The Genome Browser's Track Search feature allows users to find and display tracks of interest quickly and easily.

Searching

Search tab: "Search" is the default tab of the track search feature. To search for a track, enter search terms into the box and click search. This search looks for the user's terms in the track names, descriptions, groups, and metadata. Metadata is information, such as cell line, experiment type, and treatment, about ENCODE data.

Advanced tab: The "Advanced" tab allows users to search for terms in a specific aspect of the track (e.g. the track name, the description, and the track group) and can be especially helpful for finding ENCODE tracks by setting specific criteria in the "ENCODE terms" section of this tab.

• ENCODE terms (not available in all assemblies): This section of the Advanced tab allows users to further refine their search for ENCODE tracks using ENCODE metadata. By default, there are two rows of ENCODE metadata search criteria, but more can be added by clicking the "+" button. To remove an added metadata search row, click the "-" button. Each row is comprised of a drop-down menu followed by either a second drop-down menu or a text field. The first drop-down menu contains the searchable metadata categories available. The type of metadata term selected in the first drop-down determines the type of search available. Some metadata will have a second drop-down containing the possible metadata terms in that category available to search on. Most of these drop downs are multi-select lists, so users can select one or multiple terms. Other metadata types will have a text field for users to enter specific search terms. There are two types of text fields. If the phrase preceding the text field is "contains," then the field is a free text field, with the option of using the percent sign (%) as a wildcard. If the phrase "is among" precedes the text field, then it is possible to enter a comma-separated list to find all tracks with any of the values in the list in that metadata category. This comma-separated list also accepts the percent sign (%) as a wildcard. Because these metadata drop-downs are assembly dependent, the options available may vary from assembly to assembly. Some categories have a link to the far right of the row if there is more information available about the terms.

Results

After clicking the "Search" button, the first 100 tracks that meet the search criteria are displayed.

Check-box/Visibility: Tracks that are currently being displayed in the browser will have their check-box selected. To turn tracks on or off, select or deselect the associated check-box. To turn all tracks listed on the current results page on or off, click the "+" or "-" button at the top of the column. By default, selecting the check-box of a track turns the track to pack as long as pack is a valid view mode of the track. If it isn't, the track is set to full or show. Once the check-box of a track is selected, the visibility can be changed using the drop-down menu in the visibility column.

    This icon designates "container tracks" that can be configured by clicking the icon. Container tracks don't have data themselves; instead, they contain other tracks that do have data. Examples of container tracks are composite tracks, which have a light orange background in the search results, and super-tracks, which have a tan background; tracks that contain data have a yellow background. While tracks within a container track may show up in the search results and can be configured from the search results page, this isn't always the case. Clicking opens the container track configuration page, allowing the all the tracks within the container track to be viewed and configured. Please note, since container tracks don't have data of their own, turning one on via track search may result in no additional tracks in the browser. If this occurs, it is because none of the tracks within the container were turned on.

Track information: To find out more information about a track, click on the Track Name. The description of the track or the container track will pop-up. Click "x" at the top of the pop-up or the "OK" at the bottom to close it. For tracks that have metadata, mainly ENCODE tracks at this time, there is a "..." link on the right-hand side of the track result row. Clicking this link expands the row to show the track's metadata.

Sorting: By default, resulting tracks are listed in order of relevance. However, in the blue header of the results list, the sort order can be changed by selecting one of the other radio buttons, "Alphabetically" or "by Hierarchy" (super-tracks listed first, then composite tracks, and then data tracks).

Return to Browser/View in Browser: The "Return to Browser" button indicates that no tracks have been turned on or off. Clicking on the button returns the user to the browser. Once any track is turned on or off using the check-boxes, the button label changes to "View in Browser" (indicating changes have been made), and clicking on the button takes the user to the browser with the new track selections displayed.