v0.9.0

0.9.0 (2024-07-10)

Added

• Mantra GSC corpus for evaluation
• Loading and exporting InfoExtractionDataset as dictionaries or JSON files
• Metric support for multi-class qualifiers
• In the RuleBasedEntityMatcher, option to add terms as a dict (in addition to str, list and Term)
• In the RuleBasedEntityMatcher, option to add terms from dict (add_terms_from_dict), json (add_terms_from_json) or csv (add_terms_from_csv)
• In the Term class, an option to override arguments that were not set

Changed

• Moved regression test cases to data directory in more open format, so they are re-usable
• Made the default field for Qualifier optional
• InfoExtractionDataset and InfoExtractionMetrics use Qualifier objects for qualifiers rather than dict
• ❗ InfoExtractionDataset and InfoExtractionMetrics no longer track or use qualifier defaults
• Made qualifiers optional for metrics in Annotation
• Added a normalize method to Normalizer, so it can be used/tested directly
• The logic for determining whether the RuleBasedEntityMatcher should internally use the phrase matcher or the matcher is simplified

Deprecated

• ❗ The create_concept_dict method, which is now replaced by add_terms_from_csv in RuleBasedEntityMatcher
• ❗ In the RuleBasedEntityMatcher, the load_concepts method, which is now replaced by add_terms_from_dict and add_terms_from_json

v0.8.1

0.8.1 (2024-06-27)

Added

• Docstrings on all modules, classes, methods and functions

Changed

• In InformationExtractionDataset, renamed span_counts, label_counts and qualifier_counts to span_freqs, label_freqs and qualifier_freqs respectively.
• The clinlp_component utility now returns the class itself, rather than a helper function for making it
• Changed order of direction and qualifier arguments of ContextRule
• Simplified default settings for clinlp components and Term class
• Normalizer uses casefold rather than lower for normalizing text
• Parameterized spans_key for ie components

v0.8.0

0.8.0 (2024-06-03)

Changed

• ❗ Renamed the clinlp_entity_matcher to clinlp_rule_based_entity_matcher
• ❗ clinlp now stores entities in doc.spans['ents'] rather than doc.ents, allowing for overlap
  • ❗ Overlap in entities found by the entity matcher is no longer resolved by default (replacing old behaviour). To remove overlap, pass resolve_overlap=True.
• Refactored tests to use pytest best practices
• Changed clinlp_autocomponent to clinlp_component, which automatically registers your component with spaCy
• Codebase and linting improvements
• Renamed the other_threshold config to family_threshold in the clinlp_experiencer_transformer component

Fixed

• The clinlp_rule_based_entity_matcher no longer overwrites entities detected by other components (but appends them)

v0.7.0

0.7.0 (2024-05-16)

Added

• Integrated the clin_nlp_metrics package in this repository, specifically in clinlp.metrics.ie
• Support for non-binary qualifier in the Context Algorithm (e.g. 'Change', with values Decreasing, Stable and Increasing)
• Support for bidirectional qualifier patterns

Changed

• Moved all components related to information extraction to clinlp.ie. Please update imports accordingly (e.g. from clinlp.ie import Term).
• Updated the framework for qualifiers, to now have three qualifier classes: Presence, Temporality and Experiencer. For more details, see docs.

v0.6.6

0.6.6 (2024-04-24)

Added

• Support for Python 3.12

v0.6.5

0.6.5 (2024-02-13)

Added

• A component for transformer-based detection of Experiencer qualifiers (Patient/Other) (clinlp_experiencer_transformer)

v0.6.4

0.6.4 (2024-02-13)

Added

• A way to use a csv file as input for a conceptlist, using create_concept_dict

v0.6.3

0.6.3 (2024-01-18)

Fixed

• Fix a bug with termination trigger directly next to context trigger

v0.6.2

0.6.2 (2023-10-06)

Fixed

• replaced call to importlib.resources.path which is deprecated from python 3.11 on

v0.6.1

0.6.1 (2023-10-06)

Fixed

• a bug with adjacent entities, which were accidentally marked as overlapping