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Lee H, Jeon J, Jung D, Won JI, Kim K, Kim YJ, Yoon J. RelCurator: a text mining-based curation system for extracting gene-phenotype relationships specific to neurodegenerative disorders. Genes Genomics 2023; 45:1025-1036. [PMID: 37300788 DOI: 10.1007/s13258-023-01405-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2023] [Accepted: 05/18/2023] [Indexed: 06/12/2023]
Abstract
BACKGROUND The identification of gene-phenotype relationships is important in medical genetics as it serves as a basis for precision medicine. However, most of the gene-phenotype relationship data are buried in the biomedical literature in textual form. OBJECTIVE We propose RelCurator, a curation system that extracts sentences including both gene and phenotype entities related to specific disease categories from PubMed articles, provides rich additional information such as entity taggings, and predictions of gene-phenotype relationships. METHODS We targeted neurodegenerative disorders and developed a deep learning model using Bidirectional Gated Recurrent Unit (BiGRU) networks and BioWordVec word embeddings for predicting gene-phenotype relationships from biomedical texts. The prediction model is trained with more than 130,000 labeled PubMed sentences including gene and phenotype entities, which are related to or unrelated to neurodegenerative disorders. RESULTS We compared the performance of our deep learning model with those of Bidirectional Encoder Representations from Transformers (BERT), Support Vector Machine (SVM), and simple Recurrent Neural Network (simple RNN) models. Our model performed better with an F1-score of 0.96. Furthermore, the evaluation done using a few curation cases in the real scenario showed the effectiveness of our work. Therefore, we conclude that RelCurator can identify not only new causative genes, but also new genes associated with neurodegenerative disorders' phenotype. CONCLUSION RelCurator is a user-friendly method for accessing deep learning-based supporting information and a concise web interface to assist curators while browsing the PubMed articles. Our curation process represents an important and broadly applicable improvement to the state of the art for the curation of gene-phenotype relationships.
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Affiliation(s)
- Heonwoo Lee
- Department of Computer Engineering, Hallym University, Chuncheon, Gangwon-do, 200- 702, Republic of Korea
| | - Junbeom Jeon
- Department of Computer Engineering, Hallym University, Chuncheon, Gangwon-do, 200- 702, Republic of Korea
| | - Dawoon Jung
- Department of Computer Engineering, Hallym University, Chuncheon, Gangwon-do, 200- 702, Republic of Korea
| | - Jung-Im Won
- Center for Innovation in Engineering Education, Hanyang University, Seoul, Republic of Korea
| | - Kiyong Kim
- Department of Electronic Engineering, Kyonggi University, Suwon, Republic of Korea
| | - Yun Joong Kim
- Department of Neurology, Yonsei University College of Medicine, Seoul, Republic of Korea.
- Department of Neurology, Yongin Severance Hospital, Yonsei University College of Medicine, Yonsei University Health System, Yongin, Gyeonggi-do, 16995, Republic of Korea.
| | - Jeehee Yoon
- Department of Computer Engineering, Hallym University, Chuncheon, Gangwon-do, 200- 702, Republic of Korea.
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2
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Bokharaeian B, Dehghani M, Diaz A. Automatic extraction of ranked SNP-phenotype associations from text using a BERT-LSTM-based method. BMC Bioinformatics 2023; 24:144. [PMID: 37046202 PMCID: PMC10099837 DOI: 10.1186/s12859-023-05236-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 03/17/2023] [Indexed: 04/14/2023] Open
Abstract
Extraction of associations of singular nucleotide polymorphism (SNP) and phenotypes from biomedical literature is a vital task in BioNLP. Recently, some methods have been developed to extract mutation-diseases affiliations. However, no accessible method of extracting associations of SNP-phenotype from content considers their degree of certainty. In this paper, several machine learning methods were developed to extract ranked SNP-phenotype associations from biomedical abstracts and then were compared to each other. In addition, shallow machine learning methods, including random forest, logistic regression, and decision tree and two kernel-based methods like subtree and local context, a rule-based and a deep CNN-LSTM-based and two BERT-based methods were developed in this study to extract associations. Furthermore, the experiments indicated that although the used linguist features could be employed to implement a superior association extraction method outperforming the kernel-based counterparts, the used deep learning and BERT-based methods exhibited the best performance. However, the used PubMedBERT-LSTM outperformed the other developed methods among the used methods. Moreover, similar experiments were conducted to estimate the degree of certainty of the extracted association, which can be used to assess the strength of the reported association. The experiments revealed that our proposed PubMedBERT-CNN-LSTM method outperformed the sophisticated methods on the task.
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Affiliation(s)
| | - Mohammad Dehghani
- School of Electrical and Computer Engineering, University of Tehran, Tehran, Iran
| | - Alberto Diaz
- Facultad Informatica, Complutense University of Madrid, Madrid, Spain
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3
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Pourreza Shahri M, Kahanda I. Deep semi-supervised learning ensemble framework for classifying co-mentions of human proteins and phenotypes. BMC Bioinformatics 2021; 22:500. [PMID: 34656098 PMCID: PMC8520253 DOI: 10.1186/s12859-021-04421-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/14/2021] [Accepted: 10/04/2021] [Indexed: 11/13/2022] Open
Abstract
Background Identifying human protein-phenotype relationships has attracted researchers in bioinformatics and biomedical natural language processing due to its importance in uncovering rare and complex diseases. Since experimental validation of protein-phenotype associations is prohibitive, automated tools capable of accurately extracting these associations from the biomedical text are in high demand. However, while the manual annotation of protein-phenotype co-mentions required for training such models is highly resource-consuming, extracting millions of unlabeled co-mentions is straightforward. Results In this study, we propose a novel deep semi-supervised ensemble framework that combines deep neural networks, semi-supervised, and ensemble learning for classifying human protein-phenotype co-mentions with the help of unlabeled data. This framework allows the ability to incorporate an extensive collection of unlabeled sentence-level co-mentions of human proteins and phenotypes with a small labeled dataset to enhance overall performance. We develop PPPredSS, a prototype of our proposed semi-supervised framework that combines sophisticated language models, convolutional networks, and recurrent networks. Our experimental results demonstrate that the proposed approach provides a new state-of-the-art performance in classifying human protein-phenotype co-mentions by outperforming other supervised and semi-supervised counterparts. Furthermore, we highlight the utility of PPPredSS in powering a curation assistant system through case studies involving a group of biologists. Conclusions This article presents a novel approach for human protein-phenotype co-mention classification based on deep, semi-supervised, and ensemble learning. The insights and findings from this work have implications for biomedical researchers, biocurators, and the text mining community working on biomedical relationship extraction.
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Affiliation(s)
| | - Indika Kahanda
- School of Computing, University of North Florida, Jacksonville, USA.
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4
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Becker TE, Jakobsson E. ResidueFinder: extracting individual residue mentions from protein literature. J Biomed Semantics 2021; 12:14. [PMID: 34289903 PMCID: PMC8293528 DOI: 10.1186/s13326-021-00243-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2019] [Accepted: 05/07/2021] [Indexed: 11/10/2022] Open
Abstract
Background The revolution in molecular biology has shown how protein function and structure are based on specific sequences of amino acids. Thus, an important feature in many papers is the mention of the significance of individual amino acids in the context of the entire sequence of the protein. MutationFinder is a widely used program for finding mentions of specific mutations in texts. We report on augmenting the positive attributes of MutationFinder with a more inclusive regular expression list to create ResidueFinder, which finds mentions of native amino acids as well as mutations. We also consider parameter options for both ResidueFinder and MutationFinder to explore trade-offs between precision, recall, and computational efficiency. We test our methods and software in full text as well as abstracts. Results We find there is much more variety of formats for mentioning residues in the entire text of papers than in abstracts alone. Failure to take these multiple formats into account results in many false negatives in the program. Since MutationFinder, like several other programs, was primarily tested on abstracts, we found it necessary to build an expanded regular expression list to achieve acceptable recall in full text searches. We also discovered a number of artifacts arising from PDF to text conversion, which we wrote elements in the regular expression library to address. Taking into account those factors resulted in high recall on randomly selected primary research articles. We also developed a streamlined regular expression (called “cut”) which enables a several hundredfold speedup in both MutationFinder and ResidueFinder with only a modest compromise of recall. All regular expressions were tested using expanded F-measure statistics, i.e., we compute Fβ for various values of where the larger the value of β the more recall is weighted, the smaller the value of β the more precision is weighted. Conclusions ResidueFinder is a simple, effective, and efficient program for finding individual residue mentions in primary literature starting with text files, implemented in Python, and available in SourceForge.net. The most computationally efficient versions of ResidueFinder could enable creation and maintenance of a database of residue mentions encompassing all articles in PubMed. Supplementary Information The online version contains supplementary material available at 10.1186/s13326-021-00243-3.
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Affiliation(s)
- Ton E Becker
- Department of Molecular and Integrative Physiology, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Illinois, 61801, Urbana, USA
| | - Eric Jakobsson
- Department of Molecular and Integrative Physiology, Beckman Institute for Advanced Science and Technology, University of Illinois at Urbana-Champaign, Illinois, 61801, Urbana, USA. .,Department of Biochemistry, Program in Biophysics and Computational Biology, National Center for Supercomputing Applications, University of Illinois at Urbana-Champaign, Illinois, 61801, Urbana, USA.
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5
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Lee K, Wei CH, Lu Z. Recent advances of automated methods for searching and extracting genomic variant information from biomedical literature. Brief Bioinform 2021; 22:bbaa142. [PMID: 32770181 PMCID: PMC8138883 DOI: 10.1093/bib/bbaa142] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Revised: 06/07/2020] [Accepted: 06/25/2020] [Indexed: 12/28/2022] Open
Abstract
MOTIVATION To obtain key information for personalized medicine and cancer research, clinicians and researchers in the biomedical field are in great need of searching genomic variant information from the biomedical literature now than ever before. Due to the various written forms of genomic variants, however, it is difficult to locate the right information from the literature when using a general literature search system. To address the difficulty of locating genomic variant information from the literature, researchers have suggested various solutions based on automated literature-mining techniques. There is, however, no study for summarizing and comparing existing tools for genomic variant literature mining in terms of how to search easily for information in the literature on genomic variants. RESULTS In this article, we systematically compared currently available genomic variant recognition and normalization tools as well as the literature search engines that adopted these literature-mining techniques. First, we explain the problems that are caused by the use of non-standard formats of genomic variants in the PubMed literature by considering examples from the literature and show the prevalence of the problem. Second, we review literature-mining tools that address the problem by recognizing and normalizing the various forms of genomic variants in the literature and systematically compare them. Third, we present and compare existing literature search engines that are designed for a genomic variant search by using the literature-mining techniques. We expect this work to be helpful for researchers who seek information about genomic variants from the literature, developers who integrate genomic variant information from the literature and beyond.
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Affiliation(s)
- Kyubum Lee
- National Center for Biotechnology Information
| | | | - Zhiyong Lu
- National Center for Biotechnology Information
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6
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Dingerdissen HM, Bastian F, Vijay-Shanker K, Robinson-Rechavi M, Bell A, Gogate N, Gupta S, Holmes E, Kahsay R, Keeney J, Kincaid H, King CH, Liu D, Crichton DJ, Mazumder R. OncoMX: A Knowledgebase for Exploring Cancer Biomarkers in the Context of Related Cancer and Healthy Data. JCO Clin Cancer Inform 2020; 4:210-220. [PMID: 32142370 PMCID: PMC7101249 DOI: 10.1200/cci.19.00117] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/31/2022] Open
Abstract
PURPOSE The purpose of OncoMX1 knowledgebase development was to integrate cancer biomarker and relevant data types into a meta-portal, enabling the research of cancer biomarkers side by side with other pertinent multidimensional data types. METHODS Cancer mutation, cancer differential expression, cancer expression specificity, healthy gene expression from human and mouse, literature mining for cancer mutation and cancer expression, and biomarker data were integrated, unified by relevant biomedical ontologies, and subjected to rule-based automated quality control before ingestion into the database. RESULTS OncoMX provides integrated data encompassing more than 1,000 unique biomarker entries (939 from the Early Detection Research Network [EDRN] and 96 from the US Food and Drug Administration) mapped to 20,576 genes that have either mutation or differential expression in cancer. Sentences reporting mutation or differential expression in cancer were extracted from more than 40,000 publications, and healthy gene expression data with samples mapped to organs are available for both human genes and their mouse orthologs. CONCLUSION OncoMX has prioritized user feedback as a means of guiding development priorities. By mapping to and integrating data from several cancer genomics resources, it is hoped that OncoMX will foster a dynamic engagement between bioinformaticians and cancer biomarker researchers. This engagement should culminate in a community resource that substantially improves the ability and efficiency of exploring cancer biomarker data and related multidimensional data.
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Affiliation(s)
| | - Frederic Bastian
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | | | - Marc Robinson-Rechavi
- SIB Swiss Institute of Bioinformatics, Lausanne, Switzerland.,Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
| | - Amanda Bell
- The George Washington University, Washington DC
| | | | | | - Evan Holmes
- The George Washington University, Washington DC
| | | | | | | | | | - David Liu
- NASA Jet Propulsion Laboratory, Pasadena, CA
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7
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Rao S, Pitel B, Wagner AH, Boca SM, McCoy M, King I, Gupta S, Park BH, Warner JL, Chen J, Rogan PK, Chakravarty D, Griffith M, Griffith OL, Madhavan S. Collaborative, Multidisciplinary Evaluation of Cancer Variants Through Virtual Molecular Tumor Boards Informs Local Clinical Practices. JCO Clin Cancer Inform 2020; 4:602-613. [PMID: 32644817 PMCID: PMC7397775 DOI: 10.1200/cci.19.00169] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/18/2020] [Indexed: 12/17/2022] Open
Abstract
PURPOSE The cancer research community is constantly evolving to better understand tumor biology, disease etiology, risk stratification, and pathways to novel treatments. Yet the clinical cancer genomics field has been hindered by redundant efforts to meaningfully collect and interpret disparate data types from multiple high-throughput modalities and integrate into clinical care processes. Bespoke data models, knowledgebases, and one-off customized resources for data analysis often lack adequate governance and quality control needed for these resources to be clinical grade. Many informatics efforts focused on genomic interpretation resources for neoplasms are underway to support data collection, deposition, curation, harmonization, integration, and analytics to support case review and treatment planning. METHODS In this review, we evaluate and summarize the landscape of available tools, resources, and evidence used in the evaluation of somatic and germline tumor variants within the context of molecular tumor boards. RESULTS Molecular tumor boards (MTBs) are collaborative efforts of multidisciplinary cancer experts equipped with genomic interpretation resources to aid in the delivery of accurate and timely clinical interpretations of complex genomic results for each patient, within an institution or hospital network. Virtual MTBs (VMTBs) provide an online forum for collaborative governance, provenance, and information sharing between experts outside a given hospital network with the potential to enhance MTB discussions. Knowledge sharing in VMTBs and communication with guideline-developing organizations can lead to progress evidenced by data harmonization across resources, crowd-sourced and expert-curated genomic assertions, and a more informed and explainable usage of artificial intelligence. CONCLUSION Advances in cancer genomics interpretation aid in better patient and disease classification, more streamlined identification of relevant literature, and a more thorough review of available treatments and predicted patient outcomes.
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Affiliation(s)
- Shruti Rao
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC
| | - Beth Pitel
- Division of Laboratory Genetics and Genomics, Department of Laboratory Medicine and Pathology, Mayo Clinic, Rochester, MN
| | - Alex H. Wagner
- McDonnell Genome Institute and Department of Medicine, Washington University School of Medicine, St Louis, MO
| | - Simina M. Boca
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC
| | - Matthew McCoy
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC
| | - Ian King
- Laboratory Medicine Program, University Health Network and Department of Laboratory Medicine and Pathobiology, University of Toronto, Toronto, Ontario, Canada
| | - Samir Gupta
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC
| | - Ben Ho Park
- Division of Hematology and Oncology, Department of Medicine, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - Jeremy L. Warner
- Departments of Medicine and Biomedical Informatics, Vanderbilt-Ingram Cancer Center, Vanderbilt University Medical Center, Nashville, TN
| | - James Chen
- Division of Medical Oncology, Department of Biomedical Informatics, The Ohio State University, Columbus, OH
| | - Peter K. Rogan
- Departments of Biochemistry and Oncology, Schulich School of Medicine and Dentistry, University of Western Ontario, London, Ontario, Canada
| | - Debyani Chakravarty
- Kravis Center of Molecular Oncology, Department of Pathology, Memorial Sloan Kettering Cancer Center, New York, NY
| | - Malachi Griffith
- McDonnell Genome Institute and Department of Medicine, Washington University School of Medicine, St Louis, MO
| | - Obi L. Griffith
- McDonnell Genome Institute and Department of Medicine, Washington University School of Medicine, St Louis, MO
| | - Subha Madhavan
- Innovation Center for Biomedical Informatics, Georgetown University Medical Center, Washington, DC
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8
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Nicholson DN, Greene CS. Constructing knowledge graphs and their biomedical applications. Comput Struct Biotechnol J 2020; 18:1414-1428. [PMID: 32637040 PMCID: PMC7327409 DOI: 10.1016/j.csbj.2020.05.017] [Citation(s) in RCA: 76] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2020] [Revised: 05/22/2020] [Accepted: 05/23/2020] [Indexed: 12/31/2022] Open
Abstract
Knowledge graphs can support many biomedical applications. These graphs represent biomedical concepts and relationships in the form of nodes and edges. In this review, we discuss how these graphs are constructed and applied with a particular focus on how machine learning approaches are changing these processes. Biomedical knowledge graphs have often been constructed by integrating databases that were populated by experts via manual curation, but we are now seeing a more robust use of automated systems. A number of techniques are used to represent knowledge graphs, but often machine learning methods are used to construct a low-dimensional representation that can support many different applications. This representation is designed to preserve a knowledge graph's local and/or global structure. Additional machine learning methods can be applied to this representation to make predictions within genomic, pharmaceutical, and clinical domains. We frame our discussion first around knowledge graph construction and then around unifying representational learning techniques and unifying applications. Advances in machine learning for biomedicine are creating new opportunities across many domains, and we note potential avenues for future work with knowledge graphs that appear particularly promising.
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Affiliation(s)
- David N. Nicholson
- Department of Systems Pharmacology and Translational Therapeutics, University of Pennsylvania, United States
| | - Casey S. Greene
- Department of Systems Pharmacology and Translational Therapeutics, Perelman School of Medicine, University of Pennsylvania, Childhood Cancer Data Lab, Alex’s Lemonade Stand Foundation, United States
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9
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Wei CH, Allot A, Leaman R, Lu Z. PubTator central: automated concept annotation for biomedical full text articles. Nucleic Acids Res 2020; 47:W587-W593. [PMID: 31114887 DOI: 10.1093/nar/gkz389] [Citation(s) in RCA: 201] [Impact Index Per Article: 50.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 04/08/2019] [Accepted: 04/30/2019] [Indexed: 11/12/2022] Open
Abstract
PubTator Central (https://www.ncbi.nlm.nih.gov/research/pubtator/) is a web service for viewing and retrieving bioconcept annotations in full text biomedical articles. PubTator Central (PTC) provides automated annotations from state-of-the-art text mining systems for genes/proteins, genetic variants, diseases, chemicals, species and cell lines, all available for immediate download. PTC annotates PubMed (29 million abstracts) and the PMC Text Mining subset (3 million full text articles). The new PTC web interface allows users to build full text document collections and visualize concept annotations in each document. Annotations are downloadable in multiple formats (XML, JSON and tab delimited) via the online interface, a RESTful web service and bulk FTP. Improved concept identification systems and a new disambiguation module based on deep learning increase annotation accuracy, and the new server-side architecture is significantly faster. PTC is synchronized with PubMed and PubMed Central, with new articles added daily. The original PubTator service has served annotated abstracts for ∼300 million requests, enabling third-party research in use cases such as biocuration support, gene prioritization, genetic disease analysis, and literature-based knowledge discovery. We demonstrate the full text results in PTC significantly increase biomedical concept coverage and anticipate this expansion will both enhance existing downstream applications and enable new use cases.
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Affiliation(s)
- Chih-Hsuan Wei
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Alexis Allot
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Robert Leaman
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Zhiyong Lu
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA
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10
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Association extraction from biomedical literature based on representation and transfer learning. J Theor Biol 2020; 488:110112. [DOI: 10.1016/j.jtbi.2019.110112] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2019] [Accepted: 12/08/2019] [Indexed: 12/17/2022]
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11
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Lagunes-García G, Rodríguez-González A, Prieto-Santamaría L, García Del Valle EP, Zanin M, Menasalvas-Ruiz E. DISNET: a framework for extracting phenotypic disease information from public sources. PeerJ 2020; 8:e8580. [PMID: 32110491 PMCID: PMC7032061 DOI: 10.7717/peerj.8580] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 01/16/2020] [Indexed: 12/25/2022] Open
Abstract
Background Within the global endeavour of improving population health, one major challenge is the identification and integration of medical knowledge spread through several information sources. The creation of a comprehensive dataset of diseases and their clinical manifestations based on information from public sources is an interesting approach that allows one not only to complement and merge medical knowledge but also to increase it and thereby to interconnect existing data and analyse and relate diseases to each other. In this paper, we present DISNET (http://disnet.ctb.upm.es/), a web-based system designed to periodically extract the knowledge from signs and symptoms retrieved from medical databases, and to enable the creation of customisable disease networks. Methods We here present the main features of the DISNET system. We describe how information on diseases and their phenotypic manifestations is extracted from Wikipedia and PubMed websites; specifically, texts from these sources are processed through a combination of text mining and natural language processing techniques. Results We further present the validation of our system on Wikipedia and PubMed texts, obtaining the relevant accuracy. The final output includes the creation of a comprehensive symptoms-disease dataset, shared (free access) through the system's API. We finally describe, with some simple use cases, how a user can interact with it and extract information that could be used for subsequent analyses. Discussion DISNET allows retrieving knowledge about the signs, symptoms and diagnostic tests associated with a disease. It is not limited to a specific category (all the categories that the selected sources of information offer us) and clinical diagnosis terms. It further allows to track the evolution of those terms through time, being thus an opportunity to analyse and observe the progress of human knowledge on diseases. We further discussed the validation of the system, suggesting that it is good enough to be used to extract diseases and diagnostically-relevant terms. At the same time, the evaluation also revealed that improvements could be introduced to enhance the system's reliability.
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Affiliation(s)
- Gerardo Lagunes-García
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
| | - Alejandro Rodríguez-González
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain.,Escuela Técnica Superior de Ingenieros Informáticos, Universidad Politécnica de Madrid, Boadilla del Monte, Madrid, Spain
| | - Lucía Prieto-Santamaría
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
| | | | - Massimiliano Zanin
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
| | - Ernestina Menasalvas-Ruiz
- Centro de Tecnología Biomédica, Universidad Politécnica de Madrid, Pozuelo de Alarcón, Madrid, Spain
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12
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PGxMine: Text mining for curation of PharmGKB. PACIFIC SYMPOSIUM ON BIOCOMPUTING. PACIFIC SYMPOSIUM ON BIOCOMPUTING 2020; 25:611-622. [PMID: 31797632 PMCID: PMC6917032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
Precision medicine tailors treatment to individuals personal data including differences in their genome. The Pharmacogenomics Knowledgebase (PharmGKB) provides highly curated information on the effect of genetic variation on drug response and side effects for a wide range of drugs. PharmGKB's scientific curators triage, review and annotate a large number of papers each year but the task is challenging. We present the PGxMine resource, a text-mined resource of pharmacogenomic associations from all accessible published literature to assist in the curation of PharmGKB. We developed a supervised machine learning pipeline to extract associations between a variant (DNA and protein changes, star alleles and dbSNP identifiers) and a chemical. PGxMine covers 452 chemicals and 2,426 variants and contains 19,930 mentions of pharmacogenomic associations across 7,170 papers. An evaluation by PharmGKB curators found that 57 of the top 100 associations not found in PharmGKB led to 83 curatable papers and a further 24 associations would likely lead to curatable papers through citations. The results can be viewed at https://pgxmine.pharmgkb.org/ and code can be downloaded at https://github.com/jakelever/pgxmine.
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13
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Xu J, Yang P, Xue S, Sharma B, Sanchez-Martin M, Wang F, Beaty KA, Dehan E, Parikh B. Translating cancer genomics into precision medicine with artificial intelligence: applications, challenges and future perspectives. Hum Genet 2019; 138:109-124. [PMID: 30671672 PMCID: PMC6373233 DOI: 10.1007/s00439-019-01970-5] [Citation(s) in RCA: 95] [Impact Index Per Article: 19.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2018] [Accepted: 01/02/2019] [Indexed: 02/07/2023]
Abstract
In the field of cancer genomics, the broad availability of genetic information offered by next-generation sequencing technologies and rapid growth in biomedical publication has led to the advent of the big-data era. Integration of artificial intelligence (AI) approaches such as machine learning, deep learning, and natural language processing (NLP) to tackle the challenges of scalability and high dimensionality of data and to transform big data into clinically actionable knowledge is expanding and becoming the foundation of precision medicine. In this paper, we review the current status and future directions of AI application in cancer genomics within the context of workflows to integrate genomic analysis for precision cancer care. The existing solutions of AI and their limitations in cancer genetic testing and diagnostics such as variant calling and interpretation are critically analyzed. Publicly available tools or algorithms for key NLP technologies in the literature mining for evidence-based clinical recommendations are reviewed and compared. In addition, the present paper highlights the challenges to AI adoption in digital healthcare with regard to data requirements, algorithmic transparency, reproducibility, and real-world assessment, and discusses the importance of preparing patients and physicians for modern digitized healthcare. We believe that AI will remain the main driver to healthcare transformation toward precision medicine, yet the unprecedented challenges posed should be addressed to ensure safety and beneficial impact to healthcare.
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Affiliation(s)
- Jia Xu
- IBM Watson Health, Cambridge, MA, USA.
| | | | - Shang Xue
- IBM Watson Health, Cambridge, MA, USA
| | | | | | - Fang Wang
- IBM Watson Health, Cambridge, MA, USA
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14
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Abstract
Recent advances in technology have led to the exponential growth of scientific literature in biomedical sciences. This rapid increase in information has surpassed the threshold for manual curation efforts, necessitating the use of text mining approaches in the field of life sciences. One such application of text mining is in fostering in silico drug discovery such as drug target screening, pharmacogenomics, adverse drug event detection, etc. This chapter serves as an introduction to the applications of various text mining approaches in drug discovery. It is divided into two parts with the first half as an overview of text mining in the biosciences. The second half of the chapter reviews strategies and methods for four unique applications of text mining in drug discovery.
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Affiliation(s)
- Si Zheng
- Institute of Medical Information and Library, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Shazia Dharssi
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA
| | - Meng Wu
- Institute of Medical Information and Library, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Jiao Li
- Institute of Medical Information and Library, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing, China
| | - Zhiyong Lu
- National Center for Biotechnology Information (NCBI), National Library of Medicine (NLM), National Institutes of Health (NIH), Bethesda, MD, USA.
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15
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Islamaj Dogan R, Kim S, Chatr-Aryamontri A, Wei CH, Comeau DC, Antunes R, Matos S, Chen Q, Elangovan A, Panyam NC, Verspoor K, Liu H, Wang Y, Liu Z, Altinel B, Hüsünbeyi ZM, Özgür A, Fergadis A, Wang CK, Dai HJ, Tran T, Kavuluru R, Luo L, Steppi A, Zhang J, Qu J, Lu Z. Overview of the BioCreative VI Precision Medicine Track: mining protein interactions and mutations for precision medicine. Database (Oxford) 2019; 2019:5303240. [PMID: 30689846 PMCID: PMC6348314 DOI: 10.1093/database/bay147] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2018] [Accepted: 12/19/2018] [Indexed: 12/16/2022]
Abstract
The Precision Medicine Initiative is a multicenter effort aiming at formulating personalized treatments leveraging on individual patient data (clinical, genome sequence and functional genomic data) together with the information in large knowledge bases (KBs) that integrate genome annotation, disease association studies, electronic health records and other data types. The biomedical literature provides a rich foundation for populating these KBs, reporting genetic and molecular interactions that provide the scaffold for the cellular regulatory systems and detailing the influence of genetic variants in these interactions. The goal of BioCreative VI Precision Medicine Track was to extract this particular type of information and was organized in two tasks: (i) document triage task, focused on identifying scientific literature containing experimentally verified protein-protein interactions (PPIs) affected by genetic mutations and (ii) relation extraction task, focused on extracting the affected interactions (protein pairs). To assist system developers and task participants, a large-scale corpus of PubMed documents was manually annotated for this task. Ten teams worldwide contributed 22 distinct text-mining models for the document triage task, and six teams worldwide contributed 14 different text-mining systems for the relation extraction task. When comparing the text-mining system predictions with human annotations, for the triage task, the best F-score was 69.06%, the best precision was 62.89%, the best recall was 98.0% and the best average precision was 72.5%. For the relation extraction task, when taking homologous genes into account, the best F-score was 37.73%, the best precision was 46.5% and the best recall was 54.1%. Submitted systems explored a wide range of methods, from traditional rule-based, statistical and machine learning systems to state-of-the-art deep learning methods. Given the level of participation and the individual team results we find the precision medicine track to be successful in engaging the text-mining research community. In the meantime, the track produced a manually annotated corpus of 5509 PubMed documents developed by BioGRID curators and relevant for precision medicine. The data set is freely available to the community, and the specific interactions have been integrated into the BioGRID data set. In addition, this challenge provided the first results of automatically identifying PubMed articles that describe PPI affected by mutations, as well as extracting the affected relations from those articles. Still, much progress is needed for computer-assisted precision medicine text mining to become mainstream. Future work should focus on addressing the remaining technical challenges and incorporating the practical benefits of text-mining tools into real-world precision medicine information-related curation.
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Affiliation(s)
- Rezarta Islamaj Dogan
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Sun Kim
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | | | - Chih-Hsuan Wei
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Donald C Comeau
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
| | - Rui Antunes
- Department of Electronics, Telecommunications and Informatics (DETI)/Institute of Electronics and Informatics Engineering of Aveiro (IEETA), University of Aveiro, Aveiro, Portugal
| | - Sérgio Matos
- Department of Electronics, Telecommunications and Informatics (DETI)/Institute of Electronics and Informatics Engineering of Aveiro (IEETA), University of Aveiro, Aveiro, Portugal
| | - Qingyu Chen
- School of Computing and Information Systems, The University of Melbourne, Melbourne, VIC, Australia
| | - Aparna Elangovan
- School of Computing and Information Systems, The University of Melbourne, Melbourne, VIC, Australia
| | - Nagesh C Panyam
- School of Computing and Information Systems, The University of Melbourne, Melbourne, VIC, Australia
| | - Karin Verspoor
- School of Computing and Information Systems, The University of Melbourne, Melbourne, VIC, Australia
| | - Hongfang Liu
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
| | - Yanshan Wang
- Department of Health Science Research, Mayo Clinic, Rochester, MN, USA
| | - Zhuang Liu
- School of Computer Science and Technology, Dalian University of Technology, Dalian, China
| | - Berna Altinel
- Department of Computer Engineering, Marmara University, Istanbul, Turkey
| | | | | | - Aris Fergadis
- School of Electrical and Computer Engineering, National Technical University of Athens, Zografou, Athens, Greece
| | - Chen-Kai Wang
- Graduate Institute of Biomedical Informatics, Taipei Medical University, Taipei, Taiwan
| | - Hong-Jie Dai
- Department of Electrical Engineering, National Kaousiung University of Science and Technology, Kaohsiung, Taiwan
| | - Tung Tran
- Department of Computer Science, University of Kentucky, Lexington, KY, USA
| | - Ramakanth Kavuluru
- Division of Biomedical Informatics, Department of Internal Medicine, University of Kentucky, Lexington, KY, USA
| | - Ling Luo
- College of Computer Science and Technology, Dalian University of Technology, Dalian, China
| | - Albert Steppi
- Department of Statistics, Florida State University, Florida, USA
| | - Jinfeng Zhang
- Department of Statistics, Florida State University, Florida, USA
| | - Jinchan Qu
- Department of Statistics, Florida State University, Florida, USA
| | - Zhiyong Lu
- National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
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16
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Kordopati V, Salhi A, Razali R, Radovanovic A, Tifratene F, Uludag M, Li Y, Bokhari A, AlSaieedi A, Bin Raies A, Van Neste C, Essack M, Bajic VB. DES-Mutation: System for Exploring Links of Mutations and Diseases. Sci Rep 2018; 8:13359. [PMID: 30190574 PMCID: PMC6127254 DOI: 10.1038/s41598-018-31439-w] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2017] [Accepted: 08/17/2018] [Indexed: 12/17/2022] Open
Abstract
During cellular division DNA replicates and this process is the basis for passing genetic information to the next generation. However, the DNA copy process sometimes produces a copy that is not perfect, that is, one with mutations. The collection of all such mutations in the DNA copy of an organism makes it unique and determines the organism’s phenotype. However, mutations are often the cause of diseases. Thus, it is useful to have the capability to explore links between mutations and disease. We approached this problem by analyzing a vast amount of published information linking mutations to disease states. Based on such information, we developed the DES-Mutation knowledgebase which allows for exploration of not only mutation-disease links, but also links between mutations and concepts from 27 topic-specific dictionaries such as human genes/proteins, toxins, pathogens, etc. This allows for a more detailed insight into mutation-disease links and context. On a sample of 600 mutation-disease associations predicted and curated, our system achieves precision of 72.83%. To demonstrate the utility of DES-Mutation, we provide case studies related to known or potentially novel information involving disease mutations. To our knowledge, this is the first mutation-disease knowledgebase dedicated to the exploration of this topic through text-mining and data-mining of different mutation types and their associations with terms from multiple thematic dictionaries.
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Affiliation(s)
- Vasiliki Kordopati
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
| | - Adil Salhi
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
| | - Rozaimi Razali
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
| | - Aleksandar Radovanovic
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
| | - Faroug Tifratene
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
| | - Mahmut Uludag
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
| | - Yu Li
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
| | - Ameerah Bokhari
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
| | - Ahdab AlSaieedi
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia.,King Abdulaziz University (KAU), Faculty of Applied Medical Sciences (FAMS), Department of Medical Laboratory Technology (MLT), Jeddah, 21589-80324, Saudi Arabia
| | - Arwa Bin Raies
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
| | - Christophe Van Neste
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia.,Ghent University, Center for Medical Genetics Ghent (CMGG), B-9000, Ghent, Belgium
| | - Magbubah Essack
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia
| | - Vladimir B Bajic
- King Abdullah University of Science and Technology (KAUST), Computational Bioscience Research Center (CBRC), Thuwal, 23955-6900, Saudi Arabia.
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17
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Kveler K, Starosvetsky E, Ziv-Kenet A, Kalugny Y, Gorelik Y, Shalev-Malul G, Aizenbud-Reshef N, Dubovik T, Briller M, Campbell J, Rieckmann JC, Asbeh N, Rimar D, Meissner F, Wiser J, Shen-Orr SS. Immune-centric network of cytokines and cells in disease context identified by computational mining of PubMed. Nat Biotechnol 2018; 36:651-659. [PMID: 29912209 PMCID: PMC6035104 DOI: 10.1038/nbt.4152] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/16/2017] [Accepted: 04/05/2018] [Indexed: 02/07/2023]
Abstract
Cytokines are signaling molecules secreted and sensed by immune and other cell types, enabling dynamic intercellular communication. Although a vast amount of data on these interactions exists, this information is not compiled, integrated or easily searchable. Here we report immuneXpresso, a text-mining engine that structures and standardizes knowledge of immune intercellular communication. We applied immuneXpresso to PubMed to identify relationships between 340 cell types and 140 cytokines across thousands of diseases. The method is able to distinguish between incoming and outgoing interactions, and it includes the effect of the interaction and the cellular function involved. These factors are assigned a confidence score and linked to the disease. By leveraging the breadth of this network, we predicted and experimentally verified previously unappreciated cell-cytokine interactions. We also built a global immune-centric view of diseases and used it to predict cytokine-disease associations. This standardized knowledgebase (http://www.immunexpresso.org) opens up new directions for interpretation of immune data and model-driven systems immunology.
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Affiliation(s)
- Ksenya Kveler
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3525433, Israel
| | - Elina Starosvetsky
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3525433, Israel
| | - Amit Ziv-Kenet
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3525433, Israel
| | - Yuval Kalugny
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3525433, Israel
- CytoReason, Tel-Aviv, 67012, Israel
| | - Yuri Gorelik
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3525433, Israel
| | - Gali Shalev-Malul
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3525433, Israel
| | - Netta Aizenbud-Reshef
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3525433, Israel
| | - Tania Dubovik
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3525433, Israel
| | - Mayan Briller
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3525433, Israel
| | - John Campbell
- Northrop Grumman IT Health Solutions, Rockville, MD 20850, USA
| | - Jan C. Rieckmann
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Bayern, 82152, Germany
| | - Nuaman Asbeh
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3525433, Israel
| | - Doron Rimar
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3525433, Israel
- Rheumatology Unit, Bnai Zion Medical Center, Haifa 31048, Israel
| | - Felix Meissner
- Experimental Systems Immunology, Max Planck Institute of Biochemistry, Bayern, 82152, Germany
| | - Jeff Wiser
- Northrop Grumman IT Health Solutions, Rockville, MD 20850, USA
| | - Shai S. Shen-Orr
- Rappaport Faculty of Medicine, Technion-Israel Institute of Technology, Haifa 3525433, Israel
- Faculty of Biology, Technion-Israel Institute of Technology, Haifa 3200003, Israel
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18
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Affiliation(s)
- Nancy L. Green
- University of North Carolina Greensboro, Greensboro, NC 27402, USA. Tel.: ; Fax: ; E-mail:
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19
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Varoglu E, Seytanoglu A, Asilmaz E, Taneri B. Neurotransmitter receptor genotypes associated with mental and behavioral disorders. Per Med 2018; 14:327-338. [PMID: 29749833 DOI: 10.2217/pme-2016-0100] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
AIM Investigation of association studies within the field of mental and behavioral disorders is of value given their complex molecular etiology including epistatic interactions of multiple genes with small effects. MATERIALS & METHODS Utilizing biomedical text mining, associations are uncovered for all mental and behavioral conditions listed in Diagnostic and Statistical Manual of Mental Disorders Text Revision. Specifically, a computational pipeline is designed to retrieve neurotransmitter receptor variations from biomedical literature with a text mining approach, where unique polymorphisms are also mined. RESULTS Analyses of 1337 unique neurotransmitter receptors and 465 distinct conditions yield 1568 unique gene-disease associations. CONCLUSION This study takes an unconventional approach to association studies and generates a novel dataset of associations for disorders such as major depression and schizophrenia, which provides a global perspective for their genetic etiology.
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Affiliation(s)
- Ekrem Varoglu
- Department of Computer Engineering, Eastern Mediterranean University, Famagusta, North Cyprus 99628, Turkey
| | - Adil Seytanoglu
- Department of Biological Sciences, Eastern Mediterranean University, Famagusta, North Cyprus 99628, Turkey
| | | | - Bahar Taneri
- Department of Biological Sciences, Eastern Mediterranean University, Famagusta, North Cyprus 99628, Turkey.,Institute for Public Health Genomics, Department of Genetics & Cell Biology, Faculty of Health, Medicine & Life Sciences, Maastricht University, Maastricht, The Netherlands
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20
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Cejuela JM, Bojchevski A, Uhlig C, Bekmukhametov R, Kumar Karn S, Mahmuti S, Baghudana A, Dubey A, Satagopam VP, Rost B. nala: text mining natural language mutation mentions. Bioinformatics 2018; 33:1852-1858. [PMID: 28200120 PMCID: PMC5870606 DOI: 10.1093/bioinformatics/btx083] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/17/2016] [Accepted: 02/08/2017] [Indexed: 01/30/2023] Open
Abstract
Motivation The extraction of sequence variants from the literature remains an important task. Existing methods primarily target standard (ST) mutation mentions (e.g. ‘E6V’), leaving relevant mentions natural language (NL) largely untapped (e.g. ‘glutamic acid was substituted by valine at residue 6’). Results We introduced three new corpora suggesting named-entity recognition (NER) to be more challenging than anticipated: 28–77% of all articles contained mentions only available in NL. Our new method nala captured NL and ST by combining conditional random fields with word embedding features learned unsupervised from the entire PubMed. In our hands, nala substantially outperformed the state-of-the-art. For instance, we compared all unique mentions in new discoveries correctly detected by any of three methods (SETH, tmVar, or nala). Neither SETH nor tmVar discovered anything missed by nala, while nala uniquely tagged 33% mentions. For NL mentions the corresponding value shot up to 100% nala-only. Availability and Implementation Source code, API and corpora freely available at: http://tagtog.net/-corpora/IDP4+. Supplementary information Supplementary data are available at Bioinformatics online.
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Affiliation(s)
- Juan Miguel Cejuela
- TUM, Department of Informatics, Bioinformatics & Computational Biology - i12, Garching, Munich, Germany.,TUM Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), Garching, Germany
| | - Aleksandar Bojchevski
- TUM, Department of Informatics, Bioinformatics & Computational Biology - i12, Garching, Munich, Germany.,TUM Graduate School, Center of Doctoral Studies in Informatics and its Applications (CeDoSIA), Garching, Germany
| | - Carsten Uhlig
- TUM, Department of Informatics, Bioinformatics & Computational Biology - i12, Garching, Munich, Germany
| | - Rustem Bekmukhametov
- TUM, Department of Informatics, Bioinformatics & Computational Biology - i12, Garching, Munich, Germany.,Microsoft, WA, Bellevue, USA
| | - Sanjeev Kumar Karn
- TUM, Department of Informatics, Bioinformatics & Computational Biology - i12, Garching, Munich, Germany.,Ludwig Maximilian University, 80538 Munich & Siemens AG, Corporate Technology, Munich, Germany
| | - Shpend Mahmuti
- TUM, Department of Informatics, Bioinformatics & Computational Biology - i12, Garching, Munich, Germany
| | - Ashish Baghudana
- TUM, Department of Informatics, Bioinformatics & Computational Biology - i12, Garching, Munich, Germany.,BITS-Pilani K. K. Birla Goa Campus, Goa, India
| | - Ankit Dubey
- TUM, Department of Informatics, Bioinformatics & Computational Biology - i12, Garching, Munich, Germany.,Concur (Germany) GmbH, Frankfurt am Main, Germany
| | - Venkata P Satagopam
- Luxembourg Centre for Systems Biomedicine (LCSB), University of Luxembourg, Belvaux, Luxembourg
| | - Burkhard Rost
- TUM, Department of Informatics, Bioinformatics & Computational Biology - i12, Garching, Munich, Germany.,Institute of Advanced Study (TUM-IAS) & Institute for Food and Plant Sciences WZW - Weihenstephan & New York Consortium on Membrane Protein Structure (NYCOMPS) & Department of Biochemistry and Molecular Biophysics, Columbia University, New York, NY, USA
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21
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Abstract
Despite availability of sequence site-specific information resulting from years of sequencing and sequence feature curation, there have been few efforts to integrate and annotate this information. In this study, we update the number of human N-linked glycosylation sequons (NLGs), and we investigate cancer-relatedness of glycosylation-impacting somatic nonsynonymous single-nucleotide variation (nsSNV) by mapping human NLGs to cancer variation data and reporting the expected loss or gain of glycosylation sequon. We find 75.8% of all human proteins have at least one NLG for a total of 59,341 unique NLGs (includes predicted and experimentally validated). Only 27.4% of all NLGs are experimentally validated sites on 4,412 glycoproteins. With respect to cancer, 8,895 somatic-only nsSNVs abolish NLGs in 5,204 proteins and 12,939 somatic-only nsSNVs create NLGs in 7,356 proteins in cancer samples. nsSNVs causing loss of 24 NLGs on 23 glycoproteins and nsSNVs creating 41 NLGs on 40 glycoproteins are identified in three or more cancers. Of all identified cancer somatic variants causing potential loss or gain of glycosylation, only 36 have previously known disease associations. Although this work is computational, it builds on existing genomics and glycobiology research to promote identification and rank potential cancer nsSNV biomarkers for experimental validation.
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22
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Lee K, Kim B, Choi Y, Kim S, Shin W, Lee S, Park S, Kim S, Tan AC, Kang J. Deep learning of mutation-gene-drug relations from the literature. BMC Bioinformatics 2018; 19:21. [PMID: 29368597 PMCID: PMC5784504 DOI: 10.1186/s12859-018-2029-1] [Citation(s) in RCA: 27] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/25/2017] [Accepted: 01/17/2018] [Indexed: 12/31/2022] Open
Abstract
Background Molecular biomarkers that can predict drug efficacy in cancer patients are crucial components for the advancement of precision medicine. However, identifying these molecular biomarkers remains a laborious and challenging task. Next-generation sequencing of patients and preclinical models have increasingly led to the identification of novel gene-mutation-drug relations, and these results have been reported and published in the scientific literature. Results Here, we present two new computational methods that utilize all the PubMed articles as domain specific background knowledge to assist in the extraction and curation of gene-mutation-drug relations from the literature. The first method uses the Biomedical Entity Search Tool (BEST) scoring results as some of the features to train the machine learning classifiers. The second method uses not only the BEST scoring results, but also word vectors in a deep convolutional neural network model that are constructed from and trained on numerous documents such as PubMed abstracts and Google News articles. Using the features obtained from both the BEST search engine scores and word vectors, we extract mutation-gene and mutation-drug relations from the literature using machine learning classifiers such as random forest and deep convolutional neural networks. Our methods achieved better results compared with the state-of-the-art methods. We used our proposed features in a simple machine learning model, and obtained F1-scores of 0.96 and 0.82 for mutation-gene and mutation-drug relation classification, respectively. We also developed a deep learning classification model using convolutional neural networks, BEST scores, and the word embeddings that are pre-trained on PubMed or Google News data. Using deep learning, the classification accuracy improved, and F1-scores of 0.96 and 0.86 were obtained for the mutation-gene and mutation-drug relations, respectively. Conclusion We believe that our computational methods described in this research could be used as an important tool in identifying molecular biomarkers that predict drug responses in cancer patients. We also built a database of these mutation-gene-drug relations that were extracted from all the PubMed abstracts. We believe that our database can prove to be a valuable resource for precision medicine researchers. Electronic supplementary material The online version of this article (10.1186/s12859-018-2029-1) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kyubum Lee
- Department of Computer Science and Engineering, Korea University, Seoul, South Korea
| | - Byounggun Kim
- Interdisciplinary Graduate Program in Bioinformatics, Korea University, Seoul, South Korea
| | - Yonghwa Choi
- Department of Computer Science and Engineering, Korea University, Seoul, South Korea
| | - Sunkyu Kim
- Department of Computer Science and Engineering, Korea University, Seoul, South Korea
| | - Wonho Shin
- Interdisciplinary Graduate Program in Bioinformatics, Korea University, Seoul, South Korea
| | - Sunwon Lee
- Department of Computer Science and Engineering, Korea University, Seoul, South Korea
| | - Sungjoon Park
- Department of Computer Science and Engineering, Korea University, Seoul, South Korea
| | - Seongsoon Kim
- Department of Computer Science and Engineering, Korea University, Seoul, South Korea
| | - Aik Choon Tan
- Translational Bioinformatics and Cancer Systems Biology Laboratory, Division of Medical Oncology, Department of Medicine, University of Colorado Anschutz Medical Campus, Aurora, CO, 80045, USA.
| | - Jaewoo Kang
- Department of Computer Science and Engineering, Korea University, Seoul, South Korea. .,Interdisciplinary Graduate Program in Bioinformatics, Korea University, Seoul, South Korea.
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23
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Mahmood ASMA, Rao S, McGarvey P, Wu C, Madhavan S, Vijay-Shanker K. eGARD: Extracting associations between genomic anomalies and drug responses from text. PLoS One 2017; 12:e0189663. [PMID: 29261751 PMCID: PMC5738129 DOI: 10.1371/journal.pone.0189663] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2017] [Accepted: 11/29/2017] [Indexed: 12/25/2022] Open
Abstract
Tumor molecular profiling plays an integral role in identifying genomic anomalies which may help in personalizing cancer treatments, improving patient outcomes and minimizing risks associated with different therapies. However, critical information regarding the evidence of clinical utility of such anomalies is largely buried in biomedical literature. It is becoming prohibitive for biocurators, clinical researchers and oncologists to keep up with the rapidly growing volume and breadth of information, especially those that describe therapeutic implications of biomarkers and therefore relevant for treatment selection. In an effort to improve and speed up the process of manually reviewing and extracting relevant information from literature, we have developed a natural language processing (NLP)-based text mining (TM) system called eGARD (extracting Genomic Anomalies association with Response to Drugs). This system relies on the syntactic nature of sentences coupled with various textual features to extract relations between genomic anomalies and drug response from MEDLINE abstracts. Our system achieved high precision, recall and F-measure of up to 0.95, 0.86 and 0.90, respectively, on annotated evaluation datasets created in-house and obtained externally from PharmGKB. Additionally, the system extracted information that helps determine the confidence level of extraction to support prioritization of curation. Such a system will enable clinical researchers to explore the use of published markers to stratify patients upfront for 'best-fit' therapies and readily generate hypotheses for new clinical trials.
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Affiliation(s)
- A. S. M. Ashique Mahmood
- Department of Computer and Information Science, University of Delaware, Newark, Delaware, United States of America
- * E-mail:
| | - Shruti Rao
- Innovation Center For Biomedical Informatics, Georgetown University, Washington D.C, United States of America
| | - Peter McGarvey
- Innovation Center For Biomedical Informatics, Georgetown University, Washington D.C, United States of America
- Protein Information Resource, Georgetown University Medical Center, Washington D.C, United States of America
| | - Cathy Wu
- Department of Computer and Information Science, University of Delaware, Newark, Delaware, United States of America
- Protein Information Resource, Georgetown University Medical Center, Washington D.C, United States of America
- Center for Bioinformatics and Computational Biology, University of Delaware, Newark, Delaware, United States of America
| | - Subha Madhavan
- Innovation Center For Biomedical Informatics, Georgetown University, Washington D.C, United States of America
- Lombardi Comprehensive Cancer Center, Georgetown University Medical Center, Washington D.C, United States of America
| | - K. Vijay-Shanker
- Department of Computer and Information Science, University of Delaware, Newark, Delaware, United States of America
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24
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Khordad M, Mercer RE. Identifying genotype-phenotype relationships in biomedical text. J Biomed Semantics 2017; 8:57. [PMID: 29212530 PMCID: PMC5719522 DOI: 10.1186/s13326-017-0163-8] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2016] [Accepted: 10/28/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND One important type of information contained in biomedical research literature is the newly discovered relationships between phenotypes and genotypes. Because of the large quantity of literature, a reliable automatic system to identify this information for future curation is essential. Such a system provides important and up to date data for database construction and updating, and even text summarization. In this paper we present a machine learning method to identify these genotype-phenotype relationships. No large human-annotated corpus of genotype-phenotype relationships currently exists. So, a semi-automatic approach has been used to annotate a small labelled training set and a self-training method is proposed to annotate more sentences and enlarge the training set. RESULTS The resulting machine-learned model was evaluated using a separate test set annotated by an expert. The results show that using only the small training set in a supervised learning method achieves good results (precision: 76.47, recall: 77.61, F-measure: 77.03) which are improved by applying a self-training method (precision: 77.70, recall: 77.84, F-measure: 77.77). CONCLUSIONS Relationships between genotypes and phenotypes is biomedical information pivotal to the understanding of a patient's situation. Our proposed method is the first attempt to make a specialized system to identify genotype-phenotype relationships in biomedical literature. We achieve good results using a small training set. To improve the results other linguistic contexts need to be explored and an appropriately enlarged training set is required.
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Affiliation(s)
- Maryam Khordad
- Department of Computer Science, University of Western Ontario, 1151 Richmond Street, London, N6A 5B7 Canada
| | - Robert E. Mercer
- Department of Computer Science, University of Western Ontario, 1151 Richmond Street, London, N6A 5B7 Canada
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Névéol A, Zweigenbaum P. Making Sense of Big Textual Data for Health Care: Findings from the Section on Clinical Natural Language Processing. Yearb Med Inform 2017; 26:228-234. [PMID: 29063569 PMCID: PMC6239234 DOI: 10.15265/iy-2017-027] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/18/2017] [Indexed: 02/01/2023] Open
Abstract
Objectives: To summarize recent research and present a selection of the best papers published in 2016 in the field of clinical Natural Language Processing (NLP). Method: A survey of the literature was performed by the two section editors of the IMIA Yearbook NLP section. Bibliographic databases were searched for papers with a focus on NLP efforts applied to clinical texts or aimed at a clinical outcome. Papers were automatically ranked and then manually reviewed based on titles and abstracts. A shortlist of candidate best papers was first selected by the section editors before being peer-reviewed by independent external reviewers. Results: The five clinical NLP best papers provide a contribution that ranges from emerging original foundational methods to transitioning solid established research results to a practical clinical setting. They offer a framework for abbreviation disambiguation and coreference resolution, a classification method to identify clinically useful sentences, an analysis of counseling conversations to improve support to patients with mental disorder and grounding of gradable adjectives. Conclusions: Clinical NLP continued to thrive in 2016, with an increasing number of contributions towards applications compared to fundamental methods. Fundamental work addresses increasingly complex problems such as lexical semantics, coreference resolution, and discourse analysis. Research results translate into freely available tools, mainly for English.
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Affiliation(s)
- A. Névéol
- LIMSI, CNRS, Université Paris Saclay, Orsay, France
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Bokharaeian B, Diaz A, Taghizadeh N, Chitsaz H, Chavoshinejad R. SNPPhenA: a corpus for extracting ranked associations of single-nucleotide polymorphisms and phenotypes from literature. J Biomed Semantics 2017; 8:14. [PMID: 28388928 PMCID: PMC5383945 DOI: 10.1186/s13326-017-0116-2] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/05/2016] [Accepted: 01/13/2017] [Indexed: 11/17/2022] Open
Abstract
Background Single Nucleotide Polymorphisms (SNPs) are among the most important types of genetic variations influencing common diseases and phenotypes. Recently, some corpora and methods have been developed with the purpose of extracting mutations and diseases from texts. However, there is no available corpus, for extracting associations from texts, that is annotated with linguistic-based negation, modality markers, neutral candidates, and confidence level of associations. Method In this research, different steps were presented so as to produce the SNPPhenA corpus. They include automatic Named Entity Recognition (NER) followed by the manual annotation of SNP and phenotype names, annotation of the SNP-phenotype associations and their level of confidence, as well as modality markers. Moreover, the produced corpus was annotated with negation scopes and cues as well as neutral candidates that play crucial role as far as negation and the modality phenomenon in relation to extraction tasks. Result The agreement between annotators was measured by Cohen’s Kappa coefficient where the resulting scores indicated the reliability of the corpus. The Kappa score was 0.79 for annotating the associations and 0.80 for the confidence degree of associations. Further presented were the basic statistics of the annotated features of the corpus in addition to the results of our first experiments related to the extraction of ranked SNP-Phenotype associations. The prepared guideline documents render the corpus more convenient and facile to use. The corpus, guidelines and inter-annotator agreement analysis are available on the website of the corpus: http://nil.fdi.ucm.es/?q=node/639. Conclusion Specifying the confidence degree of SNP-phenotype associations from articles helps identify the strength of associations that could in turn assist genomics scientists in determining phenotypic plasticity and the importance of environmental factors. What is more, our first experiments with the corpus show that linguistic-based confidence alongside other non-linguistic features can be utilized in order to estimate the strength of the observed SNP-phenotype associations. Trial Registration: Not Applicable Electronic supplementary material The online version of this article (doi:10.1186/s13326-017-0116-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Behrouz Bokharaeian
- Facultad informatica, Complutense University of Madrid, Calle Profesor José García Santesmases, 9, 28040, Madrid, Spain.
| | - Alberto Diaz
- Facultad informatica, Complutense University of Madrid, Calle Profesor José García Santesmases, 9, 28040, Madrid, Spain
| | - Nasrin Taghizadeh
- School of Electrical and Computer Engineering, College of Engineering, University of Tehran, Tehran, Iran
| | - Hamidreza Chitsaz
- Department of Computer Science, Colorado State University, Fort Collins, CO, 80523, USA
| | - Ramyar Chavoshinejad
- External Collaborator, Reproductive Biomedicine Research Center, Royan Institute for Reproductive Biomedicine, Tehran, Iran
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Verspoor KM, Heo GE, Kang KY, Song M. Establishing a baseline for literature mining human genetic variants and their relationships to disease cohorts. BMC Med Inform Decis Mak 2016; 16 Suppl 1:68. [PMID: 27454860 PMCID: PMC4959367 DOI: 10.1186/s12911-016-0294-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The Variome corpus, a small collection of published articles about inherited colorectal cancer, includes annotations of 11 entity types and 13 relation types related to the curation of the relationship between genetic variation and disease. Due to the richness of these annotations, the corpus provides a good testbed for evaluation of biomedical literature information extraction systems. METHODS In this paper, we focus on assessing performance on extracting the relations in the corpus, using gold standard entities as a starting point, to establish a baseline for extraction of relations important for extraction of genetic variant information from the literature. We test the application of the Public Knowledge Discovery Engine for Java (PKDE4J) system, a natural language processing system designed for information extraction of entities and relations in text, on the relation extraction task using this corpus. RESULTS For the relations which are attested at least 100 times in the Variome corpus, we realise a performance ranging from 0.78-0.84 Precision-weighted F-score, depending on the relation. We find that the PKDE4J system adapted straightforwardly to the range of relation types represented in the corpus; some extensions to the original methodology were required to adapt to the multi-relational classification context. The results are competitive with state-of-the-art relation extraction performance on more heavily studied corpora, although the analysis shows that the Recall of a co-occurrence baseline outweighs the benefit of improved Precision for many relations, indicating the value of simple semantic constraints on relations. CONCLUSIONS This work represents the first attempt to apply relation extraction methods to the Variome corpus. The results demonstrate that automated methods have good potential to structure the information expressed in the published literature related to genetic variants, connecting mutations to genes, diseases, and patient cohorts. Further development of such approaches will facilitate more efficient biocuration of genetic variant information into structured databases, leveraging the knowledge embedded in the vast publication literature.
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Affiliation(s)
- Karin M Verspoor
- Department of Computing and Information Systems, The University of Melbourne, Melbourne, Australia
| | - Go Eun Heo
- Department of Library and Information Science, Yonsei University, Seoul, Korea
| | - Keun Young Kang
- Department of Library and Information Science, Yonsei University, Seoul, Korea
| | - Min Song
- Department of Library and Information Science, Yonsei University, Seoul, Korea.
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