diff --git a/docs/source/datasets_included.rst b/docs/source/datasets_included.rst index e505edec..c1e91421 100644 --- a/docs/source/datasets_included.rst +++ b/docs/source/datasets_included.rst @@ -75,9 +75,9 @@ The following table summarizes the number of drugs associated with each dose-res Types of dose-response metrics collected include: - AAC - Area above the response curve; the complement value of AUC. -- ABC - Area between curves, the difference between the AUC of the control and the treated cells. +- ABC - Area between curves, the difference between the AUC of the control and the treated cells. (PDX) - AUC - Area under the fitted hill slope curve across all doses present. Lower AUC signifies lower levels of growth. -- DSS - A multiparametric dose response value that takes into account control and treated cells. +- DSS - A multiparametric dose response value, that takes into account control and treated cells; the Drug Sensitivity Score is described in Yadav et al., 2014. - fit_auc - Area under the fitted hill slope curve across the common interval of −log10[M], where the molar concentration ranges from 10⁻⁴ to 10⁻¹⁰. - fit_ec50 - The fitted curve prediction of the −log10M concentration at which 50% of the maximal effect is observed. - fit_ec50se - Standard error of the Fit_EC50 estimate. @@ -85,10 +85,10 @@ Types of dose-response metrics collected include: - fit_hs - The estimated hill slope binding cooperativity, calculated as the slope of the sigmoidal hill curve. - fit_ic50 - The fitted curve prediction of the −log10M concentration required to reduce tumor growth by 50%. - fit_r2 - Coefficient of determination between observed growth and the fitted hill slope curve, indicating goodness of fit. -- lmm - The resulting “time and treatment interaction” in a linear mixed model with fixed effects as time and treatment and patient as a random effect. Indicates how much the treatment changes the slope of log(volume) over time compared to the control. -- mRESCIST - Disease status classified into PD (progressive disease), SD (stable disease), PR (partial response), and CR (complete response), based on percent volume change and cumulative average response. +- lmm - The resulting “time and treatment interaction” in a linear mixed model with fixed effects as time and treatment and with patient as a random effect. This indicates how much the treatment changes the slope of log(volume) over time compared to the control. (PDX) +- mRECIST - Disease status is classified into four categories: PD (progressive disease), SD (stable disease), PR (partial response), and CR (complete response). This is calculated as Day 10 percent volume change (%ΔV) and its cumulative average response under the following methods: CR if best %ΔV < −95% and avg < −40%, PR if %ΔV < −50% and avg < −20%, SD if %ΔV < +35% and avg < +30%, otherwise PD. (PDX) - published_auc - Published Area Under the Curve -- TG - Tumor growth inhibition between the control and treatment time-volume curves. +- TGI - The tumor growth inhibition (TGI) between the control and treatment time-volume curves. (PDX) diff --git a/schema/coderdata.yaml b/schema/coderdata.yaml index e434b47a..819e9a8f 100755 --- a/schema/coderdata.yaml +++ b/schema/coderdata.yaml @@ -200,27 +200,27 @@ enums: ResponseMetric: permissible_values: fit_auc: - description: Area under the fitted curve + description: Area under the fitted hill slope curve across the common interval of -log10[M], where the molar concentration (M) ranges from 10^-4 to 10^-10. fit_ic50: - description: Concetration at which inhibitor binding is reduced by half + description: The fitted curve prediction of the -log10M concentration required to reduce tumor growth by 50%. fit_ec50: - description: Concentration required to have half cells with adverse effect + description: The fitted curve prediction of the -log10M concentration at which 50% of the maximal effect is observed. fit_ec50se: - description: Standard error in EC50 calculation + description: Standard error of the fit_EC50 estimate. fit_einf: - description: Fraction of cells not susceptible to the drug + description: The fraction of cells that are unaffected even at an infinite dose concentration. Calculated as the lower asymptote of the hill slope function. fit_hs: - description: Hill slop binding cooperativity + description: The estimated hill slope binding cooperativity, calculated as the slope of the sigmoidal hill curve. fit_r2: - description: R2 value between fit and actual data + description: Coefficient of determination between observed growth and the fitted hill slope curve, indicating goodness of fit. aac: - description: Area above curve measured by integrating the data points + description: Area above the response curve; the complement value of AUC. auc: - description: Area under the curve measured by integrating data points + description: Area under the fitted hill slope curve across all doses present. Lower AUC signifies lower levels of growth. dss: - description: I believe this is the drug sensitivity score + description: A multiparametric dose response value, that takes into account control and treated cells; the Drug Sensitivity Score is described in Yadav et al., 2014. mrecist: - description: For PDX data this value should be either Progressive Disease, Stable Disease, Partial Response or Complete Response. + description: "Disease status is classified into four categories: PD (progressive disease), SD (stable disease), PR (partial response), and CR (complete response). This is calculated as Day 10 percent volume change (%ΔV) and its cumulative average response under the following methods: CR if best %ΔV < -95% and avg < -40%, PR if %ΔV < -50% and avg < -20%, SD if %ΔV < +35% and avg < +30%, otherwise PD." published_auc: description: AUC that has been published with the study. Currently used in organoid data. gc_auc: @@ -230,7 +230,7 @@ enums: os: description: overall survival tgi: - description: tumor growth inhibitiojn + description: The tumor growth inhibition (TGI) between the control and treatment time-volume curves. kulgap: description: kl divergence based metric CellPerturbation: