valuesets 0.3.1__py3-none-any.whl

valuesets/enums/bio/go_evidence.py

@@ -0,0 +1,129 @@
+"""
+Gene Ontology Evidence Codes
+
+Value sets for Gene Ontology evidence codes and electronic annotation methods
+
+Generated from: bio/go_evidence.yaml
+"""
+
+from __future__ import annotations
+
+from typing import Dict, Any, Optional
+from valuesets.generators.rich_enum import RichEnum
+
+class GOEvidenceCode(RichEnum):
+    """
+    Gene Ontology evidence codes mapped to Evidence and Conclusion Ontology (ECO) terms
+    """
+    # Enum members
+    EXP = "EXP"
+    IDA = "IDA"
+    IPI = "IPI"
+    IMP = "IMP"
+    IGI = "IGI"
+    IEP = "IEP"
+    HTP = "HTP"
+    HDA = "HDA"
+    HMP = "HMP"
+    HGI = "HGI"
+    HEP = "HEP"
+    IBA = "IBA"
+    IBD = "IBD"
+    IKR = "IKR"
+    IRD = "IRD"
+    ISS = "ISS"
+    ISO = "ISO"
+    ISA = "ISA"
+    ISM = "ISM"
+    IGC = "IGC"
+    RCA = "RCA"
+    TAS = "TAS"
+    NAS = "NAS"
+    IC = "IC"
+    ND = "ND"
+    IEA = "IEA"
+
+# Set metadata after class creation
+GOEvidenceCode._metadata = {
+    "EXP": {'meaning': 'ECO:0000269', 'aliases': ['experimental evidence used in manual assertion']},
+    "IDA": {'meaning': 'ECO:0000314', 'aliases': ['direct assay evidence used in manual assertion']},
+    "IPI": {'meaning': 'ECO:0000353', 'aliases': ['physical interaction evidence used in manual assertion']},
+    "IMP": {'meaning': 'ECO:0000315', 'aliases': ['mutant phenotype evidence used in manual assertion']},
+    "IGI": {'meaning': 'ECO:0000316', 'aliases': ['genetic interaction evidence used in manual assertion']},
+    "IEP": {'meaning': 'ECO:0000270', 'aliases': ['expression pattern evidence used in manual assertion']},
+    "HTP": {'meaning': 'ECO:0006056', 'aliases': ['high throughput evidence used in manual assertion']},
+    "HDA": {'meaning': 'ECO:0007005', 'aliases': ['high throughput direct assay evidence used in manual assertion']},
+    "HMP": {'meaning': 'ECO:0007001', 'aliases': ['high throughput mutant phenotypic evidence used in manual assertion']},
+    "HGI": {'meaning': 'ECO:0007003', 'aliases': ['high throughput genetic interaction phenotypic evidence used in manual assertion']},
+    "HEP": {'meaning': 'ECO:0007007', 'aliases': ['high throughput expression pattern evidence used in manual assertion']},
+    "IBA": {'meaning': 'ECO:0000318', 'aliases': ['biological aspect of ancestor evidence used in manual assertion']},
+    "IBD": {'meaning': 'ECO:0000319', 'aliases': ['biological aspect of descendant evidence used in manual assertion']},
+    "IKR": {'meaning': 'ECO:0000320', 'aliases': ['phylogenetic determination of loss of key residues evidence used in manual assertion']},
+    "IRD": {'meaning': 'ECO:0000321', 'aliases': ['rapid divergence from ancestral sequence evidence used in manual assertion']},
+    "ISS": {'meaning': 'ECO:0000250', 'aliases': ['sequence similarity evidence used in manual assertion']},
+    "ISO": {'meaning': 'ECO:0000266', 'aliases': ['sequence orthology evidence used in manual assertion']},
+    "ISA": {'meaning': 'ECO:0000247', 'aliases': ['sequence alignment evidence used in manual assertion']},
+    "ISM": {'meaning': 'ECO:0000255', 'aliases': ['match to sequence model evidence used in manual assertion']},
+    "IGC": {'meaning': 'ECO:0000317', 'aliases': ['genomic context evidence used in manual assertion']},
+    "RCA": {'meaning': 'ECO:0000245', 'aliases': ['automatically integrated combinatorial evidence used in manual assertion']},
+    "TAS": {'meaning': 'ECO:0000304', 'aliases': ['author statement supported by traceable reference used in manual assertion']},
+    "NAS": {'meaning': 'ECO:0000303', 'aliases': ['author statement without traceable support used in manual assertion']},
+    "IC": {'meaning': 'ECO:0000305', 'aliases': ['curator inference used in manual assertion']},
+    "ND": {'meaning': 'ECO:0000307', 'aliases': ['no evidence data found used in manual assertion']},
+    "IEA": {'meaning': 'ECO:0000501', 'aliases': ['evidence used in automatic assertion']},
+}
+
+class GOElectronicMethods(RichEnum):
+    """
+    Electronic annotation methods used in Gene Ontology, identified by GO_REF codes
+    """
+    # Enum members
+    INTERPRO2GO = "INTERPRO2GO"
+    EC2GO = "EC2GO"
+    UNIPROTKB_KW2GO = "UNIPROTKB_KW2GO"
+    UNIPROTKB_SUBCELL2GO = "UNIPROTKB_SUBCELL2GO"
+    HAMAP_RULE2GO = "HAMAP_RULE2GO"
+    UNIPATHWAY2GO = "UNIPATHWAY2GO"
+    UNIRULE2GO = "UNIRULE2GO"
+    RHEA2GO = "RHEA2GO"
+    ENSEMBL_COMPARA = "ENSEMBL_COMPARA"
+    PANTHER = "PANTHER"
+    REACTOME = "REACTOME"
+    RFAM2GO = "RFAM2GO"
+    DICTYBASE = "DICTYBASE"
+    MGI = "MGI"
+    ZFIN = "ZFIN"
+    FLYBASE = "FLYBASE"
+    WORMBASE = "WORMBASE"
+    SGD = "SGD"
+    POMBASE = "POMBASE"
+    METACYC2GO = "METACYC2GO"
+
+# Set metadata after class creation
+GOElectronicMethods._metadata = {
+    "INTERPRO2GO": {'meaning': 'GO_REF:0000002'},
+    "EC2GO": {'meaning': 'GO_REF:0000003'},
+    "UNIPROTKB_KW2GO": {'meaning': 'GO_REF:0000004'},
+    "UNIPROTKB_SUBCELL2GO": {'meaning': 'GO_REF:0000023'},
+    "HAMAP_RULE2GO": {'meaning': 'GO_REF:0000020'},
+    "UNIPATHWAY2GO": {'meaning': 'GO_REF:0000041'},
+    "UNIRULE2GO": {'meaning': 'GO_REF:0000104'},
+    "RHEA2GO": {'meaning': 'GO_REF:0000116'},
+    "ENSEMBL_COMPARA": {'meaning': 'GO_REF:0000107'},
+    "PANTHER": {'meaning': 'GO_REF:0000033'},
+    "REACTOME": {'meaning': 'GO_REF:0000018'},
+    "RFAM2GO": {'meaning': 'GO_REF:0000115'},
+    "DICTYBASE": {'meaning': 'GO_REF:0000015'},
+    "MGI": {'meaning': 'GO_REF:0000096'},
+    "ZFIN": {'meaning': 'GO_REF:0000031'},
+    "FLYBASE": {'meaning': 'GO_REF:0000047'},
+    "WORMBASE": {'meaning': 'GO_REF:0000003'},
+    "SGD": {'meaning': 'GO_REF:0000100'},
+    "POMBASE": {'meaning': 'GO_REF:0000024'},
+    "METACYC2GO": {'meaning': 'GO_REF:0000112'},
+}
+
+__all__ = [
+    "GOEvidenceCode",
+    "GOElectronicMethods",
+]

valuesets/enums/bio/human_developmental_stages.py

@@ -0,0 +1,62 @@
+"""
+Human Developmental Stages Value Sets
+
+Value sets for human developmental stages from fertilization through aging
+
+Generated from: bio/human_developmental_stages.yaml
+"""
+
+from __future__ import annotations
+
+from typing import Dict, Any, Optional
+from valuesets.generators.rich_enum import RichEnum
+
+class HumanDevelopmentalStage(RichEnum):
+    """
+    Human developmental stages from fertilization through aging, based on the HsapDv (Human Developmental Stages) ontology.
+    """
+    # Enum members
+    ZYGOTE_STAGE = "ZYGOTE_STAGE"
+    CLEAVAGE_STAGE = "CLEAVAGE_STAGE"
+    MORULA_STAGE = "MORULA_STAGE"
+    BLASTOCYST_STAGE = "BLASTOCYST_STAGE"
+    GASTRULA_STAGE = "GASTRULA_STAGE"
+    NEURULA_STAGE = "NEURULA_STAGE"
+    ORGANOGENESIS_STAGE = "ORGANOGENESIS_STAGE"
+    FETAL_STAGE = "FETAL_STAGE"
+    NEONATAL_STAGE = "NEONATAL_STAGE"
+    INFANT_STAGE = "INFANT_STAGE"
+    TODDLER_STAGE = "TODDLER_STAGE"
+    CHILD_STAGE = "CHILD_STAGE"
+    ADOLESCENT_STAGE = "ADOLESCENT_STAGE"
+    ADULT_STAGE = "ADULT_STAGE"
+    AGED_STAGE = "AGED_STAGE"
+    EMBRYONIC_STAGE = "EMBRYONIC_STAGE"
+    PRENATAL_STAGE = "PRENATAL_STAGE"
+    POSTNATAL_STAGE = "POSTNATAL_STAGE"
+
+# Set metadata after class creation
+HumanDevelopmentalStage._metadata = {
+    "ZYGOTE_STAGE": {'description': 'Single cell formed by fertilization (Carnegie stage 01)', 'meaning': 'HsapDv:0000003'},
+    "CLEAVAGE_STAGE": {'description': 'Early cell divisions 2-16 cells (Carnegie stage 02)', 'meaning': 'HsapDv:0000005'},
+    "MORULA_STAGE": {'description': 'Solid ball of 16-32 cells', 'meaning': 'HsapDv:0000205'},
+    "BLASTOCYST_STAGE": {'description': 'Hollow sphere with inner cell mass (Carnegie stage 03)', 'meaning': 'HsapDv:0000007'},
+    "GASTRULA_STAGE": {'description': 'Formation of three germ layers', 'meaning': 'HsapDv:0000010'},
+    "NEURULA_STAGE": {'description': 'Formation of neural tube', 'meaning': 'HsapDv:0000012'},
+    "ORGANOGENESIS_STAGE": {'description': 'Major organ systems develop (weeks 3-8)', 'meaning': 'HsapDv:0000015'},
+    "FETAL_STAGE": {'description': 'Growth and maturation of organs (week 9 to birth)', 'meaning': 'HsapDv:0000037'},
+    "NEONATAL_STAGE": {'description': 'First 28 days after birth', 'meaning': 'HsapDv:0000262'},
+    "INFANT_STAGE": {'description': 'From 1 month to 1 year', 'meaning': 'HsapDv:0000261'},
+    "TODDLER_STAGE": {'description': 'Ages 1-4 years', 'meaning': 'HsapDv:0000265'},
+    "CHILD_STAGE": {'description': 'Ages 5-14 years', 'meaning': 'HsapDv:0000271'},
+    "ADOLESCENT_STAGE": {'description': 'Ages 15-19 years', 'meaning': 'HsapDv:0000268'},
+    "ADULT_STAGE": {'description': 'Ages 20-59 years', 'meaning': 'HsapDv:0000258'},
+    "AGED_STAGE": {'description': 'Ages 60+ years', 'meaning': 'HsapDv:0000227'},
+    "EMBRYONIC_STAGE": {'description': 'From fertilization to end of week 8', 'meaning': 'HsapDv:0000002'},
+    "PRENATAL_STAGE": {'description': 'From fertilization to birth', 'meaning': 'HsapDv:0000045'},
+    "POSTNATAL_STAGE": {'description': 'After birth', 'meaning': 'HsapDv:0010000'},
+}
+
+__all__ = [
+    "HumanDevelopmentalStage",
+]