eTRANSAFE Text-Mining Workshop

The eTRANSAFE Text-Mining workshop about identification and annotation of treatment-related findings in toxicological reports was held on October 15th, just before the 7th eTRANSAFE Consortium Meeting.

The workshop was organized at Barcelona Supercomputing Center by BSC/ELIXIR-ES and IMIM text mining teams. 24 people from 16 partners attended the workshop, which included the introduction of the WebAnno annotation tool and the annotations aligned with SEND terminology that can be carried out with this tool. The workshop participants annotated over 836 representative sentences from toxicological reports (kindly donated by Bayer, Sanofi, Servier and Eisai). Ultimate goal of the exercise is the development of an automated tool which extracts the treatment-related findings and provides them as a table for inclusion into the eTRANSAFE Knowledge Hub.

The workshop finished with a discussion about what can be trained and achieved through automated text-mining pipelines once a big enough representative set of sentences is properly annotated and used as training dataset. Several EFPIA representatives promised to provide further reports and it was concluded that the developed assets shall be presented at the mid-term review of the project.

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