Skip to content

Commit

Permalink
11.4.0rc1
Browse files Browse the repository at this point in the history
  • Loading branch information
@pkalita-lbl
pkalita-lbl committed Jan 31, 2025
1 parent 1b42cef commit 6ec0d64
Show file tree
Hide file tree
Showing 5 changed files with 364 additions and 164 deletions.
60 changes: 40 additions & 20 deletions nmdc_schema/nmdc-pydantic.py
View file
Original file line number Diff line number Diff line change
Expand Up @@ -766,6 +766,26 @@ class SampleStateEnum(str, Enum):
gas = "gas"


class ChemicalEntityEnum(str, Enum):
acetonitrile = "acetonitrile"
alphaLP = "alphaLP"
ammonium_acetate = "ammonium_acetate"
ammonium_bicarbonate = "ammonium_bicarbonate"
Arg_C = "Arg-C"
Asp_N = "Asp-N"
chloroform = "chloroform"
chymotrypsin = "chymotrypsin"
formic_acid = "formic_acid"
glucose = "glucose"
Glu_C = "Glu-C"
isopropyl_alcohol = "isopropyl_alcohol"
Lys_C = "Lys-C"
Lys_N = "Lys-N"
methanol = "methanol"
trypsin = "trypsin"
water = "water"


class ArchStrucEnum(str, Enum):
building = "building"
shed = "shed"
Expand Down Expand Up @@ -2347,6 +2367,18 @@ class MetaproteomicsAnalysisCategoryEnum(str, Enum):
in_silico_metagenome = "in_silico_metagenome"


class MetabolomicsAnalysisCategoryEnum(str, Enum):
"""
The category of metabolomics analysis being performed.
"""
# A metabolomics analysis that is performed on gas chromatography mass spectrometry data.
gc_ms_metabolomics = "gc_ms_metabolomics"
# A metabolomics analysis that is performed on liquid chromatography mass spectrometry data for lipidomics annotation.
lc_ms_lipidomics = "lc_ms_lipidomics"
# A metabolomics analysis that is performed on liquid chromatography mass spectrometry data.
lc_ms_metabolomics = "lc_ms_metabolomics"



class EukEval(ConfiguredBaseModel):
"""
Expand Down Expand Up @@ -2490,9 +2522,6 @@ class Database(ConfiguredBaseModel):
calibration_set: Optional[List[CalibrationInformation]] = Field(None, description="""This property links a database object to the set of calibrations within it.""", json_schema_extra = { "linkml_meta": {'alias': 'calibration_set',
'domain_of': ['Database'],
'mixins': ['object_set']} })
chemical_entity_set: Optional[List[ChemicalEntity]] = Field(None, description="""This property links a database object to the set of chemical entities within it.""", json_schema_extra = { "linkml_meta": {'alias': 'chemical_entity_set',
'domain_of': ['Database'],
'mixins': ['object_set']} })
collecting_biosamples_from_site_set: Optional[List[CollectingBiosamplesFromSite]] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'collecting_biosamples_from_site_set',
'domain_of': ['Database'],
'mixins': ['object_set']} })
Expand Down Expand Up @@ -2611,14 +2640,14 @@ class PortionOfSubstance(ConfiguredBaseModel):
final_concentration: Optional[QuantityValue] = Field(None, description="""When solutions A (containing substance X) and B are combined together, this slot captures the concentration of X in the combination""", json_schema_extra = { "linkml_meta": {'alias': 'final_concentration',
'domain_of': ['PortionOfSubstance'],
'is_a': 'concentration'} })
known_as: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'known_as', 'domain_of': ['PortionOfSubstance']} })
mass: Optional[QuantityValue] = Field(None, title="mass", description="""A physical quality that inheres in a bearer by virtue of the proportion of the bearer's amount of matter.""", json_schema_extra = { "linkml_meta": {'alias': 'mass',
'domain_of': ['SubSamplingProcess', 'PortionOfSubstance'],
'exact_mappings': ['PATO:0000125']} })
sample_state_information: Optional[SampleStateEnum] = Field(None, description="""The chemical phase of a pure sample, or the state of a mixed sample""", json_schema_extra = { "linkml_meta": {'alias': 'sample_state_information', 'domain_of': ['PortionOfSubstance']} })
source_concentration: Optional[QuantityValue] = Field(None, description="""When solutions A (containing substance X) and B are combined together, this slot captures the concentration of X in solution A""", json_schema_extra = { "linkml_meta": {'alias': 'source_concentration',
'domain_of': ['PortionOfSubstance'],
'is_a': 'concentration'} })
known_as: Optional[ChemicalEntityEnum] = Field(None, description="""The substance from which a portion was taken.""", json_schema_extra = { "linkml_meta": {'alias': 'known_as', 'domain_of': ['PortionOfSubstance']} })
substance_role: Optional[SubstanceRoleEnum] = Field(None, description="""The role of a substance in a process""", json_schema_extra = { "linkml_meta": {'alias': 'substance_role', 'domain_of': ['PortionOfSubstance']} })
type: Literal["https://w3id.org/nmdc/PortionOfSubstance","nmdc:PortionOfSubstance"] = Field("nmdc:PortionOfSubstance", description="""the class_uri of the class that has been instantiated""", json_schema_extra = { "linkml_meta": {'alias': 'type',
'designates_type': True,
Expand Down Expand Up @@ -3793,7 +3822,7 @@ def pattern_alternative_identifiers(cls, v):

class ChemicalEntity(OntologyClass):
"""
An atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products, drugs. There may be different terms for distinct acid-base forms, protonation states
An atom or molecule that can be represented with a chemical formula. Include lipids, glycans, natural products, drugs. There may be different terms for distinct acid-base forms, protonation states. A chemical entity is a physical entity that pertains to chemistry or biochemistry.
"""
linkml_meta: ClassVar[LinkMLMeta] = LinkMLMeta({'aliases': ['metabolite',
'chemical substance',
Expand All @@ -3802,26 +3831,15 @@ class ChemicalEntity(OntologyClass):
'class_uri': 'nmdc:ChemicalEntity',
'comments': ['As with the parent OntologyClass, we will not assign an nmdc id '
'pattern or typecode to this class.'],
'deprecated': 'true; as of Jan 2025, NMDC only needs a handful of chemicals '
'and its use cases can be served via an enumeration rather than '
'supporting a full class.',
'exact_mappings': ['biolink:ChemicalSubstance'],
'from_schema': 'https://w3id.org/nmdc/nmdc',
'id_prefixes': ['cas',
'CHEBI',
'CHEMBL.COMPOUND',
'DRUGBANK',
'HMDB',
'KEGG.COMPOUND',
'MESH',
'PUBCHEM.COMPOUND'],
'id_prefixes': ['CHEBI', 'MS'],
'see_also': ['https://bioconductor.org/packages/devel/data/annotation/vignettes/metaboliteIDmapping/inst/doc/metaboliteIDmapping.html']})

chemical_formula: Optional[str] = Field(None, description="""A generic grouping for molecular formulae and empirical formulae""", json_schema_extra = { "linkml_meta": {'alias': 'chemical_formula', 'domain_of': ['ChemicalEntity']} })
inchi: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'inchi', 'domain_of': ['ChemicalEntity']} })
inchi_key: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'inchi_key',
'domain_of': ['ChemicalEntity'],
'notes': ['key set to false due to rare collisions: Pletnev I, Erin A, '
'McNaught A, Blinov K, Tchekhovskoi D, Heller S (2012) InChIKey '
'collision resistance: an experimental testing. J Cheminform. 4:12']} })
smiles: Optional[List[str]] = Field(None, description="""A string encoding of a molecular graph, no chiral or isotopic information. There are usually a large number of valid SMILES which represent a given structure. For example, CCO, OCC and C(O)C all specify the structure of ethanol.""", json_schema_extra = { "linkml_meta": {'alias': 'smiles', 'domain_of': ['ChemicalEntity']} })
alternative_names: Optional[List[str]] = Field(None, description="""A list of alternative names used to refer to the entity. The distinction between name and alternative names is application-specific.""", json_schema_extra = { "linkml_meta": {'alias': 'alternative_names',
'domain_of': ['OntologyClass', 'Study'],
'exact_mappings': ['dcterms:alternative', 'skos:altLabel']} })
Expand Down Expand Up @@ -18796,6 +18814,8 @@ class MetabolomicsAnalysis(WorkflowExecution):
'domain_of': ['MetabolomicsAnalysis', 'NomAnalysis'],
'structured_pattern': {'interpolated': True,
'syntax': '{id_nmdc_prefix}:calib-{id_shoulder}-{id_blade}$'}} })
metabolomics_analysis_category: MetabolomicsAnalysisCategoryEnum = Field(..., description="""The category of metabolomics analysis being performed.""", json_schema_extra = { "linkml_meta": {'alias': 'metabolomics_analysis_category',
'domain_of': ['MetabolomicsAnalysis']} })
ended_at_time: Optional[str] = Field(None, json_schema_extra = { "linkml_meta": {'alias': 'ended_at_time',
'domain_of': ['WorkflowExecution'],
'mappings': ['prov:endedAtTime'],
Expand Down
Loading

0 comments on commit 6ec0d64

Please sign in to comment.