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completing descriptions and validation for genomic alteration annotations #28

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86 changes: 47 additions & 39 deletions oncodashkb/adapters/copy_number_alterations.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -86,13 +86,6 @@ transformers:
- citation_PM_ids
for_objects:
- alteration
- map:
columns:
- consequence
to_property:
- consequence
for_objects:
- alteration
- map:
columns:
- level_of_evidence
Expand All @@ -103,73 +96,97 @@ transformers:
metadata:
- name: copy_number_alterations



validate: # Validation for cna labeled "external.".
columns:
patient_id:
dtype: str
description: "Cohort code from clinical data"
sample_id:
dtype: str
description: "Sample id of biopsy (origin OVCA database)"
referenceGenome:
dtype: str
description: "Standard human reference genome used in WGS read alignment"
checks:
isin:
value:
- GRCh37
- GRCh38
hugoSymbol:
dtype: str
description: "Gene name in Hugo nomenclature"
checks:
str_matches: ^[a-zA-Z0-9-]+$
alteration:
dtype: str
description: "Genomic alteration type"
checks:
isin:
value:
- AMPLIFICATION
- '4' #FIXME: possible error.
# - DELETION #FIXME: not present in data declared in source description.
# - UNKNOWN #FIXME: not present in data declared in source description.
hugoSymbol:
dtype: str
checks:
str_matches: ^[a-zA-Z0-9-]+$
- DELETION
- UNKNOWN
tumorType:
dtype: str
description: "Tumor type abbreviation (OncoTree based)"
checks:
isin:
value:
- HGSOC
- '5' #FIXME: possible error.
oncogenic:
dtype: str
description: "Indication of alteration oncogenecity"
nullable: true
checks:
isin:
value:
- Inconclusive # Not present in source documentation description.
- Inconclusive
- Likely Neutral
- Likely Oncogenic
- Oncogenic
- Unknown
- known # Not present in source documentation description.
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@mbaric758 mbaric758 May 16, 2025

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Here known still comes out as a value present in the data.

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@njmmatthieu njmmatthieu Nov 19, 2025

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I added "known" then.

mutationEffectDescription:
dtype: str
description: "Brief overview of the biological effect of the alteration with references"
nullable: true
gene_role:
dtype: str
description: "The biological effect of a mutation/alteration on the protein function"
nullable: true
checks:
isin:
value:
- Act # Not present in source documentation description.
- Gain-of-function
- Inconclusive
- Likely Gain-of-function
# - Likely Loss-of-function FIXME: not present in data declared in source description.
# - Likely Neutral FIXME: not present in data declared in source description.
# - Likely Switch-of-function FIXME: not present in data declared in source description.
# - Loss-of-function FIXME: not present in data declared in source description.
- LoF # Not present in source documentation description.
# - Neutral FIXME: not present in data declared in source description.
# - Switch-of-function FIXME: not present in data declared in source description.
- Likely Loss-of-function
- Likely Neutral
- Loss-of-function
- Unknown
- ambiguous # Not present in source documentation description.
- Act
- LoF
- ambiguous
citationPMids:
dtype: str
description: "Citations related to the biological effect separated by semicolon"
nullable: true
checks:
str_matches: ^[0-9]{7,}(,[0-9]{7,})*$
str_matches: ^[0-9]{7,}(;[0-9]{7,})*$
geneSummary:
dtype: str
description: "Brief overview of the gene and its role in cancer"
nullable: true
variantSummary:
dtype: str
description: "Brief description of the variant oncogenicity"
nullable: true
tumorTypeSummary:
dtype: str
description: "Describes the therapeutic implication that applies to the drug indication in discovered cancer"
nullable: true
level_of_evidence:
dtype: str
description: "The highest level of evidence for therapeutic implications based on OncoKB (CGI levels are mapped to this)"
nullable: true
checks:
isin:
Expand All @@ -180,13 +197,4 @@ validate: # Validation for cna labeled "external.".
- LEVEL_3B
- LEVEL_4
- LEVEL_R1
- LEVEL_R2
geneSummary:
dtype: str
nullable: true
variantSummary:
dtype: str
nullable: true
tumorTypeSummary:
dtype: str
nullable: true
- LEVEL_R2
125 changes: 65 additions & 60 deletions oncodashkb/adapters/copy_number_alterations_local.yaml
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Original file line number Diff line number Diff line change
Expand Up @@ -86,13 +86,6 @@ transformers:
- citation_PM_ids
for_objects:
- alteration
- map:
columns:
- consequence
to_property:
- consequence
for_objects:
- alteration
- map:
columns:
- level_of_evidence
Expand All @@ -106,96 +99,108 @@ metadata:

validate: # Validation for cna labeled "local.".
columns:
# unnamed:0: #FIXME: weird column.
# dtype: int64
patient_id:
dtype: str #FIXME: not present in data declared in source description.
dtype: str
description: "Cohort code from clinical data"
sample_id:
dtype: str
description: "Sample id of biopsy (origin OVCA database)"
referenceGenome:
dtype: str
description: "Standard human reference genome used in WGS read alignment"
checks:
isin:
- GRCh37
- GRCh38
- '2' #FIXME: possible error.
hugoSymbol:
dtype: str
description: "Gene name in Hugo nomenclature"
alteration:
dtype: str
description: "Genomic alteration type"
checks:
isin:
value:
- AMPLIFICATION
- '4' #FIXME: possible error.
# - DELETION FIXME: not present in data declared in source description.
# - UNKNOWN FIXME: not present in data declared in source description.
- DELETION
- UNKNOWN
tumorType:
dtype: str
description: "Tumor type abbreviation (OncoTree based)"
checks:
isin:
value:
- HGSOC
- '5' #FIXME: possible error.
nMajor: #FIXME: not present in data declared in source description.
dtype: float64
nMinor: #FIXME: not present in data declared in source description.
dtype: float64
lohstatus: #FIXME: not present in data declared in source description.
ploidy:
dtype: float64
description: "The number of complete sets of chromosomes in cancer cells"
nMinor:
dtype: int64
description: "Minor allele copynumber"
nMajor:
dtype: int64
description: "Major allele copynumber"
lohstatus:
dtype: str
description: "Loss of heterozygosity status"
checks:
isin:
value:
- HET
- '8' #FIXME: possible error.
ploidy: #FIXME: not present in data declared in source description.
dtype: float64
start: #FIXME: not present in data declared in source description.
dtype: float64
end: #FIXME: not present in data declared in source description.
dtype: float64
strand: #FIXME: not present in data declared in source description.
dtype: float64
- LOH
chromosome:
dtype: str
description: "Chromosome number where alteration is occurring"
start:
dtype: int64
description: "Start position of alteration in chromosome"
end:
dtype: int64
description: "End position of alteration in chromosome"
strand:
dtype: int64
description: "DNA strand"
checks:
isin:
value:
- -1.0
- 1.0
- 12.0 #FIXME: possible error.
band: #FIXME: not present in data declared in source description.
- -1
- 1
band:
dtype: str
nProbesCr: #FIXME: not present in data declared in source description.
dtype: float64
nProbesAf: #FIXME: not present in data declared in source description.
dtype: float64
logR: #FIXME: not present in data declared in source description.
description: "Chromosomal locus"
nProbesCr:
dtype: int64
description: "Number of probes"
nProbesAf:
dtype: int64
description: "Number of probes"
logR:
dtype: float64
baf: #FIXME: not present in data declared in source description.
description: "Signal intensity"
baf:
dtype: float64
nAraw: #FIXME: not present in data declared in source description.
description: "B-allele frequency of occurrence"
nAraw:
dtype: float64
nBraw: #FIXME: not present in data declared in source description.
description: "Calculated copy number of allele A"
nBraw:
dtype: float64
purifiedLogR: #FIXME: not present in data declared in source description.
description: "Calculated copy number of allele B"
purifiedLogR:
dtype: float64
purifiedBaf: #FIXME: not present in data declared in source description.
description: "Mean signal intensity"
purifiedBaf:
dtype: float64
purifiedLoh: #FIXME: not present in data declared in source description.
description: "B-allele frequency measurement"
purifiedLoh:
dtype: float64
minPurifiedLogR: #FIXME: not present in data declared in source description.
description: "LoH measurement"
minPurifiedLogR:
dtype: float64
maxPurifiedLogR: #FIXME: not present in data declared in source description.
description: "Minimum measured signal intensity"
maxPurifiedLogR:
dtype: float64
breaksInGene: #FIXME: not present in data declared in source description.
dtype: float64
checks:
isin:
value:
- 0.0
- 1.0
- 2.0
- 3.0
- 4.0
- 5.0
- 6.0
- 7.0
- 25.0 #FIXME: possible error.
description: "Maximum measured signal intensity"
breaksInGene:
dtype: int64
description: "Number of copy number level shift points in alteration"
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