Updating Validation lab evidence

[DSuveges]

The hypotheses data model needs to be changed: one target can be validated against different hypotheses in the cell lines. The Validation lab will provide a separate table with the following column (based on discussion with Stuart):

 gene//biomarker-name//biomarker-status-associated-with-significance//hypothesis-free-text-description

Each row is a validated hypothesis, and in the evidence will look like this:

{
  "validationHypotheses":[
    {
      "hypothesis": "KRAS-mut",
      "description": "KRAS mutation"
    },
    {
      "hypothesis": "APC-mut",
      "description": "APC mutation"
    }
  ]
}

[DSuveges]

The parser has been updated to ingest an other file with the above mentioned columns. However we still don't have the actual data. The output looks like this:

{
  "targetFromSource": "ARHGEF7",
  "validationHypotheses": [
    {
      "hypothesis": "MS_status-MSS",
      "description": "mock description"
    }
  ],
  "resourceScore": -6.49,
  "confidence": "not significant",
  "expectedConfidence": "significant",
  "statisticalTestTail": "upper tail",
  "contrast": "Loss of cell viability vs control",
  "studyOverview": "CellTtreGio measurement",
  "datasourceId": "ot_crispr_validation",
  "datatypeId": "ot_validation_lab",
  "diseaseFromSourceMappedId": "EFO_0005842",
  "diseaseFromSource": "colorectal cancer",
  "projectId": "OTAR015",
  "projectDescription": "CRISPR Cas9 Target ID",
  "diseaseCellLines": [
    {
      "name": "MDST8",
      "id": "SIDM00527",
      "tissue": "Large Intestine",
      "tissueId": "UBERON_0000059"
    }
  ],
  "biomarkers": [
    {
      "name": "MSS",
      "description": "Microsatellite stable"
    },
    {
      "name": "CRIS-D",
      "description": "WNT activation, IGF2 gene overexpression and amplification"
    },
    {
      "name": "KRAS-wt",
      "description": "KRAS mutation status: wild type"
    },
    {
      "name": "TP53-wt",
      "description": "TP53 mutation status: wild type"
    },
    {
      "name": "APC-mut",
      "description": "APC mutation status: mutant"
    }
  ]
}

However I have noticed that for certain biomarkers the parsing is not perfect:

  "biomarkers": [
    {
      "name": "MSI",
      "description": "Microsatellite instable"
    },
    null,
    {
      "name": "KRAS-wt",
      "description": "KRAS mutation status: wild type"
    },
    {
      "name": "TP53-wt",
      "description": "TP53 mutation status: wild type"
    },
    {
      "name": "APC-wt",
      "description": "APC mutation status: wild type"
    }
  ]

This issue needs to be fixed as well.

[DSuveges]

All these issues are addressed by now:

• [x] new function introduced to generate the hypothesis object. It's in mock version so far.
• [x] null values are removed from biomarkers.

The current evidence looks like this:

{
  "targetFromSource": "BRCA2",
  "validationHypotheses": [
    {
      "hypothesis": "MS_status-MSS",
      "description": "mock description"
    },
    {
      "hypothesis": "MS_status-MSS",
      "description": "mock description"
    }
  ],
  "resourceScore": 31.89,
  "confidence": "not significant",
  "expectedConfidence": "not significant",
  "statisticalTestTail": "upper tail",
  "contrast": "Loss of cell viability vs control",
  "studyOverview": "CellTtreGio measurement",
  "datasourceId": "ot_crispr_validation",
  "datatypeId": "ot_validation_lab",
  "diseaseFromSourceMappedId": "EFO_0005842",
  "diseaseFromSource": "colorectal cancer",
  "projectId": "OTAR015",
  "projectDescription": "CRISPR Cas9 Target ID",
  "biomarkers": [
    {
      "name": "MSS",
      "description": "Microsatellite stable"
    },
    {
      "name": "KRAS-mut",
      "description": "KRAS mutation status: mutant"
    },
    {
      "name": "TP53-mut",
      "description": "TP53 mutation status: mutant"
    },
    {
      "name": "APC-mut",
      "description": "APC mutation status: mutant"
    }
  ],
  "diseaseCellLines": [
    {
      "name": "SW626",
      "id": "SIDM01168",
      "tissue": "Large Intestine",
      "tissueId": "UBERON_0000059"
    }
  ]
}