• Korean Journal of Ichthyology
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• v.33 no.4
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• pp.205-216
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• 2021

Phylogenetic reconstruction based on one locus or a few loci can be misleading due to gene-tree/species-tree discordance. Species delimitation and intraspecific studies also often suffered from low resolution because of insufficient statistic power when few loci were used. Exon capture method is one of the most efficient way to collect genome-scale data, which can significantly augment studies that aimed to investigate patterns and histories of organisms at both intraspecific and high level. Here, I showed the advancement of shifting from single-gene method to genomic approach and the benefit of applying exon capture method comparing to alternative genomic techniques. Then, I explained the principle of exon capture method as well as providing detailed recommendations for applying this method. Finally, I demonstrated exon capture method using two applications and discussed future perspectives of this technology.

• Journal of Science Education
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• v.38 no.3
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• pp.670-690
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• 2014

The purpose of this study was to analyze paper and pencil test items of life science I in high school to diagnose problems of the test items developed by teachers, and to provide some implication for better assessment. 690 selection-type items and 162 supply-type items in life science I were collected from 10 general high schools. In the analysis of test items, the ratio of the selection-type item and the supply-type item was 81:19 in the number of items based on item type, while the ratio was 74.4:25.6 in the distribution of marks, indicating that the distribution of marks compared to the number of items was higher in the supply-type items. In the analysis by the Bloom's revised taxonomy of educational objectives, the items of 'conceptual knowledge' in the knowledge and those of 'understanding' in the cognition process were shown most in both the selection-type item and the supply-type item. In the analysis by the science assessment frameworks of NAEA, the items of 'knowledge' were shown 9 times more than those of 'inquiry'. When compared to the level of difficulty presented in the two-way specification table and the percentage of correct answers in the selection-type item, the concurrence was 41.5%. When compared to the ratio of number of items based on the item type of the supply-type items, the short-answer items were 34.0%, the descriptive items were 61.1%, and the drawing items were 4.9%. The drawing items were mainly developed in the unit of 'Cells and Continuity of Life'. When the descriptive items were classified by the acceptance of response, all the items were 'response restricted' type, and the items of 'restricted in content range' type among them were highest. When the items were classified by presentation of data, the items of 'presentation of data' type were highest(65.4%), and when classified by type of question, the items of 'knowledge description' type were highest(80.4%). In conclusion, it is needed to develop items belonging to 'inquiry' area more in the school, and to increase the ratio of the descriptive items, presenting various types of items.

• Korean Journal of Plant Taxonomy
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• v.34 no.1
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• pp.43-61
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• 2004

Molecular taxonomic studies were conducted to evaluate interspecific relationships in Korean Viola 34 taxa including two Japanese populations using RAPD(randornly amplified polymorphic DNA), ISSR(inter simple sequence repeat) and PCR-RFLP(restriction fragment length polymorphism) analysis. Only six and four primers out of 40 arbitrary and 12 ISSR primers were screened for 34 taxa, and were revealed 70 (98.6%) and 28 (96.6%) polymorphic bands, respectively. Fifteen restriction endonucleases produced 80 restriction sites and size variations from the large single copy region of cpDNA, 16 (20%) of which were polymorphic. The separate analyses from the RAPD, ISSR and PCR-RFLP data were incongruent in the relationships among 34 taxa, but combined data was in accordance with previous infrageneric classification system based on morphological characters, especially the subsection and series level. Section Chamaemelanium placed between subsect. Patellares and Vagimtae of section Nomimium was not formed as a distinct group. Viola alb ida complex including three very closely related taxa was recognized independent group within subsect. Patellares in combined data tree. This result strongly suggested that they should be treated to series Pinmtae. RAPD analysis was very useful to clarify the interspecific relationships among the species of Korean Viola than ISSH and PCR-RFLP analyses.

• Journal of KIISE:Software and Applications
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• v.35 no.9
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• pp.562-571
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• 2008

For the purpose of building domain ontology, this paper proposes a methodology for building core ontology first, and then enriching the core ontology with the concepts and relations in the domain thesaurus. First, the top-level concept taxonomy of the core ontology is built using domain dictionary and general domain thesaurus. Then, the concepts of the domain thesaurus are classified into top-level concepts in the core ontology, and relations between broader terms (BT) - narrower terms (NT) and related terms (RT) are classified into semantic relations defined for the core ontology. To classify concepts, a two-step approach is adopted, in which a frequency-based approach is complemented with a similarity-based approach. To classify relations, two techniques are applied: (i) for the case of insufficient training data, a rule-based module is for identifying isa relation out of non-isa ones; a pattern-based approach is for classifying non-taxonomic semantic relations from non-isa. (ii) For the case of sufficient training data, a maximum-entropy model is adopted in the feature-based classification, where k-NN approach is for noisy filtering of training data. A series of experiments show that performances of the proposed systems are quite promising and comparable to judgments by human experts.

• Korean Journal of Plant Taxonomy
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• v.36 no.3
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• pp.189-207
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• 2006

Goodyera rosulacea, which is morphologically similar to G. repens, is described recently as a new species based on its distinct morphological characters such as rosette-formed leaves, short rhizome and habitat. To verify the taxonomic identity of G. rosulacea and its taxonomic relationship within Korean Goodyera taxa, sequences of the internal transcribed spacer (ITS) region of nuclear ribosomal DNA and the trnL region of cpDNA from 24 accessions including 1 outgroup accession were analyzed. Aligned sequences were analyzed using maximum parsimony and distance method, and the taxonomic identity and the taxonomic relationships among the related taxa were estimated by the existence of private marker gene and the phylogenetic tree of the aligned sequences. Molecular data indicate that G. rosulacea gas several private marker genes and shows monophyly in phylogenetic trees of both ITS and trnL sequences. the pairwise distance between G. rosulacea and the orher taxa of Korean Goodyera was 3.49-6.68% for ITS region and 5.05-9.53% for trnL region, indicating that G. rosulacea could be treated as an independent species. Therefore, our molecular data support the taxonomic of G. rosulacea as a distinct species of Korea. In phylogenetic trees, G. rosulacea formed same clade with G. repens, which has similar morphological characters with G. rosulacea, and showed the lowest pairwise distance with G. repens among Korean Goodyera taxa. These molecular data sugguested that G. rosulacea and G. repens are closely related taxa.

• Korean Journal of Plant Taxonomy
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• v.44 no.1
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• pp.39-50
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• 2014

Phylogenetic positions of Sedirea and Neofinetia were addressed using the chloroplast matK and the nuclear ITS sequences. We also evaluate the usefulness of the makers for the identification of species and localities. Sedirea and Neofinetia form an independent monophyletic genus, respectively, in both matK and nuclear ITS trees. The sister genus of the Neofinetia was Vanda in both trees. In addition, our trees support the separate recognition of the Neofinetia from Vanda rather than the inclusion of Neofinetia into Vanda. The sister group of the Sedirea was (Dimorphorchis(Pteroceras(Saccolabiun+Phalaeonopsis))) clade. The Dimorphorchis was one of the most probable sister genus to the Sedirea. The sister group relationship between Sedirea and Aerides was suggested by their similar morphology, but not supported in molecular trees. The identification of species and localities of Neofinetia was possible using our two molecular markers. However, several pseudo-gene sequences are discovered from the public data base. In addition, the horizontal gene transfer of chloroplast genomes is frequent events in orchid hybrids. Therefore, we need a careful evaluation for the data prior to systematic use. Generation of sequence data from multiple accessions of a species may helpful to reduce these types of error.

• Korean Journal of Plant Taxonomy
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• v.41 no.2
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• pp.119-129
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• 2011

Phylogenetic studies were conducted to evaluate the taxonomic relationships among 27 taxa, including 2 outgroups of Korean Campanulaceae, using PCR-RFLP analysis and ITS sequences. In the PCR-RFLP analysis, 15 restriction endonucleases produced 244 restriction sites and size variations from the chloroplast DNA, and 59 restriction sites (24%) showed polymorphism. The length of the ITS regions ranged from 588 bp to 797 bp. The sequence divergence including the outgroups is 0-39.36%. Phylogenetic analyses based on PCR-RFLP and ITS data suggest that Campanulaceae is monophyletic; Codonopsis and Platycodon forms an independent clade; the Peracarpa and Asyneuma clade is a sister to the Adenophora-Hanabusaya clade; Campanula is monophyletic; and Wahlenbergia basally branches within the ITS tree, whereas they are placed between Campanula and the Codonopsis-Platycodon clade in the PCR-RFLP tree; Hanabusaya is placed within the Adenophora clade; and Adenophora is paraphyletic and shows discordance to the infrageneric classifications based on morphological data. The present results show two data sets, largely congruent at the generic level, but their phylogenetic positions, in particular the Wahlenbergia and Hanabusaya and the infrageneric classifications in Adenophora, show some incongruence.

• Korean Journal of Plant Taxonomy
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• v.35 no.4
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• pp.295-311
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• 2005

Starch gel electrophoretic studies using 24 populations of five Korean Orostachys species were conducted to investigate allozyme variation and to test hypotheses of systematic relationships among species. The resulting phenogram showed that the populations of five Korean Orostachys species were divided into two major groups. And they were concordant with molecular and morphological data in suggesting that Orostachys was divided into two groups corresponding to the subsect. Appendiculatae and subsect. Orostachys. The low genetic identities among Korean Orostachys species indicated that the species of Orostachys have diverged gradually through the model of geographical species. Comparing the previous genetic data from the species with similar life history and mode of reproduction, most of Korean Orostachys species revealed a significant low genetic variation, while the widespread O. japonicus showed a relatively high genetic variation among the Korean species. This kind of genetic variation pattern might be the results of the isolated habitats, limited numbers of individuals within the populations, destruction of habitats, inbreeding and asexual reproduction in Korean Orostachys populations. The Jungdongjin population (POP 21) of O. malocophyllus was genetically unrelated with remaining populations of the same species, and this interpretation was consistent to the results from the previous palynological and morphological studies. Our allozyme data supported the taxonomic treatment of recently proposed taxa, O. iwarenge (Makino) Hara for. magnus and O. margaritifolius.

• The Journal of Bigdata
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• v.6 no.1
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• pp.63-81
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• 2021

The performance of natural language processing is rapidly improving due to the recent development and application of machine learning and deep learning technologies, and as a result, the field of application is expanding. In particular, as the demand for analysis on unstructured text data increases, interest in NLP(Natural Language Processing) is also increasing. However, due to the complexity and difficulty of the natural language preprocessing process and machine learning and deep learning theories, there are still high barriers to the use of natural language processing. In this paper, for an overall understanding of NLP, by examining the main fields of NLP that are currently being actively researched and the current state of major technologies centered on machine learning and deep learning, We want to provide a foundation to understand and utilize NLP more easily. Therefore, we investigated the change of NLP in AI(artificial intelligence) through the changes of the taxonomy of AI technology. The main areas of NLP which consists of language model, text classification, text generation, document summarization, question answering and machine translation were explained with state of the art deep learning models. In addition, major deep learning models utilized in NLP were explained, and data sets and evaluation measures for performance evaluation were summarized. We hope researchers who want to utilize NLP for various purposes in their field be able to understand the overall technical status and the main technologies of NLP through this paper.

• Korean Journal of Soil Science and Fertilizer
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• v.43 no.2
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• pp.217-223
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• 2010

This study was conducted to reclassify Dongsong series based on the second edition of Soil Taxonomy and to discuss the formation of Dongsong series distributed on the lava plain at Cheolweon in Korea. Morphological properties of typifying pedon of Dongsong series were investigated, and physico-chemical properties were analyzed according to Soil Survey Laboratory Methods Manual. The typifying pedon of Dongsong series has brown (7.5YR 4/2) silty clay loam Ap horizon (0-16 cm), brown (7.5YR 4/2) silty clay loam BA horizon (16-22 cm), brown (7.5YR 4/2) silty clay Bt1 horizon (22-50 cm), reddish brown (5YR 5/4) silty clay Bt2 horizon (50-92 cm), and brown (7.5YR 4/3) silty clay loam Bt3 horizon (92-120 cm). It occurs on lava plain derived from baslt materials. The typifying pedon has higher bulk density than 0.90 Mg $m^{-3}$. That can not be classified as Andisol. But it has an argillic horizon from a depth of 22 to more than 120 cm, and a base saturation (sum of cations) of less than 35% at 125 cm below the upper boundary of the argillic horizon. It can be classified as Ultisol, not as Andisol or Alfisol. It has aquic conditions for some time in normal years in one or more horizons within 50 cm of the mineral soil surface, redoximorphic features between a depth of 25 cm, and a depth of 40 cm from the mineral soil surface, and redox concentrations, and 50%or more redox depletions with chroma of 2 or less in the matrix within the upper 12.5 cm of the argillic horizon. Therefore it can be classified as Aquult. It has episaturation, and keys out as Epiaquult. It has 50% or more chroma of 3 or more in one or more horizons between a depth of 25 cm from the mineral soil surface, and a depth of 75 cm. It can be classified as Aeric Aquult. Dongsong series have 35%or more clay at the particle-size control section, and have mesic soil temperature regime. Therefore they can be classified as fine, mesic family of Aeric Epiaquults, not as fine, mesic family of Typic Epiaqualfs. The Quarternary volcanic activities occurred in Jeju Island, Ulrung Island, Baekryeong Island, Cheolweon area, and Mt. Paekdu et al. in the Korean Penninsula. Most of them belong to the central eruption type, but Cheolweon area may be of the fissure eruption type. Dongsong series occur on Cheolweon lava plains derived from basaltic materials. Most soils distributed in Jeju Island, and derived from mainly pyroclastics are developed as Andisols. But Dongsong series distributed in Cheolweon lava plains which have a relatively dry climate and derived from basaltic materials are developed as Ultisols.