• Title/Summary/Keyword: medical ontology

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Developing a Health Informatics Conceptual Framework for Representing Clinical Findings in Traditional East Asian Medicine (한의학 임상소견 표현을 위한 개념적 프레임워크 개발 연구)

  • Kim, Seon-Ho;Park, Kyung-Mo
    • The Journal of Korean Medicine
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    • v.32 no.1
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    • pp.121-129
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    • 2011
  • Objective: The propose of this study is to build a conceptual framework for representing clinical findings in Traditional East Asian Medicine(TEAM). As the existing standard models have been developed without considering features of Traditional Medicine, in this study we introduced unique characteristics for the TEAM. Method: This study was composed of three steps. First, we analyzed whether the existing clinical information models are suitable for representing clinical findings. Second, we analyzed ISO/TS 22789 model which is a ISO medical informatics standard, to find out the problem by applying clinical findings of TEAM into the model. Finally, we defined semantic links and a concept hierarchy in our model based on the analyzed results. The model includes the concepts for clinical findings and terms, and the semantic links can be regarded as relations between concepts, so that the representating clinical findings are completed by connecting concepts with other concepts. Results: Our framework was developed by removing unnecessary semantic links, and adding some necessary ones based on ISO/TS 22789 model. The ISO/TS 22789 model has a simple concept hierarchy, but in this study we subdivided the hierarchy and also considered interoperability with other terminological systems and standard models. Conclusions: This research needs more discussions, but is meaningful as proposing a way how to develop Traditional Medicine terminological systems. This study shows the limitations of existing models in describing clinical findings for TEAM, and what should be considered to represent Traditional Medicine knowledge, and propose a solution to improve the problem.

Issues of Applying Intelligent RSS Framework to Electronic Commerce (전자상거래의 지능형 RSS 도입을 위한 이슈 분석과 지능형 RSS 프레임워크의 제안)

  • Park, Sang-Un;Kang, Ju-Young;Kim, Woo-Ju
    • The Journal of Society for e-Business Studies
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    • v.12 no.2
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    • pp.269-290
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    • 2007
  • RSS is a core component of Web 2.0 which is expected to lead the most important innovation in the new IT environment. In that sense, it is actively utilized to distribute Web contents in various areas such as news, blog, multimedia, medical information, and conference and journal information. Also, it is expected to be a major effective marketing tool in electronic commerce domain. In the paper, we analyzed the problems of current utilization of RSS in domestic shopping malls, and suggest requirements for the effective use of RSS in electronic commerce. Furthermore, we proposed various issues and answers on the implementation of the requirements, and designed the intelligent RSS framework for electronic commerce based on the issues. Syntactic and semantic interoperability between the RSS service provider and the user is one of the most important issues in the framework. We suggested how to implement the interoperability based on Semantic Web technologies.

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An Identification of the Image Retrieval Domain from the Perspective of Library and Information Science with Author Co-citation and Author Bibliographic Coupling Analyses

  • Yoon, JungWon;Chung, EunKyung;Byun, Jihye
    • Journal of the Korean Society for Library and Information Science
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    • v.49 no.4
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    • pp.99-124
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    • 2015
  • As the improvement of digital technologies increases the use of images from various fields, the domain of image retrieval has evolved and become a growing topic of research in the Library and Information Science field. The purpose of this study is to identify the knowledge structure of the image retrieval domain by using the author co-citation analysis and author bibliographic coupling as analytical tools in order to understand the domain's past and present. The data set for this study is 245 articles with 8,031 cited articles in the field of image retrieval from 1998 to 2013, from the Web of Science citation database. According to the results of author co-citation analysis for the past of the image retrieval domain, our findings demonstrate that the intellectual structure of image retrieval in the LIS field consists of predominantly user-oriented approaches, but also includes some areas influenced by the CBIR area. More specifically, the user-oriented approach contains six specific areas which include image needs, information seeking, image needs and search behavior, image indexing and access, indexing of image collection, and web image search. On the other hand, for CBIR approaches, it contains feature-based image indexing, shape-based indexing, and IR & CBIR. The recent trends of image retrieval based on the results from author bibliographic coupling analysis show that the domain is expanding to emerging areas of medical images, multimedia, ontology- and tag-based indexing which thus reflects a new paradigm of information environment.

Gene Expression Profiling of the Habenula in Rats Exposed to Chronic Restraint Stress

  • Yoo, Hyeijung;Kim, Hyun Jung;Yang, Soo Hyun;Son, Gi Hoon;Gim, Jeong-An;Lee, Hyun Woo;Kim, Hyun
    • Molecules and Cells
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    • v.45 no.5
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    • pp.306-316
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    • 2022
  • Chronic stress contributes to the risk of developing depression; the habenula, a nucleus in epithalamus, is associated with many neuropsychiatric disorders. Using genome-wide gene expression analysis, we analyzed the transcriptome of the habenula in rats exposed to chronic restraint stress for 14 days. We identified 379 differentially expressed genes (DEGs) that were affected by chronic stress. These genes were enriched in neuroactive ligand-receptor interaction, the cAMP (cyclic adenosine monophosphate) signaling pathway, circadian entrainment, and synaptic signaling from the Kyoto Encyclopedia of Genes and Genomes pathway analysis and responded to corticosteroids, positive regulation of lipid transport, anterograde trans-synaptic signaling, and chemical synapse transmission from the Gene Ontology analysis. Based on protein-protein interaction network analysis of the DEGs, we identified neuroactive ligand-receptor interactions, circadian entrainment, and cholinergic synapse-related subclusters. Additionally, cell type and habenular regional expression of DEGs, evaluated using a recently published single-cell RNA sequencing study (GSE137478), strongly suggest that DEGs related to neuroactive ligand-receptor interaction and trans-synaptic signaling are highly enriched in medial habenular neurons. Taken together, our findings provide a valuable set of molecular targets that may play important roles in mediating the habenular response to stress and the onset of chronic stress-induced depressive behaviors.

Similarity Analysis of Sibling Nodes in SNOMED CT Terminology System (SNOMED CT 용어체계에서 형제 노드의 유사도 분석 기법)

  • Woo-Seok Ryu
    • The Journal of the Korea institute of electronic communication sciences
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    • v.19 no.1
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    • pp.295-300
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    • 2024
  • This paper discusses the incompleteness of the SNOMED CT and proposes a noble metric which evaluates similarity among sibling nodes as a method to address this incompleteness. SNOMED CT encompasses an extensive range of medical terms, but it faces issues of ontology incompleteness, such as missing concepts in the hierarchy. We propose a noble metric for evaluating similarity among nodes within a node group, composed of multiple sibling nodes, to identify missing concepts, and identify groups with low similarity. Analyzing the similarity of sibling node groups in the March 2023 international release of SNOMED CT, the average similarity of 29,199 sibling node groups, which are sub-concepts of the clinical finding concept and are consist of two or more sibling nodes, was found to be 0.81. The group with the lowest similarity was associated with child concepts of poisoning, with a similarity of 0.0036.

The Improvement Plan on Unifying from Law and Regulations Related to Radiation (방사선관계법 개정 시 용어 적용에 관한 개선 방안)

  • Jeong, Dong-Kyong;Lee, Jong-Back;Park, Myeong-Hwan
    • The Journal of Korean Society for Radiation Therapy
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    • v.18 no.1
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    • pp.7-12
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    • 2006
  • Purpose: This is for the purpose to help the bill related to technologists be systematic and unitary by carefully analyzing a legislation, an enforcement ordinance, and enforcement regulations in the connection with the radiological worker and the radiation workers from the law and regulations related to technologists. Materials and Methods: Concerning technologists, a legislation, an enforcement ordinance, and enforcement regulations for a sort of medical technician, regarding the radiological worker, the rules of diagnosis radiation equipment safety management, and concerning the radiation workers, atomic energy law, an enforcement ordinance and enforcement regulations were gathered, compared with one another, and analyzed. Results: Among technologists, in the case of working in the department of diagnosis radiation, the title 'Radiological Worker' is used by the Medical Service Law, and in the case of working in the department of radiation tumors or the one of nucleus medicine, the title 'Radiation Workers' is used by the Atomic Energy Law. Conclusion: Besides the technical term that is used by characteristic tasks, unification of the terms that can be used in common is necessary for sure. And when a legislation, an enforcement ordinance, enforcement regulations, and notification, things like that in the radiation field are amended, certainly they should be done by mutual agreement through negotiation between the organization related to radiation and the governmental organization.

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Transcriptome profiling and comparative analysis of Panax ginseng adventitious roots

  • Jayakodi, Murukarthick;Lee, Sang-Choon;Park, Hyun-Seung;Jang, Woojong;Lee, Yun Sun;Choi, Beom-Soon;Nah, Gyoung Ju;Kim, Do-Soon;Natesan, Senthil;Sun, Chao;Yang, Tae-Jin
    • Journal of Ginseng Research
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    • v.38 no.4
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    • pp.278-288
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    • 2014
  • Background: Panax ginseng Meyer is a traditional medicinal plant famous for its strong therapeutic effects and serves as an important herbal medicine. To understand and manipulate genes involved in secondary metabolic pathways including ginsenosides, transcriptome profiling of P. ginseng is essential. Methods: RNA-seq analysis of adventitious roots of two P. ginseng cultivars, Chunpoong (CP) and Cheongsun (CS), was performed using the Illumina HiSeq platform. After transcripts were assembled, expression profiling was performed. Results: Assemblies were generated from ~85 million and ~77 million high-quality reads from CP and CS cultivars, respectively. A total of 35,527 and 27,716 transcripts were obtained from the CP and CS assemblies, respectively. Annotation of the transcriptomes showed that approximately 90% of the transcripts had significant matches in public databases.We identified several candidate genes involved in ginsenoside biosynthesis. In addition, a large number of transcripts (17%) with different gene ontology designations were uniquely detected in adventitious roots compared to normal ginseng roots. Conclusion: This study will provide a comprehensive insight into the transcriptome of ginseng adventitious roots, and a way for successful transcriptome analysis and profiling of resource plants with less genomic information. The transcriptome profiling data generated in this study are available in our newly created adventitious root transcriptome database (http://im-crop.snu.ac.kr/transdb/index.php) for public use.

Identification and functional prediction of long noncoding RNAs related to intramuscular fat content in Laiwu pigs

  • Wang, Lixue;Xie, Yuhuai;Chen, Wei;Zhang, Yu;Zeng, Yongqing
    • Animal Bioscience
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    • v.35 no.1
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    • pp.115-125
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    • 2022
  • Objective: Intramuscular fat (IMF) is a critical economic indicator of pork quality. Studies on IMF among different pig breeds have been performed via high-throughput sequencing, but comparisons within the same pig breed remain unreported. Methods: This study was performed to explore the gene profile and identify candidate long noncoding RNA (lncRNAs) and mRNAs associated with IMF deposition among Laiwu pigs with different IMF contents. Based on the longissimus dorsi muscle IMF content, eight pigs from the same breed and management were selected and divided into two groups: a high IMF (>12%, H) and low IMF group (<5%, L). Whole-transcriptome sequencing was performed to explore the differentially expressed (DE) genes between these two groups. Results: The IMF content varied greatly among Laiwu pig individuals (2.17% to 13.93%). Seventeen DE lncRNAs (11 upregulated and 6 downregulated) and 180 mRNAs (112 upregulated and 68 downregulated) were found. Gene Ontology analysis indicated that the following biological processes played an important role in IMF deposition: fatty acid and lipid biosynthetic processes; the extracellular signal-regulated kinase cascade; and white fat cell differentiation. In addition, the peroxisome proliferator-activated receptor, phosphatidylinositol-3-kinase-protein kinase B, and mammalian target of rapamycin pathways were enriched in the pathway analysis. Intersection analysis of the target genes of DE lncRNAs and mRNAs revealed seven candidate genes associated with IMF accumulation. Five DE lncRNAs and 20 DE mRNAs based on the pig quantitative trait locus database were identified and shown to be related to fat deposition. The expression of five DE lncRNAs and mRNAs was verified by quantitative real time polymerase chain reaction (qRT-PCR). The results of qRT-PCR and RNA-sequencing were consistent. Conclusion: These results demonstrated that the different IMF contents among pig individuals may be due to the DE lncRNAs and mRNAs associated with lipid droplets and fat deposition.

Analyzing Contextual Polarity of Unstructured Data for Measuring Subjective Well-Being (주관적 웰빙 상태 측정을 위한 비정형 데이터의 상황기반 긍부정성 분석 방법)

  • Choi, Sukjae;Song, Yeongeun;Kwon, Ohbyung
    • Journal of Intelligence and Information Systems
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    • v.22 no.1
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    • pp.83-105
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    • 2016
  • Measuring an individual's subjective wellbeing in an accurate, unobtrusive, and cost-effective manner is a core success factor of the wellbeing support system, which is a type of medical IT service. However, measurements with a self-report questionnaire and wearable sensors are cost-intensive and obtrusive when the wellbeing support system should be running in real-time, despite being very accurate. Recently, reasoning the state of subjective wellbeing with conventional sentiment analysis and unstructured data has been proposed as an alternative to resolve the drawbacks of the self-report questionnaire and wearable sensors. However, this approach does not consider contextual polarity, which results in lower measurement accuracy. Moreover, there is no sentimental word net or ontology for the subjective wellbeing area. Hence, this paper proposes a method to extract keywords and their contextual polarity representing the subjective wellbeing state from the unstructured text in online websites in order to improve the reasoning accuracy of the sentiment analysis. The proposed method is as follows. First, a set of general sentimental words is proposed. SentiWordNet was adopted; this is the most widely used dictionary and contains about 100,000 words such as nouns, verbs, adjectives, and adverbs with polarities from -1.0 (extremely negative) to 1.0 (extremely positive). Second, corpora on subjective wellbeing (SWB corpora) were obtained by crawling online text. A survey was conducted to prepare a learning dataset that includes an individual's opinion and the level of self-report wellness, such as stress and depression. The participants were asked to respond with their feelings about online news on two topics. Next, three data sources were extracted from the SWB corpora: demographic information, psychographic information, and the structural characteristics of the text (e.g., the number of words used in the text, simple statistics on the special characters used). These were considered to adjust the level of a specific SWB. Finally, a set of reasoning rules was generated for each wellbeing factor to estimate the SWB of an individual based on the text written by the individual. The experimental results suggested that using contextual polarity for each SWB factor (e.g., stress, depression) significantly improved the estimation accuracy compared to conventional sentiment analysis methods incorporating SentiWordNet. Even though literature is available on Korean sentiment analysis, such studies only used only a limited set of sentimental words. Due to the small number of words, many sentences are overlooked and ignored when estimating the level of sentiment. However, the proposed method can identify multiple sentiment-neutral words as sentiment words in the context of a specific SWB factor. The results also suggest that a specific type of senti-word dictionary containing contextual polarity needs to be constructed along with a dictionary based on common sense such as SenticNet. These efforts will enrich and enlarge the application area of sentic computing. The study is helpful to practitioners and managers of wellness services in that a couple of characteristics of unstructured text have been identified for improving SWB. Consistent with the literature, the results showed that the gender and age affect the SWB state when the individual is exposed to an identical queue from the online text. In addition, the length of the textual response and usage pattern of special characters were found to indicate the individual's SWB. These imply that better SWB measurement should involve collecting the textual structure and the individual's demographic conditions. In the future, the proposed method should be improved by automated identification of the contextual polarity in order to enlarge the vocabulary in a cost-effective manner.

Genome-Wide Analysis of DNA Methylation before- and after Exercise in the Thoroughbred Horse with MeDIP-Seq

  • Gim, Jeong-An;Hong, Chang Pyo;Kim, Dae-Soo;Moon, Jae-Woo;Choi, Yuri;Eo, Jungwoo;Kwon, Yun-Jeong;Lee, Ja-Rang;Jung, Yi-Deun;Bae, Jin-Han;Choi, Bong-Hwan;Ko, Junsu;Song, Sanghoon;Ahn, Kung;Ha, Hong-Seok;Yang, Young Mok;Lee, Hak-Kyo;Park, Kyung-Do;Do, Kyoung-Tag;Han, Kyudong;Yi, Joo Mi;Cha, Hee-Jae;Ayarpadikannan, Selvam;Cho, Byung-Wook;Bhak, Jong;Kim, Heui-Soo
    • Molecules and Cells
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    • v.38 no.3
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    • pp.210-220
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    • 2015
  • Athletic performance is an important criteria used for the selection of superior horses. However, little is known about exercise-related epigenetic processes in the horse. DNA methylation is a key mechanism for regulating gene expression in response to environmental changes. We carried out comparative genomic analysis of genome-wide DNA methylation profiles in the blood samples of two different thoroughbred horses before and after exercise by methylated-DNA immunoprecipitation sequencing (MeDIP-Seq). Differentially methylated regions (DMRs) in the pre-and post-exercise blood samples of superior and inferior horses were identified. Exercise altered the methylation patterns. After 30 min of exercise, 596 genes were hypomethy-lated and 715 genes were hypermethylated in the superior horse, whereas in the inferior horse, 868 genes were hypomethylated and 794 genes were hypermethylated. These genes were analyzed based on gene ontology (GO) annotations and the exercise-related pathway patterns in the two horses were compared. After exercise, gene regions related to cell division and adhesion were hypermethylated in the superior horse, whereas regions related to cell signaling and transport were hypermethylated in the inferior horse. Analysis of the distribution of methylated CpG islands confirmed the hypomethylation in the gene-body methylation regions after exercise. The methylation patterns of transposable elements also changed after exercise. Long interspersed nuclear elements (LINEs) showed abundance of DMRs. Collectively, our results serve as a basis to study exercise-based reprogramming of epigenetic traits.