kazu.ontology_preprocessing.autocuration¶

Functions

`initial_lowercase_then_upper_to_case_sensitive`(...)	If a synonym starts with a lowercase character followed by an uppercase character, then all synonyms should be case-sensitive.
`is_upper_case_word_to_case_insensitive`(resource)	Make Resources where all original synonyms are all uppercase alphabetical characters case-insensitive.
`multiword`(resource)	If any synonym has more than one words, it's likely a noun phase and we should mark all synonyms PROBABLE.

Classes

`AutoCurationAction`
`AutoCurator`
`IsCommmonWord`
`LikelyAcronym`	If all synonyms are less than or equal to the specified length, and are all upper case, give a confidence of POSSIBLE to all forms.
`MaxLength`	Drop resources that exceed a maximum string length.
`MinLength`
`SymbolicToCaseSensitiveAction`

class kazu.ontology_preprocessing.autocuration.AutoCurationAction[source]¶

Bases: Protocol

__call__(resource)[source]¶

Call self as a function.

Parameters:: resource (OntologyStringResource)
Return type:: OntologyStringResource

__init__(*args, **kwargs)[source]¶

class kazu.ontology_preprocessing.autocuration.AutoCurator[source]¶

Bases: object

__call__(resources)[source]¶

Call self as a function.

Parameters:: resources (set[OntologyStringResource])
Return type:: Iterable[OntologyStringResource]

__init__(actions)[source]¶

Parameters:: actions (list[AutoCurationAction])
Return type:: None

class kazu.ontology_preprocessing.autocuration.IsCommmonWord[source]¶

Bases: AutoCurationAction

__call__(resource)[source]¶

Call self as a function.

Parameters:: resource (OntologyStringResource)
Return type:: OntologyStringResource

__init__(path)[source]¶

Parameters:: path (str)
Return type:: None

class kazu.ontology_preprocessing.autocuration.LikelyAcronym[source]¶

Bases: AutoCurationAction

If all synonyms are less than or equal to the specified length, and are all upper case, give a confidence of POSSIBLE to all forms.

__call__(resource)[source]¶

Call self as a function.

Parameters:: resource (OntologyStringResource)
Return type:: OntologyStringResource

__init__(max_len_to_consider=5)[source]¶

Parameters:: max_len_to_consider (int)
Return type:: None

class kazu.ontology_preprocessing.autocuration.MaxLength[source]¶

Bases: AutoCurationAction

Drop resources that exceed a maximum string length.

__call__(resource)[source]¶

Call self as a function.

Parameters:: resource (OntologyStringResource)
Return type:: OntologyStringResource

__init__(max_len=60)[source]¶

Parameters:: max_len (int)
Return type:: None

class kazu.ontology_preprocessing.autocuration.MinLength[source]¶

Bases: AutoCurationAction

__call__(resource)[source]¶

Call self as a function.

Parameters:: resource (OntologyStringResource)
Return type:: OntologyStringResource

__init__(min_len=2)[source]¶

Parameters:: min_len (int)
Return type:: None

class kazu.ontology_preprocessing.autocuration.SymbolicToCaseSensitiveAction[source]¶

Bases: AutoCurationAction

__call__(resource)[source]¶

Call self as a function.

Parameters:: resource (OntologyStringResource)
Return type:: OntologyStringResource

__init__(entity_class)[source]¶

Parameters:: entity_class (str)
Return type:: None

kazu.ontology_preprocessing.autocuration.initial_lowercase_then_upper_to_case_sensitive(resource)[source]¶

If a synonym starts with a lowercase character followed by an uppercase character, then all synonyms should be case-sensitive.

E.g. “eGFR” vs “EGFR”.

Parameters:: resource (OntologyStringResource)
Returns:
Return type:: OntologyStringResource

kazu.ontology_preprocessing.autocuration.is_upper_case_word_to_case_insensitive(resource)[source]¶

Make Resources where all original synonyms are all uppercase alphabetical characters case-insensitive.

Some data sources use all-caps strings for nouns that can be considered case- insensitive (e.g. Chembl).

Parameters:: resource (OntologyStringResource)
Returns:
Return type:: OntologyStringResource

kazu.ontology_preprocessing.autocuration.multiword(resource)[source]¶

If any synonym has more than one words, it’s likely a noun phase and we should mark all synonyms PROBABLE.

Parameters:: resource (OntologyStringResource)
Returns:
Return type:: OntologyStringResource