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
26
27class CuratedOntologyTermList(Enum):
28    """
29    Enum for the set of curated ontology term lists supported by CZ CellXGene
30    """
31
32    CELL_CLASS = "cell_class"
33    CELL_SUBCLASS = "cell_subclass"
34    ORGAN = "organ"
35    SYSTEM = "system"
36    TISSUE_GENERAL = "tissue_general"
37    UBERON_DEVELOPMENT_STAGE = "uberon_development_stage"
38
39
40class OntologyNode:
41    """
42    Class to represent an ontology term and its subclasses
43    """
44
45    def __init__(self, term_id: str, name: str):
46        self._term_id = term_id
47        self._name = name
48        self._children: List["OntologyNode"] = []
49        self._term_counter: Counter[str] = Counter({self.term_id: 1})
50
51    @property
52    def term_id(self) -> str:
53        """
54        Ontology term ID represented by this OntologyNode.
55        """
56        return self._term_id
57
58    @property
59    def name(self) -> str:
60        """
61        Human-readable label for ontology term represented by this OntologyNode.
62        """
63        return self._name
64
65    @property
66    def children(self) -> List["OntologyNode"]:
67        """
68        List of children OntologyNode of this OntologyNode.
69        """
70        return self._children
71
72    @property
73    def term_counter(self) -> Counter[str]:
74        """
75        Mapping of unique ontology term ID descendants of this OntologyNode to the number of times each term
76        appears in the graph rooted at this node.
77        :return:
78        """
79        return self._term_counter
80
81    def add_child(self, child: "OntologyNode") -> None:
82        self._children.append(child)
83        self._term_counter.update(child.term_counter)
84
85    def to_dict(self) -> Dict[str, Any]:
86        return {
87            "term_id": self.term_id,
88            "name": self.name,
89            "children": [child.to_dict() for child in self.children],
90        }