Collaborative relation annotation and quality analysis in Markyt environment

Martín Pérez-Pérez, Gael Pérez-Rodríguez, Florentino Fdez-Riverola, Anália Lourenço
2017 Database: The Journal of Biological Databases and Curation  
Citation details: Pé rez-Pé rez,M., Pé rez-Rodríguez,G., Fdez-Riverola,F. et al. Collaborative relation annotation and quality analysis in Markyt environment. Abstract Text mining is showing potential to help in biomedical knowledge integration and discovery at various levels. However, results depend largely on the specifics of the knowledge problem and, in particular, on the ability to produce high-quality benchmarking corpora that may support the training and evaluation of automatic
more » ... systems. Annotation tools enabling the flexible and customizable production of such corpora are thus pivotal. The open-source Markyt annotation environment brings together the latest web technologies to offer a wide range of annotation capabilities in a domain-agnostic way. It enables the management of multi-user and multi-round annotation projects, including inter-annotator agreement and consensus assessments. Also, Markyt supports the description of entity and relation annotation guidelines on a project basis, being flexible to partial word tagging and the occurrence of annotation overlaps. This paper describes the current release of Markyt, namely new annotation perspectives, which enable the annotation of relations among entities, and enhanced analysis capabilities. Several demos, inspired by public biomedical corpora, are presented as means to better illustrate such functionalities. Markyt aims to bring together annotation capabilities of broad interest to those producing annotated corpora. Markyt demonstration projects describe 20 different annotation tasks of varied document sources (e.g. abstracts, twitters or drug labels) and languages (e.g. English, Spanish or Chinese). Continuous development is based on feedback from practical applications as well as community reports on shortand medium-term mining challenges. Markyt is freely available for non-commercial use at
doi:10.1093/database/bax090 pmid:29220479 pmcid:PMC5737204 fatcat:f7v2x5ge3rb3teckhmlpvcjs3y