The standalone SpaMTP release includes the pruned RaMP-DB 3.0.7 snapshot, corrected pathway graphs, legacy chemical reference tables, and precomputed SMILES features. No companion package, Hub, or download is required.
Format
Data frames (chem_props, source_df, analyte,
analytehaspathway, pathway, smiles_features, HMDB_db, Chebi_db,
Lipidmaps_db, GNPS_db, and filtered_fmp10) or named lists
(ramp_db_metadata and the four RAMP_* topology collections).
SpaMTPDatabaseInfo() reports each dataset's dimensions and resource name.
Source
RaMP-DB: https://github.com/ncats/RaMP-DB.
The bundled snapshot is shared with SpaMTP's main release. Precomputed
structure features come from the immutable resource collection
doi:10.5281/zenodo.22045311
. Topology sources and checksums are recorded
in inst/extdata/pathway_interactions_provenance.csv.
Details
chem_props contains masses, formulae, structures and RaMP/source IDs.
source_df maps source identifiers to RaMP IDs; analyte records analyte
type. analytehaspathway and pathway describe pathway membership and names.
The RAMP_* lists contain KEGG, Reactome, WikiPathways and SMPDB graphs,
including restored source_reaction_type edge labels and repair provenance.
ramp_db_metadata records upstream releases and pruning information.
smiles_features stores structure-derived fields keyed by SMILES.
Prefer LoadSpaMTPDatabase() for resource loading and provenance attributes.
Direct utils::data() access is retained for existing standalone workflows.