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From Bonnie MacKellar <bkmackel...@gmail.com>
Subject XML files as input to UIMA?
Date Wed, 20 Feb 2019 00:13:55 GMT
This is probably a very naive question, but I can't seem to find anything
about this. I currently have a lot of XML files (clinical trial
descriptions). My current workflow is to run a preprocessor that parses the
XML and generates text files in a simple format. I then run these files in
a UIMA pipeline, using FileCollectionReader to load the text files, RUTA to
parse the simple format, the Metamap annotator to do some UMLS annotations,
and finally I have a writer that generates RDF triples from the UMIA
annotations and loads the triples into a database. This has worked but is
clunky, especially the preprocessing. I feel like there has to be a better
way. Is there any support for reading XML files  or do I need to write my
own CollectionReader? Are there any other tools within UIMA for handling
XML text?

Bonnie MacKellar

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