classyfire-taxonomy-assignment
Summary
Assign standardized chemical taxonomy (kingdom, superclass, class, subclass) to molecular structures using the ClassyFire API or local instance. This skill is essential in cheminformatics pipelines to enable downstream chemical classification-based analysis and filtering of small molecules.
When to use
After molecular structures have been standardized (e.g., via PubChem standardization) and you need to enrich them with chemical taxonomy labels for cohort stratification, chemical space analysis, or retention time prediction model development. Apply when your input is a collection of standardized molecular structures (SMILES or MOL format) lacking kingdom/superclass/class/subclass annotations.
When NOT to use
- Input structures have not been standardized (use PubChem standardization first)
- Molecules are already pre-classified with an alternative taxonomy system and no re-annotation is desired
- Internet or API access to ClassyFire is unavailable and no local instance is set up
Inputs
- Standardized molecular structures (SMILES or MOL format)
- Molecular identifiers or batch file of structures
- Connection parameters to ClassyFire API or local instance
Outputs
- Aggregated classification table (CSV or JSON) with molecular identifiers and ClassyFire taxonomy (kingdom, superclass, class, subclass)
- Validation report flagging molecules with null or incomplete classification records
How to apply
Load standardized molecular structures (SMILES or MOL format) from input file. Query the ClassyFire API or local instance with each structure to retrieve the complete chemical classification taxonomy. Aggregate the returned classification results (kingdom, superclass, class, subclass) with corresponding molecular identifiers into a structured output table (CSV or JSON). Validate that each molecule has a non-null ClassyFire classification record and all available taxonomy levels are populated; flag or retry any molecules that fail classification or return incomplete taxonomy branches.
Related tools
- ClassyFire (Queries and retrieves standardized chemical classification taxonomy for each molecular structure)
- PubChem standardization (Pre-processes and standardizes input molecular structures before ClassyFire annotation)
- rcdk (Calculates molecular fingerprints and chemical descriptors, often used in conjunction with ClassyFire taxonomy for comprehensive molecular characterization)
Evaluation signals
- All input molecules have a corresponding non-null ClassyFire classification record in the output table
- Taxonomy levels (kingdom, superclass, class, subclass) are populated where available; no incomplete or truncated taxonomy branches
- Aggregated output table structure matches specified format (CSV or JSON) with all expected columns (molecular ID, kingdom, superclass, class, subclass)
- Validation report contains zero 'failed classification' flags; any molecules flagged should be manually inspected or retried
- Spot-check: verify that known reference structures (e.g., a lipid, amino acid, or drug compound) are assigned to chemically plausible taxonomy nodes
Limitations
- ClassyFire classification relies on external API availability or a maintained local instance; API rate limits or downtime may delay large batch processing
- Non-standard or highly unusual molecular structures may fail to classify or receive incomplete taxonomy annotations; such molecules should be manually reviewed
- Classification accuracy depends on the quality of input structure standardization; errors in structure standardization propagate to taxonomy assignment
Evidence
- [readme] structures are standardized using the PubChem standardization and molecular fingerprints and chemical descriptors are calculated using rcdk. Classification of molecules is performed using ClassyFire.: "structures are standardized using the PubChem standardization and molecular fingerprints and chemical descriptors are calculated using rcdk. Classification of molecules is performed using ClassyFire."
- [other] Query ClassyFire API or local instance with each structure to retrieve chemical classification taxonomy (kingdom, superclass, class, subclass).: "Query ClassyFire API or local instance with each structure to retrieve chemical classification taxonomy (kingdom, superclass, class, subclass)."
- [other] Aggregate classification results with corresponding molecular identifiers into a structured table (CSV or JSON).: "Aggregate classification results with corresponding molecular identifiers into a structured table (CSV or JSON)."
- [other] Validation: verify each molecule has a non-null ClassyFire classification record and all taxonomy levels are populated where available.: "Validation: verify each molecule has a non-null ClassyFire classification record and all taxonomy levels are populated where available."
1---2name: classyfire-taxonomy-assignment3description: Use when after molecular structures have been standardized (e.g., via PubChem standardization) and you need to enrich them with chemical taxonomy labels for cohort stratification, chemical space analysis, or retention time prediction model development.4license: CC-BY-4.05---67# classyfire-taxonomy-assignment89## Summary1011Assign standardized chemical taxonomy (kingdom, superclass, class, subclass) to molecular structures using the ClassyFire API or local instance. This skill is essential in cheminformatics pipelines to enable downstream chemical classification-based analysis and filtering of small molecules.1213## When to use1415After molecular structures have been standardized (e.g., via PubChem standardization) and you need to enrich them with chemical taxonomy labels for cohort stratification, chemical space analysis, or retention time prediction model development. Apply when your input is a collection of standardized molecular structures (SMILES or MOL format) lacking kingdom/superclass/class/subclass annotations.1617## When NOT to use1819- Input structures have not been standardized (use PubChem standardization first)20- Molecules are already pre-classified with an alternative taxonomy system and no re-annotation is desired21- Internet or API access to ClassyFire is unavailable and no local instance is set up2223## Inputs2425- Standardized molecular structures (SMILES or MOL format)26- Molecular identifiers or batch file of structures27- Connection parameters to ClassyFire API or local instance2829## Outputs3031- Aggregated classification table (CSV or JSON) with molecular identifiers and ClassyFire taxonomy (kingdom, superclass, class, subclass)32- Validation report flagging molecules with null or incomplete classification records3334## How to apply3536Load standardized molecular structures (SMILES or MOL format) from input file. Query the ClassyFire API or local instance with each structure to retrieve the complete chemical classification taxonomy. Aggregate the returned classification results (kingdom, superclass, class, subclass) with corresponding molecular identifiers into a structured output table (CSV or JSON). Validate that each molecule has a non-null ClassyFire classification record and all available taxonomy levels are populated; flag or retry any molecules that fail classification or return incomplete taxonomy branches.3738## Related tools3940- **ClassyFire** (Queries and retrieves standardized chemical classification taxonomy for each molecular structure)41- **PubChem standardization** (Pre-processes and standardizes input molecular structures before ClassyFire annotation)42- **rcdk** (Calculates molecular fingerprints and chemical descriptors, often used in conjunction with ClassyFire taxonomy for comprehensive molecular characterization)4344## Evaluation signals4546- All input molecules have a corresponding non-null ClassyFire classification record in the output table47- Taxonomy levels (kingdom, superclass, class, subclass) are populated where available; no incomplete or truncated taxonomy branches48- Aggregated output table structure matches specified format (CSV or JSON) with all expected columns (molecular ID, kingdom, superclass, class, subclass)49- Validation report contains zero 'failed classification' flags; any molecules flagged should be manually inspected or retried50- Spot-check: verify that known reference structures (e.g., a lipid, amino acid, or drug compound) are assigned to chemically plausible taxonomy nodes5152## Limitations5354- ClassyFire classification relies on external API availability or a maintained local instance; API rate limits or downtime may delay large batch processing55- Non-standard or highly unusual molecular structures may fail to classify or receive incomplete taxonomy annotations; such molecules should be manually reviewed56- Classification accuracy depends on the quality of input structure standardization; errors in structure standardization propagate to taxonomy assignment5758## Evidence5960- [readme] structures are standardized using the PubChem standardization and molecular fingerprints and chemical descriptors are calculated using rcdk. Classification of molecules is performed using ClassyFire.: "structures are standardized using the PubChem standardization and molecular fingerprints and chemical descriptors are calculated using rcdk. Classification of molecules is performed using ClassyFire."61- [other] Query ClassyFire API or local instance with each structure to retrieve chemical classification taxonomy (kingdom, superclass, class, subclass).: "Query ClassyFire API or local instance with each structure to retrieve chemical classification taxonomy (kingdom, superclass, class, subclass)."62- [other] Aggregate classification results with corresponding molecular identifiers into a structured table (CSV or JSON).: "Aggregate classification results with corresponding molecular identifiers into a structured table (CSV or JSON)."63- [other] Validation: verify each molecule has a non-null ClassyFire classification record and all taxonomy levels are populated where available.: "Validation: verify each molecule has a non-null ClassyFire classification record and all taxonomy levels are populated where available."
HolobiomicsLab