valuesets 0.3.1__py3-none-any.whl

valuesets/enums/bio/taxonomy.py

@@ -0,0 +1,238 @@
+"""
+Taxonomic Classifications
+
+Value sets for taxonomic classifications and model organisms
+
+Generated from: bio/taxonomy.yaml
+"""
+
+from __future__ import annotations
+
+from typing import Dict, Any, Optional
+from valuesets.generators.rich_enum import RichEnum
+
+class CommonOrganismTaxaEnum(RichEnum):
+    """
+    Common model organisms used in biological research, mapped to NCBI Taxonomy IDs
+    """
+    # Enum members
+    BACTERIA = "BACTERIA"
+    ARCHAEA = "ARCHAEA"
+    EUKARYOTA = "EUKARYOTA"
+    VIRUSES = "VIRUSES"
+    VERTEBRATA = "VERTEBRATA"
+    MAMMALIA = "MAMMALIA"
+    PRIMATES = "PRIMATES"
+    RODENTIA = "RODENTIA"
+    CARNIVORA = "CARNIVORA"
+    ARTIODACTYLA = "ARTIODACTYLA"
+    AVES = "AVES"
+    ACTINOPTERYGII = "ACTINOPTERYGII"
+    AMPHIBIA = "AMPHIBIA"
+    ARTHROPODA = "ARTHROPODA"
+    INSECTA = "INSECTA"
+    NEMATODA = "NEMATODA"
+    FUNGI = "FUNGI"
+    ASCOMYCOTA = "ASCOMYCOTA"
+    VIRIDIPLANTAE = "VIRIDIPLANTAE"
+    MAGNOLIOPHYTA = "MAGNOLIOPHYTA"
+    PROTEOBACTERIA = "PROTEOBACTERIA"
+    GAMMAPROTEOBACTERIA = "GAMMAPROTEOBACTERIA"
+    FIRMICUTES = "FIRMICUTES"
+    ACTINOBACTERIA = "ACTINOBACTERIA"
+    EURYARCHAEOTA = "EURYARCHAEOTA"
+    APICOMPLEXA = "APICOMPLEXA"
+    HUMAN = "HUMAN"
+    MOUSE = "MOUSE"
+    RAT = "RAT"
+    RHESUS = "RHESUS"
+    CHIMP = "CHIMP"
+    DOG = "DOG"
+    COW = "COW"
+    PIG = "PIG"
+    CHICKEN = "CHICKEN"
+    ZEBRAFISH = "ZEBRAFISH"
+    MEDAKA = "MEDAKA"
+    PUFFERFISH = "PUFFERFISH"
+    XENOPUS_TROPICALIS = "XENOPUS_TROPICALIS"
+    XENOPUS_LAEVIS = "XENOPUS_LAEVIS"
+    DROSOPHILA = "DROSOPHILA"
+    C_ELEGANS = "C_ELEGANS"
+    S_CEREVISIAE = "S_CEREVISIAE"
+    S_CEREVISIAE_S288C = "S_CEREVISIAE_S288C"
+    S_POMBE = "S_POMBE"
+    C_ALBICANS = "C_ALBICANS"
+    A_NIDULANS = "A_NIDULANS"
+    N_CRASSA = "N_CRASSA"
+    ARABIDOPSIS = "ARABIDOPSIS"
+    RICE = "RICE"
+    MAIZE = "MAIZE"
+    TOMATO = "TOMATO"
+    TOBACCO = "TOBACCO"
+    E_COLI = "E_COLI"
+    E_COLI_K12 = "E_COLI_K12"
+    B_SUBTILIS = "B_SUBTILIS"
+    M_TUBERCULOSIS = "M_TUBERCULOSIS"
+    P_AERUGINOSA = "P_AERUGINOSA"
+    S_AUREUS = "S_AUREUS"
+    S_PNEUMONIAE = "S_PNEUMONIAE"
+    H_PYLORI = "H_PYLORI"
+    M_JANNASCHII = "M_JANNASCHII"
+    H_SALINARUM = "H_SALINARUM"
+    P_FALCIPARUM = "P_FALCIPARUM"
+    T_GONDII = "T_GONDII"
+    T_BRUCEI = "T_BRUCEI"
+    DICTYOSTELIUM = "DICTYOSTELIUM"
+    TETRAHYMENA = "TETRAHYMENA"
+    PARAMECIUM = "PARAMECIUM"
+    CHLAMYDOMONAS = "CHLAMYDOMONAS"
+    PHAGE_LAMBDA = "PHAGE_LAMBDA"
+    HIV1 = "HIV1"
+    INFLUENZA_A = "INFLUENZA_A"
+    SARS_COV_2 = "SARS_COV_2"
+
+# Set metadata after class creation
+CommonOrganismTaxaEnum._metadata = {
+    "BACTERIA": {'description': 'Bacteria domain', 'meaning': 'NCBITaxon:2'},
+    "ARCHAEA": {'description': 'Archaea domain', 'meaning': 'NCBITaxon:2157'},
+    "EUKARYOTA": {'description': 'Eukaryota domain', 'meaning': 'NCBITaxon:2759'},
+    "VIRUSES": {'description': 'Viruses (not a true domain)', 'meaning': 'NCBITaxon:10239'},
+    "VERTEBRATA": {'description': 'Vertebrates', 'meaning': 'NCBITaxon:7742'},
+    "MAMMALIA": {'description': 'Mammals', 'meaning': 'NCBITaxon:40674'},
+    "PRIMATES": {'description': 'Primates', 'meaning': 'NCBITaxon:9443'},
+    "RODENTIA": {'description': 'Rodents', 'meaning': 'NCBITaxon:9989'},
+    "CARNIVORA": {'description': 'Carnivores', 'meaning': 'NCBITaxon:33554'},
+    "ARTIODACTYLA": {'description': 'Even-toed ungulates', 'meaning': 'NCBITaxon:91561'},
+    "AVES": {'description': 'Birds', 'meaning': 'NCBITaxon:8782'},
+    "ACTINOPTERYGII": {'description': 'Ray-finned fishes', 'meaning': 'NCBITaxon:7898'},
+    "AMPHIBIA": {'description': 'Amphibians', 'meaning': 'NCBITaxon:8292'},
+    "ARTHROPODA": {'description': 'Arthropods', 'meaning': 'NCBITaxon:6656'},
+    "INSECTA": {'description': 'Insects', 'meaning': 'NCBITaxon:50557'},
+    "NEMATODA": {'description': 'Roundworms', 'meaning': 'NCBITaxon:6231'},
+    "FUNGI": {'description': 'Fungal kingdom', 'meaning': 'NCBITaxon:4751'},
+    "ASCOMYCOTA": {'description': 'Sac fungi', 'meaning': 'NCBITaxon:4890'},
+    "VIRIDIPLANTAE": {'description': 'Green plants', 'meaning': 'NCBITaxon:33090'},
+    "MAGNOLIOPHYTA": {'description': 'Flowering plants', 'meaning': 'NCBITaxon:3398'},
+    "PROTEOBACTERIA": {'description': 'Proteobacteria', 'meaning': 'NCBITaxon:1224'},
+    "GAMMAPROTEOBACTERIA": {'description': 'Gamma proteobacteria', 'meaning': 'NCBITaxon:1236'},
+    "FIRMICUTES": {'description': 'Firmicutes (Gram-positive bacteria)', 'meaning': 'NCBITaxon:1239'},
+    "ACTINOBACTERIA": {'description': 'Actinobacteria', 'meaning': 'NCBITaxon:201174'},
+    "EURYARCHAEOTA": {'description': 'Euryarchaeota', 'meaning': 'NCBITaxon:28890'},
+    "APICOMPLEXA": {'description': 'Apicomplexan parasites', 'meaning': 'NCBITaxon:5794'},
+    "HUMAN": {'description': 'Homo sapiens (human)', 'meaning': 'NCBITaxon:9606'},
+    "MOUSE": {'description': 'Mus musculus (house mouse)', 'meaning': 'NCBITaxon:10090'},
+    "RAT": {'description': 'Rattus norvegicus (Norway rat)', 'meaning': 'NCBITaxon:10116'},
+    "RHESUS": {'description': 'Macaca mulatta (rhesus macaque)', 'meaning': 'NCBITaxon:9544'},
+    "CHIMP": {'description': 'Pan troglodytes (chimpanzee)', 'meaning': 'NCBITaxon:9598'},
+    "DOG": {'description': 'Canis lupus familiaris (dog)', 'meaning': 'NCBITaxon:9615'},
+    "COW": {'description': 'Bos taurus (cattle)', 'meaning': 'NCBITaxon:9913'},
+    "PIG": {'description': 'Sus scrofa (pig)', 'meaning': 'NCBITaxon:9823'},
+    "CHICKEN": {'description': 'Gallus gallus (chicken)', 'meaning': 'NCBITaxon:9031'},
+    "ZEBRAFISH": {'description': 'Danio rerio (zebrafish)', 'meaning': 'NCBITaxon:7955'},
+    "MEDAKA": {'description': 'Oryzias latipes (Japanese medaka)', 'meaning': 'NCBITaxon:8090'},
+    "PUFFERFISH": {'description': 'Takifugu rubripes (torafugu)', 'meaning': 'NCBITaxon:31033'},
+    "XENOPUS_TROPICALIS": {'description': 'Xenopus tropicalis (western clawed frog)', 'meaning': 'NCBITaxon:8364'},
+    "XENOPUS_LAEVIS": {'description': 'Xenopus laevis (African clawed frog)', 'meaning': 'NCBITaxon:8355'},
+    "DROSOPHILA": {'description': 'Drosophila melanogaster (fruit fly)', 'meaning': 'NCBITaxon:7227'},
+    "C_ELEGANS": {'description': 'Caenorhabditis elegans (roundworm)', 'meaning': 'NCBITaxon:6239'},
+    "S_CEREVISIAE": {'description': "Saccharomyces cerevisiae (baker's yeast)", 'meaning': 'NCBITaxon:4932'},
+    "S_CEREVISIAE_S288C": {'description': 'Saccharomyces cerevisiae S288C (reference strain)', 'meaning': 'NCBITaxon:559292'},
+    "S_POMBE": {'description': 'Schizosaccharomyces pombe (fission yeast)', 'meaning': 'NCBITaxon:4896'},
+    "C_ALBICANS": {'description': 'Candida albicans (pathogenic yeast)', 'meaning': 'NCBITaxon:5476'},
+    "A_NIDULANS": {'description': 'Aspergillus nidulans (filamentous fungus)', 'meaning': 'NCBITaxon:162425'},
+    "N_CRASSA": {'description': 'Neurospora crassa (red bread mold)', 'meaning': 'NCBITaxon:5141'},
+    "ARABIDOPSIS": {'description': 'Arabidopsis thaliana (thale cress)', 'meaning': 'NCBITaxon:3702'},
+    "RICE": {'description': 'Oryza sativa (rice)', 'meaning': 'NCBITaxon:4530'},
+    "MAIZE": {'description': 'Zea mays (corn)', 'meaning': 'NCBITaxon:4577'},
+    "TOMATO": {'description': 'Solanum lycopersicum (tomato)', 'meaning': 'NCBITaxon:4081'},
+    "TOBACCO": {'description': 'Nicotiana tabacum (tobacco)', 'meaning': 'NCBITaxon:4097'},
+    "E_COLI": {'description': 'Escherichia coli', 'meaning': 'NCBITaxon:562'},
+    "E_COLI_K12": {'description': 'Escherichia coli str. K-12', 'meaning': 'NCBITaxon:83333'},
+    "B_SUBTILIS": {'description': 'Bacillus subtilis', 'meaning': 'NCBITaxon:1423'},
+    "M_TUBERCULOSIS": {'description': 'Mycobacterium tuberculosis', 'meaning': 'NCBITaxon:1773'},
+    "P_AERUGINOSA": {'description': 'Pseudomonas aeruginosa', 'meaning': 'NCBITaxon:287'},
+    "S_AUREUS": {'description': 'Staphylococcus aureus', 'meaning': 'NCBITaxon:1280'},
+    "S_PNEUMONIAE": {'description': 'Streptococcus pneumoniae', 'meaning': 'NCBITaxon:1313'},
+    "H_PYLORI": {'description': 'Helicobacter pylori', 'meaning': 'NCBITaxon:210'},
+    "M_JANNASCHII": {'description': 'Methanocaldococcus jannaschii', 'meaning': 'NCBITaxon:2190'},
+    "H_SALINARUM": {'description': 'Halobacterium salinarum', 'meaning': 'NCBITaxon:2242'},
+    "P_FALCIPARUM": {'description': 'Plasmodium falciparum (malaria parasite)', 'meaning': 'NCBITaxon:5833'},
+    "T_GONDII": {'description': 'Toxoplasma gondii', 'meaning': 'NCBITaxon:5811'},
+    "T_BRUCEI": {'description': 'Trypanosoma brucei', 'meaning': 'NCBITaxon:5691'},
+    "DICTYOSTELIUM": {'description': 'Dictyostelium discoideum (slime mold)', 'meaning': 'NCBITaxon:44689'},
+    "TETRAHYMENA": {'description': 'Tetrahymena thermophila', 'meaning': 'NCBITaxon:5911'},
+    "PARAMECIUM": {'description': 'Paramecium tetraurelia', 'meaning': 'NCBITaxon:5888'},
+    "CHLAMYDOMONAS": {'description': 'Chlamydomonas reinhardtii (green alga)', 'meaning': 'NCBITaxon:3055'},
+    "PHAGE_LAMBDA": {'description': 'Escherichia phage lambda', 'meaning': 'NCBITaxon:10710'},
+    "HIV1": {'description': 'Human immunodeficiency virus 1', 'meaning': 'NCBITaxon:11676'},
+    "INFLUENZA_A": {'description': 'Influenza A virus', 'meaning': 'NCBITaxon:11320'},
+    "SARS_COV_2": {'description': 'Severe acute respiratory syndrome coronavirus 2', 'meaning': 'NCBITaxon:2697049'},
+}
+
+class TaxonomicRank(RichEnum):
+    """
+    Standard taxonomic ranks used in biological classification
+    """
+    # Enum members
+    DOMAIN = "DOMAIN"
+    KINGDOM = "KINGDOM"
+    PHYLUM = "PHYLUM"
+    CLASS = "CLASS"
+    ORDER = "ORDER"
+    FAMILY = "FAMILY"
+    GENUS = "GENUS"
+    SPECIES = "SPECIES"
+    SUBSPECIES = "SUBSPECIES"
+    STRAIN = "STRAIN"
+    VARIETY = "VARIETY"
+    FORM = "FORM"
+    CULTIVAR = "CULTIVAR"
+
+# Set metadata after class creation
+TaxonomicRank._metadata = {
+    "DOMAIN": {'description': 'Domain (highest rank)', 'meaning': 'TAXRANK:0000037'},
+    "KINGDOM": {'description': 'Kingdom', 'meaning': 'TAXRANK:0000017'},
+    "PHYLUM": {'description': 'Phylum (animals, plants, fungi) or Division (plants)', 'meaning': 'TAXRANK:0000001'},
+    "CLASS": {'description': 'Class', 'meaning': 'TAXRANK:0000002'},
+    "ORDER": {'description': 'Order', 'meaning': 'TAXRANK:0000003'},
+    "FAMILY": {'description': 'Family', 'meaning': 'TAXRANK:0000004'},
+    "GENUS": {'description': 'Genus', 'meaning': 'TAXRANK:0000005'},
+    "SPECIES": {'description': 'Species', 'meaning': 'TAXRANK:0000006'},
+    "SUBSPECIES": {'description': 'Subspecies', 'meaning': 'TAXRANK:0000023'},
+    "STRAIN": {'description': 'Strain (especially for microorganisms)', 'meaning': 'TAXRANK:0001001'},
+    "VARIETY": {'description': 'Variety (mainly plants)', 'meaning': 'TAXRANK:0000016'},
+    "FORM": {'description': 'Form (mainly plants)', 'meaning': 'TAXRANK:0000026'},
+    "CULTIVAR": {'description': 'Cultivar (cultivated variety)', 'meaning': 'TAXRANK:0000034'},
+}
+
+class BiologicalKingdom(RichEnum):
+    """
+    Major kingdoms/domains of life
+    """
+    # Enum members
+    BACTERIA = "BACTERIA"
+    ARCHAEA = "ARCHAEA"
+    EUKARYOTA = "EUKARYOTA"
+    ANIMALIA = "ANIMALIA"
+    PLANTAE = "PLANTAE"
+    FUNGI = "FUNGI"
+    PROTISTA = "PROTISTA"
+    VIRUSES = "VIRUSES"
+
+# Set metadata after class creation
+BiologicalKingdom._metadata = {
+    "BACTERIA": {'description': 'Bacteria domain', 'meaning': 'NCBITaxon:2'},
+    "ARCHAEA": {'description': 'Archaea domain', 'meaning': 'NCBITaxon:2157'},
+    "EUKARYOTA": {'description': 'Eukaryota domain', 'meaning': 'NCBITaxon:2759'},
+    "ANIMALIA": {'description': 'Animal kingdom', 'meaning': 'NCBITaxon:33208'},
+    "PLANTAE": {'description': 'Plant kingdom (Viridiplantae)', 'meaning': 'NCBITaxon:33090'},
+    "FUNGI": {'description': 'Fungal kingdom', 'meaning': 'NCBITaxon:4751'},
+    "PROTISTA": {'description': 'Protist kingdom (polyphyletic group)'},
+    "VIRUSES": {'description': 'Viruses (not a true kingdom)', 'meaning': 'NCBITaxon:10239'},
+}
+
+__all__ = [
+    "CommonOrganismTaxaEnum",
+    "TaxonomicRank",
+    "BiologicalKingdom",
+]

valuesets/enums/bio/trophic_levels.py

@@ -0,0 +1,85 @@
+"""
+
+Generated from: bio/trophic_levels.yaml
+"""
+
+from __future__ import annotations
+
+from typing import Dict, Any, Optional
+from valuesets.generators.rich_enum import RichEnum
+
+class TrophicLevelEnum(RichEnum):
+    """
+    Trophic levels are the feeding position in a food chain
+    """
+    # Enum members
+    AUTOTROPH = "AUTOTROPH"
+    CARBOXYDOTROPH = "CARBOXYDOTROPH"
+    CHEMOAUTOLITHOTROPH = "CHEMOAUTOLITHOTROPH"
+    CHEMOAUTOTROPH = "CHEMOAUTOTROPH"
+    CHEMOHETEROTROPH = "CHEMOHETEROTROPH"
+    CHEMOLITHOAUTOTROPH = "CHEMOLITHOAUTOTROPH"
+    CHEMOLITHOTROPH = "CHEMOLITHOTROPH"
+    CHEMOORGANOHETEROTROPH = "CHEMOORGANOHETEROTROPH"
+    CHEMOORGANOTROPH = "CHEMOORGANOTROPH"
+    CHEMOSYNTHETIC = "CHEMOSYNTHETIC"
+    CHEMOTROPH = "CHEMOTROPH"
+    COPIOTROPH = "COPIOTROPH"
+    DIAZOTROPH = "DIAZOTROPH"
+    FACULTATIVE = "FACULTATIVE"
+    HETEROTROPH = "HETEROTROPH"
+    LITHOAUTOTROPH = "LITHOAUTOTROPH"
+    LITHOHETEROTROPH = "LITHOHETEROTROPH"
+    LITHOTROPH = "LITHOTROPH"
+    METHANOTROPH = "METHANOTROPH"
+    METHYLOTROPH = "METHYLOTROPH"
+    MIXOTROPH = "MIXOTROPH"
+    OBLIGATE = "OBLIGATE"
+    OLIGOTROPH = "OLIGOTROPH"
+    ORGANOHETEROTROPH = "ORGANOHETEROTROPH"
+    ORGANOTROPH = "ORGANOTROPH"
+    PHOTOAUTOTROPH = "PHOTOAUTOTROPH"
+    PHOTOHETEROTROPH = "PHOTOHETEROTROPH"
+    PHOTOLITHOAUTOTROPH = "PHOTOLITHOAUTOTROPH"
+    PHOTOLITHOTROPH = "PHOTOLITHOTROPH"
+    PHOTOSYNTHETIC = "PHOTOSYNTHETIC"
+    PHOTOTROPH = "PHOTOTROPH"
+
+# Set metadata after class creation
+TrophicLevelEnum._metadata = {
+    "AUTOTROPH": {'description': 'Organism capable of synthesizing its own food from inorganic substances', 'meaning': 'ECOCORE:00000023'},
+    "CARBOXYDOTROPH": {'description': 'Organism that uses carbon monoxide as a source of carbon and energy'},
+    "CHEMOAUTOLITHOTROPH": {'description': 'Autotroph that obtains energy from inorganic compounds'},
+    "CHEMOAUTOTROPH": {'description': 'Organism that obtains energy by oxidizing inorganic compounds', 'meaning': 'ECOCORE:00000129'},
+    "CHEMOHETEROTROPH": {'description': 'Organism that obtains energy from organic compounds', 'meaning': 'ECOCORE:00000132'},
+    "CHEMOLITHOAUTOTROPH": {'description': 'Organism that uses inorganic compounds as electron donors'},
+    "CHEMOLITHOTROPH": {'description': 'Organism that obtains energy from oxidation of inorganic compounds'},
+    "CHEMOORGANOHETEROTROPH": {'description': 'Organism that uses organic compounds as both carbon and energy source'},
+    "CHEMOORGANOTROPH": {'description': 'Organism that obtains energy from organic compounds', 'meaning': 'ECOCORE:00000133'},
+    "CHEMOSYNTHETIC": {'description': 'Relating to organisms that produce organic matter through chemosynthesis'},
+    "CHEMOTROPH": {'description': 'Organism that obtains energy from chemical compounds'},
+    "COPIOTROPH": {'description': 'Organism that thrives in nutrient-rich environments'},
+    "DIAZOTROPH": {'description': 'Organism capable of fixing atmospheric nitrogen'},
+    "FACULTATIVE": {'description': 'Organism that can switch between different metabolic modes'},
+    "HETEROTROPH": {'description': 'Organism that obtains carbon from organic compounds', 'meaning': 'ECOCORE:00000010'},
+    "LITHOAUTOTROPH": {'description': 'Autotroph that uses inorganic compounds as electron donors'},
+    "LITHOHETEROTROPH": {'description': 'Heterotroph that uses inorganic compounds as electron donors'},
+    "LITHOTROPH": {'description': 'Organism that uses inorganic substrates as electron donors'},
+    "METHANOTROPH": {'description': 'Organism that uses methane as carbon and energy source'},
+    "METHYLOTROPH": {'description': 'Organism that uses single-carbon compounds'},
+    "MIXOTROPH": {'description': 'Organism that can use both autotrophic and heterotrophic methods'},
+    "OBLIGATE": {'description': 'Organism restricted to a particular metabolic mode'},
+    "OLIGOTROPH": {'description': 'Organism that thrives in nutrient-poor environments', 'meaning': 'ECOCORE:00000138'},
+    "ORGANOHETEROTROPH": {'description': 'Organism that uses organic compounds as carbon source'},
+    "ORGANOTROPH": {'description': 'Organism that uses organic compounds as electron donors'},
+    "PHOTOAUTOTROPH": {'description': 'Organism that uses light energy to synthesize organic compounds', 'meaning': 'ECOCORE:00000130'},
+    "PHOTOHETEROTROPH": {'description': 'Organism that uses light for energy but organic compounds for carbon', 'meaning': 'ECOCORE:00000131'},
+    "PHOTOLITHOAUTOTROPH": {'description': 'Photoautotroph that uses inorganic electron donors'},
+    "PHOTOLITHOTROPH": {'description': 'Organism that uses light energy and inorganic electron donors'},
+    "PHOTOSYNTHETIC": {'description': 'Relating to organisms that produce organic matter through photosynthesis'},
+    "PHOTOTROPH": {'description': 'Organism that obtains energy from light'},
+}
+
+__all__ = [
+    "TrophicLevelEnum",
+]