valuesets 0.3.1__py3-none-any.whl

valuesets/enums/analytical_chemistry/mass_spectrometry.py

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+"""
+Mass Spectrometry Value Sets
+
+Value sets for mass spectrometry and analytical chemistry, derived from MS and MSIO ontologies.
+
+Generated from: analytical_chemistry/mass_spectrometry.yaml
+"""
+
+from __future__ import annotations
+
+from typing import Dict, Any, Optional
+from valuesets.generators.rich_enum import RichEnum
+
+class RelativeTimeEnum(RichEnum):
+    # Enum members
+    BEFORE = "BEFORE"
+    AFTER = "AFTER"
+    AT_SAME_TIME_AS = "AT_SAME_TIME_AS"
+
+# Set metadata after class creation
+RelativeTimeEnum._metadata = {
+}
+
+class PresenceEnum(RichEnum):
+    # Enum members
+    PRESENT = "PRESENT"
+    ABSENT = "ABSENT"
+    BELOW_DETECTION_LIMIT = "BELOW_DETECTION_LIMIT"
+    ABOVE_DETECTION_LIMIT = "ABOVE_DETECTION_LIMIT"
+
+# Set metadata after class creation
+PresenceEnum._metadata = {
+    "PRESENT": {'description': 'The entity is present'},
+    "ABSENT": {'description': 'The entity is absent'},
+    "BELOW_DETECTION_LIMIT": {'description': 'The entity is below the detection limit'},
+    "ABOVE_DETECTION_LIMIT": {'description': 'The entity is above the detection limit'},
+}
+
+class MassSpectrometerFileFormat(RichEnum):
+    """
+    Standard file formats used in mass spectrometry
+    """
+    # Enum members
+    MZML = "MZML"
+    MZXML = "MZXML"
+    MGF = "MGF"
+    THERMO_RAW = "THERMO_RAW"
+    WATERS_RAW = "WATERS_RAW"
+    WIFF = "WIFF"
+    MZDATA = "MZDATA"
+    PKL = "PKL"
+    DTA = "DTA"
+    MS2 = "MS2"
+    BRUKER_BAF = "BRUKER_BAF"
+    BRUKER_TDF = "BRUKER_TDF"
+    BRUKER_TSF = "BRUKER_TSF"
+    MZ5 = "MZ5"
+    MZMLB = "MZMLB"
+    UIMF = "UIMF"
+
+# Set metadata after class creation
+MassSpectrometerFileFormat._metadata = {
+    "MZML": {'description': 'mzML format - PSI standard for mass spectrometry data', 'meaning': 'MS:1000584'},
+    "MZXML": {'description': 'ISB mzXML format', 'meaning': 'MS:1000566'},
+    "MGF": {'description': 'Mascot Generic Format', 'meaning': 'MS:1001062'},
+    "THERMO_RAW": {'description': 'Thermo RAW format', 'meaning': 'MS:1000563'},
+    "WATERS_RAW": {'description': 'Waters raw format', 'meaning': 'MS:1000526'},
+    "WIFF": {'description': 'ABI WIFF format', 'meaning': 'MS:1000562'},
+    "MZDATA": {'description': 'PSI mzData format', 'meaning': 'MS:1000564'},
+    "PKL": {'description': 'Micromass PKL format', 'meaning': 'MS:1000565'},
+    "DTA": {'description': 'DTA format', 'meaning': 'MS:1000613'},
+    "MS2": {'description': 'MS2 format', 'meaning': 'MS:1001466'},
+    "BRUKER_BAF": {'description': 'Bruker BAF format', 'meaning': 'MS:1000815'},
+    "BRUKER_TDF": {'description': 'Bruker TDF format', 'meaning': 'MS:1002817'},
+    "BRUKER_TSF": {'description': 'Bruker TSF format', 'meaning': 'MS:1003282'},
+    "MZ5": {'description': 'mz5 format', 'meaning': 'MS:1001881'},
+    "MZMLB": {'description': 'mzMLb format', 'meaning': 'MS:1002838'},
+    "UIMF": {'description': 'UIMF format', 'meaning': 'MS:1002531'},
+}
+
+class MassSpectrometerVendor(RichEnum):
+    """
+    Major mass spectrometer manufacturers
+    """
+    # Enum members
+    THERMO_FISHER_SCIENTIFIC = "THERMO_FISHER_SCIENTIFIC"
+    WATERS = "WATERS"
+    BRUKER_DALTONICS = "BRUKER_DALTONICS"
+    SCIEX = "SCIEX"
+    AGILENT = "AGILENT"
+    SHIMADZU = "SHIMADZU"
+    LECO = "LECO"
+
+# Set metadata after class creation
+MassSpectrometerVendor._metadata = {
+    "THERMO_FISHER_SCIENTIFIC": {'description': 'Thermo Fisher Scientific', 'meaning': 'MS:1000483'},
+    "WATERS": {'description': 'Waters Corporation', 'meaning': 'MS:1000126'},
+    "BRUKER_DALTONICS": {'description': 'Bruker Daltonics', 'meaning': 'MS:1000122'},
+    "SCIEX": {'description': 'SCIEX (formerly Applied Biosystems)', 'meaning': 'MS:1000121'},
+    "AGILENT": {'description': 'Agilent Technologies', 'meaning': 'MS:1000490'},
+    "SHIMADZU": {'description': 'Shimadzu Corporation', 'meaning': 'MS:1000124'},
+    "LECO": {'description': 'LECO Corporation', 'meaning': 'MS:1001800'},
+}
+
+class ChromatographyType(RichEnum):
+    """
+    Types of chromatographic separation methods
+    """
+    # Enum members
+    GAS_CHROMATOGRAPHY = "GAS_CHROMATOGRAPHY"
+    HIGH_PERFORMANCE_LIQUID_CHROMATOGRAPHY = "HIGH_PERFORMANCE_LIQUID_CHROMATOGRAPHY"
+    LIQUID_CHROMATOGRAPHY_MASS_SPECTROMETRY = "LIQUID_CHROMATOGRAPHY_MASS_SPECTROMETRY"
+    GAS_CHROMATOGRAPHY_MASS_SPECTROMETRY = "GAS_CHROMATOGRAPHY_MASS_SPECTROMETRY"
+    TANDEM_MASS_SPECTROMETRY = "TANDEM_MASS_SPECTROMETRY"
+    ISOTOPE_RATIO_MASS_SPECTROMETRY = "ISOTOPE_RATIO_MASS_SPECTROMETRY"
+
+# Set metadata after class creation
+ChromatographyType._metadata = {
+    "GAS_CHROMATOGRAPHY": {'description': 'Gas chromatography', 'meaning': 'MSIO:0000147'},
+    "HIGH_PERFORMANCE_LIQUID_CHROMATOGRAPHY": {'description': 'High performance liquid chromatography', 'meaning': 'MSIO:0000148'},
+    "LIQUID_CHROMATOGRAPHY_MASS_SPECTROMETRY": {'description': 'Liquid chromatography-mass spectrometry', 'meaning': 'CHMO:0000524'},
+    "GAS_CHROMATOGRAPHY_MASS_SPECTROMETRY": {'description': 'Gas chromatography-mass spectrometry', 'meaning': 'CHMO:0000497'},
+    "TANDEM_MASS_SPECTROMETRY": {'description': 'Tandem mass spectrometry', 'meaning': 'CHMO:0000575'},
+    "ISOTOPE_RATIO_MASS_SPECTROMETRY": {'description': 'Isotope ratio mass spectrometry', 'meaning': 'CHMO:0000506'},
+}
+
+class DerivatizationMethod(RichEnum):
+    """
+    Chemical derivatization methods for sample preparation
+    """
+    # Enum members
+    SILYLATION = "SILYLATION"
+    METHYLATION = "METHYLATION"
+    ACETYLATION = "ACETYLATION"
+    TRIFLUOROACETYLATION = "TRIFLUOROACETYLATION"
+    ALKYLATION = "ALKYLATION"
+    OXIMATION = "OXIMATION"
+
+# Set metadata after class creation
+DerivatizationMethod._metadata = {
+    "SILYLATION": {'description': 'Addition of silyl groups for improved volatility', 'meaning': 'MSIO:0000117'},
+    "METHYLATION": {'description': 'Addition of methyl groups', 'meaning': 'MSIO:0000115'},
+    "ACETYLATION": {'description': 'Addition of acetyl groups', 'meaning': 'MSIO:0000112'},
+    "TRIFLUOROACETYLATION": {'description': 'Addition of trifluoroacetyl groups', 'meaning': 'MSIO:0000113'},
+    "ALKYLATION": {'description': 'Addition of alkyl groups', 'meaning': 'MSIO:0000114'},
+    "OXIMATION": {'description': 'Addition of oxime groups', 'meaning': 'MSIO:0000116'},
+}
+
+class MetabolomicsAssayType(RichEnum):
+    """
+    Types of metabolomics assays and profiling approaches
+    """
+    # Enum members
+    TARGETED_METABOLITE_PROFILING = "TARGETED_METABOLITE_PROFILING"
+    UNTARGETED_METABOLITE_PROFILING = "UNTARGETED_METABOLITE_PROFILING"
+    METABOLITE_QUANTITATION_HPLC = "METABOLITE_QUANTITATION_HPLC"
+
+# Set metadata after class creation
+MetabolomicsAssayType._metadata = {
+    "TARGETED_METABOLITE_PROFILING": {'description': 'Assay targeting specific known metabolites', 'meaning': 'MSIO:0000100'},
+    "UNTARGETED_METABOLITE_PROFILING": {'description': 'Assay profiling all detectable metabolites', 'meaning': 'MSIO:0000101'},
+    "METABOLITE_QUANTITATION_HPLC": {'description': 'Metabolite quantitation using HPLC', 'meaning': 'MSIO:0000099'},
+}
+
+class AnalyticalControlType(RichEnum):
+    """
+    Types of control samples used in analytical chemistry
+    """
+    # Enum members
+    INTERNAL_STANDARD = "INTERNAL_STANDARD"
+    EXTERNAL_STANDARD = "EXTERNAL_STANDARD"
+    POSITIVE_CONTROL = "POSITIVE_CONTROL"
+    NEGATIVE_CONTROL = "NEGATIVE_CONTROL"
+    LONG_TERM_REFERENCE = "LONG_TERM_REFERENCE"
+    BLANK = "BLANK"
+    QUALITY_CONTROL = "QUALITY_CONTROL"
+
+# Set metadata after class creation
+AnalyticalControlType._metadata = {
+    "INTERNAL_STANDARD": {'description': 'Known amount of standard added to analytical sample', 'meaning': 'MSIO:0000005'},
+    "EXTERNAL_STANDARD": {'description': 'Reference standard used as external reference point', 'meaning': 'MSIO:0000004'},
+    "POSITIVE_CONTROL": {'description': 'Control providing known positive signal', 'meaning': 'MSIO:0000008'},
+    "NEGATIVE_CONTROL": {'description': 'Control providing baseline/no signal reference', 'meaning': 'MSIO:0000007'},
+    "LONG_TERM_REFERENCE": {'description': 'Stable reference for cross-batch comparisons', 'meaning': 'MSIO:0000006'},
+    "BLANK": {'description': 'Sample containing only solvent/matrix without analyte'},
+    "QUALITY_CONTROL": {'description': 'Sample with known composition for system performance monitoring'},
+}
+
+__all__ = [
+    "RelativeTimeEnum",
+    "PresenceEnum",
+    "MassSpectrometerFileFormat",
+    "MassSpectrometerVendor",
+    "ChromatographyType",
+    "DerivatizationMethod",
+    "MetabolomicsAssayType",
+    "AnalyticalControlType",
+]

valuesets/enums/bio/__init__.py

@@ -0,0 +1 @@
+"""Auto-generated package."""

valuesets/enums/bio/biological_colors.py

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+"""
+Biological Color Value Sets
+
+Color value sets for biological traits including eye colors, hair colors, flower colors, and other phenotypic color characteristics.
+
+
+Generated from: bio/biological_colors.yaml
+"""
+
+from __future__ import annotations
+
+from typing import Dict, Any, Optional
+from valuesets.generators.rich_enum import RichEnum
+
+class EyeColorEnum(RichEnum):
+    """
+    Human eye color phenotypes
+    """
+    # Enum members
+    BROWN = "BROWN"
+    BLUE = "BLUE"
+    GREEN = "GREEN"
+    HAZEL = "HAZEL"
+    AMBER = "AMBER"
+    GRAY = "GRAY"
+    HETEROCHROMIA = "HETEROCHROMIA"
+    RED_PINK = "RED_PINK"
+    VIOLET = "VIOLET"
+
+# Set metadata after class creation
+EyeColorEnum._metadata = {
+    "BROWN": {'description': 'Brown eyes', 'annotations': {'hex_range': '663300-8B4513', 'prevalence': '79% worldwide'}},
+    "BLUE": {'description': 'Blue eyes', 'meaning': 'HP:0000635', 'annotations': {'hex_range': '4169E1-87CEEB', 'prevalence': '8-10% worldwide'}},
+    "GREEN": {'description': 'Green eyes', 'annotations': {'hex_range': '2E8B57-90EE90', 'prevalence': '2% worldwide'}},
+    "HAZEL": {'description': 'Hazel eyes (brown-green mix)', 'annotations': {'hex_range': '8B7355-C9A878', 'prevalence': '5% worldwide'}},
+    "AMBER": {'description': 'Amber/golden eyes', 'annotations': {'hex_range': 'FFBF00-FFB300', 'prevalence': 'rare'}},
+    "GRAY": {'description': 'Gray eyes', 'meaning': 'HP:0007730', 'annotations': {'hex_range': '778899-C0C0C0', 'prevalence': '<1% worldwide'}},
+    "HETEROCHROMIA": {'description': 'Different colored eyes', 'meaning': 'HP:0001100', 'annotations': {'note': 'complete or sectoral heterochromia'}},
+    "RED_PINK": {'description': 'Red/pink eyes (albinism)', 'annotations': {'condition': 'associated with albinism'}},
+    "VIOLET": {'description': 'Violet eyes (extremely rare)', 'annotations': {'hex_range': '8B7AB8-9370DB', 'prevalence': 'extremely rare'}},
+}
+
+class HairColorEnum(RichEnum):
+    """
+    Human hair color phenotypes
+    """
+    # Enum members
+    BLACK = "BLACK"
+    BROWN = "BROWN"
+    DARK_BROWN = "DARK_BROWN"
+    LIGHT_BROWN = "LIGHT_BROWN"
+    BLONDE = "BLONDE"
+    DARK_BLONDE = "DARK_BLONDE"
+    LIGHT_BLONDE = "LIGHT_BLONDE"
+    PLATINUM_BLONDE = "PLATINUM_BLONDE"
+    STRAWBERRY_BLONDE = "STRAWBERRY_BLONDE"
+    RED = "RED"
+    AUBURN = "AUBURN"
+    GINGER = "GINGER"
+    GRAY = "GRAY"
+    WHITE = "WHITE"
+    SILVER = "SILVER"
+
+# Set metadata after class creation
+HairColorEnum._metadata = {
+    "BLACK": {'description': 'Black hair', 'annotations': {'hex': '000000', 'prevalence': 'most common worldwide'}},
+    "BROWN": {'description': 'Brown hair', 'annotations': {'hex_range': '654321-8B4513'}},
+    "DARK_BROWN": {'description': 'Dark brown hair', 'annotations': {'hex': '3B2F2F'}},
+    "LIGHT_BROWN": {'description': 'Light brown hair', 'annotations': {'hex': '977961'}},
+    "BLONDE": {'description': 'Blonde/blond hair', 'meaning': 'HP:0002286', 'annotations': {'hex_range': 'FAF0BE-FFF8DC'}},
+    "DARK_BLONDE": {'description': 'Dark blonde hair', 'annotations': {'hex': '9F8F71'}},
+    "LIGHT_BLONDE": {'description': 'Light blonde hair', 'annotations': {'hex': 'FFF8DC'}},
+    "PLATINUM_BLONDE": {'description': 'Platinum blonde hair', 'annotations': {'hex': 'E5E5E5'}},
+    "STRAWBERRY_BLONDE": {'description': 'Strawberry blonde hair', 'annotations': {'hex': 'FF9966'}},
+    "RED": {'description': 'Red hair', 'meaning': 'HP:0002297', 'annotations': {'hex_range': '922724-FF4500', 'prevalence': '1-2% worldwide'}},
+    "AUBURN": {'description': 'Auburn hair (reddish-brown)', 'annotations': {'hex': 'A52A2A'}},
+    "GINGER": {'description': 'Ginger hair (orange-red)', 'annotations': {'hex': 'FF6600'}},
+    "GRAY": {'description': 'Gray hair', 'meaning': 'HP:0002216', 'annotations': {'hex_range': '808080-C0C0C0'}},
+    "WHITE": {'description': 'White hair', 'meaning': 'HP:0011364', 'annotations': {'hex': 'FFFFFF'}},
+    "SILVER": {'description': 'Silver hair', 'annotations': {'hex': 'C0C0C0'}},
+}
+
+class FlowerColorEnum(RichEnum):
+    """
+    Common flower colors
+    """
+    # Enum members
+    RED = "RED"
+    PINK = "PINK"
+    ORANGE = "ORANGE"
+    YELLOW = "YELLOW"
+    WHITE = "WHITE"
+    PURPLE = "PURPLE"
+    VIOLET = "VIOLET"
+    BLUE = "BLUE"
+    LAVENDER = "LAVENDER"
+    MAGENTA = "MAGENTA"
+    BURGUNDY = "BURGUNDY"
+    CORAL = "CORAL"
+    PEACH = "PEACH"
+    CREAM = "CREAM"
+    BICOLOR = "BICOLOR"
+    MULTICOLOR = "MULTICOLOR"
+
+# Set metadata after class creation
+FlowerColorEnum._metadata = {
+    "RED": {'description': 'Red flowers', 'annotations': {'hex': 'FF0000', 'examples': 'roses, tulips, poppies'}},
+    "PINK": {'description': 'Pink flowers', 'annotations': {'hex': 'FFC0CB', 'examples': 'peonies, cherry blossoms'}},
+    "ORANGE": {'description': 'Orange flowers', 'annotations': {'hex': 'FFA500', 'examples': 'marigolds, zinnias'}},
+    "YELLOW": {'description': 'Yellow flowers', 'annotations': {'hex': 'FFFF00', 'examples': 'sunflowers, daffodils'}},
+    "WHITE": {'description': 'White flowers', 'annotations': {'hex': 'FFFFFF', 'examples': 'lilies, daisies'}},
+    "PURPLE": {'description': 'Purple flowers', 'annotations': {'hex': '800080', 'examples': 'lavender, violets'}},
+    "VIOLET": {'description': 'Violet flowers', 'annotations': {'hex': '7F00FF', 'examples': 'violets, pansies'}},
+    "BLUE": {'description': 'Blue flowers', 'annotations': {'hex': '0000FF', 'examples': 'forget-me-nots, cornflowers'}},
+    "LAVENDER": {'description': 'Lavender flowers', 'annotations': {'hex': 'E6E6FA', 'examples': 'lavender, wisteria'}},
+    "MAGENTA": {'description': 'Magenta flowers', 'annotations': {'hex': 'FF00FF', 'examples': 'fuchsias, bougainvillea'}},
+    "BURGUNDY": {'description': 'Burgundy/deep red flowers', 'annotations': {'hex': '800020', 'examples': 'dahlias, chrysanthemums'}},
+    "CORAL": {'description': 'Coral flowers', 'annotations': {'hex': 'FF7F50', 'examples': 'coral bells, begonias'}},
+    "PEACH": {'description': 'Peach flowers', 'annotations': {'hex': 'FFDAB9', 'examples': 'roses, dahlias'}},
+    "CREAM": {'description': 'Cream flowers', 'annotations': {'hex': 'FFFDD0', 'examples': 'roses, tulips'}},
+    "BICOLOR": {'description': 'Two-colored flowers', 'annotations': {'note': 'flowers with two distinct colors'}},
+    "MULTICOLOR": {'description': 'Multi-colored flowers', 'annotations': {'note': 'flowers with more than two colors'}},
+}
+
+class AnimalCoatColorEnum(RichEnum):
+    """
+    Animal coat/fur colors
+    """
+    # Enum members
+    BLACK = "BLACK"
+    WHITE = "WHITE"
+    BROWN = "BROWN"
+    TAN = "TAN"
+    CREAM = "CREAM"
+    GRAY = "GRAY"
+    RED = "RED"
+    GOLDEN = "GOLDEN"
+    FAWN = "FAWN"
+    BRINDLE = "BRINDLE"
+    SPOTTED = "SPOTTED"
+    MERLE = "MERLE"
+    PIEBALD = "PIEBALD"
+    CALICO = "CALICO"
+    TABBY = "TABBY"
+    TORTOISESHELL = "TORTOISESHELL"
+    ROAN = "ROAN"
+    PALOMINO = "PALOMINO"
+    CHESTNUT = "CHESTNUT"
+    BAY = "BAY"
+
+# Set metadata after class creation
+AnimalCoatColorEnum._metadata = {
+    "BLACK": {'description': 'Black coat', 'annotations': {'hex': '000000'}},
+    "WHITE": {'description': 'White coat', 'annotations': {'hex': 'FFFFFF'}},
+    "BROWN": {'description': 'Brown coat', 'annotations': {'hex': '964B00'}},
+    "TAN": {'description': 'Tan coat', 'annotations': {'hex': 'D2B48C'}},
+    "CREAM": {'description': 'Cream coat', 'annotations': {'hex': 'FFFDD0'}},
+    "GRAY": {'description': 'Gray coat', 'annotations': {'hex': '808080'}},
+    "RED": {'description': 'Red/rust coat', 'annotations': {'hex': 'B22222'}},
+    "GOLDEN": {'description': 'Golden coat', 'annotations': {'hex': 'FFD700'}},
+    "FAWN": {'description': 'Fawn coat', 'annotations': {'hex': 'E5AA70'}},
+    "BRINDLE": {'description': 'Brindle pattern (striped)', 'annotations': {'pattern': 'striped mixture of colors'}},
+    "SPOTTED": {'description': 'Spotted pattern', 'annotations': {'pattern': 'spots on base color'}},
+    "MERLE": {'description': 'Merle pattern (mottled)', 'annotations': {'pattern': 'mottled patches'}},
+    "PIEBALD": {'description': 'Piebald pattern (patches)', 'annotations': {'pattern': 'irregular patches'}},
+    "CALICO": {'description': 'Calico pattern (tri-color)', 'annotations': {'pattern': 'tri-color patches', 'species': 'primarily cats'}},
+    "TABBY": {'description': 'Tabby pattern (striped)', 'annotations': {'pattern': 'striped or spotted', 'species': 'primarily cats'}},
+    "TORTOISESHELL": {'description': 'Tortoiseshell pattern', 'annotations': {'pattern': 'mottled orange and black', 'species': 'primarily cats'}},
+    "ROAN": {'description': 'Roan pattern (mixed white)', 'annotations': {'pattern': 'white mixed with base color', 'species': 'primarily horses'}},
+    "PALOMINO": {'description': 'Palomino (golden with white mane)', 'annotations': {'hex': 'DEC05F', 'species': 'horses'}},
+    "CHESTNUT": {'description': 'Chestnut/sorrel', 'annotations': {'hex': 'CD5C5C', 'species': 'horses'}},
+    "BAY": {'description': 'Bay (brown with black points)', 'annotations': {'species': 'horses'}},
+}
+
+class SkinToneEnum(RichEnum):
+    """
+    Human skin tone classifications (Fitzpatrick scale based)
+    """
+    # Enum members
+    TYPE_I = "TYPE_I"
+    TYPE_II = "TYPE_II"
+    TYPE_III = "TYPE_III"
+    TYPE_IV = "TYPE_IV"
+    TYPE_V = "TYPE_V"
+    TYPE_VI = "TYPE_VI"
+
+# Set metadata after class creation
+SkinToneEnum._metadata = {
+    "TYPE_I": {'description': 'Very pale white skin', 'annotations': {'fitzpatrick': 'Type I', 'hex_range': 'FFE0BD-FFDFC4', 'sun_reaction': 'always burns, never tans'}},
+    "TYPE_II": {'description': 'Fair white skin', 'annotations': {'fitzpatrick': 'Type II', 'hex_range': 'F0D5BE-E8C5A0', 'sun_reaction': 'burns easily, tans minimally'}},
+    "TYPE_III": {'description': 'Light brown skin', 'annotations': {'fitzpatrick': 'Type III', 'hex_range': 'DDA582-CD9766', 'sun_reaction': 'burns moderately, tans gradually'}},
+    "TYPE_IV": {'description': 'Moderate brown skin', 'annotations': {'fitzpatrick': 'Type IV', 'hex_range': 'B87659-A47148', 'sun_reaction': 'burns minimally, tans easily'}},
+    "TYPE_V": {'description': 'Dark brown skin', 'annotations': {'fitzpatrick': 'Type V', 'hex_range': '935D37-7C4E2A', 'sun_reaction': 'rarely burns, tans darkly'}},
+    "TYPE_VI": {'description': 'Very dark brown to black skin', 'annotations': {'fitzpatrick': 'Type VI', 'hex_range': '5C3A1E-3D2314', 'sun_reaction': 'never burns, always tans darkly'}},
+}
+
+class PlantLeafColorEnum(RichEnum):
+    """
+    Plant leaf colors (including seasonal changes)
+    """
+    # Enum members
+    GREEN = "GREEN"
+    DARK_GREEN = "DARK_GREEN"
+    LIGHT_GREEN = "LIGHT_GREEN"
+    YELLOW_GREEN = "YELLOW_GREEN"
+    YELLOW = "YELLOW"
+    ORANGE = "ORANGE"
+    RED = "RED"
+    PURPLE = "PURPLE"
+    BRONZE = "BRONZE"
+    SILVER = "SILVER"
+    VARIEGATED = "VARIEGATED"
+    BROWN = "BROWN"
+
+# Set metadata after class creation
+PlantLeafColorEnum._metadata = {
+    "GREEN": {'description': 'Green leaves (healthy/summer)', 'meaning': 'PATO:0000320', 'annotations': {'hex_range': '228B22-90EE90', 'season': 'spring/summer'}},
+    "DARK_GREEN": {'description': 'Dark green leaves', 'annotations': {'hex': '006400'}},
+    "LIGHT_GREEN": {'description': 'Light green leaves', 'annotations': {'hex': '90EE90'}},
+    "YELLOW_GREEN": {'description': 'Yellow-green leaves', 'annotations': {'hex': '9ACD32', 'condition': 'new growth or nutrient deficiency'}},
+    "YELLOW": {'description': 'Yellow leaves (autumn or chlorosis)', 'meaning': 'PATO:0000324', 'annotations': {'hex': 'FFD700', 'season': 'autumn'}},
+    "ORANGE": {'description': 'Orange leaves (autumn)', 'annotations': {'hex': 'FF8C00', 'season': 'autumn'}},
+    "RED": {'description': 'Red leaves (autumn or certain species)', 'meaning': 'PATO:0000322', 'annotations': {'hex': 'DC143C', 'season': 'autumn'}},
+    "PURPLE": {'description': 'Purple leaves (certain species)', 'annotations': {'hex': '800080', 'examples': 'purple basil, Japanese maple'}},
+    "BRONZE": {'description': 'Bronze leaves', 'annotations': {'hex': 'CD7F32'}},
+    "SILVER": {'description': 'Silver/gray leaves', 'annotations': {'hex': 'C0C0C0', 'examples': 'dusty miller, artemisia'}},
+    "VARIEGATED": {'description': 'Variegated leaves (multiple colors)', 'annotations': {'pattern': 'mixed colors/patterns'}},
+    "BROWN": {'description': 'Brown leaves (dead/dying)', 'annotations': {'hex': '964B00', 'condition': 'senescent or dead'}},
+}
+
+__all__ = [
+    "EyeColorEnum",
+    "HairColorEnum",
+    "FlowerColorEnum",
+    "AnimalCoatColorEnum",
+    "SkinToneEnum",
+    "PlantLeafColorEnum",
+]

valuesets/enums/bio/cell_cycle.py

@@ -0,0 +1,180 @@
+"""
+Cell Cycle Value Sets
+
+Value sets for cell cycle phases, checkpoints, and related concepts
+
+Generated from: bio/cell_cycle.yaml
+"""
+
+from __future__ import annotations
+
+from typing import Dict, Any, Optional
+from valuesets.generators.rich_enum import RichEnum
+
+class CellCyclePhase(RichEnum):
+    """
+    Major phases of the eukaryotic cell cycle
+    """
+    # Enum members
+    G0 = "G0"
+    G1 = "G1"
+    S = "S"
+    G2 = "G2"
+    M = "M"
+    INTERPHASE = "INTERPHASE"
+
+# Set metadata after class creation
+CellCyclePhase._metadata = {
+    "G0": {'description': 'G0 phase (quiescent/resting phase)', 'meaning': 'GO:0044838', 'annotations': {'aliases': 'quiescent phase, resting phase'}},
+    "G1": {'description': 'G1 phase (Gap 1)', 'meaning': 'GO:0051318', 'annotations': {'aliases': 'Gap 1, first gap phase', 'duration': 'variable (hours to years)'}},
+    "S": {'description': 'S phase (DNA synthesis)', 'meaning': 'GO:0051320', 'annotations': {'aliases': 'synthesis phase, DNA replication phase', 'duration': '6-8 hours'}},
+    "G2": {'description': 'G2 phase (Gap 2)', 'meaning': 'GO:0051319', 'annotations': {'aliases': 'Gap 2, second gap phase', 'duration': '3-4 hours'}},
+    "M": {'description': 'M phase (mitosis and cytokinesis)', 'meaning': 'GO:0000279', 'annotations': {'aliases': 'mitotic phase, division phase', 'duration': '~1 hour'}},
+    "INTERPHASE": {'description': 'Interphase (G1, S, and G2 phases combined)', 'meaning': 'GO:0051325', 'annotations': {'includes': 'G1, S, G2'}},
+}
+
+class MitoticPhase(RichEnum):
+    """
+    Stages of mitosis (M phase)
+    """
+    # Enum members
+    PROPHASE = "PROPHASE"
+    PROMETAPHASE = "PROMETAPHASE"
+    METAPHASE = "METAPHASE"
+    ANAPHASE = "ANAPHASE"
+    TELOPHASE = "TELOPHASE"
+    CYTOKINESIS = "CYTOKINESIS"
+
+# Set metadata after class creation
+MitoticPhase._metadata = {
+    "PROPHASE": {'description': 'Prophase', 'meaning': 'GO:0051324', 'annotations': {'order': 1, 'features': 'chromatin condensation, spindle formation begins'}},
+    "PROMETAPHASE": {'description': 'Prometaphase', 'meaning': 'GO:0007080', 'annotations': {'order': 2, 'features': 'nuclear envelope breakdown, kinetochore attachment'}},
+    "METAPHASE": {'description': 'Metaphase', 'meaning': 'GO:0051323', 'annotations': {'order': 3, 'features': 'chromosomes aligned at metaphase plate'}},
+    "ANAPHASE": {'description': 'Anaphase', 'meaning': 'GO:0051322', 'annotations': {'order': 4, 'features': 'sister chromatid separation'}},
+    "TELOPHASE": {'description': 'Telophase', 'meaning': 'GO:0051326', 'annotations': {'order': 5, 'features': 'nuclear envelope reformation'}},
+    "CYTOKINESIS": {'description': 'Cytokinesis', 'meaning': 'GO:0000910', 'annotations': {'order': 6, 'features': 'cytoplasmic division'}},
+}
+
+class CellCycleCheckpoint(RichEnum):
+    """
+    Cell cycle checkpoints that regulate progression
+    """
+    # Enum members
+    G1_S_CHECKPOINT = "G1_S_CHECKPOINT"
+    INTRA_S_CHECKPOINT = "INTRA_S_CHECKPOINT"
+    G2_M_CHECKPOINT = "G2_M_CHECKPOINT"
+    SPINDLE_CHECKPOINT = "SPINDLE_CHECKPOINT"
+
+# Set metadata after class creation
+CellCycleCheckpoint._metadata = {
+    "G1_S_CHECKPOINT": {'description': 'G1/S checkpoint (Restriction point)', 'meaning': 'GO:0000082', 'annotations': {'aliases': 'Start checkpoint, Restriction point, R point', 'regulator': 'p53, Rb'}},
+    "INTRA_S_CHECKPOINT": {'description': 'Intra-S checkpoint', 'meaning': 'GO:0031573', 'annotations': {'function': 'monitors DNA replication', 'regulator': 'ATR, CHK1'}},
+    "G2_M_CHECKPOINT": {'description': 'G2/M checkpoint', 'meaning': 'GO:0031571', 'annotations': {'function': 'ensures DNA properly replicated', 'regulator': 'p53, CHK1, CHK2'}},
+    "SPINDLE_CHECKPOINT": {'description': 'Spindle checkpoint (M checkpoint)', 'meaning': 'GO:0031577', 'annotations': {'aliases': 'SAC, spindle assembly checkpoint', 'function': 'ensures proper chromosome attachment', 'regulator': 'MAD2, BubR1'}},
+}
+
+class MeioticPhase(RichEnum):
+    """
+    Phases specific to meiotic cell division
+    """
+    # Enum members
+    MEIOSIS_I = "MEIOSIS_I"
+    PROPHASE_I = "PROPHASE_I"
+    METAPHASE_I = "METAPHASE_I"
+    ANAPHASE_I = "ANAPHASE_I"
+    TELOPHASE_I = "TELOPHASE_I"
+    MEIOSIS_II = "MEIOSIS_II"
+    PROPHASE_II = "PROPHASE_II"
+    METAPHASE_II = "METAPHASE_II"
+    ANAPHASE_II = "ANAPHASE_II"
+    TELOPHASE_II = "TELOPHASE_II"
+
+# Set metadata after class creation
+MeioticPhase._metadata = {
+    "MEIOSIS_I": {'description': 'Meiosis I (reductional division)', 'meaning': 'GO:0007127', 'annotations': {'result': 'reduction from diploid to haploid'}},
+    "PROPHASE_I": {'description': 'Prophase I', 'meaning': 'GO:0007128', 'annotations': {'substages': 'leptotene, zygotene, pachytene, diplotene, diakinesis'}},
+    "METAPHASE_I": {'description': 'Metaphase I', 'meaning': 'GO:0007132', 'annotations': {'feature': 'homologous pairs align'}},
+    "ANAPHASE_I": {'description': 'Anaphase I', 'meaning': 'GO:0007133', 'annotations': {'feature': 'homologous chromosomes separate'}},
+    "TELOPHASE_I": {'description': 'Telophase I', 'meaning': 'GO:0007134'},
+    "MEIOSIS_II": {'description': 'Meiosis II (equational division)', 'meaning': 'GO:0007135', 'annotations': {'similarity': 'similar to mitosis'}},
+    "PROPHASE_II": {'description': 'Prophase II', 'meaning': 'GO:0007136'},
+    "METAPHASE_II": {'description': 'Metaphase II', 'meaning': 'GO:0007137'},
+    "ANAPHASE_II": {'description': 'Anaphase II', 'meaning': 'GO:0007138', 'annotations': {'feature': 'sister chromatids separate'}},
+    "TELOPHASE_II": {'description': 'Telophase II', 'meaning': 'GO:0007139'},
+}
+
+class CellCycleRegulator(RichEnum):
+    """
+    Types of cell cycle regulatory molecules
+    """
+    # Enum members
+    CYCLIN = "CYCLIN"
+    CDK = "CDK"
+    CDK_INHIBITOR = "CDK_INHIBITOR"
+    CHECKPOINT_KINASE = "CHECKPOINT_KINASE"
+    TUMOR_SUPPRESSOR = "TUMOR_SUPPRESSOR"
+    E3_UBIQUITIN_LIGASE = "E3_UBIQUITIN_LIGASE"
+    PHOSPHATASE = "PHOSPHATASE"
+
+# Set metadata after class creation
+CellCycleRegulator._metadata = {
+    "CYCLIN": {'description': 'Cyclin proteins', 'meaning': 'GO:0016538', 'annotations': {'examples': 'Cyclin A, B, D, E'}},
+    "CDK": {'description': 'Cyclin-dependent kinase', 'meaning': 'GO:0004693', 'annotations': {'examples': 'CDK1, CDK2, CDK4, CDK6'}},
+    "CDK_INHIBITOR": {'description': 'CDK inhibitor', 'meaning': 'GO:0004861', 'annotations': {'examples': 'p21, p27, p57'}},
+    "CHECKPOINT_KINASE": {'description': 'Checkpoint kinase', 'meaning': 'GO:0000077', 'annotations': {'examples': 'CHK1, CHK2, ATR, ATM'}},
+    "TUMOR_SUPPRESSOR": {'description': 'Tumor suppressor involved in cell cycle', 'meaning': 'GO:0051726', 'annotations': {'examples': 'p53, Rb, BRCA1, BRCA2'}},
+    "E3_UBIQUITIN_LIGASE": {'description': 'E3 ubiquitin ligase (cell cycle)', 'meaning': 'GO:0051437', 'annotations': {'examples': 'APC/C, SCF'}},
+    "PHOSPHATASE": {'description': 'Cell cycle phosphatase', 'meaning': 'GO:0004721', 'annotations': {'examples': 'CDC25A, CDC25B, CDC25C'}},
+}
+
+class CellProliferationState(RichEnum):
+    """
+    Cell proliferation and growth states
+    """
+    # Enum members
+    PROLIFERATING = "PROLIFERATING"
+    QUIESCENT = "QUIESCENT"
+    SENESCENT = "SENESCENT"
+    DIFFERENTIATED = "DIFFERENTIATED"
+    APOPTOTIC = "APOPTOTIC"
+    NECROTIC = "NECROTIC"
+
+# Set metadata after class creation
+CellProliferationState._metadata = {
+    "PROLIFERATING": {'description': 'Actively proliferating cells', 'meaning': 'GO:0008283'},
+    "QUIESCENT": {'description': 'Quiescent cells (reversibly non-dividing)', 'meaning': 'GO:0044838', 'annotations': {'phase': 'G0', 'reversible': True}},
+    "SENESCENT": {'description': 'Senescent cells (permanently non-dividing)', 'meaning': 'GO:0090398', 'annotations': {'reversible': False, 'markers': 'SA-β-gal, p16'}},
+    "DIFFERENTIATED": {'description': 'Terminally differentiated cells', 'meaning': 'GO:0030154', 'annotations': {'examples': 'neurons, cardiomyocytes'}},
+    "APOPTOTIC": {'description': 'Cells undergoing apoptosis', 'meaning': 'GO:0006915', 'annotations': {'aliases': 'programmed cell death'}},
+    "NECROTIC": {'description': 'Cells undergoing necrosis', 'meaning': 'GO:0070265', 'annotations': {'type': 'uncontrolled cell death'}},
+}
+
+class DNADamageResponse(RichEnum):
+    """
+    DNA damage response pathways during cell cycle
+    """
+    # Enum members
+    CELL_CYCLE_ARREST = "CELL_CYCLE_ARREST"
+    DNA_REPAIR = "DNA_REPAIR"
+    APOPTOSIS_INDUCTION = "APOPTOSIS_INDUCTION"
+    SENESCENCE_INDUCTION = "SENESCENCE_INDUCTION"
+    CHECKPOINT_ADAPTATION = "CHECKPOINT_ADAPTATION"
+
+# Set metadata after class creation
+DNADamageResponse._metadata = {
+    "CELL_CYCLE_ARREST": {'description': 'Cell cycle arrest', 'meaning': 'GO:0051726', 'aliases': ['regulation of cell cycle']},
+    "DNA_REPAIR": {'description': 'DNA repair', 'meaning': 'GO:0006281'},
+    "APOPTOSIS_INDUCTION": {'description': 'Induction of apoptosis', 'meaning': 'GO:0043065', 'aliases': ['positive regulation of apoptotic process']},
+    "SENESCENCE_INDUCTION": {'description': 'Induction of senescence', 'meaning': 'GO:0090400'},
+    "CHECKPOINT_ADAPTATION": {'description': 'Checkpoint adaptation', 'annotations': {'description': 'override of checkpoint despite damage'}},
+}
+
+__all__ = [
+    "CellCyclePhase",
+    "MitoticPhase",
+    "CellCycleCheckpoint",
+    "MeioticPhase",
+    "CellCycleRegulator",
+    "CellProliferationState",
+    "DNADamageResponse",
+]