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Use when when you have raw PubChem compound records or other public chemical structure databases and need to supply candidate metabolite structures to a mass spectrometry annotation workflow like MAGMa.
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SOC 職業分類に基づく
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| name | annotation-pipeline-data-preparation |
| description | Use when when you have raw PubChem compound records or other public chemical structure databases and need to supply candidate metabolite structures to a mass spectrometry annotation workflow like MAGMa. |
| license | CC-BY-4.0 |
| metadata | {"edam_operation":"http://edamontology.org/operation_3443","edam_topics":["http://edamontology.org/topic_0218","http://edamontology.org/topic_3172","http://edamontology.org/topic_3375"],"tools":["MAGMa","pubchem (subproject)"],"techniques":["LC-MS"],"license_tier":"open"} |
| derived_from | [{"doi":"10.5702/massspectrometry.S0033","title":"magma"}] |
| evidence_spans | ["MAGMa is a abbreviation for 'Ms Annotation based on in silico Generated Metabolites'."] |
| claims | [] |
| provenance | {"collection":"https://w3id.org/holobiomicslab/asb-skill/collection/metabolomics/v2","assembled_by":"scripts/collect_metabolomics_collection.py","sources":[{"build":"coll_magma_cq","doi":"10.5702/massspectrometry.S0033","title":"magma"}],"dedup_kept_from":"coll_magma_cq"} |
| schema_version | 0.2.0 |
| attribution | {"generator":"AgenticScienceBuilder","original_doi":"10.5702/massspectrometry.S0033","all_source_dois":["10.5702/massspectrometry.S0033"],"zenodo_doi":"10.5281/zenodo.20794027","curators":[],"promoter":"Louis-Félix Nothias","sponsor":"CNRS & Université Côte d'Azur"} |
Prepare and standardize chemical structure data from public databases (PubChem) into a validated candidate set formatted for metabolite annotation pipelines (MAGMa). This skill bridges raw compound record extraction and annotation-ready structure libraries by filtering, standardizing molecular representations, and validating schema compliance.
When you have raw PubChem compound records or other public chemical structure databases and need to supply candidate metabolite structures to a mass spectrometry annotation workflow like MAGMa. Specifically: you are starting a metabolite identification project, you have liquid chromatography–mass spectrometry (LC-MS) data without pre-filtered candidates, and you need to generate or compile a validated lookup database that MAGMa's in silico annotation engine can query by mass and chemical properties.
Extract and parse PubChem compound records from the public PubChem database using the PubChem API or bulk downloads. Filter and standardize chemical structures to ensure compatibility with MAGMa's annotation pipeline—this includes normalizing molecular representations, removing duplicates, and reconciling stereochemistry and ionization states. Generate or compile candidate structure identifiers and molecular properties (e.g., monoisotopic mass, formula, InChI). Validate the candidate set for completeness (no missing critical fields) and format compliance against MAGMa's expected input schema. Finally, export the processed candidate structures to the binary or text format required by MAGMa job calculation. The rationale is that MAGMa's accuracy depends on the quality and coverage of its input candidate pool; standardization ensures structures are correctly parseable by the annotation engine and reduces false negatives in metabolite identification.
job calculation requires a pubchem lookup database which can be made using the pubchem application."