cellxgene_ontology_guide.entities

 1from collections import Counter
 2from enum import Enum
 3from typing import Any, Dict, List
 4
 5
 6class Ontology(Enum):
 7    """
 8    Enum for the set of ontologies supported by CZ CellXGene.
 9    """
10
11    CL = "cl"
12    EFO = "efo"
13    MONDO = "mondo"
14    UBERON = "uberon"
15    HANCESTRO = "hancestro"
16    HsapDv = "hsapdv"
17    MmusDv = "mmusdv"
18    PATO = "pato"
19    NCBITaxon = "ncbitaxon"
20    FBbt = "fbbt"
21    FBdv = "fbdv"
22    ZFA = "zfa"
23    WBbt = "wbbt"
24    WBls = "wbls"
25    CVCL = "cvcl"
26    CHEBI = "chebi"
27    # NOTE: UniProt is a special case. Unlike OBO/OWL ontologies, UniProt does not expose a
28    # parseable is-a hierarchy through this pipeline. The ``ancestors`` field is empty for
29    # all UniProt terms. Hierarchy support (e.g. via Gene Ontology molecular-function
30    # annotations) is not yet implemented in cellxgene-ontology-guide.
31    UniProt = "uniprot"
32
33
34class CuratedOntologyTermList(Enum):
35    """
36    Enum for the set of curated ontology term lists supported by CZ CellXGene
37    """
38
39    CELL_CLASS = "cell_class"
40    CELL_SUBCLASS = "cell_subclass"
41    ORGAN = "organ"
42    SYSTEM = "system"
43    TISSUE_GENERAL = "tissue_general"
44    UBERON_DEVELOPMENT_STAGE = "uberon_development_stage"
45
46
47class OntologyNode:
48    """
49    Class to represent an ontology term and its subclasses
50    """
51
52    def __init__(self, term_id: str, name: str):
53        self._term_id = term_id
54        self._name = name
55        self._children: List["OntologyNode"] = []
56        self._term_counter: Counter[str] = Counter({self.term_id: 1})
57
58    @property
59    def term_id(self) -> str:
60        """
61        Ontology term ID represented by this OntologyNode.
62        """
63        return self._term_id
64
65    @property
66    def name(self) -> str:
67        """
68        Human-readable label for ontology term represented by this OntologyNode.
69        """
70        return self._name
71
72    @property
73    def children(self) -> List["OntologyNode"]:
74        """
75        List of children OntologyNode of this OntologyNode.
76        """
77        return self._children
78
79    @property
80    def term_counter(self) -> Counter[str]:
81        """
82        Mapping of unique ontology term ID descendants of this OntologyNode to the number of times each term
83        appears in the graph rooted at this node.
84        :return:
85        """
86        return self._term_counter
87
88    def add_child(self, child: "OntologyNode") -> None:
89        self._children.append(child)
90        self._term_counter.update(child.term_counter)
91
92    def to_dict(self) -> Dict[str, Any]:
93        return {
94            "term_id": self.term_id,
95            "name": self.name,
96            "children": [child.to_dict() for child in self.children],
97        }