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ChEMU 2020: Natural Language Processing Methods Are Effective for Information Extraction From Chemical Patents.

ABSTRACT: 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.

SUBMITTER: He J

PROVIDER: S-EPMC8028406 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:BackgroundHealth researchers are increasingly using natural language processing (NLP) to study various mental health conditions using both social media and electronic health records (EHRs). There is currently no published synthesis that relates specifically to the use of NLP methods for bipolar disorder, and this scoping review was conducted to synthesize valuable insights that have been presented in the literature.ObjectiveThis scoping review explored how NLP methods have been used in research to better understand bipolar disorder and identify opportunities for further use of these methods.MethodsA systematic, computerized search of index and free-text terms related to bipolar disorder and NLP was conducted using 5 databases and 1 anthology: MEDLINE, PsycINFO, Academic Search Ultimate, Scopus, Web of Science Core Collection, and the ACL Anthology.ResultsOf 507 identified studies, a total of 35 (6.9%) studies met the inclusion criteria. A narrative synthesis was used to describe the data, and the studies were grouped into four objectives: prediction and classification (n=25), characterization of the language of bipolar disorder (n=13), use of EHRs to measure health outcomes (n=3), and use of EHRs for phenotyping (n=2). Ethical considerations were reported in 60% (21/35) of the studies.ConclusionsThe current literature demonstrates how language analysis can be used to assist in and improve the provision of care for people living with bipolar disorder. Individuals with bipolar disorder and the medical community could benefit from research that uses NLP to investigate risk-taking, web-based services, social and occupational functioning, and the representation of gender in bipolar disorder populations on the web. Future research that implements NLP methods to study bipolar disorder should be governed by ethical principles, and any decisions regarding the collection and sharing of data sets should ultimately be made on a case-by-case basis, considering the risk to the data participants and whether their privacy can be ensured.

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ChEMU 2020: Natural Language Processing Methods Are Effective for Information Extraction From Chemical Patents.

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