valuesets 0.3.1__py3-none-any.whl

valuesets/enums/bio/insdc_missing_values.py

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+"""
+
+Generated from: bio/insdc_missing_values.yaml
+"""
+
+from __future__ import annotations
+
+from typing import Dict, Any, Optional
+from valuesets.generators.rich_enum import RichEnum
+
+class InsdcMissingValueEnum(RichEnum):
+    """
+    INSDC (International Nucleotide Sequence Database Collaboration) controlled vocabulary for missing values in sequence records
+    """
+    # Enum members
+    NOT_APPLICABLE = "NOT_APPLICABLE"
+    MISSING = "MISSING"
+    NOT_COLLECTED = "NOT_COLLECTED"
+    NOT_PROVIDED = "NOT_PROVIDED"
+    RESTRICTED_ACCESS = "RESTRICTED_ACCESS"
+    MISSING_CONTROL_SAMPLE = "MISSING_CONTROL_SAMPLE"
+    MISSING_SAMPLE_GROUP = "MISSING_SAMPLE_GROUP"
+    MISSING_SYNTHETIC_CONSTRUCT = "MISSING_SYNTHETIC_CONSTRUCT"
+    MISSING_LAB_STOCK = "MISSING_LAB_STOCK"
+    MISSING_THIRD_PARTY_DATA = "MISSING_THIRD_PARTY_DATA"
+    MISSING_DATA_AGREEMENT_ESTABLISHED_PRE_2023 = "MISSING_DATA_AGREEMENT_ESTABLISHED_PRE_2023"
+    MISSING_ENDANGERED_SPECIES = "MISSING_ENDANGERED_SPECIES"
+    MISSING_HUMAN_IDENTIFIABLE = "MISSING_HUMAN_IDENTIFIABLE"
+
+# Set metadata after class creation
+InsdcMissingValueEnum._metadata = {
+    "NOT_APPLICABLE": {'description': 'Information is inappropriate to report, can indicate that the standard itself fails to model or represent the information appropriately', 'meaning': 'NCIT:C48660'},
+    "MISSING": {'description': 'Not stated explicitly or implied by any other means', 'meaning': 'NCIT:C54031'},
+    "NOT_COLLECTED": {'description': 'Information of an expected format was not given because it has never been collected', 'meaning': 'NCIT:C142610', 'annotations': {'note': 'NCIT:C142610 represents Missing Data which encompasses data not collected'}},
+    "NOT_PROVIDED": {'description': 'Information of an expected format was not given, a value may be given at the later stage', 'meaning': 'NCIT:C126101', 'annotations': {'note': 'Using NCIT:C126101 (Not Available) as a general term for data not provided'}},
+    "RESTRICTED_ACCESS": {'description': 'Information exists but cannot be released openly because of privacy concerns', 'meaning': 'NCIT:C67110', 'annotations': {'note': 'NCIT:C67110 represents Data Not Releasable due to confidentiality'}},
+    "MISSING_CONTROL_SAMPLE": {'description': 'Information is not applicable to control samples, negative control samples (e.g. blank sample or clear sample)', 'annotations': {'note': 'No specific ontology term found for missing control sample data'}},
+    "MISSING_SAMPLE_GROUP": {'description': 'Information can not be provided for a sample group where a selection of samples is used to represent a species, location or some other attribute/metric', 'annotations': {'note': 'No specific ontology term found for missing sample group data'}},
+    "MISSING_SYNTHETIC_CONSTRUCT": {'description': 'Information does not exist for a synthetic construct', 'annotations': {'note': 'No specific ontology term found for missing synthetic construct data'}},
+    "MISSING_LAB_STOCK": {'description': 'Information is not collected for a lab stock and its cultivation, e.g. stock centers, culture collections, seed banks', 'annotations': {'note': 'No specific ontology term found for missing lab stock data'}},
+    "MISSING_THIRD_PARTY_DATA": {'description': 'Information has not been revealed by another party', 'meaning': 'NCIT:C67329', 'annotations': {'note': 'NCIT:C67329 represents Source Data Not Available'}},
+    "MISSING_DATA_AGREEMENT_ESTABLISHED_PRE_2023": {'description': 'Information can not be reported due to a data agreement established before metadata standards were introduced in 2023', 'annotations': {'note': 'No specific ontology term for data missing due to pre-2023 agreements'}},
+    "MISSING_ENDANGERED_SPECIES": {'description': 'Information can not be reported due to endangered species concerns', 'annotations': {'note': 'No specific ontology term for data withheld due to endangered species'}},
+    "MISSING_HUMAN_IDENTIFIABLE": {'description': 'Information can not be reported due to identifiable human data concerns', 'annotations': {'note': 'No specific ontology term for data withheld due to human identifiability'}},
+}
+
+__all__ = [
+    "InsdcMissingValueEnum",
+]

valuesets/enums/bio/lipid_categories.py

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+"""
+Lipid Categories
+
+Major lipid categories from SwissLipids classification
+
+Generated from: bio/lipid_categories.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 LipidCategory(RichEnum):
+    """
+    Major categories of lipids based on SwissLipids classification
+    """
+    # Enum members
+    LIPID = "LIPID"
+    FATTY_ACYLS_AND_DERIVATIVES = "FATTY_ACYLS_AND_DERIVATIVES"
+    GLYCEROLIPIDS = "GLYCEROLIPIDS"
+    GLYCEROPHOSPHOLIPIDS = "GLYCEROPHOSPHOLIPIDS"
+    SPHINGOLIPIDS = "SPHINGOLIPIDS"
+    STEROIDS_AND_DERIVATIVES = "STEROIDS_AND_DERIVATIVES"
+    PRENOL_LIPIDS = "PRENOL_LIPIDS"
+
+# Set metadata after class creation
+LipidCategory._metadata = {
+    "LIPID": {'description': 'Lipid', 'meaning': 'CHEBI:18059'},
+    "FATTY_ACYLS_AND_DERIVATIVES": {'description': 'Fatty acyls and derivatives', 'meaning': 'CHEBI:24027', 'aliases': ['fatty-acyl group']},
+    "GLYCEROLIPIDS": {'description': 'Glycerolipids', 'meaning': 'CHEBI:35741', 'aliases': ['glycerolipid']},
+    "GLYCEROPHOSPHOLIPIDS": {'description': 'Glycerophospholipids', 'meaning': 'CHEBI:37739', 'aliases': ['glycerophospholipid']},
+    "SPHINGOLIPIDS": {'description': 'Sphingolipids', 'meaning': 'CHEBI:26739', 'aliases': ['sphingolipid']},
+    "STEROIDS_AND_DERIVATIVES": {'description': 'Steroids and derivatives', 'meaning': 'CHEBI:35341', 'aliases': ['steroid']},
+    "PRENOL_LIPIDS": {'description': 'Prenol Lipids', 'meaning': 'CHEBI:24913', 'aliases': ['isoprenoid']},
+}
+
+__all__ = [
+    "RelativeTimeEnum",
+    "PresenceEnum",
+    "LipidCategory",
+]

valuesets/enums/bio/mouse_developmental_stages.py

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+"""
+Mouse Developmental Stages Value Sets
+
+Value sets for mouse developmental stages from fertilization through aging
+
+Generated from: bio/mouse_developmental_stages.yaml
+"""
+
+from __future__ import annotations
+
+from typing import Dict, Any, Optional
+from valuesets.generators.rich_enum import RichEnum
+
+class MouseDevelopmentalStage(RichEnum):
+    """
+    Mouse developmental stages from fertilization through aging, based on the MmusDv (Mouse Developmental Stages) ontology and Theiler staging system.
+    """
+    # Enum members
+    ZYGOTE_STAGE = "ZYGOTE_STAGE"
+    TWO_CELL_STAGE = "TWO_CELL_STAGE"
+    FOUR_CELL_STAGE = "FOUR_CELL_STAGE"
+    EIGHT_CELL_STAGE = "EIGHT_CELL_STAGE"
+    MORULA_STAGE = "MORULA_STAGE"
+    BLASTOCYST_STAGE = "BLASTOCYST_STAGE"
+    GASTRULA_STAGE = "GASTRULA_STAGE"
+    NEURULA_STAGE = "NEURULA_STAGE"
+    ORGANOGENESIS_STAGE = "ORGANOGENESIS_STAGE"
+    E0_5 = "E0_5"
+    E9_5 = "E9_5"
+    E14_5 = "E14_5"
+    P0_NEWBORN = "P0_NEWBORN"
+    P21_WEANING = "P21_WEANING"
+    P42_JUVENILE = "P42_JUVENILE"
+    P56_ADULT = "P56_ADULT"
+    AGED_12_MONTHS = "AGED_12_MONTHS"
+    THEILER_STAGE = "THEILER_STAGE"
+
+# Set metadata after class creation
+MouseDevelopmentalStage._metadata = {
+    "ZYGOTE_STAGE": {'description': 'Single cell after fertilization (Theiler stage 01, E0.5)', 'meaning': 'MmusDv:0000003'},
+    "TWO_CELL_STAGE": {'description': 'Two-cell embryo (Theiler stage 02, E1.5)', 'meaning': 'MmusDv:0000005'},
+    "FOUR_CELL_STAGE": {'description': 'Four-cell embryo (Theiler stage 02, E2)', 'meaning': 'MmusDv:0000005'},
+    "EIGHT_CELL_STAGE": {'description': 'Eight-cell embryo (Theiler stage 03, E2.5)', 'meaning': 'MmusDv:0000006'},
+    "MORULA_STAGE": {'description': 'Compact morula (Theiler stage 03, E2.5-3)', 'meaning': 'MmusDv:0000006'},
+    "BLASTOCYST_STAGE": {'description': 'Blastocyst with inner cell mass (Theiler stage 05, E3.5-4.5)', 'meaning': 'MmusDv:0000009'},
+    "GASTRULA_STAGE": {'description': 'Formation of three germ layers (E6.5-7.5)', 'meaning': 'MmusDv:0000013'},
+    "NEURULA_STAGE": {'description': 'Neural tube formation (Theiler stage 11, E8)', 'meaning': 'MmusDv:0000017'},
+    "ORGANOGENESIS_STAGE": {'description': 'Major organ development (E8.5-14.5)', 'meaning': 'MmusDv:0000018'},
+    "E0_5": {'description': 'Embryonic day 0.5 - fertilization', 'meaning': 'MmusDv:0000003'},
+    "E9_5": {'description': 'Embryonic day 9.5 - early organogenesis', 'meaning': 'MmusDv:0000023'},
+    "E14_5": {'description': 'Embryonic day 14.5 - late organogenesis', 'meaning': 'MmusDv:0000029'},
+    "P0_NEWBORN": {'description': 'Birth/postnatal day 0', 'meaning': 'MmusDv:0000036'},
+    "P21_WEANING": {'description': 'Postnatal day 21 - weaning age', 'meaning': 'MmusDv:0000141'},
+    "P42_JUVENILE": {'description': 'Postnatal day 42 - juvenile/sexually mature', 'meaning': 'MmusDv:0000151'},
+    "P56_ADULT": {'description': 'Postnatal day 56 - young adult', 'meaning': 'MmusDv:0000154'},
+    "AGED_12_MONTHS": {'description': '12+ months - aged mouse', 'meaning': 'MmusDv:0000135'},
+    "THEILER_STAGE": {'description': 'Reference to Theiler staging system for mouse development'},
+}
+
+__all__ = [
+    "MouseDevelopmentalStage",
+]

valuesets/enums/bio/plant_biology.py

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+"""
+Plant Biology Value Sets
+
+Value sets related to plant biology, including reproductive systems,
+breeding systems, and other plant-specific characteristics.
+
+Generated from: bio/plant_biology.yaml
+"""
+
+from __future__ import annotations
+
+from typing import Dict, Any, Optional
+from valuesets.generators.rich_enum import RichEnum
+
+class PlantSexualSystem(RichEnum):
+    """
+    Sexual systems in plants, describing the distribution and types of
+    reproductive organs (flowers) within and among individual plants.
+    """
+    # Enum members
+    ANDRODIOECIOUS = "ANDRODIOECIOUS"
+    ANDROECIOUS = "ANDROECIOUS"
+    ANDROGYNOMONOECIOUS = "ANDROGYNOMONOECIOUS"
+    ANDROGYNOUS = "ANDROGYNOUS"
+    ANDROMONOECIOUS = "ANDROMONOECIOUS"
+    BISEXUAL = "BISEXUAL"
+    DICHOGAMOUS = "DICHOGAMOUS"
+    DICLINOUS = "DICLINOUS"
+    DIOECIOUS = "DIOECIOUS"
+    GYNODIOECIOUS = "GYNODIOECIOUS"
+    GYNOECIOUS = "GYNOECIOUS"
+    GYNOMONOECIOUS = "GYNOMONOECIOUS"
+    HERMAPHRODITIC = "HERMAPHRODITIC"
+    IMPERFECT = "IMPERFECT"
+    MONOCLINOUS = "MONOCLINOUS"
+    MONOECIOUS = "MONOECIOUS"
+    PERFECT = "PERFECT"
+    POLYGAMODIOECIOUS = "POLYGAMODIOECIOUS"
+    POLYGAMOMONOECIOUS = "POLYGAMOMONOECIOUS"
+    POLYGAMOUS = "POLYGAMOUS"
+    PROTANDROUS = "PROTANDROUS"
+    PROTOGYNOUS = "PROTOGYNOUS"
+    SUBANDROECIOUS = "SUBANDROECIOUS"
+    SUBDIOECIOUS = "SUBDIOECIOUS"
+    SUBGYNOECIOUS = "SUBGYNOECIOUS"
+    SYNOECIOUS = "SYNOECIOUS"
+    TRIMONOECIOUS = "TRIMONOECIOUS"
+    TRIOECIOUS = "TRIOECIOUS"
+    UNISEXUAL = "UNISEXUAL"
+
+# Set metadata after class creation
+PlantSexualSystem._metadata = {
+    "ANDRODIOECIOUS": {'description': 'A sexual system in which males and hermaphrodites coexist in a population', 'meaning': 'GSSO:011874'},
+    "ANDROECIOUS": {'description': 'Having only male flowers (staminate flowers)'},
+    "ANDROGYNOMONOECIOUS": {'description': 'Having male, female, and bisexual flowers on the same plant'},
+    "ANDROGYNOUS": {'description': 'Having both male and female reproductive organs; hermaphroditic'},
+    "ANDROMONOECIOUS": {'description': 'Having both male and hermaphroditic flowers on the same plant', 'meaning': 'GSSO:011870'},
+    "BISEXUAL": {'description': 'Having both male and female reproductive organs in the same flower'},
+    "DICHOGAMOUS": {'description': 'Having male and female organs that mature at different times'},
+    "DICLINOUS": {'description': 'Having unisexual flowers (either male or female, not both)'},
+    "DIOECIOUS": {'description': 'Having male and female flowers on separate plants', 'meaning': 'GSSO:011872'},
+    "GYNODIOECIOUS": {'description': 'Having female and hermaphroditic plants in the same population', 'meaning': 'GSSO:011873'},
+    "GYNOECIOUS": {'description': 'Having only female flowers (pistillate flowers)'},
+    "GYNOMONOECIOUS": {'description': 'Having both female and hermaphroditic flowers on the same plant', 'meaning': 'GSSO:011869'},
+    "HERMAPHRODITIC": {'description': 'Having both male and female reproductive organs', 'meaning': 'PATO:0001340'},
+    "IMPERFECT": {'description': 'Flowers lacking either stamens or pistils (unisexual)'},
+    "MONOCLINOUS": {'description': 'Having bisexual flowers (both male and female organs)'},
+    "MONOECIOUS": {'description': 'Having separate male and female flowers on the same plant', 'meaning': 'GSSO:011868'},
+    "PERFECT": {'description': 'Flowers having both stamens and pistils (bisexual)'},
+    "POLYGAMODIOECIOUS": {'description': 'Having male, female, and bisexual flowers on separate plants'},
+    "POLYGAMOMONOECIOUS": {'description': 'Having male, female, and bisexual flowers on the same plant'},
+    "POLYGAMOUS": {'description': 'Having male, female, and bisexual flowers'},
+    "PROTANDROUS": {'description': 'Starting as male and changing to female at a later stage', 'meaning': 'PATO:0040053'},
+    "PROTOGYNOUS": {'description': 'Starting as female and changing to male at a later stage', 'meaning': 'PATO:0040052'},
+    "SUBANDROECIOUS": {'description': 'Predominantly male plants with occasional hermaphroditic flowers'},
+    "SUBDIOECIOUS": {'description': 'Predominantly dioecious with occasional hermaphroditic individuals'},
+    "SUBGYNOECIOUS": {'description': 'Predominantly female plants with occasional hermaphroditic flowers'},
+    "SYNOECIOUS": {'description': 'Having male and female organs in the same structure'},
+    "TRIMONOECIOUS": {'description': 'Having male, female, and bisexual flowers on the same plant'},
+    "TRIOECIOUS": {'description': 'Having males, females, and hermaphrodites in the same population', 'meaning': 'GSSO:011875'},
+    "UNISEXUAL": {'description': 'Having only one sex (either male or female reproductive organs)'},
+}
+
+__all__ = [
+    "PlantSexualSystem",
+]

valuesets/enums/bio/plant_developmental_stages.py

@@ -0,0 +1,54 @@
+"""
+Plant Developmental Stages Value Sets
+
+Value sets for plant developmental stages from germination through senescence
+
+Generated from: bio/plant_developmental_stages.yaml
+"""
+
+from __future__ import annotations
+
+from typing import Dict, Any, Optional
+from valuesets.generators.rich_enum import RichEnum
+
+class PlantDevelopmentalStage(RichEnum):
+    """
+    Major developmental stages in the plant life cycle, from seed germination through senescence. Based on the Plant Ontology (PO) standardized stages.
+    """
+    # Enum members
+    SEED_GERMINATION_STAGE = "SEED_GERMINATION_STAGE"
+    SEEDLING_STAGE = "SEEDLING_STAGE"
+    VEGETATIVE_GROWTH_STAGE = "VEGETATIVE_GROWTH_STAGE"
+    FLOWERING_STAGE = "FLOWERING_STAGE"
+    FRUIT_DEVELOPMENT_STAGE = "FRUIT_DEVELOPMENT_STAGE"
+    SEED_DEVELOPMENT_STAGE = "SEED_DEVELOPMENT_STAGE"
+    SENESCENCE_STAGE = "SENESCENCE_STAGE"
+    DORMANCY_STAGE = "DORMANCY_STAGE"
+    EMBRYO_DEVELOPMENT_STAGE = "EMBRYO_DEVELOPMENT_STAGE"
+    ROOT_DEVELOPMENT_STAGE = "ROOT_DEVELOPMENT_STAGE"
+    LEAF_DEVELOPMENT_STAGE = "LEAF_DEVELOPMENT_STAGE"
+    REPRODUCTIVE_STAGE = "REPRODUCTIVE_STAGE"
+    MATURITY_STAGE = "MATURITY_STAGE"
+    POST_HARVEST_STAGE = "POST_HARVEST_STAGE"
+
+# Set metadata after class creation
+PlantDevelopmentalStage._metadata = {
+    "SEED_GERMINATION_STAGE": {'description': 'Stage beginning with seed imbibition and ending with radicle emergence', 'meaning': 'PO:0007057'},
+    "SEEDLING_STAGE": {'description': 'Stage from germination until development of first adult vascular leaf', 'meaning': 'PO:0007131', 'aliases': ['seedling development stage']},
+    "VEGETATIVE_GROWTH_STAGE": {'description': 'Stage of growth before reproductive structure formation', 'meaning': 'PO:0007134', 'aliases': ['sporophyte vegetative stage']},
+    "FLOWERING_STAGE": {'description': 'Stage when flowers open with pollen release and/or receptive stigma', 'meaning': 'PO:0007616'},
+    "FRUIT_DEVELOPMENT_STAGE": {'description': 'Stage of fruit formation through ripening', 'meaning': 'PO:0001002'},
+    "SEED_DEVELOPMENT_STAGE": {'description': 'Stage from fertilization to mature seed', 'meaning': 'PO:0001170'},
+    "SENESCENCE_STAGE": {'description': 'Stage of aging with loss of function and organ deterioration', 'meaning': 'PO:0007017', 'aliases': ['sporophyte senescent stage']},
+    "DORMANCY_STAGE": {'description': 'Stage of suspended physiological activity and growth', 'meaning': 'PO:0007132', 'aliases': ['sporophyte dormant stage']},
+    "EMBRYO_DEVELOPMENT_STAGE": {'description': 'Stage from zygote first division to seed germination initiation', 'meaning': 'PO:0007631', 'aliases': ['plant embryo development stage']},
+    "ROOT_DEVELOPMENT_STAGE": {'description': 'Stages in root growth and development', 'meaning': 'PO:0007520'},
+    "LEAF_DEVELOPMENT_STAGE": {'description': 'Stages in leaf formation and expansion', 'meaning': 'PO:0001050'},
+    "REPRODUCTIVE_STAGE": {'description': 'Stage from reproductive structure initiation to senescence onset', 'meaning': 'PO:0007130', 'aliases': ['sporophyte reproductive stage']},
+    "MATURITY_STAGE": {'description': 'Stage when plant or plant embryo reaches full development', 'meaning': 'PO:0001081', 'aliases': ['mature plant embryo stage']},
+    "POST_HARVEST_STAGE": {'description': 'Stage after harvest when plant parts are detached from parent plant'},
+}
+
+__all__ = [
+    "PlantDevelopmentalStage",
+]

valuesets/enums/bio/plant_sex.py

@@ -0,0 +1,81 @@
+"""
+
+Generated from: bio/plant_sex.yaml
+"""
+
+from __future__ import annotations
+
+from typing import Dict, Any, Optional
+from valuesets.generators.rich_enum import RichEnum
+
+class PlantSexEnum(RichEnum):
+    """
+    Plant reproductive and sexual system types
+    """
+    # Enum members
+    ANDRODIOECIOUS = "ANDRODIOECIOUS"
+    ANDROECIOUS = "ANDROECIOUS"
+    ANDROGYNOMONOECIOUS = "ANDROGYNOMONOECIOUS"
+    ANDROGYNOUS = "ANDROGYNOUS"
+    ANDROMONOECIOUS = "ANDROMONOECIOUS"
+    BISEXUAL = "BISEXUAL"
+    DICHOGAMOUS = "DICHOGAMOUS"
+    DICLINOUS = "DICLINOUS"
+    DIOECIOUS = "DIOECIOUS"
+    GYNODIOECIOUS = "GYNODIOECIOUS"
+    GYNOECIOUS = "GYNOECIOUS"
+    GYNOMONOECIOUS = "GYNOMONOECIOUS"
+    HERMAPHRODITIC = "HERMAPHRODITIC"
+    IMPERFECT = "IMPERFECT"
+    MONOCLINOUS = "MONOCLINOUS"
+    MONOECIOUS = "MONOECIOUS"
+    PERFECT = "PERFECT"
+    POLYGAMODIOECIOUS = "POLYGAMODIOECIOUS"
+    POLYGAMOMONOECIOUS = "POLYGAMOMONOECIOUS"
+    POLYGAMOUS = "POLYGAMOUS"
+    PROTANDROUS = "PROTANDROUS"
+    PROTOGYNOUS = "PROTOGYNOUS"
+    SUBANDROECIOUS = "SUBANDROECIOUS"
+    SUBDIOECIOUS = "SUBDIOECIOUS"
+    SUBGYNOECIOUS = "SUBGYNOECIOUS"
+    SYNOECIOUS = "SYNOECIOUS"
+    TRIMONOECIOUS = "TRIMONOECIOUS"
+    TRIOECIOUS = "TRIOECIOUS"
+    UNISEXUAL = "UNISEXUAL"
+
+# Set metadata after class creation
+PlantSexEnum._metadata = {
+    "ANDRODIOECIOUS": {'description': 'Having male and hermaphrodite flowers on separate plants'},
+    "ANDROECIOUS": {'description': 'Having only male flowers'},
+    "ANDROGYNOMONOECIOUS": {'description': 'Having male, female, and hermaphrodite flowers on the same plant'},
+    "ANDROGYNOUS": {'description': 'Having both male and female reproductive organs in the same flower'},
+    "ANDROMONOECIOUS": {'description': 'Having male and hermaphrodite flowers on the same plant'},
+    "BISEXUAL": {'description': 'Having both male and female reproductive organs'},
+    "DICHOGAMOUS": {'description': 'Male and female organs mature at different times'},
+    "DICLINOUS": {'description': 'Having male and female reproductive organs in separate flowers'},
+    "DIOECIOUS": {'description': 'Having male and female flowers on separate plants', 'meaning': 'GSSO:011872'},
+    "GYNODIOECIOUS": {'description': 'Having female and hermaphrodite flowers on separate plants'},
+    "GYNOECIOUS": {'description': 'Having only female flowers'},
+    "GYNOMONOECIOUS": {'description': 'Having female and hermaphrodite flowers on the same plant'},
+    "HERMAPHRODITIC": {'description': 'Having both male and female reproductive organs', 'meaning': 'UBERON:0007197'},
+    "IMPERFECT": {'description': 'Flower lacking either male or female reproductive organs'},
+    "MONOCLINOUS": {'description': 'Having both male and female reproductive organs in the same flower'},
+    "MONOECIOUS": {'description': 'Having male and female flowers on the same plant', 'meaning': 'GSSO:011868'},
+    "PERFECT": {'description': 'Flower having both male and female reproductive organs'},
+    "POLYGAMODIOECIOUS": {'description': 'Having male, female, and hermaphrodite flowers on separate plants'},
+    "POLYGAMOMONOECIOUS": {'description': 'Having male, female, and hermaphrodite flowers on the same plant'},
+    "POLYGAMOUS": {'description': 'Having male, female, and hermaphrodite flowers'},
+    "PROTANDROUS": {'description': 'Male organs mature before female organs'},
+    "PROTOGYNOUS": {'description': 'Female organs mature before male organs'},
+    "SUBANDROECIOUS": {'description': 'Mostly male flowers with occasional hermaphrodite flowers'},
+    "SUBDIOECIOUS": {'description': 'Mostly dioecious with occasional hermaphrodite flowers'},
+    "SUBGYNOECIOUS": {'description': 'Mostly female flowers with occasional hermaphrodite flowers'},
+    "SYNOECIOUS": {'description': 'Having male and female organs fused together'},
+    "TRIMONOECIOUS": {'description': 'Having male, female, and hermaphrodite flowers on the same plant'},
+    "TRIOECIOUS": {'description': 'Having male, female, and hermaphrodite flowers on separate plants'},
+    "UNISEXUAL": {'description': 'Having only one sex of reproductive organs'},
+}
+
+__all__ = [
+    "PlantSexEnum",
+]

valuesets/enums/bio/protein_evidence.py

@@ -0,0 +1,61 @@
+"""
+Protein Evidence Value Sets
+
+Value sets related to protein evidence and annotation status
+
+Generated from: bio/protein_evidence.yaml
+"""
+
+from __future__ import annotations
+
+from typing import Dict, Any, Optional
+from valuesets.generators.rich_enum import RichEnum
+
+class ProteinEvidenceForExistence(RichEnum):
+    """
+    The evidence for the existence of a biological entity. See https://www.uniprot.org/help/protein_existence and https://www.ncbi.nlm.nih.gov/genbank/evidence/.
+    """
+    # Enum members
+    EXPERIMENTAL_EVIDENCE_AT_PROTEIN_LEVEL = "EXPERIMENTAL_EVIDENCE_AT_PROTEIN_LEVEL"
+    EXPERIMENTAL_EVIDENCE_AT_TRANSCRIPT_LEVEL = "EXPERIMENTAL_EVIDENCE_AT_TRANSCRIPT_LEVEL"
+    PROTEIN_INFERRED_BY_HOMOLOGY = "PROTEIN_INFERRED_BY_HOMOLOGY"
+    PROTEIN_PREDICTED = "PROTEIN_PREDICTED"
+    PROTEIN_UNCERTAIN = "PROTEIN_UNCERTAIN"
+
+# Set metadata after class creation
+ProteinEvidenceForExistence._metadata = {
+    "EXPERIMENTAL_EVIDENCE_AT_PROTEIN_LEVEL": {'description': 'Indicates that there is clear experimental evidence for the existence of the protein. The criteria include partial or complete Edman sequencing, clear identification by mass spectrometry, X-ray or NMR structure, good quality protein-protein interaction or detection of the protein by antibodies.'},
+    "EXPERIMENTAL_EVIDENCE_AT_TRANSCRIPT_LEVEL": {'description': 'Indicates that the existence of a protein has not been strictly proven but that expression data (such as existence of cDNA(s), RT-PCR or Northern blots) indicate the existence of a transcript.'},
+    "PROTEIN_INFERRED_BY_HOMOLOGY": {'description': 'Indicates that the existence of a protein is probable because clear orthologs exist in closely related species.'},
+    "PROTEIN_PREDICTED": {'description': 'Used for entries without evidence at protein, transcript, or homology levels.'},
+    "PROTEIN_UNCERTAIN": {'description': 'Indicates that the existence of the protein is unsure.'},
+}
+
+class RefSeqStatusType(RichEnum):
+    """
+    RefSeq status codes, taken from https://www.ncbi.nlm.nih.gov/genbank/evidence/.
+    """
+    # Enum members
+    MODEL = "MODEL"
+    INFERRED = "INFERRED"
+    PREDICTED = "PREDICTED"
+    PROVISIONAL = "PROVISIONAL"
+    REVIEWED = "REVIEWED"
+    VALIDATED = "VALIDATED"
+    WGS = "WGS"
+
+# Set metadata after class creation
+RefSeqStatusType._metadata = {
+    "MODEL": {'description': 'The RefSeq record is provided by the NCBI Genome Annotation pipeline and is not subject to individual review or revision between annotation runs.'},
+    "INFERRED": {'description': 'The RefSeq record has been predicted by genome sequence analysis, but it is not yet supported by experimental evidence. The record may be partially supported by homology data.'},
+    "PREDICTED": {'description': 'The RefSeq record has not yet been subject to individual review, and some aspect of the RefSeq record is predicted.'},
+    "PROVISIONAL": {'description': 'The RefSeq record has not yet been subject to individual review. The initial sequence-to-gene association has been established by outside collaborators or NCBI staff.'},
+    "REVIEWED": {'description': 'The RefSeq record has been reviewed by NCBI staff or by a collaborator. The NCBI review process includes assessing available sequence data and the literature. Some RefSeq records may incorporate expanded sequence and annotation information.'},
+    "VALIDATED": {'description': 'The RefSeq record has undergone an initial review to provide the preferred sequence standard. The record has not yet been subject to final review at which time additional functional information may be provided.'},
+    "WGS": {'description': 'The RefSeq record is provided to represent a collection of whole genome shotgun sequences. These records are not subject to individual review or revisions between genome updates.'},
+}
+
+__all__ = [
+    "ProteinEvidenceForExistence",
+    "RefSeqStatusType",
+]

valuesets/enums/bio/proteomics_standards.py

@@ -0,0 +1,123 @@
+"""
+Proteomics Standards
+
+Controlled vocabularies for mass spectrometry and proteomics data annotation from HUPO-PSI standards
+
+Generated from: bio/proteomics_standards.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 PeakAnnotationSeriesLabel(RichEnum):
+    """
+    Types of peak annotations in mass spectrometry data
+    """
+    # Enum members
+    PEPTIDE = "PEPTIDE"
+    INTERNAL = "INTERNAL"
+    PRECURSOR = "PRECURSOR"
+    IMMONIUM = "IMMONIUM"
+    REFERENCE = "REFERENCE"
+    NAMED_COMPOUND = "NAMED_COMPOUND"
+    FORMULA = "FORMULA"
+    SMILES = "SMILES"
+    UNANNOTATED = "UNANNOTATED"
+
+# Set metadata after class creation
+PeakAnnotationSeriesLabel._metadata = {
+    "PEPTIDE": {'description': 'Peptide fragment ion'},
+    "INTERNAL": {'description': 'Internal fragment ion'},
+    "PRECURSOR": {'description': 'Precursor ion'},
+    "IMMONIUM": {'description': 'Immonium ion'},
+    "REFERENCE": {'description': 'Reference peak or calibrant'},
+    "NAMED_COMPOUND": {'description': 'Named chemical compound'},
+    "FORMULA": {'description': 'Chemical formula'},
+    "SMILES": {'description': 'SMILES structure notation'},
+    "UNANNOTATED": {'description': 'Unannotated peak'},
+}
+
+class PeptideIonSeries(RichEnum):
+    """
+    Types of peptide fragment ion series in mass spectrometry
+    """
+    # Enum members
+    B = "B"
+    Y = "Y"
+    A = "A"
+    X = "X"
+    C = "C"
+    Z = "Z"
+    D = "D"
+    V = "V"
+    W = "W"
+    DA = "DA"
+    DB = "DB"
+    WA = "WA"
+    WB = "WB"
+
+# Set metadata after class creation
+PeptideIonSeries._metadata = {
+    "B": {'description': 'B ion series - N-terminal fragment with CO'},
+    "Y": {'description': 'Y ion series - C-terminal fragment with H'},
+    "A": {'description': 'A ion series - N-terminal fragment minus CO'},
+    "X": {'description': 'X ion series - C-terminal fragment plus CO'},
+    "C": {'description': 'C ion series - N-terminal fragment with NH3'},
+    "Z": {'description': 'Z ion series - C-terminal fragment minus NH'},
+    "D": {'description': 'D ion series - partial side chain cleavage'},
+    "V": {'description': 'V ion series - side chain loss from y ion'},
+    "W": {'description': 'W ion series - side chain loss from z ion'},
+    "DA": {'description': 'DA ion series - a ion with side chain loss'},
+    "DB": {'description': 'DB ion series - b ion with side chain loss'},
+    "WA": {'description': 'WA ion series - a ion with tryptophan side chain loss'},
+    "WB": {'description': 'WB ion series - b ion with tryptophan side chain loss'},
+}
+
+class MassErrorUnit(RichEnum):
+    """
+    Units for expressing mass error in mass spectrometry
+    """
+    # Enum members
+    PPM = "PPM"
+    DA = "DA"
+
+# Set metadata after class creation
+MassErrorUnit._metadata = {
+    "PPM": {'description': 'Parts per million - relative mass error'},
+    "DA": {'description': 'Dalton - absolute mass error', 'aliases': ['Dalton', 'u', 'amu']},
+}
+
+__all__ = [
+    "RelativeTimeEnum",
+    "PresenceEnum",
+    "PeakAnnotationSeriesLabel",
+    "PeptideIonSeries",
+    "MassErrorUnit",
+]