• Title/Summary/Keyword: core ontology

Search Result 77, Processing Time 0.02 seconds

Linking OntoCloud to WordNet (OntoCloud와 워드넷 연결)

  • Park, Kwang-Hee;Kim, Eun-Kyung;Choi, DongHyun;Choi, Key-Sun
    • Annual Conference on Human and Language Technology
    • /
    • 2010.10a
    • /
    • pp.172-176
    • /
    • 2010
  • 본 논문에서는 위키피디아의 '틀(temp late)'을 기조로 하여 작성된 온톨로지인 OntoCloud의 신뢰도를 보장하고 공유 및 재사용을 가능하게 하기 위하여 또 다른 어휘집합체인 워드넷(WordNet)과의 매핑을 한다. 온톨로지 매핑 기술은 온톨로지 개발 기술의 한 방법으로, 서로 비슷한 도메인을 대상으로 이미 구축되어진 서로 다른 다수의 온롤로지를 연결시킴으로서 하나의 풍부한 정보를 가지고 있는 연결망을 구축하는 방법이다. 본 논문에서는 OntoCloud와 워드넷을 두개의 온톨로지로 정의하고 각 온톨로지의 개념에 대한 정의문 비교 방법을 통해서 두개의 온톨로지에 존재하는 유사한 개념을 연결한다. 이렇게 매핑된 정보들은 OntoCloud 개념을 워드넷 어휘로 연결함으로써 개념에 대한 직관적인 이해를 돕고, 워드넷에 연결된 다른 시소러스 (예: SUMO, CoreNet 등)와 간접적으로 연결할 수 있는 틀을 마련한다. 또한 온톨로지의 상하위 계층정보를 자동으로 보강하는 등의 OntoCloud 유지보수에 활용될 수 있다. 본 논문의 실험에서는 두개의 서로 다른 온톨로지의 정의문에 사용된 어휘의 겹침 정도로 두개의 개념의 유사성을 판별하는 방법을 보인다. 본 논문에서 제시한 방법으로 약 73%의 개념 매핑에 성공하였으나, 추후 매핑 프로세스의 전처리 과정(약자 처리 및 복합명사 대응 모듈)을 추가하고 온톨로지의 구조적 특성을 활용하여 유사 개념 자동 매핑 기술을 향상시키고자 한다.

  • PDF

Comprehensive Transcriptomic Analysis of Cordyceps militaris Cultivated on Germinated Soybeans

  • Yoo, Chang-Hyuk;Sadat, Md. Abu;Kim, Wonjae;Park, Tae-Sik;Park, Dong Ki;Choi, Jaehyuk
    • Mycobiology
    • /
    • v.50 no.1
    • /
    • pp.1-11
    • /
    • 2022
  • The ascomycete fungus Cordyceps militaris infects lepidopteran larvae and pupae and forms characteristic fruiting bodies. Owing to its immune-enhancing effects, the fungus has been used as a medicine. For industrial application, this fungus can be grown on geminated soybeans as an alternative protein source. In our study, we performed a comprehensive transcriptomic analysis to identify core gene sets during C. militaris cultivation on germinated soybeans. RNA-Seq technology was applied to the fungal cultures at seven-time points (2, 4, and 7-day and 2, 3, 5, 7-week old cultures) to investigate the global transcriptomic change. We conducted a time-series analysis using a two-step regression strategy and chose 1460 significant genes and assigned them into five clusters. Characterization of each cluster based on Gene Ontology and Kyoto Encyclopedia of Genes and Genomes databases revealed that transcription profiles changed after two weeks of incubation. Gene mapping of cordycepin biosynthesis and isoflavone modification pathways also confirmed that gene expression in the early stage of GSC cultivation is important for these metabolic pathways. Our transcriptomic analysis and selected genes provided a comprehensive molecular basis for the cultivation of C. militaris on germinated soybeans.

Comparative transcriptome analysis of Cordyceps militaris grown on germinated soybean media

  • Yoo, Chang-Hyuk;Choi, Jaehyuk
    • Journal of Mushroom
    • /
    • v.20 no.1
    • /
    • pp.7-12
    • /
    • 2022
  • The ascomycete fungus Cordyceps militaris infects lepidopteran insect pupae, forming characteristic fruiting bodies called "Dong Chung Ha Cho" in Korean. They have been used as medicines owing to their anti-allergic, anti-inflammatory, and immune-enhancing effects. This fungus can be grown on the geminated soybeans Rhynchosia nulubilis, which also contains several novel isoflavones. We performed a comparative transcriptome analysis to determine core gene sets or pathways contributing to biologically active products such as isoflavone. Initially, we sequenced 2-week-old fungal cultures on different soybean agar media, where different amounts of water agar were implemented to show different surface topology. We selected 830 upregulated and 188 downregulated genes by comparing linear models of the samples (two-fold change threshold). Gene ontology analysis identified that the "IMP biosynthesis" term was significantly found in the upregulated gene sets. The pathway is involved in the synthesis of cordycepin, the reference chemical for C. militaris. This finding in the transcriptome data is consistent with the previous observation: increased cordycepin concentrations in the C. militaris cultured on germinated soybean.

A Mobile Semantic Integrated Search System of National Defense Research Information (국방연구정보의 모바일 시맨틱 통합검색 시스템)

  • Yoo, Dong-Hee;Ra, Min-Young
    • The KIPS Transactions:PartB
    • /
    • v.18B no.5
    • /
    • pp.295-304
    • /
    • 2011
  • To effectively manage research information in the field of national defense, metadata about the information should be managed systematically, and an integrated system to help convergence and management of the information should be implemented based on the metadata. In addition, the system should provide the users with effective integrated search services in a mobile environment, because searching via the use of mobile devices is increasing. The objective of this paper is to suggest a MSISS (Mobile Semantic Integrated Search System), which satisfies the requirements for effective management of the national defense research information. Specifically, we defined national defense research ontologies and national defense research rules after analyzing the Dublin Core metadata and database information of the major military research institutions. We implemented a prototype system for MSISS to demonstrate the use of the ontologies and rules for semantic integrated searching of the military research information. We also presented a triple-based search service to support semantic integrated search in a mobile environment and suggested future mobile semantic integrated search services.

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
    • /
    • v.12 no.2
    • /
    • pp.269-290
    • /
    • 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.

  • PDF

siRNAs Derived from Cymbidium Mosaic Virus and Odontoglossum Ringspot Virus Down-modulated the Expression Levels of Endogenous Genes in Phalaenopsis equestris

  • Lan, Han-hong;Wang, Cui-mei;Chen, Shuang-shuang;Zheng, Jian-ying
    • The Plant Pathology Journal
    • /
    • v.35 no.5
    • /
    • pp.508-520
    • /
    • 2019
  • Interplay between Cymbidium mosaic virus (CymMV)/Odontoglossum ringspot virus (ORSV) and its host plant Phalaenopsis equestris remain largely unknown, which led to deficiency of effective measures to control disease of P. equestris caused by infecting viruses. In this study, for the first time, we characterized viral small interfering RNAs (vsiRNAs) profiles in P. equestris co-infected with CymMV and ORSV through small RNA sequencing technology. CymMV and ORSV small interfering RNAs (siRNAs) demonstrated several general and specific/new characteristics. vsiRNAs, with A/U bias at the first nucleotide, were predominantly 21-nt long and they were derived predominantly (90%) from viral positive-strand RNA. 21-nt siRNA duplexes with 0-nt overhangs were the most abundant 21-nt duplexes, followed by 2-nt overhangs and then 1-nt overhangs 21-nt duplexes in infected P. equestris. Continuous but heterogeneous distribution and secondary structures prediction implied that vsiRNAs originate predominantly by direct Dicer-like enzymes cleavage of imperfect duplexes in the most folded regions of the positive strand of both viruses RNA molecular. Furthermore, we totally predicted 54 target genes by vsiRNAs with psRNATarget server, including disease/stress response-related genes, RNA interference core components, cytoskeleton-related genes, photosynthesis or energy supply related genes. Gene Ontology classification showed that a majority of the predicted targets were related to cellular components and cellular processes and performed a certain function. All target genes were down-regulated with different degree by vsiRNAs as shown by real-time reverse transcription polymerase chain reaction. Taken together, CymMV and ORSV siRNAs played important roles in interplay with P. equestris by down modulating the expression levels of endogenous genes in host plant.

Identification of genomic diversity and selection signatures in Luxi cattle using whole-genome sequencing data

  • Mingyue Hu;Lulu Shi;Wenfeng Yi;Feng Li;Shouqing Yan
    • Animal Bioscience
    • /
    • v.37 no.3
    • /
    • pp.461-470
    • /
    • 2024
  • Objective: The objective of this study was to investigate the genetic diversity, population structure and whole-genome selection signatures of Luxi cattle to reveal its genomic characteristics in terms of meat and carcass traits, skeletal muscle development, body size, and other traits. Methods: To further analyze the genomic characteristics of Luxi cattle, this study sequenced the whole-genome of 16 individuals from the core conservation farm in Shandong region, and collected 174 published genomes of cattle for conjoint analysis. Furthermore, three different statistics (pi, Fst, and XP-EHH) were used to detect potential positive selection signatures related to selection in Luxi cattle. Moreover, gene ontology and Kyoto encyclopedia of genes and genomes pathway enrichment analyses were performed to reveal the potential biological function of candidate genes harbored in selected regions. Results: The results showed that Luxi cattle had high genomic diversity and low inbreeding levels. Using three complementary methods (pi, Fst, and XP-EHH) to detect the signatures of selection in the Luxi cattle genome, there were 2,941, 2,221 and 1,304 potentially selected genes identified, respectively. Furthermore, there were 45 genes annotated in common overlapping genomic regions covered 0.723 Mb, including PLAG1 zinc finger (PLAG1), dedicator of cytokinesis 3 (DOCK3), ephrin A2 (EFNA2), DAZ associated protein 1 (DAZAP1), Ral GTPase activating protein catalytic subunit alpha 1 (RALGAPA1), mediator complex subunit 13 (MED13), and decaprenyl diphosphate synthase subunit 2 (PDSS2), most of which were enriched in pathways related to muscle growth and differentiation and immunity. Conclusion: In this study, we provided a series of genes associated with important economic traits were found in positive selection regions, and a scientific basis for the scientific conservation and genetic improvement of Luxi cattle.

Network Pharmacology Analysis and Efficacy Prediction of GunryeongTang Constituents in Diabetic Complications (당뇨 합병증과 군령탕 구성성분의 네트워크 약리학 분석 및 효능 예측)

  • Jung Joo Yoon;Hye Yoom Kim;Ai Lin Tai;Ho Sub Lee;Dae Gill Kang
    • Herbal Formula Science
    • /
    • v.32 no.1
    • /
    • pp.11-28
    • /
    • 2024
  • Objectives : GunRyeong-Tang(GRT) is a traditional herbal prescription that combines Oryeongsan and Sagunja-tang. This study employed network analysis methods on the components of GRT and target genes related to diabetes complications to predict the improvement effects of GRT on diabetes complications. Methods : The collection of active compounds of GRT and related target genes involved the utilization of public databases and the PubChem database. We selected diabetes complication-related genes using GeneCards and confirmed their correlation through comparative analysis with the target genes of GRT. We constructed a network using Cytoscape 3.9.1 and conducted topological analysis. To predict the mechanism, we performed functional enrichment analysis based on Gene Ontology (GO) biological processes and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways. Results : Through network analysis, 234 active compounds and 1361 related genes were collected from GRT. A total of 9,136 genes related to diabetes complications were collected, and 1,039 target genes overlapping with the components of GRT were identified. The core genes of this network were TP53, INS, AKT1, ALB, and EGFR. In addition, GRT significantly reduced the H9c2 cell size and the expression of myocardial hypertrophy biomarkers (ANP, BNP), which were increased by high glucose (HG). Conclusions : Through this study, we were able to predict the activity and mechanism of action of GRT on diabetes and diabetic complications, and confirmed the potential of GRT as a treatment for diabetes complications through the effect of GRT on improving myocardial hypertrophy for diabetic cardiomyopathy.

Analyzing Disaster Response Terminologies by Text Mining and Social Network Analysis (텍스트 마이닝과 소셜 네트워크 분석을 이용한 재난대응 용어분석)

  • Kang, Seong Kyung;Yu, Hwan;Lee, Young Jai
    • Information Systems Review
    • /
    • v.18 no.1
    • /
    • pp.141-155
    • /
    • 2016
  • This study identified terminologies related to the proximity and frequency of disaster by social network analysis (SNA) and text mining, and then expressed the outcome into a mind map. The termdocument matrix of text mining was utilized for the terminology proximity analysis, and the SNA closeness centrality was calculated to organically express the relationship of the terminologies through a mind map. By analyzing terminology proximity and selecting disaster response-related terminologies, this study identified the closest field among all the disaster response fields to disaster response and the core terms in each disaster response field. This disaster response terminology analysis could be utilized in future core term-based terminology standardization, disaster-related knowledge accumulation and research, and application of various response scenario compositions, among others.

The Adoption and Diffusion of Semantic Web Technology Innovation: Qualitative Research Approach (시맨틱 웹 기술혁신의 채택과 확산: 질적연구접근법)

  • Joo, Jae-Hun
    • Asia pacific journal of information systems
    • /
    • v.19 no.1
    • /
    • pp.33-62
    • /
    • 2009
  • Internet computing is a disruptive IT innovation. Semantic Web can be considered as an IT innovation because the Semantic Web technology possesses the potential to reduce information overload and enable semantic integration, using capabilities such as semantics and machine-processability. How should organizations adopt the Semantic Web? What factors affect the adoption and diffusion of Semantic Web innovation? Most studies on adoption and diffusion of innovation use empirical analysis as a quantitative research methodology in the post-implementation stage. There is criticism that the positivist requiring theoretical rigor can sacrifice relevance to practice. Rapid advances in technology require studies relevant to practice. In particular, it is realistically impossible to conduct quantitative approach for factors affecting adoption of the Semantic Web because the Semantic Web is in its infancy. However, in an early stage of introduction of the Semantic Web, it is necessary to give a model and some guidelines and for adoption and diffusion of the technology innovation to practitioners and researchers. Thus, the purpose of this study is to present a model of adoption and diffusion of the Semantic Web and to offer propositions as guidelines for successful adoption through a qualitative research method including multiple case studies and in-depth interviews. The researcher conducted interviews with 15 people based on face-to face and 2 interviews by telephone and e-mail to collect data to saturate the categories. Nine interviews including 2 telephone interviews were from nine user organizations adopting the technology innovation and the others were from three supply organizations. Semi-structured interviews were used to collect data. The interviews were recorded on digital voice recorder memory and subsequently transcribed verbatim. 196 pages of transcripts were obtained from about 12 hours interviews. Triangulation of evidence was achieved by examining each organization website and various documents, such as brochures and white papers. The researcher read the transcripts several times and underlined core words, phrases, or sentences. Then, data analysis used the procedure of open coding, in which the researcher forms initial categories of information about the phenomenon being studied by segmenting information. QSR NVivo version 8.0 was used to categorize sentences including similar concepts. 47 categories derived from interview data were grouped into 21 categories from which six factors were named. Five factors affecting adoption of the Semantic Web were identified. The first factor is demand pull including requirements for improving search and integration services of the existing systems and for creating new services. Second, environmental conduciveness, reference models, uncertainty, technology maturity, potential business value, government sponsorship programs, promising prospects for technology demand, complexity and trialability affect the adoption of the Semantic Web from the perspective of technology push. Third, absorptive capacity is an important role of the adoption. Fourth, suppler's competence includes communication with and training for users, and absorptive capacity of supply organization. Fifth, over-expectance which results in the gap between user's expectation level and perceived benefits has a negative impact on the adoption of the Semantic Web. Finally, the factor including critical mass of ontology, budget. visible effects is identified as a determinant affecting routinization and infusion. The researcher suggested a model of adoption and diffusion of the Semantic Web, representing relationships between six factors and adoption/diffusion as dependent variables. Six propositions are derived from the adoption/diffusion model to offer some guidelines to practitioners and a research model to further studies. Proposition 1 : Demand pull has an influence on the adoption of the Semantic Web. Proposition 1-1 : The stronger the degree of requirements for improving existing services, the more successfully the Semantic Web is adopted. Proposition 1-2 : The stronger the degree of requirements for new services, the more successfully the Semantic Web is adopted. Proposition 2 : Technology push has an influence on the adoption of the Semantic Web. Proposition 2-1 : From the perceptive of user organizations, the technology push forces such as environmental conduciveness, reference models, potential business value, and government sponsorship programs have a positive impact on the adoption of the Semantic Web while uncertainty and lower technology maturity have a negative impact on its adoption. Proposition 2-2 : From the perceptive of suppliers, the technology push forces such as environmental conduciveness, reference models, potential business value, government sponsorship programs, and promising prospects for technology demand have a positive impact on the adoption of the Semantic Web while uncertainty, lower technology maturity, complexity and lower trialability have a negative impact on its adoption. Proposition 3 : The absorptive capacities such as organizational formal support systems, officer's or manager's competency analyzing technology characteristics, their passion or willingness, and top management support are positively associated with successful adoption of the Semantic Web innovation from the perceptive of user organizations. Proposition 4 : Supplier's competence has a positive impact on the absorptive capacities of user organizations and technology push forces. Proposition 5 : The greater the gap of expectation between users and suppliers, the later the Semantic Web is adopted. Proposition 6 : The post-adoption activities such as budget allocation, reaching critical mass, and sharing ontology to offer sustainable services are positively associated with successful routinization and infusion of the Semantic Web innovation from the perceptive of user organizations.