valuesets 0.3.1__py3-none-any.whl

valuesets/enums/bio/psi_mi.py

@@ -0,0 +1,306 @@
+"""
+PSI-MI (Molecular Interactions) Value Sets
+
+Common value sets from the PSI-MI (Molecular Interactions) controlled vocabulary used for annotating protein-protein interaction experiments.
+
+Generated from: bio/psi_mi.yaml
+"""
+
+from __future__ import annotations
+
+from typing import Dict, Any, Optional
+from valuesets.generators.rich_enum import RichEnum
+
+class InteractionDetectionMethod(RichEnum):
+    """
+    Methods used to detect molecular interactions
+    """
+    # Enum members
+    TWO_HYBRID = "TWO_HYBRID"
+    COIMMUNOPRECIPITATION = "COIMMUNOPRECIPITATION"
+    PULL_DOWN = "PULL_DOWN"
+    TANDEM_AFFINITY_PURIFICATION = "TANDEM_AFFINITY_PURIFICATION"
+    FLUORESCENCE_RESONANCE_ENERGY_TRANSFER = "FLUORESCENCE_RESONANCE_ENERGY_TRANSFER"
+    SURFACE_PLASMON_RESONANCE = "SURFACE_PLASMON_RESONANCE"
+    CROSS_LINKING = "CROSS_LINKING"
+    X_RAY_CRYSTALLOGRAPHY = "X_RAY_CRYSTALLOGRAPHY"
+    NMR = "NMR"
+    ELECTRON_MICROSCOPY = "ELECTRON_MICROSCOPY"
+    MASS_SPECTROMETRY = "MASS_SPECTROMETRY"
+    PROXIMITY_LIGATION_ASSAY = "PROXIMITY_LIGATION_ASSAY"
+    BIMOLECULAR_FLUORESCENCE_COMPLEMENTATION = "BIMOLECULAR_FLUORESCENCE_COMPLEMENTATION"
+    YEAST_TWO_HYBRID = "YEAST_TWO_HYBRID"
+    MAMMALIAN_TWO_HYBRID = "MAMMALIAN_TWO_HYBRID"
+
+# Set metadata after class creation
+InteractionDetectionMethod._metadata = {
+    "TWO_HYBRID": {'description': 'Classical two-hybrid system using transcriptional activity', 'meaning': 'MI:0018'},
+    "COIMMUNOPRECIPITATION": {'description': 'Using antibody to capture bait and its ligands', 'meaning': 'MI:0019'},
+    "PULL_DOWN": {'description': 'Affinity capture using immobilized bait', 'meaning': 'MI:0096'},
+    "TANDEM_AFFINITY_PURIFICATION": {'description': 'TAP tagging for protein complex purification', 'meaning': 'MI:0676'},
+    "FLUORESCENCE_RESONANCE_ENERGY_TRANSFER": {'description': 'FRET for detecting proximity between molecules', 'meaning': 'MI:0055', 'aliases': ['fluorescent resonance energy transfer']},
+    "SURFACE_PLASMON_RESONANCE": {'description': 'SPR for real-time binding analysis', 'meaning': 'MI:0107'},
+    "CROSS_LINKING": {'description': 'Chemical cross-linking of interacting proteins', 'meaning': 'MI:0030', 'aliases': ['cross-linking study']},
+    "X_RAY_CRYSTALLOGRAPHY": {'description': 'Crystal structure determination', 'meaning': 'MI:0114'},
+    "NMR": {'description': 'Nuclear magnetic resonance spectroscopy', 'meaning': 'MI:0077', 'aliases': ['nuclear magnetic resonance']},
+    "ELECTRON_MICROSCOPY": {'description': 'EM for structural determination', 'meaning': 'MI:0040'},
+    "MASS_SPECTROMETRY": {'description': 'MS-based interaction detection', 'meaning': 'MI:0943', 'aliases': ['detection by mass spectrometry']},
+    "PROXIMITY_LIGATION_ASSAY": {'description': 'PLA for detecting protein proximity', 'meaning': 'MI:0813'},
+    "BIMOLECULAR_FLUORESCENCE_COMPLEMENTATION": {'description': 'BiFC split fluorescent protein assay', 'meaning': 'MI:0809'},
+    "YEAST_TWO_HYBRID": {'description': 'Y2H screening in yeast', 'meaning': 'MI:0018', 'aliases': ['two hybrid']},
+    "MAMMALIAN_TWO_HYBRID": {'description': 'Two-hybrid in mammalian cells', 'meaning': 'MI:2413', 'aliases': ['mammalian membrane two hybrid']},
+}
+
+class InteractionType(RichEnum):
+    """
+    Types of molecular interactions
+    """
+    # Enum members
+    PHYSICAL_ASSOCIATION = "PHYSICAL_ASSOCIATION"
+    DIRECT_INTERACTION = "DIRECT_INTERACTION"
+    ASSOCIATION = "ASSOCIATION"
+    COLOCALIZATION = "COLOCALIZATION"
+    FUNCTIONAL_ASSOCIATION = "FUNCTIONAL_ASSOCIATION"
+    ENZYMATIC_REACTION = "ENZYMATIC_REACTION"
+    PHOSPHORYLATION_REACTION = "PHOSPHORYLATION_REACTION"
+    UBIQUITINATION_REACTION = "UBIQUITINATION_REACTION"
+    ACETYLATION_REACTION = "ACETYLATION_REACTION"
+    METHYLATION_REACTION = "METHYLATION_REACTION"
+    CLEAVAGE_REACTION = "CLEAVAGE_REACTION"
+    GENETIC_INTERACTION = "GENETIC_INTERACTION"
+    SELF_INTERACTION = "SELF_INTERACTION"
+
+# Set metadata after class creation
+InteractionType._metadata = {
+    "PHYSICAL_ASSOCIATION": {'description': 'Molecules within the same physical complex', 'meaning': 'MI:0915'},
+    "DIRECT_INTERACTION": {'description': 'Direct physical contact between molecules', 'meaning': 'MI:0407'},
+    "ASSOCIATION": {'description': 'May form one or more physical complexes', 'meaning': 'MI:0914'},
+    "COLOCALIZATION": {'description': 'Coincident occurrence in subcellular location', 'meaning': 'MI:0403'},
+    "FUNCTIONAL_ASSOCIATION": {'description': 'Functional modulation without direct contact', 'meaning': 'MI:2286'},
+    "ENZYMATIC_REACTION": {'description': 'Enzyme-substrate relationship', 'meaning': 'MI:0414'},
+    "PHOSPHORYLATION_REACTION": {'description': 'Kinase-substrate phosphorylation', 'meaning': 'MI:0217'},
+    "UBIQUITINATION_REACTION": {'description': 'Ubiquitin ligase-substrate relationship', 'meaning': 'MI:0220'},
+    "ACETYLATION_REACTION": {'description': 'Acetyltransferase-substrate relationship', 'meaning': 'MI:0192'},
+    "METHYLATION_REACTION": {'description': 'Methyltransferase-substrate relationship', 'meaning': 'MI:0213'},
+    "CLEAVAGE_REACTION": {'description': 'Protease-substrate relationship', 'meaning': 'MI:0194'},
+    "GENETIC_INTERACTION": {'description': 'Genetic epistatic relationship', 'meaning': 'MI:0208', 'aliases': ['genetic interaction (sensu unexpected)']},
+    "SELF_INTERACTION": {'description': 'Intra-molecular interaction', 'meaning': 'MI:1126'},
+}
+
+class ExperimentalRole(RichEnum):
+    """
+    Role played by a participant in the experiment
+    """
+    # Enum members
+    BAIT = "BAIT"
+    PREY = "PREY"
+    NEUTRAL_COMPONENT = "NEUTRAL_COMPONENT"
+    ENZYME = "ENZYME"
+    ENZYME_TARGET = "ENZYME_TARGET"
+    SELF = "SELF"
+    PUTATIVE_SELF = "PUTATIVE_SELF"
+    ANCILLARY = "ANCILLARY"
+    COFACTOR = "COFACTOR"
+    INHIBITOR = "INHIBITOR"
+    STIMULATOR = "STIMULATOR"
+    COMPETITOR = "COMPETITOR"
+
+# Set metadata after class creation
+ExperimentalRole._metadata = {
+    "BAIT": {'description': 'Molecule used to capture interacting partners', 'meaning': 'MI:0496'},
+    "PREY": {'description': 'Molecule captured by the bait', 'meaning': 'MI:0498'},
+    "NEUTRAL_COMPONENT": {'description': 'Participant with no specific role', 'meaning': 'MI:0497'},
+    "ENZYME": {'description': 'Catalytically active participant', 'meaning': 'MI:0501'},
+    "ENZYME_TARGET": {'description': 'Target of enzymatic activity', 'meaning': 'MI:0502'},
+    "SELF": {'description': 'Self-interaction participant', 'meaning': 'MI:0503'},
+    "PUTATIVE_SELF": {'description': 'Potentially self-interacting', 'meaning': 'MI:0898'},
+    "ANCILLARY": {'description': 'Supporting but not directly interacting', 'meaning': 'MI:0684'},
+    "COFACTOR": {'description': 'Required cofactor for interaction', 'meaning': 'MI:0682'},
+    "INHIBITOR": {'description': 'Inhibitor of the interaction', 'meaning': 'MI:0586'},
+    "STIMULATOR": {'description': 'Enhancer of the interaction', 'meaning': 'MI:0840'},
+    "COMPETITOR": {'description': 'Competitive inhibitor', 'meaning': 'MI:0941'},
+}
+
+class BiologicalRole(RichEnum):
+    """
+    Physiological role of an interactor
+    """
+    # Enum members
+    ENZYME = "ENZYME"
+    ENZYME_TARGET = "ENZYME_TARGET"
+    ELECTRON_DONOR = "ELECTRON_DONOR"
+    ELECTRON_ACCEPTOR = "ELECTRON_ACCEPTOR"
+    INHIBITOR = "INHIBITOR"
+    COFACTOR = "COFACTOR"
+    LIGAND = "LIGAND"
+    AGONIST = "AGONIST"
+    ANTAGONIST = "ANTAGONIST"
+    PHOSPHATE_DONOR = "PHOSPHATE_DONOR"
+    PHOSPHATE_ACCEPTOR = "PHOSPHATE_ACCEPTOR"
+
+# Set metadata after class creation
+BiologicalRole._metadata = {
+    "ENZYME": {'description': 'Catalytically active molecule', 'meaning': 'MI:0501'},
+    "ENZYME_TARGET": {'description': 'Substrate of enzymatic activity', 'meaning': 'MI:0502'},
+    "ELECTRON_DONOR": {'description': 'Donates electrons in reaction', 'meaning': 'MI:0579'},
+    "ELECTRON_ACCEPTOR": {'description': 'Accepts electrons in reaction', 'meaning': 'MI:0580'},
+    "INHIBITOR": {'description': 'Inhibits activity or interaction', 'meaning': 'MI:0586'},
+    "COFACTOR": {'description': 'Required for activity', 'meaning': 'MI:0682'},
+    "LIGAND": {'description': 'Small molecule binding partner'},
+    "AGONIST": {'description': 'Activates receptor', 'meaning': 'MI:0625'},
+    "ANTAGONIST": {'description': 'Blocks receptor activation', 'meaning': 'MI:0626'},
+    "PHOSPHATE_DONOR": {'description': 'Provides phosphate group', 'meaning': 'MI:0842'},
+    "PHOSPHATE_ACCEPTOR": {'description': 'Receives phosphate group', 'meaning': 'MI:0843'},
+}
+
+class ParticipantIdentificationMethod(RichEnum):
+    """
+    Methods to identify interaction participants
+    """
+    # Enum members
+    MASS_SPECTROMETRY = "MASS_SPECTROMETRY"
+    WESTERN_BLOT = "WESTERN_BLOT"
+    SEQUENCE_TAG_IDENTIFICATION = "SEQUENCE_TAG_IDENTIFICATION"
+    ANTIBODY_DETECTION = "ANTIBODY_DETECTION"
+    PREDETERMINED = "PREDETERMINED"
+    NUCLEIC_ACID_SEQUENCING = "NUCLEIC_ACID_SEQUENCING"
+    PROTEIN_SEQUENCING = "PROTEIN_SEQUENCING"
+
+# Set metadata after class creation
+ParticipantIdentificationMethod._metadata = {
+    "MASS_SPECTROMETRY": {'description': 'MS-based protein identification', 'meaning': 'MI:0943', 'aliases': ['detection by mass spectrometry']},
+    "WESTERN_BLOT": {'description': 'Antibody-based detection', 'meaning': 'MI:0113'},
+    "SEQUENCE_TAG_IDENTIFICATION": {'description': 'Using affinity tags', 'meaning': 'MI:0102'},
+    "ANTIBODY_DETECTION": {'description': 'Direct antibody recognition', 'meaning': 'MI:0678', 'aliases': ['antibody array']},
+    "PREDETERMINED": {'description': 'Known from experimental design', 'meaning': 'MI:0396', 'aliases': ['predetermined participant']},
+    "NUCLEIC_ACID_SEQUENCING": {'description': 'DNA/RNA sequencing', 'meaning': 'MI:0078', 'aliases': ['nucleotide sequence identification']},
+    "PROTEIN_SEQUENCING": {'description': 'Direct protein sequencing'},
+}
+
+class FeatureType(RichEnum):
+    """
+    Molecular features affecting interactions
+    """
+    # Enum members
+    BINDING_SITE = "BINDING_SITE"
+    MUTATION = "MUTATION"
+    POST_TRANSLATIONAL_MODIFICATION = "POST_TRANSLATIONAL_MODIFICATION"
+    TAG = "TAG"
+    CROSS_LINK = "CROSS_LINK"
+    LIPIDATION_SITE = "LIPIDATION_SITE"
+    PHOSPHORYLATION_SITE = "PHOSPHORYLATION_SITE"
+    UBIQUITINATION_SITE = "UBIQUITINATION_SITE"
+    METHYLATION_SITE = "METHYLATION_SITE"
+    ACETYLATION_SITE = "ACETYLATION_SITE"
+    SUMOYLATION_SITE = "SUMOYLATION_SITE"
+    NECESSARY_BINDING_REGION = "NECESSARY_BINDING_REGION"
+    SUFFICIENT_BINDING_REGION = "SUFFICIENT_BINDING_REGION"
+
+# Set metadata after class creation
+FeatureType._metadata = {
+    "BINDING_SITE": {'description': 'Region involved in binding', 'meaning': 'MI:0117', 'aliases': ['binding-associated region']},
+    "MUTATION": {'description': 'Sequence alteration', 'meaning': 'MI:0118'},
+    "POST_TRANSLATIONAL_MODIFICATION": {'description': 'PTM site', 'meaning': 'MI:0121', 'aliases': ['acetylated residue']},
+    "TAG": {'description': 'Affinity or epitope tag', 'meaning': 'MI:0507'},
+    "CROSS_LINK": {'description': 'Cross-linking site'},
+    "LIPIDATION_SITE": {'description': 'Lipid modification site'},
+    "PHOSPHORYLATION_SITE": {'description': 'Phosphorylated residue', 'meaning': 'MI:0170', 'aliases': ['phosphorylated residue']},
+    "UBIQUITINATION_SITE": {'description': 'Ubiquitinated residue'},
+    "METHYLATION_SITE": {'description': 'Methylated residue'},
+    "ACETYLATION_SITE": {'description': 'Acetylated residue'},
+    "SUMOYLATION_SITE": {'description': 'SUMOylated residue'},
+    "NECESSARY_BINDING_REGION": {'description': 'Required for binding', 'meaning': 'MI:0429'},
+    "SUFFICIENT_BINDING_REGION": {'description': 'Sufficient for binding', 'meaning': 'MI:0442'},
+}
+
+class InteractorType(RichEnum):
+    """
+    Types of molecular species in interactions
+    """
+    # Enum members
+    PROTEIN = "PROTEIN"
+    PEPTIDE = "PEPTIDE"
+    SMALL_MOLECULE = "SMALL_MOLECULE"
+    DNA = "DNA"
+    RNA = "RNA"
+    PROTEIN_COMPLEX = "PROTEIN_COMPLEX"
+    GENE = "GENE"
+    BIOPOLYMER = "BIOPOLYMER"
+    POLYSACCHARIDE = "POLYSACCHARIDE"
+    LIPID = "LIPID"
+    NUCLEIC_ACID = "NUCLEIC_ACID"
+    SYNTHETIC_POLYMER = "SYNTHETIC_POLYMER"
+    METAL_ION = "METAL_ION"
+
+# Set metadata after class creation
+InteractorType._metadata = {
+    "PROTEIN": {'description': 'Polypeptide molecule', 'meaning': 'MI:0326'},
+    "PEPTIDE": {'description': 'Short polypeptide', 'meaning': 'MI:0327'},
+    "SMALL_MOLECULE": {'description': 'Small chemical compound', 'meaning': 'MI:0328'},
+    "DNA": {'description': 'Deoxyribonucleic acid', 'meaning': 'MI:0319', 'aliases': ['deoxyribonucleic acid']},
+    "RNA": {'description': 'Ribonucleic acid', 'meaning': 'MI:0320', 'aliases': ['ribonucleic acid']},
+    "PROTEIN_COMPLEX": {'description': 'Multi-protein assembly', 'meaning': 'MI:0314', 'aliases': ['complex']},
+    "GENE": {'description': 'Gene locus', 'meaning': 'MI:0250'},
+    "BIOPOLYMER": {'description': 'Biological polymer', 'meaning': 'MI:0383'},
+    "POLYSACCHARIDE": {'description': 'Carbohydrate polymer', 'meaning': 'MI:0904'},
+    "LIPID": {'description': 'Lipid molecule'},
+    "NUCLEIC_ACID": {'description': 'DNA or RNA', 'meaning': 'MI:0318'},
+    "SYNTHETIC_POLYMER": {'description': 'Artificial polymer'},
+    "METAL_ION": {'description': 'Metal ion cofactor'},
+}
+
+class ConfidenceScore(RichEnum):
+    """
+    Types of confidence scoring methods
+    """
+    # Enum members
+    INTACT_MISCORE = "INTACT_MISCORE"
+    AUTHOR_CONFIDENCE = "AUTHOR_CONFIDENCE"
+    INTACT_CONFIDENCE = "INTACT_CONFIDENCE"
+    MINT_SCORE = "MINT_SCORE"
+    MATRIXDB_SCORE = "MATRIXDB_SCORE"
+
+# Set metadata after class creation
+ConfidenceScore._metadata = {
+    "INTACT_MISCORE": {'description': 'IntAct molecular interaction score'},
+    "AUTHOR_CONFIDENCE": {'description': 'Author-provided confidence', 'meaning': 'MI:0621'},
+    "INTACT_CONFIDENCE": {'description': 'IntAct curation confidence'},
+    "MINT_SCORE": {'description': 'MINT database score'},
+    "MATRIXDB_SCORE": {'description': 'MatrixDB confidence score'},
+}
+
+class ExperimentalPreparation(RichEnum):
+    """
+    Sample preparation methods
+    """
+    # Enum members
+    RECOMBINANT_EXPRESSION = "RECOMBINANT_EXPRESSION"
+    NATIVE_SOURCE = "NATIVE_SOURCE"
+    IN_VITRO_EXPRESSION = "IN_VITRO_EXPRESSION"
+    OVEREXPRESSION = "OVEREXPRESSION"
+    KNOCKDOWN = "KNOCKDOWN"
+    KNOCKOUT = "KNOCKOUT"
+    ENDOGENOUS_LEVEL = "ENDOGENOUS_LEVEL"
+
+# Set metadata after class creation
+ExperimentalPreparation._metadata = {
+    "RECOMBINANT_EXPRESSION": {'description': 'Expressed in heterologous system'},
+    "NATIVE_SOURCE": {'description': 'From original organism'},
+    "IN_VITRO_EXPRESSION": {'description': 'Cell-free expression'},
+    "OVEREXPRESSION": {'description': 'Above physiological levels', 'meaning': 'MI:0506', 'aliases': ['over expressed level']},
+    "KNOCKDOWN": {'description': 'Reduced expression'},
+    "KNOCKOUT": {'description': 'Gene deletion', 'meaning': 'MI:0788', 'aliases': ['knock out']},
+    "ENDOGENOUS_LEVEL": {'description': 'Physiological expression'},
+}
+
+__all__ = [
+    "InteractionDetectionMethod",
+    "InteractionType",
+    "ExperimentalRole",
+    "BiologicalRole",
+    "ParticipantIdentificationMethod",
+    "FeatureType",
+    "InteractorType",
+    "ConfidenceScore",
+    "ExperimentalPreparation",
+]

valuesets/enums/bio/relationship_to_oxygen.py

@@ -0,0 +1,37 @@
+"""
+
+Generated from: bio/relationship_to_oxygen.yaml
+"""
+
+from __future__ import annotations
+
+from typing import Dict, Any, Optional
+from valuesets.generators.rich_enum import RichEnum
+
+class RelToOxygenEnum(RichEnum):
+    """
+    Organism's relationship to oxygen for growth and survival
+    """
+    # Enum members
+    AEROBE = "AEROBE"
+    ANAEROBE = "ANAEROBE"
+    FACULTATIVE = "FACULTATIVE"
+    MICROAEROPHILIC = "MICROAEROPHILIC"
+    MICROANAEROBE = "MICROANAEROBE"
+    OBLIGATE_AEROBE = "OBLIGATE_AEROBE"
+    OBLIGATE_ANAEROBE = "OBLIGATE_ANAEROBE"
+
+# Set metadata after class creation
+RelToOxygenEnum._metadata = {
+    "AEROBE": {'description': 'Organism that can survive and grow in an oxygenated environment', 'meaning': 'ECOCORE:00000173'},
+    "ANAEROBE": {'description': 'Organism that does not require oxygen for growth', 'meaning': 'ECOCORE:00000172'},
+    "FACULTATIVE": {'description': 'Organism that can grow with or without oxygen', 'meaning': 'ECOCORE:00000177', 'annotations': {'note': 'Maps to facultative anaerobe in ECOCORE'}},
+    "MICROAEROPHILIC": {'description': 'Organism that requires oxygen at lower concentrations than atmospheric', 'meaning': 'MICRO:0000515'},
+    "MICROANAEROBE": {'description': 'Organism that can tolerate very small amounts of oxygen'},
+    "OBLIGATE_AEROBE": {'description': 'Organism that requires oxygen to grow', 'meaning': 'ECOCORE:00000179'},
+    "OBLIGATE_ANAEROBE": {'description': 'Organism that cannot grow in the presence of oxygen', 'meaning': 'ECOCORE:00000178'},
+}
+
+__all__ = [
+    "RelToOxygenEnum",
+]