In specialized domains that require expert annotators and high inter-annotator agreement, high-quality datasets with span-bound semantic concept annotations remain expensive to develop. Substantial resources are typically spent on unitizing, the task of identifying precise span boundaries for entity mentions. Unitizing is a significant source of inter-annotator disagreement, a poor use of expensive domain expertise, and very time-consuming. We propose a lighter annotation procedure that concentrates manual efforts on typed position annotations, marking positions in the text that overlap with mentions of each entity type, abstracting away span boundary decisions. With as few as 100-200 example sentences, we train span boundary detection models to unitize typed position annotations. Through evaluation over three datasets: CRAFT (biomedical), GENIA (molecular biology), and POLIANNA (climate/energy policy text), we demonstrate that (1) annotating typed positions in the text instead of full concept annotation is a more efficient use of time in low-resource settings, and (2) model-inferred span boundaries result in higher agreement at both the annotator training and corpus annotation phases, without sacrificing utility.

As part of the BioNLP Open Shared Tasks 2019, the CRAFT Shared Tasks 2019 provides a platform to gauge the state of the art for three fundamental language processing tasks — dependency parse construction, coreference resolution, and ontology concept identification — over full-text biomedical articles. The structural annotation task requires the automatic generation of dependency parses for each sentence of an article given only the article text. The coreference resolution task focuses on linking coreferring base noun phrase mentions into chains using the symmetrical and transitive identity relation. The ontology concept annotation task involves the identification of concept mentions within text using the classes of ten distinct ontologies in the biomedical domain, both unmodified and augmented with extension classes. This paper provides an overview of each task, including descriptions of the data provided to participants and the evaluation metrics used, and discusses participant results relative to baseline performances for each of the three tasks.