• Journal of Computing Science and Engineering
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• v.2 no.2
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• pp.109-136
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• 2008

In this survey paper, we discuss biomedical ontologies and major text mining techniques applied to biomedicine and healthcare. Biomedical ontologies such as UMLS are currently being adopted in text mining approaches because they provide domain knowledge for text mining approaches. In addition, biomedical ontologies enable us to resolve many linguistic problems when text mining approaches handle biomedical literature. As the first example of text mining, document clustering is surveyed. Because a document set is normally multiple topic, text mining approaches use document clustering as a preprocessing step to group similar documents. Additionally, document clustering is able to inform the biomedical literature searches required for the practice of evidence-based medicine. We introduce Swanson's UnDiscovered Public Knowledge (UDPK) model to generate biomedical hypotheses from biomedical literature such as MEDLINE by discovering novel connections among logically-related biomedical concepts. Another important area of text mining is document classification. Document classification is a valuable tool for biomedical tasks that involve large amounts of text. We survey well-known classification techniques in biomedicine. As the last example of text mining in biomedicine and healthcare, we survey information extraction. Information extraction is the process of scanning text for information relevant to some interest, including extracting entities, relations, and events. We also address techniques and issues of evaluating text mining applications in biomedicine and healthcare.

• Genomics & Informatics
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• v.16 no.3
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• pp.75-77
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• 2018

Genomics & Informatics (NLM title abbreviation: Genomics Inform) is the official journal of the Korea Genome Organization. Text corpus for this journal annotated with various levels of linguistic information would be a valuable resource as the process of information extraction requires syntactic, semantic, and higher levels of natural language processing. In this study, we publish our new corpus called GNI Corpus version 1.0, extracted and annotated from full texts of Genomics & Informatics, with NLTK (Natural Language ToolKit)-based text mining script. The preliminary version of the corpus could be used as a training and testing set of a system that serves a variety of functions for future biomedical text mining.

• Genomics & Informatics
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• v.2 no.2
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• pp.99-106
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• 2004

In this paper we introduce PubMiner, an intelligent machine learning based text mining system for mining biological information from the literature. PubMiner employs natural language processing techniques and machine learning based data mining techniques for mining useful biological information such as protein­protein interaction from the massive literature. The system recognizes biological terms such as gene, protein, and enzymes and extracts their interactions described in the document through natural language processing. The extracted interactions are further analyzed with a set of features of each entity that were collected from the related public databases to infer more interactions from the original interactions. An inferred interaction from the interaction analysis and native interaction are provided to the user with the link of literature sources. The performance of entity and interaction extraction was tested with selected MEDLINE abstracts. The evaluation of inference proceeded using the protein interaction data of S. cerevisiae (bakers yeast) from MIPS and SGD.

• Journal of Information Processing Systems
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• v.8 no.4
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• pp.575-588
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• 2012

Exploiting unlabeled text data with a relatively small labeled corpus has been an active and challenging research topic in text mining, due to the recent growth of the amount of biomedical literature. Biomedical named-entity recognition is an essential prerequisite task before effective text mining of biomedical literature can begin. This paper proposes an Active Co-Training (ACT) algorithm for biomedical named-entity recognition. ACT is a semi-supervised learning method in which two classifiers based on two different feature sets iteratively learn from informative examples that have been queried from the unlabeled data. We design a new classification problem to measure the informativeness of an example in unlabeled data. In this classification problem, the examples are classified based on a joint view of a feature set to be informative/non-informative to both classifiers. To form the training data for the classification problem, we adopt a query-by-committee method. Therefore, in the ACT, both classifiers are considered to be one committee, which is used on the labeled data to give the informativeness label to each example. The ACT method outperforms the traditional co-training algorithm in terms of f-measure as well as the number of training iterations performed to build a good classification model. The proposed method tends to efficiently exploit a large amount of unlabeled data by selecting a small number of examples having not only useful information but also a comprehensive pattern.

• Genomics & Informatics
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• v.18 no.2
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• pp.15.1-15.6
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• 2020

Named entity recognition tools are used to identify mentions of biomedical entities in free text and are essential components of high-quality information retrieval and extraction systems. Without good entity recognition, methods will mislabel searched text and will miss important information or identify spurious text that will frustrate users. Most tools do not capture non-contiguous entities which are separate spans of text that together refer to an entity, e.g., the entity "type 1 diabetes" in the phrase "type 1 and type 2 diabetes." This type is commonly found in biomedical texts, especially in lists, where multiple biomedical entities are named in shortened form to avoid repeating words. Most text annotation systems, that enable users to view and edit entity annotations, do not support non-contiguous entities. Therefore, experts cannot even visualize non-contiguous entities, let alone annotate them to build valuable datasets for machine learning methods. To combat this problem and as part of the BLAH6 hackathon, we extended the TextAE platform to allow visualization and annotation of non-contiguous entities. This enables users to add new subspans to existing entities by selecting additional text. We integrate this new functionality with TextAE's existing editing functionality to allow easy changes to entity annotation and editing of relation annotations involving non-contiguous entities, with importing and exporting to the PubAnnotation format. Finally, we roughly quantify the problem across the entire accessible biomedical literature to highlight that there are a substantial number of non-contiguous entities that appear in lists that would be missed by most text mining systems.

• Journal of the Korean Society for information Management
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• v.31 no.1
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• pp.231-250
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• 2014

Due to the recent development of Information and Communication Technologies (ICT), the amount of research publications has increased exponentially. In response to this rapid growth, the demand of automated text processing methods has risen to deal with massive amount of text data. Biomedical text mining discovering hidden biological meanings and treatments from biomedical literatures becomes a pivotal methodology and it helps medical disciplines reduce the time and cost. Many researchers have conducted literature-based discovery studies to generate new hypotheses. However, existing approaches either require intensive manual process of during the procedures or a semi-automatic procedure to find and select biomedical entities. In addition, they had limitations of showing one dimension that is, the cause-and-effect relationship between two concepts. Thus;this study proposed a novel approach to discover various relationships among source and target concepts and their intermediate concepts by expanding intermediate concepts to multi-levels. This study provided distinct perspectives for literature-based discovery by not only discovering the meaningful relationship among concepts in biomedical literature through graph-based path interference but also being able to generate feasible new hypotheses.

• Genomics & Informatics
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• v.18 no.2
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• pp.13.1-13.6
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• 2020

The prototype version of the full-text corpus of Genomics & Informatics has recently been archived in a GitHub repository. The full-text publications of volumes 10 through 17 are also directly downloadable from PubMed Central (PMC) as XML files. During the Biomedical Linked Annotation Hackathon 6 (BLAH6), we experimented with converting, annotating, and updating 301 PMC full-text articles of Genomics & Informatics using PubAnnotation, a system that provides a convenient way to add PMC publications based on PMCID. Thus, this review aims to provide a tutorial overview of practicing the iterative task of named entity recognition with the PubAnnotation/PubDictionaries/TextAE ecosystem. We also describe developing a conversion tool between the Genia tagger output and the JSON format of PubAnnotation during the hackathon.

• Korean Journal of Clinical Pharmacy
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• v.27 no.4
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• pp.221-227
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• 2017

Background: As personalized healthcare industry has attracted much attention, big data analysis of healthcare data is essential. Lots of healthcare data such as product labeling, biomedical literature and social media data are unstructured, extracting meaningful information from the unstructured text data are becoming important. In particular, text mining for adverse drug reactions (ADRs) reports is able to provide signal information to predict and detect adverse drug reactions. There has been no study on text analysis of expert opinion on Korea Adverse Event Reporting System (KAERS) databases in Korea. Methods: Expert opinion text of KAERS database provided by Korea Institute of Drug Safety & Risk Management (KIDS-KD) are analyzed. To understand the whole text, word frequency analysis are performed, and to look for important keywords from the text TF-IDF weight analysis are performed. Also, related keywords with the important keywords are presented by calculating correlation coefficient. Results: Among total 90,522 reports, 120 insulin ADR report and 858 tramadol ADR report were analyzed. The ADRs such as dizziness, headache, vomiting, dyspepsia, and shock were ranked in order in the insulin data, while the ADR symptoms such as vomiting, 어지러움, dizziness, dyspepsia and constipation were ranked in order in the tramadol data as the most frequently used keywords. Conclusion: Using text mining of the expert opinion in KIDS-KD, frequently mentioned ADRs and medications are easily recovered. Text mining in ADRs research is able to play an important role in detecting signal information and prediction of ADRs.

• Genomics & Informatics
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• v.16 no.4
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• pp.40.1-40.3
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• 2018

There is a communal need for an annotated corpus consisting of the full texts of biomedical journal articles. In response to community needs, a prototype version of the full-text corpus of Genomics & Informatics, called GNI version 1.0, has recently been published, with 499 annotated full-text articles available as a corpus resource. However, GNI needs to be updated, as the texts were shallow-parsed and annotated with several existing parsers. I list issues associated with upgrading annotations and give an opinion on the methodology for developing the next version of the GNI corpus, based on a semi-automatic strategy for more linguistically rich corpus annotation.

• International Journal of Fuzzy Logic and Intelligent Systems
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• v.15 no.2
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• pp.111-120
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• 2015

Protein named entity identification is one of the most essential and fundamental predecessor for extracting information about protein-protein interactions from biomedical literature. In this paper, we explore the use of abstracts of biomedical literature in MEDLINE for protein name identification and present the results of the conducted experiments. We present a robust and effective approach to classify biomedical named entities into protein and non-protein classes, based on a rich set of features: orthographic, keyword, morphological and newly introduced Protein-Score features. Our procedure shows significant performance in the experiments on GENIA corpus using Random Forest, achieving the highest values of precision 92.7%, recall 91.7%, and F-measure 92.2% for protein identification, while reducing the training and testing time significantly.