Xenobiotic Phase Audit
Audit observed xenobiotic reaction order and phase coverage.
Description
A xenobiotic phase-label audit checks a declared sequence against an I-then-II ordering rule.
A xenobiotic phase-label audit checks a declared sequence against an I-then-II ordering rule. Such a checklist does not model actual reaction mechanisms.1
Audit observed xenobiotic reaction order and phase coverage.
When to use Xenobiotic Phase Audit
Use this tool to audit observed xenobiotic reaction order and phase coverage.
Prepare the measured profile, formula counts, upstream model outputs or caller-defined reference criteria requested. Keep paired entries aligned and units, sample basis and preprocessing consistent.
How to use Xenobiotic Phase Audit and understand its results
- Prepare the measured profile, formula counts, upstream model outputs or caller-defined reference criteria requested. Keep paired entries aligned and units, sample basis and preprocessing consistent.
- Enter reactionPhases, minimumPhaseOneCount, minimumPhaseTwoCount using the field table and calculation rules, then run the tool.
- Read phaseOneCount, phaseTwoCount, orderingValid, complete. The explanation below defines the units, signs, ordering and any flags or placeholder values.
- If the tool reports an input issue, correct the values and run it again. Apply the stated assumptions when interpreting a successfully returned result.
| Input field | Meaning | Value type; see rules below | Requirement |
|---|---|---|---|
| reactionPhases | Reaction phases | list of string | Required |
| minimumPhaseOneCount | Minimum phase one count | number | Required |
| minimumPhaseTwoCount | Minimum phase two count | number | Required |
Enter a nonempty list containing exactly I or II and finite minimum counts. Count each phase and forbid I after the first II; an all-I or all-II list remains ordered. Return counts and ordering/completeness flags.
complete=orderingValid AND count(I)≥minimumI AND count(II)≥minimumII Units, indexing, boundary conditions and exceptional cases are defined in the calculation rules above.
| Output field | Meaning | Value type |
|---|---|---|
| phaseOneCount | Phase one count | number |
| phaseTwoCount | Phase two count | number |
| orderingValid | Ordering valid | boolean |
| complete | Complete | boolean |
{
"input": {
"reactionPhases": [
"I",
"I",
"II"
],
"minimumPhaseOneCount": 1,
"minimumPhaseTwoCount": 1
},
"output": {
"phaseOneCount": 2,
"phaseTwoCount": 1,
"orderingValid": true,
"complete": true
}
}Limitations and assumptions
Minimum counts are not constrained to nonnegative integers. Real metabolic reactions need not follow this simplified checklist order; no chemistry is inspected.
Numeric inputs must be finite. Follow the calculation-specific rules for overflow, underflow and exceptional cases. Lists are limited to 100,000 entries; the rules above may require smaller limits. Missing required fields, extra fields, wrong value types and violations of the calculation rules are input errors. A successfully returned false flag is an evaluated outcome; its meaning is explained above.
Alternative or Complementary methods
Use Stoichiometric Flux Balance: Check S·v steady-state residuals against a supplied flux-balance tolerance. For a complementary task, use Pathway Overrepresentation: Calculate hypergeometric pathway over-representation and upper-tail probability.
References
-
Xenobiotic Phase Audit — tool.io
Similar or alternative tools
- Stoichiometric Flux Balance
Check S·v steady-state residuals against a supplied flux-balance tolerance.
- Pathway Overrepresentation
Calculate hypergeometric pathway over-representation and upper-tail probability.