Adding OncoKB and CancerHotspots annotation into cBioPortal database

[jjgao]

We would like to do this for two reasons:

1. OncoKB and CancerHotspots annotation has become a bottleneck when loading oncoprint for big queries oncokb calls are slow for large query #5167
2. Supporting OncoKB analysis in study view #5212

A high-level to-do list:

• extend database scheme to add OncoKB and CancerHotspots annotation
• change import pipeline to add annotation
• set up a process and scripts to update annotation when there is new OncoKB or CancerHotspots releases
  • the scripts could be used for importing too
• documentation of the process so that others can use it
• modify frontend code

Questions:

• What data to add?
  • To address # 1, we could add information about whether an alteration is Oncogenic or a hotspot into our database.
  • For # 2, we may need additional information such as oncokb levels. (would on-the-fly loading of levels for oncogenic events fast enough? If so, maybe we don't have to save them in cBioPortal?)
• Where to add annotation?
  • For mutations, we could add it to either mutation_event or mutation table
    • note: level data has to add to mutation table since it's cancer type specific
  • For CNAs, cna_event?
  • How about fusions? Currently we are modeled as mutations but we will separate them into the structural_variant table.
  • Or should we separate them and have a variant_annotation table? Maybe cleaner?
  • Should we consider re-using the DRIVER_FILTER/TIERS columns?

cc'ing @pieterlukasse @schultzn

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[zhx828]

I think we like to keep this open.

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[jjgao]

unstale

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[stale]

This issue has been automatically marked as stale because it has not had recent activity. It will be closed if no further activity occurs. Thank you for your contributions.

[jjgao]

This is being implemented based on RFC56.