Wiki Browser Track

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Wiki Browser Track

A user modified track on the genome browser.

Purpose

Allows any user of the genome browser to add their own annotations to the genome at any place of interest.

Features

Originating user can add and edit features. Other users can add comments to include with the feature. TrackUi options could include:

  • The usual track visibilities
  • pull down filter menu: "show all features", "show only my features", "show only other's features"
  • date of creation filter
  • date last modified filter

Implementation

An entry system allows the creation of the feature. Users are authenticated via genomewiki. Other users will see the features on the genome browser and they can add notes to the feature. To allow any edits, a user would need to go through the genomewiki login.

Details

Entry system characteristics would allow the selection of start and stop coordinates of the feature with the initial coordinate defaults the current browser view. You could also allow coordinate entry with a start and length specification. These could be three entry boxes with java script to allow an alteration to the start or end coordinates to change the length field, or a change to the length field to alter the end coordinate. There could be a simple color choice pull-down menu for the item. A name entry field for the item. A strand pull-down choice. Description page text contents would be started at this initial creation time. Characteristics such as originating owner, date of initial creation would automatically be added to the feature. There would also be a date of last modification.

An originating owner of a feature could change any of the initial characteristics. The edit system needs to have a "preview" mode and a "submit" mode.

Other uses can add notations to the details page.

A user could enter the add or edit system via any details page or the trackUi page. Only originating users would see the "edit" option when they view their features. Others would only see "add comments".

Potentially

Added features to one genome could automatically be lifted over to other genomes. Thus an addition to any one genome would add the feature to other genome browsers too.

Where is the data

The data tables for the features need to be kept in a separate and unique database that is available to all the RR machines. Note potential synchronization, backup, and mirror site difficulties to be solved.

Feature Structure

It can be a bed 6+ data type, and thus displayed in hgTracks as a bed track, and manipulated in hgTables as a bed track.

  • chrom
  • chromStart
  • chromEnd
  • name
  • score
  • strand
  • db - database for this item - since this table is most-likely in hgcentral
  • owner - creator of item - enables special editing privs, useful in filter
  • color - useful ?
  • class - classification of item (perhaps browser group)
  • creationDate - perhaps useful in a filter
  • lastModifiedDate - perhaps useful in a filter
  • descriptionKey - reference to Wiki page where description edits are maintained
  • id - auto-increment item ID

To Do

  • TrackUi filter functions
  • Table browser functions
  • probably better to return to the browser after add item rather than item display
  • also return to genome browser after adding comments to an existing item
  • possible a special entry box area for publication reference links
  • this all may be more useful as an annotation mechanism for UCSC genes