• Journal of the Korean Society for Library and Information Science
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• v.50 no.2
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• pp.309-336
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• 2016

This paper introduces a relation extraction system that can be used in identifying and classifying semantic relations between biomedical entities in scientific texts using machine learning methods such as Support Vector Machines (SVM). The suggested system includes many useful functions capable of extracting various linguistic features from sentences having a pair of biomedical entities and applying them into training relation extraction models for maximizing their performance. Three globally representative collections in biomedical domains were used in the experiments which demonstrate its superiority in various biomedical domains. As a result, it is most likely that the intensive experimental study conducted in this paper will provide meaningful foundations for research on bio-text analysis based on machine learning.

• Genomics & Informatics
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• v.19 no.3
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• pp.28.1-28.4
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• 2021

Since only a small number of patients have a rare disease, it is difficult to identify all of the features of these diseases. This is especially true for patients uncommonly presenting with rare diseases. It can also be difficult for the patient, their families, and even clinicians to know which one of a number of disease phenotypes the patient is exhibiting. To address this issue, during Biomedical Linked Annotation Hackathon 7 (BLAH7), we tried to extract Alexander disease patient data in Portable Document Format. We then visualized the phenotypic diversity of those Alexander disease patients with uncommon presentations. This led to us identifying several issues that we need to overcome in our future work.

• Genomics & Informatics
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• v.17 no.2
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• pp.14.1-14.6
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• 2019

The total number of scholarly publications grows day by day, making it necessary to explore and use simple yet effective ways to expose their metadata. Schema.org supports adding structured metadata to web pages via markup, making it easier for data providers but also for search engines to provide the right search results. Bioschemas is based on the standards of schema.org, providing new types, properties and guidelines for metadata, i.e., providing metadata profiles tailored to the Life Sciences domain. Here we present our proposed contribution to Bioschemas (from the project "Biotea"), which supports metadata contributions for scholarly publications via profiles and web components. Biotea comprises a semantic model to represent publications together with annotated elements recognized from the scientific text; our Biotea model has been mapped to schema.org following Bioschemas standards.

• Journal of the Korean Society for information Management
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• v.35 no.2
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• pp.63-88
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• 2018

This research evaluated differences of classification performance for feature selection methods using LDA topic model and Doc2Vec which is based on word embedding using deep learning, feature corpus sizes and classification algorithms. In addition to find the feature corpus with high performance of classification, an experiment was conducted using feature corpus was composed differently according to the location of the document and by adjusting the size of the feature corpus. Conclusionally, in the experiments using deep learning evaluate training frequency and specifically considered information for context inference. This study constructed biomedical document dataset, Disease-35083 which consisted biomedical scholarly documents provided by PMC and categorized by the disease category. Throughout the study this research verifies which type and size of feature corpus produces the highest performance and, also suggests some feature corpus which carry an extensibility to specific feature by displaying efficiency during the training time. Additionally, this research compares the differences between deep learning and existing method and suggests an appropriate method by classification environment.

• KIISE Transactions on Computing Practices
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• v.23 no.1
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• pp.28-36
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• 2017

After the genome projects of the 90s, a vast number of gene studies have been stored in online databases. By using these databases, several biological relationships can be inferred. In this study, we proposed a method to infer disease-gene relationships using title and body in biomedical text. The title was used to extract hub genes from data in the literature; whereas, the body of the literature was used to extract sub genes that are related to hub genes. Through these steps, we were able to construct a local gene-network for each report in the literature. By integrating the local gene-networks, we then constructed a global gene-network. Subsequent analyses of the global gene-network allowed inference of disease-related genes with high rank. We validated the proposed method by comparing with previous methods. The results indicated that the proposed method is a meaningful approach to infer disease-related genes.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2003.10a
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• pp.3-3
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• 2003

With biomedical literature expanding so rapidly, there is an urgent need to discover and organize knowledge extracted from texts. Although factual databases contain crucial information the overwhelming amount of new knowledge remains in textual form (e.g. MEDLINE). In addition, new terms are constantly coined as the relationships linking new genes, drugs, proteins etc. As the size of biomedical literature is expanding, more systems are applying a variety of methods to automate the process of knowledge acquisition and management. In my talk, I focus on the project, GENIA, of our group at the University of Tokyo, the objective of which is to construct an information extraction system of protein - protein interaction from abstracts of MEDLINE. The talk includes (1) Techniques we use fDr named entity recognition (1-a) SOHMM (Self-organized HMM) (1-b) Maximum Entropy Model (1-c) Lexicon-based Recognizer (2) Treatment of term variants and acronym finders (3) Event extraction using a full parser (4) Linguistic resources for text mining (GENIA corpus) (4-a) Semantic Tags (4-b) Structural Annotations (4-c) Co-reference tags (4-d) GENIA ontology I will also talk about possible extension of our work that links the findings of molecular biology with clinical findings, and claim that textual based or conceptual based biology would be a viable alternative to system biology that tends to emphasize the role of simulation models in bioinformatics.

• Genomics & Informatics
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• v.18 no.2
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• pp.24.1-24.7
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• 2020

Despite a growing number of natural language processing shared-tasks dedicated to the use of Twitter data, there is currently no ad-hoc annotation tool for the purpose. During the 6th edition of Biomedical Linked Annotation Hackathon (BLAH), after a short review of 19 generic annotation tools, we adapted GATE and TextAE for annotating Twitter timelines. Although none of the tools reviewed allow the annotation of all information inherent of Twitter timelines, a few may be suitable provided the willingness by annotators to compromise on some functionality.

• Journal of the Korean Society for Library and Information Science
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• v.51 no.4
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• pp.77-97
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• 2017

A recent sharp increase of the biomedical literature causes researchers to struggle to grasp the current research trends and conduct creative studies based on the previous results. In order to alleviate their difficulties in keeping up with the latest scholarly trends, numerous attempts have been made to develop specialized analytic services that can provide direct, intuitive and formalized scholarly information by using various text mining technologies such as information extraction and event detection. This paper introduces and evaluates total 8 Convolutional Neural Network (CNN) models for extracting biomedical events from academic abstracts by applying various feature utilization approaches. Also, this paper conducts performance comparison evaluation for the proposed models. As a result of the comparison, we confirmed that the Entity-Type-Fully-Connected model, one of the introduced models in the paper, showed the most promising performance (72.09% in F-score) in the event classification task while it achieved a relatively low but comparable result (21.81%) in the entire event extraction process due to the imbalance problem of the training collections and event identify model's low performance.

• Journal of the Korean Society for Library and Information Science
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• v.51 no.4
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• pp.227-248
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• 2017

This paper introduces an integrated model for systematically constructing a linguistic resource database that can be used by machine learning-based biomedical information extraction systems. The proposed method suggests an orderly process of collecting and constructing dictionaries and training sets for both named-entity recognition and relation extraction. Multiple heterogeneous structures for the resources which are collected from diverse sources are analyzed to derive essential items and fields for constructing the integrated database. All the collected resources are converted and refined to build an integrated linguistic resource storage. In this paper, we constructed entity dictionaries of gene, protein, disease and drug, which are considered core linguistic elements or core named entities in the biomedical domains and conducted verification tests to measure their acceptability.

• Journal of the Korean Society for information Management
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• v.36 no.1
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• pp.191-213
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• 2019

The process of obtaining scientific knowledge is conducted through research. Researchers deal with the uncertainty of science and establish certainty of scientific knowledge. In other words, in order to obtain scientific knowledge, uncertainty is an essential step that must be performed. The existing studies were predominantly performed through a hedging study of linguistic approaches and constructed corpus with uncertainty word manually in computational linguistics. They have only been able to identify characteristics of uncertainty in a particular research field based on the simple frequency. Therefore, in this study, we examine pattern of scientific knowledge based on uncertainty word according to the passage of time in biomedical literature where biomedical claims in sentences play an important role. For this purpose, biomedical propositions are analyzed based on semantic predications provided by UMLS and DMR topic modeling which is useful method to identify patterns in disciplines is applied to understand the trend of entity based topic with uncertainty. As time goes by, the development of research has been confirmed that uncertainty in scientific knowledge is moving toward a decreasing pattern.