diff --git a/README.md b/README.md index 58d4c3e..b84abc1 100644 --- a/README.md +++ b/README.md @@ -1,5 +1,8 @@ -## UPDATE: v3.4 allows you to include descriptions into the annotated files. See [Columns added section](#columns-added) for more details +## UPDATE: +- v3.4 allows you to include descriptions into the annotated files with `-d` parameter. +- When annotating genomic change, HGVSg, three additional columns will be added. `ONCOKB_HUGO_SYMBOL`, `ONCOKB_PROTEIN_CHANGE` and `ONCOKB_CONSEQUENCE` +- See [Columns added section](#columns-added) for more details # oncokb-annotator API token required, please see [OncoKB™ API section](#oncokb-api) for more information @@ -116,33 +119,34 @@ python ${FILE_NAME.py} -i ${INPUT_FILE} -o ${OUTPUT_FILE} -b ${ONCOKB_API_TOKEN} ## Columns added ### MafAnnotator/CnaAnnotator/StructuralVariantAnnotator/FusionAnnotator - -| Column | Possible Values, Conditions | Description | -|-----------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|-----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| -| ANNOTATED | True, False | Whether the variant is annotated by OncoKB successfully. | -| GENE_IN_ONCOKB | True, False | Whether the gene has been curated by the OncoKB Team. | -| VARIANT_IN_ONCOKB | True, False | Whether the variant has been curated by the OncoKB Team. Note: when a variant does not exist, it may still have annotations. | -| MUTATION_EFFECT | Gain-of-function, Likely Gain-of-function, Loss-of-function, Likely Loss-of-function, Switch-of-function, Likely Switch-of-function, Neutral, Likely Neutral, Inconclusive, Unknown | The biological effect of a mutation/alteration on the protein function that gives rise to changes in the biological properties of cells expressing the mutant/altered protein compared to cells expressing the wildtype protein. | -| MUTATION_EFFECT_CITATIONS | PMID, Abstract, Website link | All citations related to the biological effect. | -| ONCOGENIC | Oncogenic, Likely Oncogenic, Likely Neutral, Inconclusive, Unknown, Resistance | In OncoKB™, “oncogenic” is defined as “referring to the ability to induce or cause cancer” as described in the second edition of The Biology of Cancer by Robert Weinberg (2014). | -| LEVEL_* | Therapeutic implications | The leveled therapeutic implications. | -| HIGHEST_LEVEL | LEVEL_1, LEVEL_2, LEVEL_3A, LEVEL_3B, LEVEL_4, LEVEL_R1, LEVEL_R2 | The highest level of evidence for therapeutic implications. Order: LEVEL_R1 > LEVEL_1 > LEVEL_2 > LEVEL_3A > LEVEL_3B > LEVEL_4 > LEVEL_R2 | -| HIGHEST_SENSITIVE_LEVEL | LEVEL_1, LEVEL_2, LEVEL_3A, LEVEL_3B, LEVEL_4 | The highest sensitive level of evidence for therapeutic implications. Order: LEVEL_1 > LEVEL_2 > LEVEL_3A > LEVEL_3B > LEVEL_4 | -| HIGHEST_RESISTANCE_LEVEL | LEVEL_R1, LEVEL_R2 | The highest resistance level of evidence for therapeutic implications. Order: LEVEL_R1 > LEVEL_R2 | -| TX_CITATIONS | PMID, Abstract, Website link | All citations related to therapeutic implications. | -| LEVEL_Dx* | Tumor type the level of evidence is assigned to | The leveled diagnostic implications. | -| HIGHEST_DX_LEVEL | LEVEL_Dx1, LEVEL_Dx2, LEVEL_Dx3 | The highest level of evidence for diagnostic implications. | -| DX_CITATIONS | PMID, Abstract, Website link | All citations related to diagnostic implications. | -| LEVEL_Px* | Tumor type the level of evidence is assigned to | The leveled prognostic implications. | -| HIGHEST_PX_LEVEL | LEVEL_Px1, LEVEL_Px2, LEVEL_Px3 | The highest level of evidence for prognostic implications. | -| PX_CITATIONS | PMID, Abstract, Website link | All citations related to prognostic implications. | -| GENE_SUMMARY (Optional) | Only when parameter -d is specified | Brief overview of the gene and its role in cancer | -| VARIANT_SUMMARY (Optional) | Only when parameter -d is specified | Variant summary describes the variant oncogenicity, last review if it is VUS | -| TUMOR_TYPE_SUMMARY (Optional) | Only when parameter -d is specified | Tumor type summary describes the therapeutic implication that applies to the indication | -| DIAGNOSTIC_SUMMARY (Optional) | Only when parameter -d is specified | Diagnostic summary that applies to the indication, for hematologic malignancies only | -| PROGNOSTIC_SUMMARY (Optional) | Only when parameter -d is specified | Prognostic summary that applies to the indication, for hematologic malignancies only | -| MUTATION_EFFECT_DESCRIPTION (Optional) | Only when parameter -d is specified | The mutation effect description provides a brief overview of the biological and oncogenic effect of the VPS and includes appropriate references to peer-reviewed literature. | - +| Column | Conditions | Possible Values | Description | +|-----------------------------|----------------------------------------------------|-------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------|----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------| +| ANNOTATED | | True, False | Whether the variant is annotated by OncoKB successfully. | +| ONCOKB_HUGO_SYMBOL | Only added when annotating genomic change or HGVSg | | When annotating genomic change, we obtained gene hugo symbol from GenomeNexus. This can be cross-referenced with your own gene name. | +| ONCOKB_PROTEIN_CHANGE | Only added when annotating genomic change or HGVSg | | When annotating genomic change, we obtained alteration protein change from GenomeNexus. This can be cross-referenced with your own protein change. | +| ONCOKB_CONSEQUENCE | Only added when annotating genomic change or HGVSg | | When annotating genomic change, we obtained alteration consequence from GenomeNexus. This can be cross-referenced with your own consequence/Variant Class. | +| GENE_IN_ONCOKB | | True, False | Whether the gene has been curated by the OncoKB Team. | +| VARIANT_IN_ONCOKB | | True, False | Whether the variant has been curated by the OncoKB Team. Note: when a variant does not exist, it may still have annotations. | +| MUTATION_EFFECT | | Gain-of-function, Likely Gain-of-function, Loss-of-function, Likely Loss-of-function, Switch-of-function, Likely Switch-of-function, Neutral, Likely Neutral, Inconclusive, Unknown | The biological effect of a mutation/alteration on the protein function that gives rise to changes in the biological properties of cells expressing the mutant/altered protein compared to cells expressing the wildtype protein. | +| MUTATION_EFFECT_CITATIONS | | PMID, Abstract, Website link | All citations related to the biological effect. | +| ONCOGENIC | | Oncogenic, Likely Oncogenic, Likely Neutral, Inconclusive, Unknown, Resistance | In OncoKB™, “oncogenic” is defined as “referring to the ability to induce or cause cancer” as described in the second edition of The Biology of Cancer by Robert Weinberg (2014). | +| LEVEL_* | | Therapeutic implications | The leveled therapeutic implications. | +| HIGHEST_LEVEL | | LEVEL_1, LEVEL_2, LEVEL_3A, LEVEL_3B, LEVEL_4, LEVEL_R1, LEVEL_R2 | The highest level of evidence for therapeutic implications. Order: LEVEL_R1 > LEVEL_1 > LEVEL_2 > LEVEL_3A > LEVEL_3B > LEVEL_4 > LEVEL_R2 | +| HIGHEST_SENSITIVE_LEVEL | | LEVEL_1, LEVEL_2, LEVEL_3A, LEVEL_3B, LEVEL_4 | The highest sensitive level of evidence for therapeutic implications. Order: LEVEL_1 > LEVEL_2 > LEVEL_3A > LEVEL_3B > LEVEL_4 | +| HIGHEST_RESISTANCE_LEVEL | | LEVEL_R1, LEVEL_R2 | The highest resistance level of evidence for therapeutic implications. Order: LEVEL_R1 > LEVEL_R2 | +| TX_CITATIONS | | PMID, Abstract, Website link | All citations related to therapeutic implications. | +| LEVEL_Dx* | | Tumor type the level of evidence is assigned to | The leveled diagnostic implications. | +| HIGHEST_DX_LEVEL | | LEVEL_Dx1, LEVEL_Dx2, LEVEL_Dx3 | The highest level of evidence for diagnostic implications. | +| DX_CITATIONS | | PMID, Abstract, Website link | All citations related to diagnostic implications. | +| LEVEL_Px* | | Tumor type the level of evidence is assigned to | The leveled prognostic implications. | +| HIGHEST_PX_LEVEL | | LEVEL_Px1, LEVEL_Px2, LEVEL_Px3 | The highest level of evidence for prognostic implications. | +| PX_CITATIONS | | PMID, Abstract, Website link | All citations related to prognostic implications. | +| GENE_SUMMARY | Only when parameter -d is specified | | Brief overview of the gene and its role in cancer | +| VARIANT_SUMMARY | Only when parameter -d is specified | | Variant summary describes the variant oncogenicity, last review if it is VUS | +| TUMOR_TYPE_SUMMARY | Only when parameter -d is specified | | Tumor type summary describes the therapeutic implication that applies to the indication | +| DIAGNOSTIC_SUMMARY | Only when parameter -d is specified | | Diagnostic summary that applies to the indication, for hematologic malignancies only | +| PROGNOSTIC_SUMMARY | Only when parameter -d is specified | | Prognostic summary that applies to the indication, for hematologic malignancies only | +| MUTATION_EFFECT_DESCRIPTION | Only when parameter -d is specified | | The mutation effect description provides a brief overview of the biological and oncogenic effect of the VPS and includes appropriate references to peer-reviewed literature. | ### ClinicalDataAnnotator Please see description above for columns LEVEL_*, HIGHEST_LEVEL, HIGHEST_SENSITIVE_LEVEL, HIGHEST_RESISTANCE_LEVEL, LEVEL_Dx*, HIGHEST_DX_LEVEL, LEVEL_Px*, HIGHEST_PX_LEVEL.