pubmad.types

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 0from datetime import datetime
 1from typing import Optional, List
 2from dataclasses import dataclass
 3
 4@dataclass
 5class Article:
 6    title: str
 7    abstract: Optional[str]
 8    full_text: Optional[str]
 9    pmid: str
10    publication_data: datetime
11
12
13class Entity:
14    '''
15    Entity defines a gene or a disease in a text.
16
17        Parameters
18
19            mesh_id (List[str]): List of Unique identifier for the entity, e.g. MESH:D001234. (You can use the MESH ID to look up the name of the entity in the MESH database.)
20            mention (str): The string that is associated with the entity in the text (e.g. "BRCA1").
21            type (str): The type of the entity. Can be 'gene' or 'disease'.
22            prob (float): The probability of the entity, it indicates the confidence of the model prediction.
23            span_begin (int): The begin of the span of the entity.
24            span_end (int): The end of the span of the entity.
25            article (Article): The article the entity is associated with.
26            source (str): The source of the entity within the article. Can be 'abstract' or 'full_text'. Defaults to 'abstract'.
27            pmid (str): The PubMed ID of the article.
28    '''
29    def __init__(self, mesh_id: List[str], mention: str, type: str, prob: float, span_begin: int, span_end: int, article: Article = None, source: str = 'abstract', pmid: str = ''):
30        self.mesh_id = mesh_id
31        self.mention = mention
32        self.type = type
33        self.prob = prob
34        self.span_begin = span_begin
35        self.span_end = span_end
36        self.article = article
37        self.source = source
38        self.pmid = pmid

@dataclass

class Article:

View Source

 5@dataclass
 6class Article:
 7    title: str
 8    abstract: Optional[str]
 9    full_text: Optional[str]
10    pmid: str
11    publication_data: datetime

Article(title: str, abstract: Optional[str], full_text: Optional[str], pmid: str, publication_data: datetime.datetime)

# Article( title: str, abstract: Optional[str], full_text: Optional[str], pmid: str, publication_data: datetime.datetime )

# class Entity:

View Source

14class Entity:
15    '''
16    Entity defines a gene or a disease in a text.
17
18        Parameters
19
20            mesh_id (List[str]): List of Unique identifier for the entity, e.g. MESH:D001234. (You can use the MESH ID to look up the name of the entity in the MESH database.)
21            mention (str): The string that is associated with the entity in the text (e.g. "BRCA1").
22            type (str): The type of the entity. Can be 'gene' or 'disease'.
23            prob (float): The probability of the entity, it indicates the confidence of the model prediction.
24            span_begin (int): The begin of the span of the entity.
25            span_end (int): The end of the span of the entity.
26            article (Article): The article the entity is associated with.
27            source (str): The source of the entity within the article. Can be 'abstract' or 'full_text'. Defaults to 'abstract'.
28            pmid (str): The PubMed ID of the article.
29    '''
30    def __init__(self, mesh_id: List[str], mention: str, type: str, prob: float, span_begin: int, span_end: int, article: Article = None, source: str = 'abstract', pmid: str = ''):
31        self.mesh_id = mesh_id
32        self.mention = mention
33        self.type = type
34        self.prob = prob
35        self.span_begin = span_begin
36        self.span_end = span_end
37        self.article = article
38        self.source = source
39        self.pmid = pmid

Entity defines a gene or a disease in a text.

Parameters

    mesh_id (List[str]): List of Unique identifier for the entity, e.g. MESH:D001234. (You can use the MESH ID to look up the name of the entity in the MESH database.)
    mention (str): The string that is associated with the entity in the text (e.g. "BRCA1").
    type (str): The type of the entity. Can be 'gene' or 'disease'.
    prob (float): The probability of the entity, it indicates the confidence of the model prediction.
    span_begin (int): The begin of the span of the entity.
    span_end (int): The end of the span of the entity.
    article (Article): The article the entity is associated with.
    source (str): The source of the entity within the article. Can be 'abstract' or 'full_text'. Defaults to 'abstract'.
    pmid (str): The PubMed ID of the article.

# Entity( mesh_id: List[str], mention: str, type: str, prob: float, span_begin: int, span_end: int, article: pubmad.types.Article = None, source: str = 'abstract', pmid: str = '' )

View Source

30    def __init__(self, mesh_id: List[str], mention: str, type: str, prob: float, span_begin: int, span_end: int, article: Article = None, source: str = 'abstract', pmid: str = ''):
31        self.mesh_id = mesh_id
32        self.mention = mention
33        self.type = type
34        self.prob = prob
35        self.span_begin = span_begin
36        self.span_end = span_end
37        self.article = article
38        self.source = source
39        self.pmid = pmid