diff --git a/vignettes/Introduction_Appendices.Rmd b/vignettes/Introduction_Appendices.Rmd index 6199ffa..0d9f5a1 100644 --- a/vignettes/Introduction_Appendices.Rmd +++ b/vignettes/Introduction_Appendices.Rmd @@ -2383,31 +2383,42 @@ Field <- c("dtxsid", "chnm", "spid", "qc_level", "pass_or_caution", "t0", "t4", Description <- c("Unique identifier from U.S. EPA Distributed Structure-Searchable Toxicity (DSSTox) Database", "Chemical name", "Sample ID", "Level of analytical QC: substance or sample", - "Indication of analytical QC pass or caution. Considered caution unless T0 or T4 is A, B or T0 and T4 are I with S call", - "Grade at T0. Grade options include:

- A: Molecular Weight (MW) Confirmed, Purity >90%
- B: MW Confirmed, Purity 75-90%
- C: MW Confirmed, Purity 50-75%
- D: CAUTION Purity <50%
- Ac: Purity > 90% CAUTION Low Conc. 5-30% of expected value
- Bc: Purity 75-90% CAUTION, Low Conc. 5-30% of expected value
- Cc: Purity 50-75% CAUTION, Low Conc. 5-30% of expected value
- Fc: CAUTION Very Low Conc. <5% of expected value. Biological Activity Unreliable
- Z: MW Confirmed, No Purity Info
- I: ISOMERS Two or more isomers detected
- M: DEFINED MIXTURE Two or more components
- F: CAUTION Incorrect MW. Biological Activity Unreliable
- Fns: CAUTION No Sample Detected. Biological Activity Unreliable
- U: Unknown/Inconclusive
- ND: Not Determined,W:Sample Withdrawn", - "Grade at T4. Same options at T0.", - "Call options include:

- S: Stable
- T: CAUTION Chemical transformation
- L: CAUTION Physical loss
- X: CAUTION Unstable, reason undetermined", + "Indication of analytical QC pass or caution. Considered caution unless T0 or T4 in (A, B), or T0 and T4 are I with S call", + "Grade at T0 (Time zero: Compounds freshly taken out of freezer). Grade options include:
+ **A**: Molecular Weight (MW) Confirmed, Purity >90%
+ **B**: MW Confirmed, Purity 75-90%
+ **C**: MW Confirmed, Purity 50-75%
+ **D**: CAUTION Purity <50%
+ **Ac**: Purity > 90% CAUTION Low Conc. 5-30% of expected value
+ **Bc**: Purity 75-90% CAUTION, Low Conc. 5-30% of expected value
+ **Cc**: Purity 50-75% CAUTION, Low Conc. 5-30% of expected value
+ **Fc**: CAUTION Very Low Conc. <5% of expected value. Biological Activity Unreliable
+ **Z**: MW Confirmed, No Purity Info
+ **I**: ISOMERS Two or more isomers detected
+ **M**: DEFINED MIXTURE Two or more components
+ **F**: CAUTION Incorrect MW. Biological Activity Unreliable
+ **Fns**: CAUTION No Sample Detected. Biological Activity Unreliable
+ **U**: Unknown/Inconclusive
+ **ND**: Not Determined
+ **W**: Sample Withdrawn", + "Grade at T4 (Time 4 months: Compounds kept at room temperature for 4 months). Same options at T0.", + "Call options include:
+ **S**: Stable
+ **T**: CAUTION Chemical transformation
+ **L**: CAUTION Physical loss
+ **X**: CAUTION Unstable, reason undetermined", "Annotation note from analytical QC manual curation", -"Interpretative flags set based on observed substance or sample level QC (T0, T4, calls) or physicochemical properties", +"Interpretative flags set based on observed substance or sample level QC (T0, T4, calls) or physicochemical properties. Flag options incude:
+**Room temperature stability decreases over time**: T0 in (A, B, C) *AND* call is in (T,L,X))
+**Low concentration possible**: T0 *OR* T4 in (Ac,Bc,Cc). Call may be pass or caution depending on T0
+**Extreme loss at room temperature over time**: T0 in (A, B, C) *AND* t4 in (Fc, Fns)
+**Missing data for room temperature stability**: T4 in (U,ND,NA,Z,W)
+**Initial purity between 75-90%**: T0 in (B, Bc)
+**Initial purity between 50-75%**: T0 in (C,Cc)
+**Likely fail**: t0 in (D, F, Fns, W) OR T0 in (Z) & T4 in (D, F,Fc,Fns)
+**Examine physicochemical properties**: Predicted log10-VP >= 1 *OR* logKow >= 6.5
+**Confirmed isomer or mixture**: T0 in (M,I) *AND* T4 in (M,ND,I)
+**Missing purity information**: T0 in (Z) *AND* T4 in (A,Ac,B,C)", "Mass", "OPERA predicted log10 vapor pressure", "OPERA predicted Octanol-water partition coefficient")