MetaTron: advancing biomedical annotation empowering relation annotation and collaboration.

ABSTRACT

BACKGROUND: The constant growth of biomedical data is accompanied by the need for new methodologies to effectively and efficiently extract machine-readable knowledge for training and testing purposes. A crucial aspect in this regard is creating large, often manually or semi-manually, annotated corpora vital for developing effective and efficient methods for tasks like relation extraction, topic recognition, and entity linking. However, manual annotation is expensive and time-consuming especially if not assisted by interactive, intuitive, and collaborative computer-aided tools. To support healthcare experts in the annotation process and foster annotated corpora creation, we present MetaTron. MetaTron is an open-source and free-to-use web-based annotation tool to annotate biomedical data interactively and collaboratively; it supports both mention-level and document-level annotations also integrating automatic built-in predictions. Moreover, MetaTron enables relation annotation with the support of ontologies, functionalities often overlooked by off-the-shelf annotation tools. RESULTS: We conducted a qualitative analysis to compare MetaTron with a set of manual annotation tools including TeamTat, INCEpTION, LightTag, MedTAG, and brat, on three sets of criteria technical, data, and functional. A quantitative evaluation allowed us to assess MetaTron performances in terms of time and number of clicks to annotate a set of documents. The results indicated that MetaTron fulfills almost all the selected criteria and achieves the best performances. CONCLUSIONS: MetaTron stands out as one of the few annotation tools targeting the biomedical domain supporting the annotation of relations, and fully customizable with documents in several formats-PDF included, as well as abstracts retrieved from PubMed, Semantic Scholar, and OpenAIRE. To meet any user need, we released MetaTron both as an online instance and as a Docker image locally deployable.