We introduce a new evaluation lab named ChEMU (Cheminformatics Elsevier Melbourne University), part of the 11th Conference and Labs of the Evaluation Forum (CLEF-2020). ChEMU involves two key information extraction tasks over chemical reactions from patents. Task 1-Named entity recognition-involves identifying chemical compounds as well as their types in context, i.e., to assign the label of a chemical compound according to the role which the compound plays within a chemical reaction. Task 2-Event extraction over chemical reactions-involves event trigger detection and argument recognition. We briefly present the motivations and goals of the ChEMU tasks, as well as resources and evaluation methodology.
Chemical patents represent a valuable source of information about new chemical compounds, which is critical to the drug discovery process. Automated information extraction over chemical patents is, however, a challenging task due to the large volume of existing patents and the complex linguistic properties of chemical patents. The Cheminformatics Elsevier Melbourne University (ChEMU) evaluation lab 2020, part of the Conference and Labs of the Evaluation Forum 2020 (CLEF2020), was introduced to support the development of advanced text mining techniques for chemical patents. The ChEMU 2020 lab proposed two fundamental information extraction tasks focusing on chemical reaction processes described in chemical patents: (1) chemical named entity recognition, requiring identification of essential chemical entities and their roles in chemical reactions, as well as reaction conditions; and (2) event extraction, which aims at identification of event steps relating the entities involved in chemical reactions. The ChEMU 2020 lab received 37 team registrations and 46 runs. Overall, the performance of submissions for these tasks exceeded our expectations, with the top systems outperforming strong baselines. We further show the methods to be robust to variations in sampling of the test data. We provide a detailed overview of the ChEMU 2020 corpus and its annotation, showing that inter-annotator agreement is very strong. We also present the methods adopted by participants, provide a detailed analysis of their performance, and carefully consider the potential impact of data leakage on interpretation of the results. The ChEMU 2020 Lab has shown the viability of automated methods to support information extraction of key information in chemical patents.
We present COVID-SEE, a system for medical literature discovery based on the concept of information exploration, which builds on several distinct text analysis and natural language processing methods to structure and organise information in publications, and augments search through a visual overview of a collection enabling exploration to identify key articles of interest. We developed this system over COVID-19 literature to help medical professionals and researchers explore the literature evidence, and improve findability of relevant information. COVID-SEE is available at http://covid-see.com.
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