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Utilities for health informatics

Project description


A collection of utilities for health informatics

This is pre-alpha, anything might change, i.e. not ready for production use.

Application areas

Text annotation / NLP


Knowledge graphs

Statistics / summary data


pip install hiutils



We assume that annotations are in the format:

	document_id: {
		entities: {
			entitiy_id: {,
				cui : "concept_id",
				meta_anns: {
					'meta_ann_name': {'value': 'meta_ann_value',
					'confidence': confidence,
					'name': 'meta_ann_name'},
					...other meta...


Basic process

The aim is to:

  1. keep only some annotations based on context
  2. convert from document->concepts to patient->concepts
  3. limit to a subset of concepts relevant to our project
  4. group some specific concepts into more general concepts e.g. specific subtypes of a disease -> any occurence of a that disease

To achieve these aims:

  • 1 filter by meta_anns:
filtered = hi.annotations.filter_anns_meta(anns, {'Subject': ['Other']}, inplace=False)
  • 2 aggregate to patient level
agg = hi.annotations.aggregate_docs(filtered, item2doc=pt2doc)
  • 3+4 group relevant concepts and drop other concepts
groups = {'Group 1': set(['286933003', '70582006']), 'My other group': set(['60046008'])}
merged = hi.merge_concepts(agg, groups, keep_empty=False)

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