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In addition, analysis of disagreement between two annotators showed that most of discrepancies were also from gene-related categories.
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As such, a disagreement between two annotators is recorded if both have marked up slightly different beginnings and endings.
The calculated Kappa score between two annotators was 0.837, which indicates a reasonable agreement between two annotators.
When comparing the annotation of entities between the two annotators, there is agreement if each annotator annotates the same entity: i.e., both the textual span (begin/end boundaries) of the annotated entity and the entity type match.
The initial annotation phase then involved the two annotators annotating five full articles, according to the Guidelines; the resulting annotated documents were examined for agreement between the annotators, and particularly for any differences in the way categories were filled.
After individual annotation, we collected all the discrepancies between the two annotators' results and presented them to the annotators.
During the harmonization process only the non-overlapping instances between the two annotators were investigated.
Inter-rater reliability was tested between the two annotators resulting in percentage agreement of 93.0% (Cohen's κ 0.85).
Disagreements between the two annotators were forwarded to a third physician adjudicator, who made the final decision regarding the conflicting annotations.
In the next step, the two annotators annotated 50 abstracts and the inter-annotator agreement was calculated.
There was a good to excellent agreement between the two annotators (kappa scores of 0.74 (95% CI 0.59-0.89) and 0.90 (95% CI 0.83-0.97) for the hepatobiliary and acute renal failure data sets, respectively).
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Justyna Jupowicz-Kozak
CEO of Professional Science Editing for Scientists @ prosciediting.com