Entity recognition in parallel multi-lingual biomedical corpora: the CLEF-ER laboratory overview

Dietrich Rebholz-Schuhmann, Simon Clematide, Fabio Rinaldi, Senay Kafkas, Erik M. van Mulligen, Chinh Bui, Johannes Hellrich, Ian Lewin, David Milward, Michael Poprat, Antonio Jimeno-Yepes, Udo Hahn, Jan A. Kors

Lecture Notes in Computer Science. 2013; 8138:353-367




The identification and normalisation of biomedical entities from the scientific literature has a long tradition and a number of challenges have contributed to the development of reliable solutions. Increasingly patient records are processed to align their content with other biomedical data resources, but this approach requires analysing documents in different languages across Europe [1,2].  The CLEF-ER challenge has been organized by the Mantra project partners to improve entity recognition (ER) in multilingual documents. Several corpora in different languages, i.e. Medline titles, EMEA documents and patent claims, have been prepared to enable ER in parallel documents.

The participants have been ask to annotate entity mentions with concept unique identifiers (CUIs) in the documents of their preferred non-English language. 

The evaluation determines the number of correctly identified entity mentions against a silver standard (Task A) and the performance measures for the identification of CUIs in the non-English corpora. The participants could make use of the prepared terminological resources for entity normalisation and of the English silver standard corpora (SSCs) as input for concept candidates in the non-English documents.  The participants used different approaches including translation techniques and word or phrase alignments apart from lexical lookup and other text mining techniques. The performances for task A and B was lower for the patent corpus in comparison to Medline titles and EMEA documents.

In the patent documents, chemical entities were identified at higher performance, whereas the other two document types cover a higher portion of medical terms. The number of novel terms provided from all corpora is currently under investigation.  Altogether, the CLEF-ER challenge demonstrates the performances of annotation solutions in different languages against an SSC.