compound-class-annotation-parsing
Summary
Parse and validate structured compound-class annotation results returned by CANOPUS web service queries, extracting predicted compound classes and confidence scores into a standardized tabular or JSON format. This skill ensures annotation completeness and conformance before downstream structural or metabolomic interpretation.
When to use
Apply this skill after submitting a fingerprint or spectrum query to the CANOPUS web service and receiving a structured response. Use it when you need to validate that the response contains all required fields (compound class, probability/confidence), standardize the format for downstream analysis, and ensure the annotation result is ready for integration into a metabolite identification workflow.
When NOT to use
- Input is raw MS/MS spectra or fingerprints not yet submitted to CANOPUS—submit to the web service first.
- You need structural candidate ranking or de novo structure generation—use CSI:FingerID or MSNovelist instead.
- Annotation results are already integrated into a SIRIUS GUI session—the GUI handles parsing internally.
Inputs
- CANOPUS web service JSON or tabular response
- structured annotation result containing compound-class predictions
Outputs
- parsed and validated compound-class annotation table (CSV/TSV/JSON)
- standardized records with compound class and confidence score fields
- validation report (records passed, failed, or incomplete)
How to apply
Retrieve the structured JSON or tabular response from the CANOPUS web service endpoint. Parse the response to extract predicted compound classes and their associated confidence scores or probabilities. Validate that all required fields (compound class, probability/confidence) are present in each annotation record. Check that confidence scores fall within the expected range (typically 0–1 or 0–100%). Convert the parsed data into a standardized format (e.g., CSV, TSV, or JSON) suitable for storage or downstream analysis. Log any malformed or incomplete records for review.
Related tools
Evaluation signals
- All returned records contain non-empty compound-class field.
- All confidence/probability scores are numeric and fall within valid range (0–1 or 0–100%).
- Parsed output schema matches expected structure: compound class, confidence score, and optional metadata (e.g., query ID, timestamp).
- No truncation, encoding errors, or malformed JSON/CSV in parsed output.
- Validation report accurately counts and categorizes passed and failed records with descriptive error messages for any malformed entries.
Limitations
- CANOPUS web service is available for academic research and education use only; non-academic users require licenses from Bright Giant GmbH.
- Confidence scores reflect model predictions and should not be interpreted as ground truth; low-confidence predictions may require manual review or additional validation.
- Parsing assumes CANOPUS returns consistent JSON/tabular schema; changes in API response format may require script updates.
- This skill validates structure only; it does not assess biological relevance, consistency with reference databases, or cross-validation with other tools (CSI:FingerID, ZODIAC).
Evidence
- [other] retrieve and parse the annotation result: "Retrieve the structured JSON or tabular response containing predicted compound classes and confidence scores. Parse and validate the annotation result to ensure required fields (compound class,"
- [readme] CANOPUS web service integration in SIRIUS: "Fragmentation trees and spectra can be directly uploaded from SIRIUS to the CSI:FingerID, CANOPUS and MSNovelist web services. Results are retrieved from the web service and can be displayed in the"
- [readme] academic-only restriction: "The SIRIUS web services (CSI:FingerID, CANOPUS, MSNovelist and others) hosted by the Böcker group are for academic research and education use only."
- [readme] SIRIUS integration of CANOPUS: "SIRIUS integrates a collection of our tools, including CSI:FingerID (with COSMIC), ZODIAC, CANOPUS."
1---2name: compound-class-annotation-parsing-23description: Use when after submitting a fingerprint or spectrum query to the CANOPUS web service and receiving a structured response.4license: CC-BY-4.05---67# compound-class-annotation-parsing89## Summary1011Parse and validate structured compound-class annotation results returned by CANOPUS web service queries, extracting predicted compound classes and confidence scores into a standardized tabular or JSON format. This skill ensures annotation completeness and conformance before downstream structural or metabolomic interpretation.1213## When to use1415Apply this skill after submitting a fingerprint or spectrum query to the CANOPUS web service and receiving a structured response. Use it when you need to validate that the response contains all required fields (compound class, probability/confidence), standardize the format for downstream analysis, and ensure the annotation result is ready for integration into a metabolite identification workflow.1617## When NOT to use1819- Input is raw MS/MS spectra or fingerprints not yet submitted to CANOPUS—submit to the web service first.20- You need structural candidate ranking or de novo structure generation—use CSI:FingerID or MSNovelist instead.21- Annotation results are already integrated into a SIRIUS GUI session—the GUI handles parsing internally.2223## Inputs2425- CANOPUS web service JSON or tabular response26- structured annotation result containing compound-class predictions2728## Outputs2930- parsed and validated compound-class annotation table (CSV/TSV/JSON)31- standardized records with compound class and confidence score fields32- validation report (records passed, failed, or incomplete)3334## How to apply3536Retrieve the structured JSON or tabular response from the CANOPUS web service endpoint. Parse the response to extract predicted compound classes and their associated confidence scores or probabilities. Validate that all required fields (compound class, probability/confidence) are present in each annotation record. Check that confidence scores fall within the expected range (typically 0–1 or 0–100%). Convert the parsed data into a standardized format (e.g., CSV, TSV, or JSON) suitable for storage or downstream analysis. Log any malformed or incomplete records for review.3738## Related tools3940- **CANOPUS** (web service that generates the structured compound-class annotation result to be parsed and validated) — https://bio.informatik.uni-jena.de/software/canopus/41- **SIRIUS** (Java-based framework that seamlessly integrates the CANOPUS web service and handles result retrieval and display) — https://github.com/sirius-ms/sirius4243## Evaluation signals4445- All returned records contain non-empty compound-class field.46- All confidence/probability scores are numeric and fall within valid range (0–1 or 0–100%).47- Parsed output schema matches expected structure: compound class, confidence score, and optional metadata (e.g., query ID, timestamp).48- No truncation, encoding errors, or malformed JSON/CSV in parsed output.49- Validation report accurately counts and categorizes passed and failed records with descriptive error messages for any malformed entries.5051## Limitations5253- CANOPUS web service is available for academic research and education use only; non-academic users require licenses from Bright Giant GmbH.54- Confidence scores reflect model predictions and should not be interpreted as ground truth; low-confidence predictions may require manual review or additional validation.55- Parsing assumes CANOPUS returns consistent JSON/tabular schema; changes in API response format may require script updates.56- This skill validates structure only; it does not assess biological relevance, consistency with reference databases, or cross-validation with other tools (CSI:FingerID, ZODIAC).5758## Evidence5960- [other] retrieve and parse the annotation result: "Retrieve the structured JSON or tabular response containing predicted compound classes and confidence scores. Parse and validate the annotation result to ensure required fields (compound class,"61- [readme] CANOPUS web service integration in SIRIUS: "Fragmentation trees and spectra can be directly uploaded from SIRIUS to the CSI:FingerID, CANOPUS and MSNovelist web services. Results are retrieved from the web service and can be displayed in the"62- [readme] academic-only restriction: "The SIRIUS web services (CSI:FingerID, CANOPUS, MSNovelist and others) hosted by the Böcker group are for academic research and education use only."63- [readme] SIRIUS integration of CANOPUS: "SIRIUS integrates a collection of our tools, including CSI:FingerID (with COSMIC), ZODIAC, CANOPUS."
HolobiomicsLab 