Fields

Fields are grouped by availability. Fields marked reserved belong to the semantic schema designed for the database's continued development; they carry no data in this release but are retained because they define future extensions. They are hidden by default. Show reserved fields

Compound fields

Field	Type	Non-null	Description
molecule_uid	VARCHAR	1,391,199	Canonical compound key: full InChIKey, lipid shorthand, name key, or registry id
uuid_type	VARCHAR	1,391,199	Type of molecule_uid: inchikey / lipidkey / namekey / registry
uid_source	VARCHAR	1,391,199	Raw source string from which molecule_uid was derived
inchikey	VARCHAR	1,067,791	Full 27-character InChIKey including stereochemistry
inchi	VARCHAR	767,675	InChI string
smiles	VARCHAR[]	1,334,186	SMILES strings (list)
smiles_canonical	VARCHAR	540,042	Canonicalised SMILES; UNPARSABLE when structure could not be parsed
formula	VARCHAR	1,075,625	Molecular formula
molecular_weight	DOUBLE	304,858	Molecular weight (Da)
exact_mass	DOUBLE	747,076	Monoisotopic neutral mass (Da)
charge	BIGINT	24,884	Net formal charge
name	VARCHAR[]	1,391,138	Compound names (list)
iupac_name	VARCHAR[]	301,462	IUPAC names (list)
synonyms	VARCHAR[]	952,894	Synonyms (list)
kingdom	VARCHAR	23,788	ClassyFire kingdom
superclass	VARCHAR	33,629	ClassyFire superclass
class	VARCHAR	33,484	ClassyFire class
subclass	VARCHAR	28,263	ClassyFire subclass
direct_parent	VARCHAR	33,581	ClassyFire direct parent
molecular_framework	VARCHAR	29,994	ClassyFire molecular framework
taxonomy_alternative_parents	VARCHAR[]	14,479	ClassyFire alternative parents
taxonomy_substituents	VARCHAR[]	14,537	ClassyFire substituents
taxonomy_external_descriptors	VARCHAR[]	6,146	ClassyFire external descriptors
state	VARCHAR	5,730	Physical state reported by source
logp	DOUBLE	55,877	Predicted logP
logs	DOUBLE	0	Predicted logS
pka_acidic	DOUBLE	0	Predicted acidic pKa
pka_basic	DOUBLE	0	Predicted basic pKa
hba	DOUBLE	48,876	Hydrogen-bond acceptors
hbd	DOUBLE	48,876	Hydrogen-bond donors
tpsa	DOUBLE	48,876	Topological polar surface area
water_solubility	DOUBLE	0	Experimental water solubility
melting_point	DOUBLE	0	Melting point
boiling_point	DOUBLE	0	Boiling point
source_category	VARCHAR[]	29,192	Organism classes reported for this compound (plant / animal / fungi / bacterium / human / microbe)
molecule_type	VARCHAR	30,807	Entity type: small_molecule / protein / biotech / oligonucleotide / oligosaccharide
origin	VARCHAR	26	Exogenous vs endogenous annotation from source
max_phase	VARCHAR	6,183	Maximum clinical phase (drug sources)
source_organism_class	VARCHAR[]	639	Organism class labels (reserved)
occurrence_context	VARCHAR[]	0	Context of occurrence (reserved; not populated)
mixture	STRUCT("system" VARCHAR, id VARCHAR, "label" VARCHAR, rank VARCHAR, "value" VARCHAR, evidence VARCHAR[])[]	0	Mixture membership records (reserved)
cas	VARCHAR[]	47,289	CAS registry numbers (list)
pubchem_cid	VARCHAR[]	301,674	PubChem CIDs (list)
hmdb_id	VARCHAR	15,141	HMDB identifier
chemspider_id	VARCHAR	11,884	ChemSpider identifier
kegg_id	VARCHAR	5,390	KEGG compound identifier
chebi_id	VARCHAR	9,234	ChEBI identifier
drugbank_id	VARCHAR	3,813	DrugBank identifier
foodb_id	VARCHAR	5,688	FooDB identifier
metlin_id	VARCHAR	1,289	METLIN identifier
pdb_id	VARCHAR	368	PDB ligand identifier
biocyc_id	VARCHAR	1,793	BioCyc identifier
bigg_id	VARCHAR	437	BiGG identifier
knapsack_id	VARCHAR	3,072	KNApSAcK identifier
wikipedia_id	VARCHAR	5,311	Wikipedia page title
phenolexplorer_id	VARCHAR	201	Phenol-Explorer identifier
vmh_id	VARCHAR	865	VMH identifier
registry	STRUCT("system" VARCHAR, id VARCHAR, "label" VARCHAR, rank VARCHAR, "value" VARCHAR, evidence VARCHAR[])[]	926,080	Registry records with provenance evidence (list of structs)
hmdb_diseases	VARCHAR[]	0	Diseases associated with this compound in HMDB (reserved)
hmdb_disease_omim	VARCHAR[]	0	OMIM ids for HMDB diseases (reserved)
disease	STRUCT("system" VARCHAR, id VARCHAR, "label" VARCHAR, rank VARCHAR, "value" VARCHAR, evidence VARCHAR[])[]	0	Disease associations (reserved)
molecule_relation	STRUCT("system" VARCHAR, id VARCHAR, "label" VARCHAR, rank VARCHAR, "value" VARCHAR, evidence VARCHAR[])[]	0	Relations to other molecules (reserved)
hmdb_pathways	VARCHAR[]	0	HMDB pathway names (reserved)
pathway	STRUCT("system" VARCHAR, id VARCHAR, "label" VARCHAR, rank VARCHAR, "value" VARCHAR, evidence VARCHAR[])[]	29,105	NPClassifier pathway / class annotation
hmdb_targets	VARCHAR[]	0	HMDB protein targets (reserved)
target	STRUCT("system" VARCHAR, id VARCHAR, "label" VARCHAR, rank VARCHAR, "value" VARCHAR, evidence VARCHAR[])[]	0	Protein targets (reserved)
taxon	STRUCT("system" VARCHAR, id VARCHAR, "label" VARCHAR, rank VARCHAR, "value" VARCHAR, evidence VARCHAR[])[]	26,291	Taxonomic occurrence annotations (LOTUS / COCONUT / MycoBank / LPSN)
reaction	STRUCT("system" VARCHAR, id VARCHAR, "label" VARCHAR, rank VARCHAR, "value" VARCHAR, evidence VARCHAR[])[]	0	Reaction records (reserved)
license	STRUCT(license VARCHAR, licensor VARCHAR)[]	1,391,199	License records: license name and licensor
provenance	STRUCT(distributor VARCHAR, dataset VARCHAR, file VARCHAR, source_id VARCHAR)[]	1,391,199	Source records: distributor, dataset, file, source_id
record_quality_grade	VARCHAR	1,391,199	Structure completeness: M0 full structure, M1 lipid shorthand, M2 name only, M3 registry id
ccs	DOUBLE	0	Collision cross section (molecule level; reserved)
standard_available	BOOLEAN	1,391,199	True when at least one spectrum comes from an AGIS-JBLab authentic standard
spectrum_count	BIGINT	0	Number of spectra linked to this compound (reserved; use spectrum table)

Spectrum fields

Field	Type	Non-null	Description
spectrum_uid	VARCHAR	8,155,799	Spectrum identifier; the SOL: prefix marks spectra imported from the AGIS-JBLab dataset
peaks_mz	DOUBLE[]	8,155,799	Fragment m/z values (list)
peaks_intensity	DOUBLE[]	8,155,799	Fragment intensities (list)
content_hash	VARCHAR	8,155,799	Normalised content fingerprint (peaks, precursor, adduct, polarity, CE)
splash	VARCHAR	3,522,497	SPLASH spectral hash
molecule_uid	VARCHAR	8,150,202	Compound key the spectrum is assigned to
annotation_level	VARCHAR	0	Annotation confidence level (reserved)
mass_error	DOUBLE	0	Precursor mass error (reserved)
annotations	STRUCT(molecule_uid VARCHAR, annotation_level VARCHAR, mass_error DOUBLE, rank BIGINT)[]	0	Alternative annotations (reserved)
precursor_mz	DOUBLE	7,824,243	Precursor m/z
precursor_type	VARCHAR	7,784,033	Adduct type (e.g. [M+H]+, [M-H]-)
charge	BIGINT	7,365,879	Precursor charge
ionization_mode	VARCHAR	8,150,791	Ionization polarity
ion_source	VARCHAR	3,725,725	Ion source (ESI, APCI, ...)
mass_analyzer	VARCHAR	7,086	Mass analyser
instrument	VARCHAR[]	5,813,538	Instrument model(s) (list)
instrument_type	VARCHAR[]	3,712,017	Instrument family (list)
resolution	VARCHAR	44,457	Resolving power as reported by source
fragmentation_mode	VARCHAR	416,779	Fragmentation method (HCD, CID, ...)
collision_energy	STRUCT("value" DOUBLE, unit VARCHAR, "level" VARCHAR)	6,105,224	Collision energy: value, unit, level
isolation_window	VARCHAR	0	Precursor isolation window (reserved)
derivative_type	VARCHAR	0	Derivatization type (reserved)
derivative_form	VARCHAR	0	Derivatization form (reserved)
derivative_smiles	VARCHAR	0	Derivatized SMILES (reserved)
scan_number	BIGINT	0	Original scan number (reserved)
scan_filter	VARCHAR	0	Original scan filter (reserved)
retention_time	DOUBLE	4,474,730	Retention time as reported (units follow source)
retention_index	DOUBLE	0	Retention index (reserved)
ccs	DOUBLE	1,436,982	Collision cross section
lc_column	VARCHAR	1,557	LC column description
solvent	VARCHAR	0	Solvent (reserved)
flow_rate	VARCHAR	0	Flow rate (reserved)
mobile_phase	VARCHAR	1,557	Mobile phase description
chromatography_type	VARCHAR	0	Chromatography type (reserved)
column_type	VARCHAR	0	Column type (reserved)
technique	VARCHAR	0	Technique (reserved)
ms_level	VARCHAR	6,368,072	MS level as reported (MS2 / MS3 / ... / missing)
base_peak	DOUBLE	0	Base peak intensity (reserved)
precursor_intensity	DOUBLE	0	Precursor intensity (reserved)
origin	VARCHAR	540,502	experimental; populated only where the source reported it
sample_class	VARCHAR	0	Sample class (reserved)
source_organism	VARCHAR	0	Source organism (reserved)
sample_material	VARCHAR	0	Sample material (reserved)
sample_mass	VARCHAR	0	Sample mass (reserved)
sample_concentration	VARCHAR	0	Sample concentration (reserved)
sample_ph	VARCHAR	0	Sample pH (reserved)
spectral_entropy	DOUBLE	458,350	Spectral entropy
normalized_entropy	DOUBLE	458,350	Normalised spectral entropy
quality	STRUCT(metric VARCHAR, "value" DOUBLE, "method" VARCHAR)[]	8,155,799	Quality records: major_frac / base_frac / major_cv / major_median / grade_* / imputed_*
license	STRUCT(license VARCHAR, licensor VARCHAR)[]	8,155,799	License records: license name and licensor
provenance	STRUCT(distributor VARCHAR, dataset VARCHAR, file VARCHAR, source_id VARCHAR)[]	8,155,799	Source records: distributor, dataset, file, source_id
spectrum_quality_str	VARCHAR	8,155,799	Compact quality string: (major_frac,base_frac,major_cv,major_median)-Px-Ax-Bx