modos.codes#

Utilities to automatically find / recommend terminology codes from text.

Attributes#

SLOT_TERMINOLOGIES

Classes#

`Code`
`CodeMatcher`	Base class for protocol classes.
`LocalCodeMatcher`	Find ontology codes for a given text by running a local term matcher.
`RemoteCodeMatcher`	Find ontology codes for a given text relying on a remote term matcher.

Functions#

`get_slot_matcher`(slot[, endpoint])	Instantiates a code matcher based on input slot name.
`get_slot_matchers`([endpoint])	Instantiates a code matcher for each slot. If the endpoint is provided, remote matchers are used.

Module Contents#

modos.codes.SLOT_TERMINOLOGIES[source]#

class modos.codes.Code[source]#

label: str[source]#

uri: str[source]#

class modos.codes.CodeMatcher[source]#

Bases: Protocol

Base class for protocol classes.

Protocol classes are defined as:

class Proto(Protocol):
    def meth(self) -> int:
        ...

Such classes are primarily used with static type checkers that recognize structural subtyping (static duck-typing), for example:

class C:
    def meth(self) -> int:
        return 0

def func(x: Proto) -> int:
    return x.meth()

func(C())  # Passes static type check

See PEP 544 for details. Protocol classes decorated with @typing.runtime_checkable act as simple-minded runtime protocols that check only the presence of given attributes, ignoring their type signatures. Protocol classes can be generic, they are defined as:

class GenProto(Protocol[T]):
    def meth(self) -> T:
        ...

endpoint: str | None[source]#

slot: str[source]#

top: int[source]#

find_codes(query)[source]#

Parameters:: query (str)
Return type:: list[Code]

class modos.codes.LocalCodeMatcher(slot, top=50)[source]#

Bases: CodeMatcher

Find ontology codes for a given text by running a local term matcher.

Parameters:

slot (str)
top (int)

endpoint = None[source]#

slot[source]#

top[source]#

sources[source]#

find_codes(query)[source]#

Parameters:: query (str)
Return type:: list[Code]

class modos.codes.RemoteCodeMatcher(slot, endpoint, top=50)[source]#

Bases: CodeMatcher

Find ontology codes for a given text relying on a remote term matcher.

Parameters:

slot (str)
endpoint (str)
top (int)

endpoint[source]#

slot[source]#

top[source]#

find_codes(query)[source]#

Parameters:: query (str)
Return type:: list[Code]

modos.codes.get_slot_matcher(slot, endpoint=None)[source]#

Instantiates a code matcher based on input slot name.

Parameters:

slot (str)
endpoint (Optional[str])

Return type:

CodeMatcher

modos.codes.get_slot_matchers(endpoint=None)[source]#

Instantiates a code matcher for each slot. If the endpoint is provided, remote matchers are used.

Parameters:: endpoint (Optional[str])
Return type:: dict[str, CodeMatcher]