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In the trial descriptions from clinicaltrials.gov, eligibility criteria are provided in free text sentences.
Zhang et al. recently reported on their subtree match method, which finds structural patterns in free text sentences and thus allows to find similar sentences in other documents [ 27].
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All logical relations between these characteristics as stated in the criterion's original free text sentence were discarded in this process.
It should be stressed that ICD-10 codes, i.e. possible free-text sentences that mention an ICD-10 code, are not included in the queries when conducting the experiment.
Then two researchers (SL, MB) independently analyzed each free text answer sentence by sentence and coded line by line according to qualitative content analysis [ 17].
Additionally, we performed a free text query, using the whole sentence as input into the tools repository, in order to compare the automated results of our system to those obtained with a full text query (a complete list of the full text results can be found in Additional file 1: Table S2).
Syntactic parsing is a critical component of BioNLP applications that rely on correctly determining the sentence and phrase structure of free text.
This includes that sentences mentioning ICD-10 codes in free text are excluded from the query episodes.
They also randomly selected 200 sentences from recently published books, gathered from free text on Amazon.com.
For each relevant section of the EHR, CDAPubMed analyzes the content using an NLP package, i.e., OpenNLP [ 32], extracting sentences and words (or tokens) from the free text content.
Similar to the other models/methods, all of the free text in the query episode, excluding the discharge summary and any sentence mentioning ICD-10 codes, served as the query string provided to Lucene.
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