Ronald B. Wilkinson

Unable to serialize medspacy Doc object that contains Sections

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Trying to serialize medspacy documents using the SpaCy doc.to_bytes() or doc_bin.add() methods fails when the doc contains Sections. The error message is: TypeError: can not serialize 'Section' object My understanding...

Trying to save a model using the serialization methods nlp.to_disk or nlp.to_bytes fails if one of the model components is the medspacy_sectionizer. In particular, these serialization methods make use of...

medspacy QuickUMLS syntax

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With the version of MedSpacy prior to support of the SpaCy 3 use of pipe names to add pipes, I used the following syntax to add a QuickUMLS pipe with...

Incorrect matching of subsections with parent sections

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Hello Alec, Your post processing suggestion took care of that problem. However, I believe I have found a problem that is more fundamental. Attached is a Notebook in which I...

Why does this warning suppression code not work?

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I have some section rules where where two distinct literals map to a single category and that common category is the parent of some subcategories. The Sectionizer allows this but...

Making a pattern match conditional on the Section in which it is found.

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I would like the text "Qual" to be flagged as "qualitative lab result" only if the text occurs in a Section with the section_category "lab_results". The TargetMatcher pattern I tried...

Would like suggestion for implementing (if necessary, an equivalent to) overlapping entities

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The following text is a fragment of a clinical note: "HEENT: Tympanic membranes are normal bilaterally. Oropharynx is normal, no exudate no erythema. Neck is supple no anterior cervical lymphadenopathy....

How to break out section_parent attributes with DocConsumer?

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Specifying the section_parent attribute for ents in DocConsumer results in a table in which all the attributes of the section_parent are listed in one cell.   Is there a...

As of SpaCy v3.3, displacy can visualize Span Groups, so this feature can be added to MedSpaCy

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The MedSpaCy notebook on Span Groups says that SpaCy's displacy does not support Span Groups, which is why MedSpacy's visualizers which are built on displacy do not support them. Actually,...