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
27
28class CuratedOntologyTermList(Enum):
29    """
30    Enum for the set of curated ontology term lists supported by CZ CellXGene
31    """
32
33    CELL_CLASS = "cell_class"
34    CELL_SUBCLASS = "cell_subclass"
35    ORGAN = "organ"
36    SYSTEM = "system"
37    TISSUE_GENERAL = "tissue_general"
38    UBERON_DEVELOPMENT_STAGE = "uberon_development_stage"
39
40
41class OntologyNode:
42    """
43    Class to represent an ontology term and its subclasses
44    """
45
46    def __init__(self, term_id: str, name: str):
47        self._term_id = term_id
48        self._name = name
49        self._children: List["OntologyNode"] = []
50        self._term_counter: Counter[str] = Counter({self.term_id: 1})
51
52    @property
53    def term_id(self) -> str:
54        """
55        Ontology term ID represented by this OntologyNode.
56        """
57        return self._term_id
58
59    @property
60    def name(self) -> str:
61        """
62        Human-readable label for ontology term represented by this OntologyNode.
63        """
64        return self._name
65
66    @property
67    def children(self) -> List["OntologyNode"]:
68        """
69        List of children OntologyNode of this OntologyNode.
70        """
71        return self._children
72
73    @property
74    def term_counter(self) -> Counter[str]:
75        """
76        Mapping of unique ontology term ID descendants of this OntologyNode to the number of times each term
77        appears in the graph rooted at this node.
78        :return:
79        """
80        return self._term_counter
81
82    def add_child(self, child: "OntologyNode") -> None:
83        self._children.append(child)
84        self._term_counter.update(child.term_counter)
85
86    def to_dict(self) -> Dict[str, Any]:
87        return {
88            "term_id": self.term_id,
89            "name": self.name,
90            "children": [child.to_dict() for child in self.children],
91        }