SmallMoleculeSummary

Properties

Name (Alias)	Type (Default)	Constraints	Description
prefix	str (SML)	required pattern: SML Validation type: error	The small molecule table row prefix. SML MUST be used for rows of the small molecule table.
header_prefix	str (SMH)	required pattern: SMH Validation type: error	The small molecule table header prefix. SMH MUST be used for the small molecule table header line (the column labels).
comment	List of Comment	-
sml_id (SML_ID)	int	required format: non-negative-integer Validation type: error	A within file unique identifier for the small molecule summary.
smf_id_refs (SMF_ID_REFS)	List of int	format: non-negative-integer Validation type: error	References to the small molecule features (SMF elements) via referencing SMF_ID values. Multiple values MAY be provided as a | separated list to indicate which features were used to aggregate the SML row.
database_identifier	List of str	-	A list of | separated possible identifiers for the small molecule; multiple values MUST only be provided to indicate ambiguity in the identification of the molecule and not to demonstrate different identifier types for the same molecule. Alternative identifiers for the same molecule MAY be provided as optional columns. The database identifier must be preceded by the resource description (prefix) followed by a colon, as specified in the metadata section. A null value MAY be provided if the identification is sufficiently ambiguous as to be meaningless for reporting or the small molecule has not been identified.
chemical_formula	List of str	-	The chemical formula of the identified compound e.g. in a database, assumed to match the theoretical mass to charge (in some cases this will be the derivatized form, including adducts and protons). This should be specified in Hill notation (EA Hill 1900), i.e. elements in the order C, H and then alphabetically all other elements. Counts of one may be omitted. Elements should be capitalized properly to avoid confusion (e.g., “CO” vs. “Co”). The chemical formula reported should refer to the neutral form. Charge state is reported by the charge field in the SME and SMF section.<br/>Example N-acetylglucosamine would be encoded by the string “C8H15NO6”
smiles	List of str	-	The potential molecule’s structure in the simplified molecular-input line-entry system (SMILES) for the small molecule.
inchi	List of str	-	A standard IUPAC International Chemical Identifier (InChI) for the given substance.
chemical_name	List of str	-	The small molecule’s chemical/common name, or general description if a chemical name is unavailable.
uri	List of str	min: 1 format: any-url Validation type: error	A URI pointing to the small molecule’s entry in a database (e.g., the small molecule’s HMDB, Chebi or KEGG entry).
theoretical_neutral_mass	List of float	-	The theoretical neutral mass of the small molecule. This should be calculated from the chemical formula.
adduct_ions	List of str	-	A | separated list of the detected adduct ion forms for this small molecule. The terms should follow the general style in the 2013 IUPAC recommendations on terms relating to MS e.g. [M+H]1+, [M+Na]1+, [M+NH4]1+, [M-H]1-, [M+Cl]1-.
reliability	str	-	The reliability of the given small molecule identification. This must be supplied by the resource and should be reported as an integer between 1-4:<br/><br/>1: identified, rigorous. ...<br/>2: identified. ...<br/>3: putatively characterized class. ...<br/>4: unknown. ...
best_id_confidence_measure	Parameter	-	The small molecule confidence measure/score of the best identification for this small molecule summary. The type of the value is defined by the best_id_confidence_measure CV parameter. The value is reported in the best_id_confidence_value column.
best_id_confidence_value	float	required Validation type: warn	The small molecule confidence measure/score value of the best identification for this small molecule summary.
abundance_assay	List of float	-	The small molecule’s abundance in every assay described in the metadata section MUST be reported. Null or zero values may be reported as appropriate.
abundance_study_variable	List of float	-	The small molecule’s abundance in every study variable described in the metadata section. Null or zero values may be reported as appropriate.
abundance_variation_study_variable	List of float	-	The small molecule’s abundance variation in every study variable described in the metadata section. Null or zero values may be reported as appropriate.
opt	List of OptColumnMapping	-	Additional columns can be added to the end of the small molecule table. These column headers MUST start with the prefix “opt_” followed by the {identifier} of the object they reference: assay, study variable, MS run or “global” (if the value relates to all replicates). Column names MUST only contain the following characters: 'A'-'Z', 'a'-'z', '0'-'9', '', '-', '[', ']', and ':'. CV parameter accessions MAY be used for optional columns following the format: opt{identifier}_cv_{accession}_{parameter name}. Spaces within the parameter's name MUST be replaced by '_'.