The medical concept normalisation task aims to map textual descriptions to standard terminologies such as SNOMED-CT or MedDRA. Existing publicly available datasets annotated using different terminologies cannot be simply merged and utilised, and therefore become less valuable when developing machine learning-based concept normalisation systems. To address that, we designed a data harmonisation pipeline and engineered a corpus of 27,979 textual descriptions simultaneously mapped to both MedDRA and SNOMED-CT, sourced from five publicly available datasets across biomedical and social media domains. The pipeline can be used in the future to integrate new datasets into the corpus and also could be applied in relevant data curation tasks. We also described a method to merge different terminologies into a single concept graph preserving their relations and demonstrated that representation learning approach based on random walks on a graph can efficiently encode both hierarchical and equivalent relations and capture semantic similarities not only between concepts inside a given terminology but also between concepts from different terminologies. We believe that making a corpus and embeddings for cross-terminology medical concept normalisation available to the research community would contribute to a better understanding of the task.
{"title":"MedNorm: A Corpus and Embeddings for Cross-terminology Medical Concept Normalisation","authors":"M. Belousov, W. Dixon, G. Nenadic","doi":"10.18653/v1/W19-3204","DOIUrl":"https://doi.org/10.18653/v1/W19-3204","url":null,"abstract":"The medical concept normalisation task aims to map textual descriptions to standard terminologies such as SNOMED-CT or MedDRA. Existing publicly available datasets annotated using different terminologies cannot be simply merged and utilised, and therefore become less valuable when developing machine learning-based concept normalisation systems. To address that, we designed a data harmonisation pipeline and engineered a corpus of 27,979 textual descriptions simultaneously mapped to both MedDRA and SNOMED-CT, sourced from five publicly available datasets across biomedical and social media domains. The pipeline can be used in the future to integrate new datasets into the corpus and also could be applied in relevant data curation tasks. We also described a method to merge different terminologies into a single concept graph preserving their relations and demonstrated that representation learning approach based on random walks on a graph can efficiently encode both hierarchical and equivalent relations and capture semantic similarities not only between concepts inside a given terminology but also between concepts from different terminologies. We believe that making a corpus and embeddings for cross-terminology medical concept normalisation available to the research community would contribute to a better understanding of the task.","PeriodicalId":265570,"journal":{"name":"Proceedings of the Fourth Social Media Mining for Health Applications (#SMM4H) Workshop & Shared Task","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"123339584","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
Samarth Rawal, S. Rawal, Saadat Anwar, Chitta Baral
Analyzing social media posts can offer insights into a wide range of topics that are commonly discussed online, providing valuable information for studying various health-related phenomena reported online. The outcome of this work can offer insights into pharmacovigilance research to monitor the adverse effects of medications. This research specifically looks into mentions of adverse drug reactions (ADRs) in Twitter data through the Social Media Mining for Health Applications (SMM4H) Shared Task 2019. Adverse drug reactions are undesired harmful effects which can arise from medication or other methods of treatment. The goal of this research is to build accurate models using natural language processing techniques to detect reports of adverse drug reactions in Twitter data and extract these words or phrases.
{"title":"Identification of Adverse Drug Reaction Mentions in Tweets – SMM4H Shared Task 2019","authors":"Samarth Rawal, S. Rawal, Saadat Anwar, Chitta Baral","doi":"10.18653/v1/W19-3225","DOIUrl":"https://doi.org/10.18653/v1/W19-3225","url":null,"abstract":"Analyzing social media posts can offer insights into a wide range of topics that are commonly discussed online, providing valuable information for studying various health-related phenomena reported online. The outcome of this work can offer insights into pharmacovigilance research to monitor the adverse effects of medications. This research specifically looks into mentions of adverse drug reactions (ADRs) in Twitter data through the Social Media Mining for Health Applications (SMM4H) Shared Task 2019. Adverse drug reactions are undesired harmful effects which can arise from medication or other methods of treatment. The goal of this research is to build accurate models using natural language processing techniques to detect reports of adverse drug reactions in Twitter data and extract these words or phrases.","PeriodicalId":265570,"journal":{"name":"Proceedings of the Fourth Social Media Mining for Health Applications (#SMM4H) Workshop & Shared Task","volume":null,"pages":null},"PeriodicalIF":0.0,"publicationDate":"1900-01-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"132045535","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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