GlycanFormatConverter

GlycanFormatConverter converts WURCS and other glycan notations to and from standard IUPAC-based, KCF, and LinearCode formats to enable standardized, human-readable representations and interoperability of glycan structural data.

Key Features:

• WURCS to IUPAC conversion: Converts WURCS linear notation into IUPAC-Extended, IUPAC-Condensed, and IUPAC-Short formats.
• Import formats: Supports importing glycans in IUPAC-Extended, KEGG Chemical Function (KCF), and LinearCode formats.
• Bidirectional conversion: Provides conversion capability between WURCS and other supported formats to enable data exchange.
• Support for complex structures: Handles complex glycan architectures represented in WURCS, including branched and cyclic forms.
• Validation against GlyTouCan: Conversion functionality has been tested against all glycans registered in the GlyTouCan repository.
• Format-limitation reporting: Identifies conversion exceptions that arise from limitations within the original source formats.

Scientific Applications:

• Data interoperability: Enables standardized exchange of glycan structural data across databases and analysis tools.
• Human-readable representation: Produces IUPAC formats to facilitate manual curation and interpretation of glycan structures.
• Integration of external formats: Allows incorporation of glycans from KEGG KCF and LinearCode into glycomics workflows.
• Repository-scale validation: Supports large-scale testing and validation of format conversions using the GlyTouCan dataset.

Methodology:

Performs computational format conversion between WURCS and IUPAC-Extended/IUPAC-Condensed/IUPAC-Short, imports IUPAC-Extended, KCF, and LinearCode formats, and was validated by testing conversions across all glycans in the GlyTouCan repository, with noted exceptions attributed to source-format limitations.