Title
An Extended Overview of the CLEF 2020 ChEMU Lab: Information Extraction of Chemical Reactions from Patents
Date Issued
01 January 2020
Access level
metadata only access
Resource Type
conference paper
Author(s)
He J.
Nguyen D.Q.
Akhondi S.A.
Druckenbrodt C.
Thorne C.
Hoessel R.
Afzal Z.
Zhai Z.
Fang B.
Yoshikawa H.
Albahem A.
Wang J.
Ren Y.
Zhang Z.
Zhang Y.
Dao M.H.
Ruas P.
Lamurias A.
Couto F.M.
Naderi N.
Knafou J.
Ruch P.
Teodoro D.
Lowe D.
Mayfield J.
Köksal A.
Dönmez H.
Özkırımlı E.
Özgür A.
Mahendran D.
Gurdin G.
Lewinski N.
Tang C.
McInnes B.T.
Malarkodi C.S.
Rao P.R.K.
Devi S.L.
Cavedon L.
Cohn T.
Baldwin T.
Verspoor K.
Uni. of Applied Sciences & Arts of Western Switzerland
Publisher(s)
CEUR-WS
Abstract
The discovery of new chemical compounds is perceived as a key driver of the chemistry industry and many other economic sectors. The information about the new discoveries are usually disclosed in scientific literature and in particular, in chemical patents, since patents are often the first venues where the new chemical compounds are publicized. Despite the significance of the information provided in chemical patents, extracting the information from patents is costly due to the large volume of existing patents and its drastic expansion rate. The Cheminformatics Elsevier Melbourne University (ChEMU) evaluation lab 2020, part of the Conference and Labs of the Evaluation Forum 2020 (CLEF2020), provides a platform to advance the state-of-the-arts in automatic information extraction systems over chemical patents. In particular, we focus on extracting synthesis process of new chemical compounds from chemical patents. Using the ChEMU corpus of 1500 “snippets” (text segments) sampled from 170 patent documents and annotated by chemical experts, we defined two key information extraction tasks. Task 1 targets at chemical named entity recognition, i.e., the identification of chemical compounds and their specific roles in chemical reactions. Task 2 targets at event extraction, i.e., the identification of reaction steps, relating the chemical compounds involved in a chemical reaction. In this paper, we provide an overview of our ChEMU2020 lab. Herein, we describe the resources created for the two tasks, the evaluation methodology adopted, and participants results. We also provide a brief summary of the methods employed by participants of this lab and the results obtained across 46 runs from 11 teams, finding that several submissions achieve substantially better results than the baseline methods prepared by the organizers.
Volume
2696
Language
English
OCDE Knowledge area
Química Ingeniería de sistemas y comunicaciones
Scopus EID
2-s2.0-85121760827
ISSN of the container
16130073
Conference
CEUR Workshop Proceedings
Sponsor(s)
We are grateful for the detailed excerption and annotation work of the domain experts that support Reaxys, and the support of Ivan Krstic, Director of Chemistry Solutions at Elsevier. Funding for the ChEMU project is provided by an Australian Research Council Linkage Project, project number LP160101469, and Elsevier.
Sources of information: Directorio de Producción Científica Scopus