metabolism-prediction-result-aggregation
License: restricted — no clear open-source license detected for the underlying tool; verify licensing before commercial use or redistribution.
Summary
Aggregate cytochrome P450 (CYP) metabolism predictions across multiple isoforms into a single consolidated result file. This skill enables comprehensive metabolic profiling by collecting per-isoform predictions and merging them for downstream pharmacokinetic or drug metabolism analysis.
When to use
When you have run CypReact predictions on a molecular dataset against multiple CYP isoforms (e.g., 1A2, 2A6, 2B6) and need to consolidate the per-isoform output files into a single combined result file for cross-isoform comparison, visualization, or downstream metabolite identification.
When NOT to use
- Predictions have only been generated for a single CYP isoform (aggregation is unnecessary).
- Output files from different molecular input datasets are being mixed (cross-contamination risk).
- Per-isoform predictions use incompatible or non-aligned molecular identifier schemes.
Inputs
- Multiple per-isoform CypReact output files in .sdf format
- Multiple per-isoform CypReact output files in .csv format
- Metadata mapping molecule identifiers to isoforms tested
Outputs
- Merged prediction file (.sdf or .csv) containing all isoform results
- Consolidated metabolite list with isoform attribution
How to apply
After invoking CypReact with comma-separated isoform codes (e.g., '1A2,2A6,2B6'), the tool generates per-isoform predictions. Collect all output files (.sdf or .csv format) corresponding to each isoform, then merge them using a standard consolidation workflow: (1) ensure all per-isoform files share the same molecular identifier column and prediction schema; (2) concatenate records while preserving isoform source attribution (e.g., add an 'isoform' column); (3) deduplicate on molecule ID if necessary, retaining all isoform-specific metabolite predictions; (4) validate that the merged file contains predictions from all requested isoforms and that no records were lost during aggregation.
Related tools
- CypReact (Generates per-isoform cytochrome P450 metabolism predictions that are aggregated into a consolidated result) — github:bitbucket.org__Leon_Ti__cypreact
Examples
java -jar cypreact.jar /path/to/input.sdf /path/to/output_merged.sdf 1A2,2A6,2B6
Evaluation signals
- Merged file contains records from all requested CYP isoforms (verify isoform column has no missing values for any molecule).
- Row count in merged file equals the sum of rows across all per-isoform input files (no records lost during aggregation).
- Molecular identifiers are consistent and non-duplicated across the merged file (one row per molecule per isoform).
- Prediction fields (e.g., metabolite structures, reaction types) are preserved and non-null for all isoforms.
- Metadata schema (column names, data types) matches the original CypReact output specification for .sdf or .csv format.
Limitations
- CypReact must be invoked with the multi-isoform parameter format (comma-separated, no spaces) to generate all per-isoform predictions before aggregation can occur.
- No automated conflict resolution is specified if the same metabolite is predicted by multiple isoforms with different reaction mechanisms; manual review may be required.
- Aggregation workflow (file merging) is not automated within CypReact; external scripting or data-wrangling tools are required to execute the consolidation steps.
Evidence
- [other] Consolidation step: "Collect and merge the per-isoform predictions into a single combined result file (.sdf or .csv) for downstream analysis."
- [other] Multi-isoform invocation format: "Multiple CYP isoforms are specified as a comma-separated list without spaces by replacing the single isoform parameter (e.g., replacing "1A2" with "1A2,2A6,2B6")."
- [intro] Output format options: "The user can output a .sdf file or a .csv file."
- [intro] Multi-isoform testing instruction: "if the user wants to test his/her molecules on CYP1A2,2A6 and 2B6, he/she can simply replace "1A2" with "1A2,2A6,2B6""
1---2name: metabolism-prediction-result-aggregation3description: Use when when you have run CypReact predictions on a molecular dataset against multiple CYP isoforms (e.g., 1A2, 2A6, 2B6) and need to consolidate the per-isoform output files into a single combined result file for cross-isoform comparison, visualization, or downstream metabolite identification.4license: CC-BY-4.05---67# metabolism-prediction-result-aggregation89> **License: restricted** — no clear open-source license detected for the underlying tool; verify licensing before commercial use or redistribution. <!-- asb-license-banner -->10## Summary1112Aggregate cytochrome P450 (CYP) metabolism predictions across multiple isoforms into a single consolidated result file. This skill enables comprehensive metabolic profiling by collecting per-isoform predictions and merging them for downstream pharmacokinetic or drug metabolism analysis.1314## When to use1516When you have run CypReact predictions on a molecular dataset against multiple CYP isoforms (e.g., 1A2, 2A6, 2B6) and need to consolidate the per-isoform output files into a single combined result file for cross-isoform comparison, visualization, or downstream metabolite identification.1718## When NOT to use1920- Predictions have only been generated for a single CYP isoform (aggregation is unnecessary).21- Output files from different molecular input datasets are being mixed (cross-contamination risk).22- Per-isoform predictions use incompatible or non-aligned molecular identifier schemes.2324## Inputs2526- Multiple per-isoform CypReact output files in .sdf format27- Multiple per-isoform CypReact output files in .csv format28- Metadata mapping molecule identifiers to isoforms tested2930## Outputs3132- Merged prediction file (.sdf or .csv) containing all isoform results33- Consolidated metabolite list with isoform attribution3435## How to apply3637After invoking CypReact with comma-separated isoform codes (e.g., '1A2,2A6,2B6'), the tool generates per-isoform predictions. Collect all output files (.sdf or .csv format) corresponding to each isoform, then merge them using a standard consolidation workflow: (1) ensure all per-isoform files share the same molecular identifier column and prediction schema; (2) concatenate records while preserving isoform source attribution (e.g., add an 'isoform' column); (3) deduplicate on molecule ID if necessary, retaining all isoform-specific metabolite predictions; (4) validate that the merged file contains predictions from all requested isoforms and that no records were lost during aggregation.3839## Related tools4041- **CypReact** (Generates per-isoform cytochrome P450 metabolism predictions that are aggregated into a consolidated result) — github:bitbucket.org__Leon_Ti__cypreact4243## Examples4445```46java -jar cypreact.jar /path/to/input.sdf /path/to/output_merged.sdf 1A2,2A6,2B647```4849## Evaluation signals5051- Merged file contains records from all requested CYP isoforms (verify isoform column has no missing values for any molecule).52- Row count in merged file equals the sum of rows across all per-isoform input files (no records lost during aggregation).53- Molecular identifiers are consistent and non-duplicated across the merged file (one row per molecule per isoform).54- Prediction fields (e.g., metabolite structures, reaction types) are preserved and non-null for all isoforms.55- Metadata schema (column names, data types) matches the original CypReact output specification for .sdf or .csv format.5657## Limitations5859- CypReact must be invoked with the multi-isoform parameter format (comma-separated, no spaces) to generate all per-isoform predictions before aggregation can occur.60- No automated conflict resolution is specified if the same metabolite is predicted by multiple isoforms with different reaction mechanisms; manual review may be required.61- Aggregation workflow (file merging) is not automated within CypReact; external scripting or data-wrangling tools are required to execute the consolidation steps.6263## Evidence6465- [other] Consolidation step: "Collect and merge the per-isoform predictions into a single combined result file (.sdf or .csv) for downstream analysis."66- [other] Multi-isoform invocation format: "Multiple CYP isoforms are specified as a comma-separated list without spaces by replacing the single isoform parameter (e.g., replacing "1A2" with "1A2,2A6,2B6")."67- [intro] Output format options: "The user can output a .sdf file or a .csv file."68- [intro] Multi-isoform testing instruction: "if the user wants to test his/her molecules on CYP1A2,2A6 and 2B6, he/she can simply replace "1A2" with "1A2,2A6,2B6""
HolobiomicsLab