5.1.0

This release adds the ability to query the termexists cNLP transformer when listing polarity. It's another polarity model that's similar to the default negation model, but may be a bit better.

The model can be installed from docker hub.

Set URL_CNLP_TERM_EXISTS to point at the correct endpoint (defaults to http://localhost:8000/termexists/process).

Use it like so:

from ctakesclient.transformer import TransformerModel, list_polarity

list_polarity(text, spans, model=TransformerModel.TERM_EXISTS)

5.0.0

Whoops, one more tweak to the ICD10 codes, with another major version bump with it.

4.0.0

No Python changes, but the ICD10 list for covid symptoms has been modified. So just be aware of that before you upgrade, as it may affect clinical results based on it.

3.0.0

A few breaking changes in this major release:

• Support for Python 3.7 has been dropped (slightly before it goes end-of-life)
• All network calls have been changed to be async methods. Specifically, the following API calls are now async:
  • client.post
  • client.extract
  • transformer.list_polarity
  • transformer.map_polarity

These new async calls also take an optional client kwarg parameter, to provide an existing
httpx.AsyncClient session.

2.1.1

Fixes accidentally duplicating CUI codes in text2fhir output.

2.1.0

Add filesystem.covid_symptoms_path() and filesystem.umls_semantic_groups_path() to get direct access to the .bsv files for each.

2.0.0

Drops support for Python 3.6 and adds a new ctakesclient.text2fhir.nlp_fhir method that returns all FHIR resources found in a cTAKES response

1.3.1

Updates the covid symptoms dictionary to include SOB (shortness of breath) and some other fixes

1.3.0

Adds a new submodule ctakesclient.text2fhir which holds some methods for converting from MatchText to FHIR resources (for example, converting cTAKES symptoms to FHIR Observations).

1.2.0

New API

• ctakesclient.filesystem.covid_symptoms() -> List[BsvConcept]

  • Returns a list of known covid symptoms

• ctakesclient.filesystem.umls_semantic_groups() -> List[BsvSemanticType]

  • Returns a list of UMLS semantic groups

Changed API

• ctakesclient.filesystem.map_cui_pref()
  • now accepts either a string or a list of BsvConcepts (previously it only accepted a filename string). This is to make it easier to use with the above new API.

Features

• polarity-diff-report now has a --mention argument that lets you filter by certain kinds of mentions (e.g. --mention=DiseaseDisorderMention)

Fixes

• Non-latin1 characters in physician notes no longer throws an exception
• An exception is now thrown if there was an error talking to the cTAKES or cNLP servers