An annotated corpus of clinical trial publications supporting schema-based relational information extraction

Background: The evidence-based medicine paradigm requires the ability to aggregate and compare outcomes of interventions across different trials. This can be facilitated and partially automatized by information extraction systems. In order to support the development of systems that can extract information from published clinical trials at a fine-grained and comprehensive level to populate a knowledge base, we present a richly annotated corpus at two levels. At the first level, entities that describe components of the PICO elements (e.g., population's age and pre-conditions, dosage of a treatment, etc.) are annotated. The second level comprises schema-level (i.e., slot-filling templates) annotations corresponding to complex PICO elements and other concepts related to a clinical trial (e.g. the relation between an intervention and an arm, the relation between an outcome and an intervention, etc.).

Results: The final corpus includes 211 annotated clinical trial abstracts with substantial agreement between annotators at the entity and scheme level. The mean Kappa value for the glaucoma and T2DM corpora was 0.74 and 0.68, respectively, for single entities. The micro-averaged F1 score to measure inter-annotator agreement for complex entities (i.e. slot-filling templates) was 0.81.The BERT-base baseline method for entity recognition achieved average micro- F1 scores of 0.76 for glaucoma and 0.77 for diabetes with exact matching.

Conclusions: In this work, we have created a corpus that goes beyond the existing clinical trial corpora, since it is annotated in a schematic way that represents the classes and properties defined in an ontology. Although the corpus is small, it has fine-grained annotations and could be used to fine-tune pre-trained machine learning models and transformers to the specific task of extracting information about clinical trial abstracts.For future work, we will use the corpus for training information extraction systems that extract single entities, and predict template slot-fillers (i.e., class data/object properties) to populate a knowledge base that relies on the C-TrO ontology for the description of clinical trials. The resulting corpus and the code to measure inter-annotation agreement and the baseline method are publicly available at https://zenodo.org/record/6365890.