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medcat.cdb.concepts

Classes:

Functions:

CUIInfo

Bases: TypedDict

Attributes:

average_confidence instance-attribute 

average_confidence: float

context_vectors instance-attribute 

context_vectors: Optional[dict[str, ndarray]]

count_train instance-attribute 

count_train: int

cui instance-attribute 

cui: str

description instance-attribute 

description: Optional[str]

group instance-attribute 

group: Optional[str]

in_other_ontology instance-attribute 

in_other_ontology: Optional[set[str]]

names instance-attribute 

names: set[str]

original_names instance-attribute 

original_names: Optional[set[str]]

preferred_name instance-attribute 

preferred_name: str

subnames instance-attribute 

subnames: set[str]

tags instance-attribute 

tags: Optional[list[str]]

type_ids instance-attribute 

type_ids: set[str]

NameInfo

Bases: TypedDict

Attributes:

count_train instance-attribute 

count_train: int

is_upper instance-attribute 

is_upper: bool

name instance-attribute 

name: str

per_cui_status instance-attribute 

per_cui_status: dict[str, str]

TypeInfo dataclass 

TypeInfo(type_id: str, name: str, cuis: set[str] = set())

Represents all the info regarding a type ID.

Attributes:

cuis class-attribute instance-attribute 

cuis: set[str] = field(default_factory=set)

name instance-attribute 

name: str

type_id instance-attribute 

type_id: str

get_new_cui_info 

get_new_cui_info(cui: str, preferred_name: str, names: set[str] = set(), subnames: set[str] = set(), type_ids: set[str] = set(), description: Optional[str] = None, original_names: Optional[set[str]] = None, tags: Optional[list[str]] = None, group: Optional[str] = None, in_other_ontology: Optional[set[str]] = None, count_train: int = 0, context_vectors: Optional[dict[str, ndarray]] = None, average_confidence: float = 0.0) -> CUIInfo
Source code in medcat-v2/medcat/cdb/concepts.py 
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def get_new_cui_info(cui: str, preferred_name: str,
                     names: set[str] = set(),
                     subnames: set[str] = set(),
                     type_ids: set[str] = set(),
                     description: Optional[str] = None,
                     original_names: Optional[set[str]] = None,
                     tags: Optional[list[str]] = None,
                     group: Optional[str] = None,
                     in_other_ontology: Optional[set[str]] = None,
                     count_train: int = 0,
                     context_vectors: Optional[dict[str, np.ndarray]] = None,
                     average_confidence: float = 0.0) -> CUIInfo:
    return {
        'cui': cui,
        'preferred_name': preferred_name,
        'names': names or names.copy(),
        'subnames': subnames or subnames.copy(),
        'type_ids': type_ids or type_ids.copy(),
        'description': description,
        'original_names': original_names,
        'tags': tags,
        'group': group,
        'in_other_ontology': in_other_ontology,
        'count_train': count_train,
        'context_vectors': context_vectors,
        'average_confidence': average_confidence
    }

get_new_name_info 

get_new_name_info(name: str, per_cui_status: dict[str, str] = {}, is_upper: bool = False, count_train: int = 0) -> NameInfo
Source code in medcat-v2/medcat/cdb/concepts.py 
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def get_new_name_info(name: str,
                      per_cui_status: dict[str, str] = {},
                      is_upper: bool = False,
                      count_train: int = 0) -> NameInfo:
    return {
        'name': name,
        'per_cui_status': per_cui_status or per_cui_status.copy(),
        'is_upper': is_upper,
        'count_train': count_train
    }

reset_cui_training 

reset_cui_training(cui_info: CUIInfo) -> None
Source code in medcat-v2/medcat/cdb/concepts.py 
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def reset_cui_training(cui_info: CUIInfo) -> None:
    cui_info['context_vectors'] = None
    cui_info['count_train'] = 0
    cui_info['average_confidence'] = 0