medkit.text.context.family_detector#

Classes:

FamilyDetector(output_label[, rules, uid])

Annotator creating family attributes with boolean values indicating if a family reference has been detected.

FamilyDetectorRule(regexp[, ...])

Regexp-based rule to use with FamilyDetector

FamilyMetadata(_typename[, _fields])

Metadata dict added to family attributes with True value.
class FamilyDetector(output_label, rules=None, uid=None)[source]#

Annotator creating family attributes with boolean values indicating if a family reference has been detected.

Because family attributes will be attached to whole annotations, each input annotation should be “local”-enough rather than a big chunk of text (ie a sentence or a syntagma).

For detecting family references, the module uses rules that may be sensitive to unicode or not. When the rule is not sensitive to unicode, we try to convert unicode chars to the closest ascii chars. However, some characters need to be pre-processed before (e.g., n° -> number). So, if the text lengths are different, we fall back on initial unicode text for detection even if rule is not unicode-sensitive. In this case, a warning is logged for recommending to pre-process data.

Note that for better results, family detection should be run at the sentence level (ie on sentence segments) rather than at the syntagma level [1].

[1] N. Garcelon, A. Neuraz, V. Benoit, R. Salomon, A. Burgun, “Improving a full-text search engine: the importance of negation detection and family history context to identify cases in a biomedical data warehouse”, Journal of the American Medical Informatics Association, Volume 24, Issue 3, May 2017

Parameters

  • output_label (str) – The label of the created attributes

  • rules (Optional[List[FamilyDetectorRule]]) – The set of rules to use when detecting family references. If none provided, the rules in “family_detector_default_rules.yml” will be used

  • uid (str) – Identifier of the detector

Methods:

check_rules_sanity(rules)

Check consistency of a set of rules

load_rules(path_to_rules[, encoding])

Load all rules stored in a yml file

run(segments)

Add a family attribute to each segment with a boolean value indicating if a family reference has been detected.

save_rules(rules, path_to_rules[, encoding])

Store rules in a yml file

set_prov_tracer(prov_tracer)

Enable provenance tracing.

Attributes:

description

Contains all the operation init parameters.
run(segments)[source]#

Add a family attribute to each segment with a boolean value indicating if a family reference has been detected.

Family attributes with a True value have a metadata dict with fields described in FamilyMetadata.

Parameters

segments (List[Segment]) – List of segments to detect as being family references or not

static load_rules(path_to_rules, encoding=None)[source]#

Load all rules stored in a yml file

Parameters

  • path_to_rules (Path) – Path to a yml file containing a list of mappings with the same structure as FamilyDetectorRule

  • encoding (Optional[str]) – Encoding of the file to open

Return type

List[FamilyDetectorRule]

Returns

List[FamilyDetectorRule] – List of all the rules in path_to_rules, can be used to init a FamilyDetector

static check_rules_sanity(rules)[source]#

Check consistency of a set of rules

static save_rules(rules, path_to_rules, encoding=None)[source]#

Store rules in a yml file

Parameters

  • rules (List[FamilyDetectorRule]) – The rules to save

  • path_to_rules (Path) – Path to a .yml file that will contain the rules

  • encoding (Optional[str]) – Encoding of the .yml file

property description: medkit.core.operation_desc.OperationDescription#

Contains all the operation init parameters.

Return type

OperationDescription

set_prov_tracer(prov_tracer)#

Enable provenance tracing.

Parameters

prov_tracer (ProvTracer) – The provenance tracer used to trace the provenance.

class FamilyDetectorRule(regexp, exclusion_regexps=<factory>, id=None, case_sensitive=False, unicode_sensitive=False)[source]#

Regexp-based rule to use with FamilyDetector

Input text may be converted before detecting rule.

Parameters

  • regexp (str) – The regexp pattern used to match a family reference

  • exclusion_regexps (List[str]) – Optional exclusion patterns

  • id (Optional[str]) – Unique identifier of the rule to store in the metadata of the entities

  • case_sensitive (bool) – Whether to consider case when running regexp and `exclusion_regexs

  • unicode_sensitive (bool) – If True, rule matches are searched on unicode text. So, regexp and exclusion_regexps shall not contain non-ASCII chars because they would never be matched. If False, rule matches are searched on closest ASCII text when possible. (cf. FamilyDetector)

class FamilyMetadata(_typename, _fields=None, /, **kwargs)[source]#

Metadata dict added to family attributes with True value.

Parameters

rule_id (Union[str, int]) – Identifier of the rule used to detect a family reference. If the rule has no id, then the index of the rule in the list of rules is used instead.