Text Mining the History of Medicine
Historical text archives constitute a rich and diverse source of information, which is becoming increasingly readily accessible, due to large-scale digitisation efforts. However, it can be difficult for researchers to explore and search such large volumes of data in an efficient manner. Text mining...
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Published in | PloS one Vol. 11; no. 1; p. e0144717 |
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Main Authors | , , , , , , , , |
Format | Journal Article |
Language | English |
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United States
Public Library of Science
06.01.2016
Public Library of Science (PLoS) |
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Abstract | Historical text archives constitute a rich and diverse source of information, which is becoming increasingly readily accessible, due to large-scale digitisation efforts. However, it can be difficult for researchers to explore and search such large volumes of data in an efficient manner. Text mining (TM) methods can help, through their ability to recognise various types of semantic information automatically, e.g., instances of concepts (places, medical conditions, drugs, etc.), synonyms/variant forms of concepts, and relationships holding between concepts (which drugs are used to treat which medical conditions, etc.). TM analysis allows search systems to incorporate functionality such as automatic suggestions of synonyms of user-entered query terms, exploration of different concepts mentioned within search results or isolation of documents in which concepts are related in specific ways. However, applying TM methods to historical text can be challenging, according to differences and evolutions in vocabulary, terminology, language structure and style, compared to more modern text. In this article, we present our efforts to overcome the various challenges faced in the semantic analysis of published historical medical text dating back to the mid 19th century. Firstly, we used evidence from diverse historical medical documents from different periods to develop new resources that provide accounts of the multiple, evolving ways in which concepts, their variants and relationships amongst them may be expressed. These resources were employed to support the development of a modular processing pipeline of TM tools for the robust detection of semantic information in historical medical documents with varying characteristics. We applied the pipeline to two large-scale medical document archives covering wide temporal ranges as the basis for the development of a publicly accessible semantically-oriented search system. The novel resources are available for research purposes, while the processing pipeline and its modules may be used and configured within the Argo TM platform. |
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AbstractList | Historical text archives constitute a rich and diverse source of information, which is becoming increasingly readily accessible, due to large-scale digitisation efforts. However, it can be difficult for researchers to explore and search such large volumes of data in an efficient manner. Text mining (TM) methods can help, through their ability to recognise various types of semantic information automatically, e.g., instances of concepts (places, medical conditions, drugs, etc.), synonyms/variant forms of concepts, and relationships holding between concepts (which drugs are used to treat which medical conditions, etc.). TM analysis allows search systems to incorporate functionality such as automatic suggestions of synonyms of user-entered query terms, exploration of different concepts mentioned within search results or isolation of documents in which concepts are related in specific ways. However, applying TM methods to historical text can be challenging, according to differences and evolutions in vocabulary, terminology, language structure and style, compared to more modern text. In this article, we present our efforts to overcome the various challenges faced in the semantic analysis of published historical medical text dating back to the mid 19th century. Firstly, we used evidence from diverse historical medical documents from different periods to develop new resources that provide accounts of the multiple, evolving ways in which concepts, their variants and relationships amongst them may be expressed. These resources were employed to support the development of a modular processing pipeline of TM tools for the robust detection of semantic information in historical medical documents with varying characteristics. We applied the pipeline to two large-scale medical document archives covering wide temporal ranges as the basis for the development of a publicly accessible semantically-oriented search system. The novel resources are available for research purposes, while the processing pipeline and its modules may be used and configured within the Argo TM platform. Historical text archives constitute a rich and diverse source of information, which is becoming increasingly readily accessible, due to large-scale digitisation efforts. However, it can be difficult for researchers to explore and search such large volumes of data in an efficient manner. Text mining (TM) methods can help, through their ability to recognise various types of semantic information automatically, e.g., instances of concepts (places, medical conditions, drugs, etc.), synonyms/variant forms of concepts, and relationships holding between concepts (which drugs are used to treat which medical conditions, etc.). TM analysis allows search systems to incorporate functionality such as automatic suggestions of synonyms of user-entered query terms, exploration of different concepts mentioned within search results or isolation of documents in which concepts are related in specific ways. However, applying TM methods to historical text can be challenging, according to differences and evolutions in vocabulary, terminology, language structure and style, compared to more modern text. In this article, we present our efforts to overcome the various challenges faced in the semantic analysis of published historical medical text dating back to the mid 19 th century. Firstly, we used evidence from diverse historical medical documents from different periods to develop new resources that provide accounts of the multiple, evolving ways in which concepts, their variants and relationships amongst them may be expressed. These resources were employed to support the development of a modular processing pipeline of TM tools for the robust detection of semantic information in historical medical documents with varying characteristics. We applied the pipeline to two large-scale medical document archives covering wide temporal ranges as the basis for the development of a publicly accessible semantically-oriented search system. The novel resources are available for research purposes, while the processing pipeline and its modules may be used and configured within the Argo TM platform. Historical text archives constitute a rich and diverse source of information, which is becoming increasingly readily accessible, due to large-scale digitisation efforts. However, it can be difficult for researchers to explore and search such large volumes of data in an efficient manner. Text mining (TM) methods can help, through their ability to recognise various types of semantic information automatically, e.g., instances of concepts (places, medical conditions, drugs, etc.), synonyms/variant forms of concepts, and relationships holding between concepts (which drugs are used to treat which medical conditions, etc.). TM analysis allows search systems to incorporate functionality such as automatic suggestions of synonyms of user-entered query terms, exploration of different concepts mentioned within search results or isolation of documents in which concepts are related in specific ways. However, applying TM methods to historical text can be challenging, according to differences and evolutions in vocabulary, terminology, language structure and style, compared to more modern text. In this article, we present our efforts to overcome the various challenges faced in the semantic analysis of published historical medical text dating back to the mid 19.sup.th century. Firstly, we used evidence from diverse historical medical documents from different periods to develop new resources that provide accounts of the multiple, evolving ways in which concepts, their variants and relationships amongst them may be expressed. These resources were employed to support the development of a modular processing pipeline of TM tools for the robust detection of semantic information in historical medical documents with varying characteristics. We applied the pipeline to two large-scale medical document archives covering wide temporal ranges as the basis for the development of a publicly accessible semantically-oriented search system. The novel resources are available for research purposes, while the processing pipeline and its modules may be used and configured within the Argo TM platform. Historical text archives constitute a rich and diverse source of information, which is becoming increasingly readily accessible, due to large-scale digitisation efforts. However, it can be difficult for researchers to explore and search such large volumes of data in an efficient manner. Text mining (TM) methods can help, through their ability to recognise various types of semantic information automatically, e.g., instances of concepts (places, medical conditions, drugs, etc.), synonyms/variant forms of concepts, and relationships holding between concepts (which drugs are used to treat which medical conditions, etc.). TM analysis allows search systems to incorporate functionality such as automatic suggestions of synonyms of user-entered query terms, exploration of different concepts mentioned within search results or isolation of documents in which concepts are related in specific ways. However, applying TM methods to historical text can be challenging, according to differences and evolutions in vocabulary, terminology, language structure and style, compared to more modern text. In this article, we present our efforts to overcome the various challenges faced in the semantic analysis of published historical medical text dating back to the mid 19 th century. Firstly, we used evidence from diverse historical medical documents from different periods to develop new resources that provide accounts of the multiple, evolving ways in which concepts, their variants and relationships amongst them may be expressed. These resources were employed to support the development of a modular processing pipeline of TM tools for the robust detection of semantic information in historical medical documents with varying characteristics. We applied the pipeline to two large-scale medical document archives covering wide temporal ranges as the basis for the development of a publicly accessible semantically-oriented search system. The novel resources are available for research purposes, while the processing pipeline and its modules may be used and configured within the Argo TM platform. |
Audience | Academic |
Author | Carter, Jacob Thompson, Paul Worboys, Michael Kontonatsios, Georgios Ananiadou, Sophia Batista-Navarro, Riza Theresa Toon, Elizabeth McNaught, John Timmermann, Carsten |
AuthorAffiliation | 1 National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, United Kingdom 2 Centre for the History of Science, Technology and Medicine, University of Manchester, Manchester, United Kingdom Indiana University, UNITED STATES |
AuthorAffiliation_xml | – name: 1 National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, United Kingdom – name: 2 Centre for the History of Science, Technology and Medicine, University of Manchester, Manchester, United Kingdom – name: Indiana University, UNITED STATES |
Author_xml | – sequence: 1 givenname: Paul surname: Thompson fullname: Thompson, Paul organization: National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, United Kingdom – sequence: 2 givenname: Riza Theresa surname: Batista-Navarro fullname: Batista-Navarro, Riza Theresa organization: National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, United Kingdom – sequence: 3 givenname: Georgios surname: Kontonatsios fullname: Kontonatsios, Georgios organization: National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, United Kingdom – sequence: 4 givenname: Jacob surname: Carter fullname: Carter, Jacob organization: National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, United Kingdom – sequence: 5 givenname: Elizabeth surname: Toon fullname: Toon, Elizabeth organization: Centre for the History of Science, Technology and Medicine, University of Manchester, Manchester, United Kingdom – sequence: 6 givenname: John surname: McNaught fullname: McNaught, John organization: National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, United Kingdom – sequence: 7 givenname: Carsten surname: Timmermann fullname: Timmermann, Carsten organization: Centre for the History of Science, Technology and Medicine, University of Manchester, Manchester, United Kingdom – sequence: 8 givenname: Michael surname: Worboys fullname: Worboys, Michael organization: Centre for the History of Science, Technology and Medicine, University of Manchester, Manchester, United Kingdom – sequence: 9 givenname: Sophia surname: Ananiadou fullname: Ananiadou, Sophia organization: National Centre for Text Mining, School of Computer Science, University of Manchester, Manchester, United Kingdom |
BackLink | https://www.ncbi.nlm.nih.gov/pubmed/26734936$$D View this record in MEDLINE/PubMed |
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Notes | ObjectType-Article-1 SourceType-Scholarly Journals-1 ObjectType-Feature-2 content type line 23 Conceived and designed the experiments: SA MW JM CT. Performed the experiments: PT RB GK ET. Analyzed the data: PT RB GK ET. Wrote the paper: PT SA JM RB GK. Developed the semantic search interface: JC. Competing Interests: The authors have declared that no competing interests exist. |
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SubjectTerms | Accessibility Analysis Archives Archives & records Bioinformatics Causality Computer science Data Mining Data processing Dating techniques Digitization Disease Drugs History of Medicine History, 19th Century Keywords Medical research Medical services Medicine Queries Query expansion Researchers Science history Searching Semantics Studies Terminology Texts Tuberculosis |
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Title | Text Mining the History of Medicine |
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