select how each correspondence type will be handled. Choose to ignore (not display), or use a correspondence type. Or you may use only those correspondences that have a score greater than or less than the specified score.needs explanation - how are scores created?
• Aggregate Correspondences - Choose to draw all of the correspondences individually, or draw all the correspondenses between each map as one line (the average location on each map) or two lines (the span of locations on each map).
• Correspondence lines drawn to - Have the individual correspondence lines drawn to either the feature or the map (the vertical scale bar).
• View Intra-slot Correspondences - If you have selected multiple maps from a map set to be drawn together, they will appear within a single slot (panel). If correspondences have been created between the maps in the same map set, you can select this option to display them.
• Aggregate Evidence Types Separately - If you have selected to aggregate correspondences (previously in correspondence options), correspondences with different evidence types can be separated with this option.

c. Display Options Menu (Customize the Map Display)

• Map Size - Select the relative display size of a reference map.
• Font Size - Select the desired size of the fonts.
• Image Type - Select the image format you prefer.
• Clean View - Do not display the navigation buttons on the image. This is useful for publications.

d. Advanced Options Menu (Customize Map displays in comparison to each other)

• Draw Maps to Scale - Draw the maps that have the same base units to scale with respect to each other. The base units must be defined as scalable in the config file.
• Clickable Image - To increase render time for views that display a lot of features, you can choose not to have clickable features (which leaves the navigation buttons intact) or to remove all clickable elements from the image.
• Menu Order of Comparative Maps - Order the maps in the comparative map menu by their predefined order (specified in the database) or by the number of correspondences.
• Ignore Image Map Sanity Check - If an image has an insane number of clickable elements on it this can cause a browser (IE) to crash, and increases transmission and render time. When a threshold of the number of elements on an image is crossed (the number defined in the config file), Maps will disable all clickable elements and print a warning. The user can ignore this warning (at the user's peril).

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Other Help

Evidence Types	This page lists the name an evidence type, its accession ID, rank (in relation to other evidence types), the color of the line representing the correspondence, and any attributes or cross-references established by the curators.
Saved Links	Links can be created using the "Save Link" button on the map viewer page. Links are organized and accessed by link group. This can be anything the user wants. Some suggestions are some combination of user, project, department or date. Permanent Links have the session information stored in the server's database which makes it stable to use for bookmarking and for sharing. Legacy Links use the legacy link parameters. The advantage of this link is that it will be stable across different servers (with the same data). The disadvantages are that it can get longer than a browser (IE) can handle. It also cannot handle the complex options such as minimum correspondences (which can be different for each map set added in the image). Hidden links - When there are a lot of saved links, the saved link viewer page might get cluttered. Hidding a link makes it invisible to the saved link viewer (unless specifically looking for hidden links) but is still in the database so that it can be accessed (via bookmark or other system). Importing Links - Links can be imported from xml file using the cmap_admin.pl script on the server. Ask you administrator to view the ADMINISTRATION document if you wish to utilize this feature.
Tutorial	More in-depth than the help pages, use the tutorial for an exaple of using the database, see how it integrates other datasets, and get tips to increase your data search efficiency.
FAQ	Frequently Asked Questions - see what questions users have asked, and get the developers answers.
Release Notes	For more information about the most recent release.

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