bel/schemas/constants.py
"""Constants and Enums"""
# Standard Library
# cSpell:disable
import enum
class EntityTypesEnum(str, enum.Enum):
"""Namespace Entity types"""
Abundance = "Abundance"
Protein = "Protein"
RNA = "RNA"
Micro_RNA = "Micro_RNA"
Gene = "Gene"
Complex = "Complex"
BiologicalProcess = "BiologicalProcess"
Pathology = "Pathology"
Activity = "Activity"
Variant = "Variant"
ProteinModification = "ProteinModification"
AminoAcid = "AminoAcid"
Location = "Location"
Species = "Species"
Cell = "Cell"
All = "All"
class AnnotationTypesEnum(str, enum.Enum):
"""Namespace entity annotation types"""
Anatomy = "Anatomy"
Cell = "Cell"
CellLine = "CellLine"
CellStructure = "CellStructure"
Disease = "Disease"
Evidence = "Evidence"
Species = "Species"
All = "All"
# Used for validation of pmod()
AminoAcid = [
"Alanine",
"Ala",
"A",
"Arginine",
"Arg",
"R",
"Asparagine",
"Asn",
"N",
"Aspartic Acid",
"Asp",
"D",
"Cysteine",
"Cys",
"C",
"Glutamic Acid",
"Glu",
"E",
"Glutamine",
"Gln",
"Q",
"Glycine",
"Gly",
"G",
"Histidine",
"His",
"H",
"Isoleucine",
"Ile",
"I",
"Leucine",
"Leu",
"L",
"Lysine",
"Lys",
"K",
"Methionine",
"Met",
"M",
"Phenylalanine",
"Phe",
"F",
"Proline",
"Pro",
"P",
"Serine",
"Ser",
"S",
"Threonine",
"Thr",
"T",
"Tryptophan",
"Trp",
"W",
"Tyrosine",
"Tyr",
"Y",
"Valine",
"Val",
"V",
]
AminoAcidCompletion = {
"Alanine": "Ala",
"Ala": "Ala",
"Arginine": "Arg",
"Arg": "Arg",
"Asparagine": "Asn",
"Asn": "Asn",
"Aspartic Acid": "Asp",
"Asp": "Asp",
"Cysteine": "Cys",
"Cys": "Cys",
"Glutamic Acid": "Glu",
"Glu": "Glu",
"Glutamine": "Gln",
"Gln": "Gln",
"Glycine": "Gly",
"Gly": "Gly",
"Histidine": "His",
"His": "His",
"Isoleucine": "Ile",
"Ile": "Ile",
"Leucine": "Leu",
"Leu": "Leu",
"Lysine": "Lys",
"Lys": "Lys",
"Methionine": "Met",
"Met": "Met",
"Phenylalanine": "Phe",
"Phe": "Phe",
"Proline": "Pro",
"Pro": "Pro",
"Serine": "Ser",
"Ser": "Ser",
"Threonine": "Thr",
"Thr": "Thr",
"Tryptophan": "Trp",
"Trp": "Trp",
"Tyrosine": "Tyr",
"Tyr": "Tyr",
"Valine": "Val",
"Val": "Val",
}
# Used for validation of ma()
Activity = [
"catalyticActivity",
"cat",
"chaperoneActivity",
"chap",
"gtpBoundActivity",
"gtp",
"kinaseActivity",
"kin",
"molecularActivity",
"act",
"peptidaseActivity",
"pep",
"phosphataseActivity",
"phos",
"ribosylationActivity",
"ribo",
"transcriptionalActivity",
"tscript",
"transportActivity",
"tport",
]
ActivityCompletion = {
"catalyticActivity": "cat",
"cat": "cat",
"chaperoneActivity": "chap",
"chap": "chap",
"gtpBoundActivity": "gtp",
"gtp": "gtp",
"kinaseActivity": "kin",
"kin": "kin",
"molecularActivity": "act",
"act": "act",
"peptidaseActivity": "pep",
"pep": "pep",
"phosphataseActivity": "phos",
"phos": "phos",
"ribosylationActivity": "ribo",
"ribo": "ribo",
"transcriptionalActivity": "tscript",
"tscript": "tscript",
"transportActivity": "tport",
"tport": "tport",
}
# Used for validation of pmod()
ProteinModification = [
"acetylation",
"Ac",
"ADP-ribosylation",
"ADPRib",
"farnesylation",
"Farn",
"geranylgeranylation",
"Gerger",
"glycosylation",
"Glyco",
"hydroxylation",
"Hy",
"ISG15-protein conjugation",
"ISG",
"methylation",
"Me",
"mono-methylation",
"Me1",
"di-methylation",
"Me2",
"tri-methylation",
"Me3",
"myristoylation",
"Myr",
"neddylation",
"Nedd",
"N-linked glycosylation",
"NGlyco",
"Nitrosylation",
"NO",
"O-linked glycosylation",
"OGlyco",
"palmitoylation",
"Palm",
"phosphorylation",
"Ph",
"sulfonation",
"Sulf",
"SUMOylation",
"Sumo",
"ubiquitination",
"Ub",
"Lysine 48-linked polyubiquitination",
"UbK48",
"Lysine 63-linked polyubiquitination",
"UbK63",
"mono-ubiquitination",
"UbMono",
"poly-ubiquitination",
"UbPoly",
]
ProteinModificationCompletion = {
"acetylation": "Ac",
"Ac": "Ac",
"ADP-ribosylation": "ADPRib",
"ADPRib": "ADPRib",
"farnesylation": "Farn",
"Farn": "Farn",
"geranylgeranylation": "Gerger",
"Gerger": "Gerger",
"glycosylation": "Glyco",
"Glyco": "Glyco",
"hydroxylation": "Hy",
"Hy": "Hy",
"ISG15-protein conjugation": "ISG",
"ISG": "ISG",
"methylation": "Me",
"Me": "Me",
"mono-methylation": "Me1",
"Me1": "Me1",
"di-methylation": "Me2",
"Me2": "Me2",
"tri-methylation": "Me3",
"Me3": "Me3",
"myristoylation": "Myr",
"Myr": "Myr",
"neddylation": "Nedd",
"Nedd": "Nedd",
"N-linked glycosylation": "NGlyco",
"NGlyco": "NGlyco",
"Nitrosylation": "NO",
"NO": "NO",
"O-linked glycosylation": "OGlyco",
"OGlyco": "OGlyco",
"palmitoylation": "Palm",
"Palm": "Palm",
"phosphorylation": "Ph",
"Ph": "Ph",
"sulfonation": "Sulf",
"Sulf": "Sulf",
"SUMOylation": "Sumo",
"Sumo": "Sumo",
"ubiquitination": "Ub",
"Ub": "Ub",
"Lysine 48-linked polyubiquitination": "UbK48",
"UbK48": "UbK48",
"Lysine 63-linked polyubiquitination": "UbK63",
"UbK63": "UbK63",
"mono-ubiquitination": "UbMono",
"UbMono": "UbMono",
"poly-ubiquitination": "UbPoly",
"UbPoly": "UbPoly",
}
strarg_validation_lists = {
"Activity": Activity,
"ProteinModification": ProteinModification,
"AminoAcid": AminoAcid,
}
strarg_completions = {
"Activity": ActivityCompletion,
"AminoAcid": AminoAcidCompletion,
"ProteinModification": ProteinModificationCompletion,
}