swagger_client.models.small_molecule_summary module

mzTab-M reference implementation and validation API.

This is the mzTab-M reference implementation and validation API service. # noqa: E501

OpenAPI spec version: 2.0.0 Contact: nils.hoffmann@isas.de Generated by: https://github.com/swagger-api/swagger-codegen.git

class swagger_client.models.small_molecule_summary.SmallMoleculeSummary(prefix='SML', header_prefix='SMH', sml_id=None, smf_id_refs=None, database_identifier=None, chemical_formula=None, smiles=None, inchi=None, chemical_name=None, uri=None, theoretical_neutral_mass=None, adduct_ions=None, reliability=None, best_id_confidence_measure=None, best_id_confidence_value=None, abundance_assay=None, abundance_study_variable=None, abundance_variation_study_variable=None, opt=None, comment=None)

Bases: object

NOTE: This class is auto generated by the swagger code generator program.

Do not edit the class manually.

SmallMoleculeSummary - a model defined in Swagger

property abundance_assay

Gets the abundance_assay of this SmallMoleculeSummary. # noqa: E501

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. “null” SHOULD be used to report missing quantities, while zero SHOULD be used to indicate a present but not reliably quantifiable value (e.g. below a minimum noise threshold). # noqa: E501

Returns

The abundance_assay of this SmallMoleculeSummary. # noqa: E501

Return type

list[float]

property abundance_study_variable

Gets the abundance_study_variable of this SmallMoleculeSummary. # noqa: E501

The small molecule’s abundance in all the study variables described in the metadata section (study_variable[1-n]_average_function), calculated using the method as described in the Metadata section (default = arithmetic mean across assays). Null or zero values may be reported as appropriate. “null” SHOULD be used to report missing quantities, while zero SHOULD be used to indicate a present but not reliably quantifiable value (e.g. below a minimum noise threshold). # noqa: E501

Returns

The abundance_study_variable of this SmallMoleculeSummary. # noqa: E501

Return type

list[float]

property abundance_variation_study_variable

Gets the abundance_variation_study_variable of this SmallMoleculeSummary. # noqa: E501

A measure of the variability of the study variable abundance measurement, calculated using the method as described in the metadata section (study_variable[1-n]_average_function), with a default = arithmethic co-efficient of variation of the small molecule’s abundance in the given study variable. # noqa: E501

Returns

The abundance_variation_study_variable of this SmallMoleculeSummary. # noqa: E501

Return type

list[float]

property adduct_ions

Gets the adduct_ions of this SmallMoleculeSummary. # noqa: E501

A “|” separated list of detected adducts for this this molecule, following 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-, [M+H]1+. If the adduct classification is ambiguous with regards to identification evidence it MAY be null. # noqa: E501

Returns

The adduct_ions of this SmallMoleculeSummary. # noqa: E501

Return type

list[str]

attribute_map = {'abundance_assay': 'abundance_assay', 'abundance_study_variable': 'abundance_study_variable', 'abundance_variation_study_variable': 'abundance_variation_study_variable', 'adduct_ions': 'adduct_ions', 'best_id_confidence_measure': 'best_id_confidence_measure', 'best_id_confidence_value': 'best_id_confidence_value', 'chemical_formula': 'chemical_formula', 'chemical_name': 'chemical_name', 'comment': 'comment', 'database_identifier': 'database_identifier', 'header_prefix': 'header_prefix', 'inchi': 'inchi', 'opt': 'opt', 'prefix': 'prefix', 'reliability': 'reliability', 'smf_id_refs': 'smf_id_refs', 'smiles': 'smiles', 'sml_id': 'sml_id', 'theoretical_neutral_mass': 'theoretical_neutral_mass', 'uri': 'uri'}

property best_id_confidence_measure

Gets the best_id_confidence_measure of this SmallMoleculeSummary. # noqa: E501

The approach or database search that identified this small molecule with highest confidence. # noqa: E501

Returns

The best_id_confidence_measure of this SmallMoleculeSummary. # noqa: E501

Return type

Parameter

property best_id_confidence_value

Gets the best_id_confidence_value of this SmallMoleculeSummary. # noqa: E501

The best confidence measure in identification (for this type of score) for the given small molecule across all assays. The type of score MUST be defined in the metadata section. If the small molecule was not identified by the specified search engine, “null” MUST be reported. If the confidence measure does not report a numerical confidence value, “null” SHOULD be reported. # noqa: E501

Returns

The best_id_confidence_value of this SmallMoleculeSummary. # noqa: E501

Return type

float

property chemical_formula

Gets the chemical_formula of this SmallMoleculeSummary. # noqa: E501

A list of “|” separated potential chemical formulae of the reported compound. The number of values provided MUST match the number of entities reported under “database_identifier”, even if this leads to redundant reporting of information (i.e. if ambiguity can be resolved in the chemical formula), and the validation software will throw an error if the number of “|” symbols does not match. “null” values between bars are allowed. 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. Example: N-acetylglucosamine would be encoded by the string “C8H15NO6”. # noqa: E501

Returns

The chemical_formula of this SmallMoleculeSummary. # noqa: E501

Return type

list[str]

property chemical_name

Gets the chemical_name of this SmallMoleculeSummary. # noqa: E501

A list of “|” separated possible chemical/common names for the small molecule, or general description if a chemical name is unavailable. Multiple names are only to demonstrate ambiguity in the identification. The number of values provided MUST match the number of entities reported under “database_identifier”, and the validation software will throw an error if the number of “|” symbols does not match. “null” values between bars are allowed. # noqa: E501

Returns

The chemical_name of this SmallMoleculeSummary. # noqa: E501

Return type

list[str]

property comment

Gets the comment of this SmallMoleculeSummary. # noqa: E501

Returns

The comment of this SmallMoleculeSummary. # noqa: E501

Return type

list[Comment]

property database_identifier

Gets the database_identifier of this SmallMoleculeSummary. # noqa: E501

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. # noqa: E501

Returns

The database_identifier of this SmallMoleculeSummary. # noqa: E501

Return type

list[str]

property header_prefix

Gets the header_prefix of this SmallMoleculeSummary. # noqa: E501

The small molecule table header prefix. SMH MUST be used for the small molecule table header line (the column labels). # noqa: E501

Returns

The header_prefix of this SmallMoleculeSummary. # noqa: E501

Return type

str

property inchi

Gets the inchi of this SmallMoleculeSummary. # noqa: E501

A list of “|” separated potential standard IUPAC International Chemical Identifier (InChI) of the given substance. The number of values provided MUST match the number of entities reported under “database_identifier”, even if this leads to redundant information being reported (i.e. if ambiguity can be resolved in the InChi), and the validation software will throw an error if the number of “|” symbols does not match. “null” values between bars are allowed. # noqa: E501

Returns

The inchi of this SmallMoleculeSummary. # noqa: E501

Return type

list[str]

property opt

Gets the opt of this SmallMoleculeSummary. # noqa: E501

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 ‘_’. # noqa: E501

Returns

The opt of this SmallMoleculeSummary. # noqa: E501

Return type

list[OptColumnMapping]

property prefix

Gets the prefix of this SmallMoleculeSummary. # noqa: E501

The small molecule table row prefix. SML MUST be used for rows of the small molecule table. # noqa: E501

Returns

The prefix of this SmallMoleculeSummary. # noqa: E501

Return type

str

property reliability

Gets the reliability of this SmallMoleculeSummary. # noqa: E501

The reliability of the given small molecule identification. This must be supplied by the resource and MUST be reported as an integer between 1-4: identified metabolite (1) putatively annotated compound (2) putatively characterized compound class (3) unknown compound (4) These MAY be replaced using a suitable CV term in the metadata section e.g. to use MSI recommendation levels (see Section 6.2.57 for details). The following CV terms are already available within the PSI MS CV. Future schemes may be implemented by extending the PSI MS CV with new terms and associated levels. The MSI has recently discussed an extension of the original four level scheme into a five level scheme MS:1002896 (compound identification confidence level) with levels isolated, pure compound, full stereochemistry (0) reference standard match or full 2D structure (1) unambiguous diagnostic evidence (literature, database) (2) most likely structure, including isomers, substance class or substructure match (3) unknown compound (4) For high-resolution MS, the following term and its levels may be used: MS:1002955 (hr-ms compound identification confidence level) with levels confirmed structure (1) probable structure (2) unambiguous ms library match (2a) diagnostic evidence (2b) tentative candidates (3) unequivocal molecular formula (4) exact mass (5) A String data type is set to allow for different systems to be specified in the metadata section. # noqa: E501

Returns

The reliability of this SmallMoleculeSummary. # noqa: E501

Return type

str

property smf_id_refs

Gets the smf_id_refs of this SmallMoleculeSummary. # noqa: E501

References to all the features on which quantitation has been based (SMF elements) via referencing SMF_ID values. Multiple values SHOULD be provided as a “|” separated list. This MAY be null only if this is a Summary file. # noqa: E501

Returns

The smf_id_refs of this SmallMoleculeSummary. # noqa: E501

Return type

list[int]

property smiles

Gets the smiles of this SmallMoleculeSummary. # noqa: E501

A list of “|” separated potential molecule structures in the simplified molecular-input line-entry system (SMILES) for the small molecule. The number of values provided MUST match the number of entities reported under “database_identifier”, and the validation software will throw an error if the number of “|” symbols does not match. “null” values between bars are allowed. # noqa: E501

Returns

The smiles of this SmallMoleculeSummary. # noqa: E501

Return type

list[str]

property sml_id

Gets the sml_id of this SmallMoleculeSummary. # noqa: E501

A within file unique identifier for the small molecule. # noqa: E501

Returns

The sml_id of this SmallMoleculeSummary. # noqa: E501

Return type

int

swagger_types = {'abundance_assay': 'list[float]', 'abundance_study_variable': 'list[float]', 'abundance_variation_study_variable': 'list[float]', 'adduct_ions': 'list[str]', 'best_id_confidence_measure': 'Parameter', 'best_id_confidence_value': 'float', 'chemical_formula': 'list[str]', 'chemical_name': 'list[str]', 'comment': 'list[Comment]', 'database_identifier': 'list[str]', 'header_prefix': 'str', 'inchi': 'list[str]', 'opt': 'list[OptColumnMapping]', 'prefix': 'str', 'reliability': 'str', 'smf_id_refs': 'list[int]', 'smiles': 'list[str]', 'sml_id': 'int', 'theoretical_neutral_mass': 'list[float]', 'uri': 'list[str]'}

property theoretical_neutral_mass

Gets the theoretical_neutral_mass of this SmallMoleculeSummary. # noqa: E501

The small molecule’s precursor’s theoretical neutral mass. The number of values provided MUST match the number of entities reported under “database_identifier”, and the validation software will throw an error if the number of “|” symbols does not match. “null” values (in general and between bars) are allowed for molecules that have not been identified only, or for molecules where the neutral mass cannot be calculated. In these cases, the SML entry SHOULD reference features in which exp_mass_to_charge values are captured. # noqa: E501

Returns

The theoretical_neutral_mass of this SmallMoleculeSummary. # noqa: E501

Return type

list[float]

to_dict()

Returns the model properties as a dict

to_str()

Returns the string representation of the model

property uri

Gets the uri of this SmallMoleculeSummary. # noqa: E501

A URI pointing to the small molecule’s entry in a reference database (e.g., the small molecule’s HMDB or KEGG entry). The number of values provided MUST match the number of entities reported under “database_identifier”, and the validation software will throw an error if the number of “|” symbols does not match. “null” values between bars are allowed. # noqa: E501

Returns

The uri of this SmallMoleculeSummary. # noqa: E501

Return type

list[str]