Browsing Features

When browsing the different Features that have been curated in CIViC, users select the type of Feature they wish to browse first.

Browsing Features

Figure 1: When browsing Features, users select the type of Feature to browse. Note that Complex Molecular Profiles can consist of combinations of Feature-Variant pairs with multiple Feature types

In order to browse the selection of Features that have been curated in CIViC, a user can simply use the left menu selection in the user interface, and click on the Features button as outlined in red in the figure below. After that, the Feature Browse table is shown. This table shows Genes by default. Other Features may be viewed by utilizing the Feature Type pulldown menu with the green outline around it in the figure.

Browsing Features in the CIViC user interface

Figure 2: Users should use the left sidebar in the user interface to select the Features view. Users may then select the Feature type they wish to browse.

If Factor is selected under Feature Type, then the Factors for which curation has been done in CIViC are shown:

Browsing view of Factors in the CIViC user interface

Figure 3: Factors in CIViC for which curation has been performed are listed in the Feature browse view, after the Factor Feature type was selected by the user.

This browse view also displays other useful fields associated with the given Feature, including Full Name, which is helpful particularly for Factors which are often abbreviations, such as TMB for Tumor Mutation Burden. Curated Aliases as well as Evidence-associated Diseases and Therapies curated for the given Feature are also shown. In addition, the count of curated Evidence Items, number of Variants, Assertions, and Molecular Profiles associated with the Feature are shown.

Users should also keep in mind that Molecular Profiles, Features, and Variants are almost always clickable in the CIViC interface, and will bring you to the page for the entity of interest. Hovering over these entities can show additional data.

Navigating the Feature-Variant pairs for a Molecular Profile in the Evidence Item view

Figure 4: A CIViC Evidence Item (EID) for the Molecular Profile (MP) EML4::ALK Fusion AND ALK L1198F AND ALK C1156Y is shown. Note that Molecular Profiles in the EID are listed both in the full Molecular Profile form, which lists the entire name, and brings the user to the corresponding Complex MP page when clicked, and also the MP Elements form, which gives explicit links for each element of the Complex MP Feature-Variant pairs. Multiple fields are clickable in EIDs, and also generally throughout the pages of the CIViC interface, and each bring the user to a new page. MPs, Features, and Variants each have their own symbol in the CIViC interface as shown above. Other clickable entities in the EID are the submitter and Editor names, as well as Disease, Therapy, Source, and Clinical Trial fields. The tabs below the EID number EID844 are all clickable, as are the Revise, Flag, and other buttons on the upper right.