oncokb / matchminer-curate Goto Github PK

oncokb_variant: Oncogenic Mutations
matching_examples(optional, manual curated): V600E, V30del

For the current endpoint of "http://oncokb.org/api/v1/variants", provide a boolean option called "includeGeneralMutations". When this option is set to true, return the original oncokb variants plus the general mutations such as "Oncogenic Mutations", "Truncating Mutations" etc.

Create a new endpoint for the matching examples validation.
Input: Hugo Symbol, OncoKB Variant and Matching example.
Supposed return: a boolean value to indicate is the matching example valid.

Check trial status. Hide "Finish Curation" button when status is "In progress".
Delete a trial in MongoDB when the trial is archived.

Store mapping result like patient-trial? Or store result like patient-variant-trial? Or store mapping result like variant-trial?

Also can visualize the matches for specific sample/patient

For a trial having multiple arms, adding new sections will cause some previously added sections to be deleted

Each OncoKB trial has an oncokb_variant attribute. Before we match trials to patients, we need to have an API on OncoKB side to return relative variants of oncokb_variant. Next, load clinical data and variant list to Mongo DB. After all required data load in Mongo, we can start matching.

This file is the project front-end configuration file. Instead of ignoring the file, we need to track it with example data. Otherwise, the front-end built will fail.

1. Prepare a sheet for curators to clean up about the main types
2. Clean up main type data (manually or script)
3. Only use the subtype nodes in the drop-down list

The purpose of this feature is to make curation more flexible. Currently, we strictly stick to the YAML format defined by Match Miner in the curation interface. This caused lots of inconveniences, such as to enter age_input greater than 12 and less than 18, curator have to enter a "Or" section containing two Clinical Section.

Below are two nominated features:
a) Genomic Section
annotated_variant: allow curator to enter multiple variants separated by a comma, such as "V600E,V600K,V600M"

b) Clinical Section
age_input: allow curator to enter an age in the format of ">=12,<=18"

Use this version:
May/1 + development version(Lymphoid and Myeloid)

Angular CLI

1. loop through trials to get a status vocabulary
2. replace current trial status with a dropdown list
3. add an arm status dropdown list

Here is the API end point to use to get all trials info https://discover.mskcc.org:443/api/trials/

For MSK trials, use the discovery API return first(current_accrual and all other fields). If not found, use the clinical trials gov API return.

After adding some sections, can't add a new arm

METHOD
POST

Request

{
  "oncokbVariants": [{
     "hugoSymbol": "",
     "alteration": ""
  }],
  "queries": [{
      "id": "",
      "hugoSymbol": "",
      "alteration": ""
  }]
}

Response:

[
 {
    "query": {
    },
    "result": [{
      "hugoSymbol": "",
      "alteration": ""
    }]
 }
]

• genomic/clinical data formats need to be discussed.
• the output format