Skip to content

HpoConceptRecognizer

This abstract class acts as an interface for classes that implement parse_cell to perform HPO-based concept recognition.

Source code in pyphetools/creation/hpo_cr.py 
 7
 8
 9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
55
56
57
58
59
60
61
62
class HpoConceptRecognizer(metaclass=abc.ABCMeta):
    """
    This abstract class acts as an interface for classes that implement parse_cell to perform HPO-based concept recognition.
    """

    @abc.abstractmethod
    def parse_cell(self, cell_contents, custom_d=None) -> List[HpTerm]:
        """
        parse HPO Terms from the contents of a cell of the original table

        :param cell_contents: a cell of the original table
        :type cell_contents: str
        :param custom_d: a dictionary with keys for strings in the original table and their mappings to HPO labels
        :type custom_d: Dict[str,str], optional
        """
        pass


    @abc.abstractmethod
    def parse_cell_for_exact_matches(self, cell_contents, custom_d) -> List[HpTerm]:
        """
        Identify HPO Terms from the contents of a cell whose label exactly matches a string in the custom dictionary

        :param cell_contents: a cell of the original table
        :type cell_contents: str
        :param custom_d: a dictionary with keys for strings in the original table and their mappings to HPO labels
        :type custom_d: Dict[str,str]
        """
        pass

    @abc.abstractmethod
    def get_term_from_id(self, hpo_id) -> HpTerm:
        """
        :param hpo_id: an HPO identifier, e.g., HP:0004372
        :type hpo_id: str
        :returns: corresponding HPO term
        :rtype: HpTerm
        """
        pass

    @abc.abstractmethod
    def get_term_from_label(self, label) -> HpTerm:
        """
        :param label: an HPO label, e.g., Arachnodactyly
        :type label: str
        :returns: corresponding HPO term
        :rtype: HpTerm
        """
        pass

    @abc.abstractmethod
    def initialize_simple_column_maps(self, column_name_to_hpo_label_map, observed, excluded, non_measured=None):
        """
        Create a dictionary of SimpleColumnMappers
        """
        pass

get_term_from_id(hpo_id) abstractmethod

Parameters:

Name Type Description Default
hpo_id str

an HPO identifier, e.g., HP:0004372

 required

Returns:

Type Description
HpTerm

corresponding HPO term
Source code in pyphetools/creation/hpo_cr.py 
37
38
39
40
41
42
43
44
45
@abc.abstractmethod
def get_term_from_id(self, hpo_id) -> HpTerm:
    """
    :param hpo_id: an HPO identifier, e.g., HP:0004372
    :type hpo_id: str
    :returns: corresponding HPO term
    :rtype: HpTerm
    """
    pass

get_term_from_label(label) abstractmethod

Parameters:

Name Type Description Default
label str

an HPO label, e.g., Arachnodactyly

 required

Returns:

Type Description
HpTerm

corresponding HPO term
Source code in pyphetools/creation/hpo_cr.py 
47
48
49
50
51
52
53
54
55
@abc.abstractmethod
def get_term_from_label(self, label) -> HpTerm:
    """
    :param label: an HPO label, e.g., Arachnodactyly
    :type label: str
    :returns: corresponding HPO term
    :rtype: HpTerm
    """
    pass

initialize_simple_column_maps(column_name_to_hpo_label_map, observed, excluded, non_measured=None) abstractmethod

Create a dictionary of SimpleColumnMappers

Source code in pyphetools/creation/hpo_cr.py 
57
58
59
60
61
62
@abc.abstractmethod
def initialize_simple_column_maps(self, column_name_to_hpo_label_map, observed, excluded, non_measured=None):
    """
    Create a dictionary of SimpleColumnMappers
    """
    pass

parse_cell(cell_contents, custom_d=None) abstractmethod

parse HPO Terms from the contents of a cell of the original table

Parameters:

Name Type Description Default
cell_contents str

a cell of the original table

 required
custom_d Dict[str,str], optional

a dictionary with keys for strings in the original table and their mappings to HPO labels

 None
Source code in pyphetools/creation/hpo_cr.py 
12
13
14
15
16
17
18
19
20
21
22
@abc.abstractmethod
def parse_cell(self, cell_contents, custom_d=None) -> List[HpTerm]:
    """
    parse HPO Terms from the contents of a cell of the original table

    :param cell_contents: a cell of the original table
    :type cell_contents: str
    :param custom_d: a dictionary with keys for strings in the original table and their mappings to HPO labels
    :type custom_d: Dict[str,str], optional
    """
    pass

parse_cell_for_exact_matches(cell_contents, custom_d) abstractmethod

Identify HPO Terms from the contents of a cell whose label exactly matches a string in the custom dictionary

Parameters:

Name Type Description Default
cell_contents str

a cell of the original table

 required
custom_d Dict[str,str]

a dictionary with keys for strings in the original table and their mappings to HPO labels

 required
Source code in pyphetools/creation/hpo_cr.py 
25
26
27
28
29
30
31
32
33
34
35
@abc.abstractmethod
def parse_cell_for_exact_matches(self, cell_contents, custom_d) -> List[HpTerm]:
    """
    Identify HPO Terms from the contents of a cell whose label exactly matches a string in the custom dictionary

    :param cell_contents: a cell of the original table
    :type cell_contents: str
    :param custom_d: a dictionary with keys for strings in the original table and their mappings to HPO labels
    :type custom_d: Dict[str,str]
    """
    pass