• 한국언어정보학회:학술대회논문집
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• 한국언어정보학회 2007년도 정기학술대회
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• pp.13-28
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• 2007

This is a speculative paper, describing a recently started effort to give a formal semantics to semantic annotation schemes. Semantic annotations are intended to capture certain semantic information in a text, which means that it only makes sense to use semantic annotations if these have a well-defined semantics. In practice, however, semantic annotation schemes are used that lack any formal semantics. In this paper we outline how existing approaches to the annotation of temporal information, semantic roles, and reference relations can be integrated in a single XML-based format and can be given a formal semantics by translating them into second-order logic. This is argued to offer an incremental aproach to the incorporation of semantic information in natural language processing that does not suffer from the problems of ambiguity and lack of robustness that are common to traditional approaches to computational semantics.

• 한국언어정보학회:학술대회논문집
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• 한국언어정보학회 2002년도 Language, Information, and Computation Proceedings of The 16th Pacific Asia Conference
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• pp.1-1
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• 2002

This talk provides an overview of current work in my research group on the syntactic annotation of the T bingen corpus of spoken German and of the German Reference Corpus (Deutsches Referenzkorpus: DEREKO) of written texts. Morpho-syntactic and syntactic annotation as well as annotation of function-argument structure for these corpora is performed automatically by a hybrid architecture that combines robust symbolic parsing with finite-state methods ("chunk parsing" in the sense Abney) with memory-based parsing (in the sense of Daelemans). The resulting robust annotations can be used by theoretical linguists, who lire interested in large-scale, empirical data, and by computational linguists, who are in need of training material for a wide range of language technology applications. To aid retrieval of annotated trees from the treebank, a query tool VIQTORYA with a graphical user interface and a logic-based query language has been developed. VIQTORYA allows users to query the treebanks for linguistic structures at the word level, at the level of individual phrases, and at the clausal level.

• Genomics & Informatics
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• 제3권3호
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• pp.94-97
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• 2005

We have built a database server called Patome which contains the annotation information for patented bio-sequences from the Korean Intellectual Property Office (KIPO). The aims of the Patome are to annotate Korean patent bio-sequences and to provide information on patent relationship of public database entries. The patent sequences were annotated with Reference Sequence (RefSeq) or NCBI's nr database. The raw patent data and the annotated data were stored in the database. Annotation information can be used to determine whether a particular RefSeq ID or NCBI's nr ID is related to Korean patent. Patome infrastructure consists of three components­the database itself, a sequence data loader, and an online database query interface. The database can be queried using submission number, organism, title, applicant name, or accession number. Patome can be accessed at http://www.patome.net. The information will be updated every two months.

• 한국언어정보학회지:언어와정보
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• 제18권2호
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• pp.141-168
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• 2014

Recognizing spatial information associated with events expressed in natural language text is essential not only for the interpretation of such events and but also for the understanding of the relations among them. However, spatial information is rarely mentioned as compared to events and the association between event and spatial expressions is also highly implicit in a text. This would make it difficult to automate the extraction of spatial information associated with events from the text. In this paper, we give a linguistic analysis of how spatial expressions are associated with event expressions in a text. We first present issues in annotating narrative texts with reference relations between event and spatial expressions, and then discuss surface-level linguistic characteristics of such relations based on the annotated corpus to give a helpful insight into developing an automated recognition method.

• Genomics & Informatics
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• 제17권4호
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• pp.46.1-46.7
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• 2019

The implications of germline de novo variants (DNVs) in diseases are well documented. Despite extensive research, inconsistencies between studies remain a challenge, and the distribution and genetic characteristics of DNVs need to be precisely evaluated. To address this issue at the whole-genome scale, a large number of DNVs identified from the whole-genome sequencing of 1,902 healthy trios (i.e., parents and progeny) from the Simons Foundation for Autism Research Initiative study and 20 healthy Korean trios were analyzed. These apparently nonpathogenic DNVs were enriched in functional elements of the genome but relatively depleted in regions of common copy number variants, implying their potential function as triggers of evolution even in healthy groups. No strong mutational hotspots were identified. The pathogenicity of the DNVs was not strongly elevated, reflecting the health status of the cohort. The mutational signatures were consistent with previous studies. This study will serve as a reference for future DNV studies.

• 한국도서관정보학회지
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• 제25권
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• pp.143-166
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• 1996

Recently Orientalism becomes the center of public interest. So many books related to Cheon Pu Kyung(천부경) are published in Korea. But the present writer thinks that such literature doesn#t communicate us, as it is, the original meaning of Cheon Pu Kyung. Most specialists concentrate on not so much the original text interpretation as annotation in reference to Cheon Pu Kyung. If so, it is difficult for us to find out precisely the real intention of it. Consequently the present writer in the interpretation of Cheon Pu Kyung makes plans to carry out the real intention interpretation and annotation based on Cheon Pu Kyung interpretation of Seok-Kok(석곡) Lee, Kyu-Jun(이규준). Together, the contents on which this article is based on were investigated as follows: 1. words go into 2. the limit of the original text interpretation 3. why does it need the real intention interpretation of Cheon Pu Kyung 4. the interpretative limit of Cheon Pu Kyung literature 5. Cheon Pu Kyung interpretation of Seok-Kok(석곡) Lee, Kyu-Jun(이규준) 6. words go out.

• Genomics & Informatics
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• 제4권4호
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• pp.182-187
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• 2006

6-Phosphogluconolactonase (6PGL) is one of the key enzymes in the ubiquitous pathways of central carbon metabolism, but bacterial 6PGL had been long known as a missing enzyme even after complete bacterial genome sequence information became available. Although recent experimental characterization suggests that there are two types of 6PGLs (DevB and YbhE), their phylogenetic distribution is severely biased. Here we present that proteins in COG group previously described as 3-oarboxymuconate cyclase (COG2706) are actually the YbhE-type 6PGLs, which are widely distributed in Proteobacteria and Fimicutes. This case exemplifies how erroneous functional description of a member in the reference database commonly used in transitive genome annotation cause systematic problem in the prediction of genes even with universal cellular functions.

• Asian-Australasian Journal of Animal Sciences
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• 제32권7호
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• pp.1044-1051
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• 2019

Objective: Recent studies have implied that gene expression has high tissue-specificity, and therefore it is essential to investigate gene expression in a variety of tissues when performing the transcriptomic analysis. In addition, the gradual increase of long non-coding RNA (lncRNA) annotation database has increased the importance and proportion of mapped reads accordingly. Methods: We employed simple statistical models to detect the sexually biased/dimorphic genes and their conjugate lncRNAs in 40 RNA-seq samples across two factors: sex and tissue. We employed two quantification pipeline: mRNA annotation only and mRNA+lncRNA annotation. Results: As a result, the tissue-specific sexually dimorphic genes are affected by the addition of lncRNA annotation at a non-negligible level. In addition, many lncRNAs are expressed in a more tissue-specific fashion and with greater variation between tissues compared to protein-coding genes. Due to the genic region lncRNAs, the differentially expressed gene list changes, which results in certain sexually biased genes to become ambiguous across the tissues. Conclusion: In a past study, it has been reported that tissue-specific patterns can be seen throughout the differentially expressed genes between sexes in cattle. Using the same dataset, this study used a more recent reference, and the addition of conjugate lncRNA information, which revealed alterations of differentially expressed gene lists that result in an apparent distinction in the downstream analysis and interpretation. We firmly believe such misquantification of genic lncRNAs can be vital in both future and past studies.

• 한국의사학회지
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• 제23권2호
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• pp.81-87
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• 2010

1. An analysis of "GuGeupGanIBang(救急簡易方)" through Gwakran(霍亂) showed that the reference books are not concretely cited, but the symptoms are described in detail ed to let the common people understand and deal with Gwakran(霍亂) easily. It has the most detailed among Korean annotation emergency treatment books. It focuses on moxibustion and hot medicinal compress rather than acupuncture. The Korean annotation is translated in the order of the Korean language, so anyone can execute the treatments. The annotation used a lot of active verbs, so it is more of a book for the patient, not the doctor. So we can understand that this book is focused on the practical tips at an actual emergency situation. 2. "GuGeupGanIBang(救急簡易方)" is the most complete emergency treatment book and a Hangul medical book, which is scarce. It was published shortly after the invention of Hangul. It is an important material showing how terms related to medicine such as disease, prescriptions, symptoms were understood and expressed. As it is important in both medical book presswork study and Korean language study, it is designated as treasure. 3. The existing "GuGeupGanIBang(救急簡易方)" seem to be a reissued version. It is also not complete and scattered in several places. Volumes 1,2,3,6 and 7 survived, and volumes 4,5 and 8 have not been found yet.

• Molecules and Cells
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• 제21권2호
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• pp.269-275
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• 2006

A recent report of the Korean Intellectual Property Office(KIPO) showed that the number of biological sequence-based patents is rapidly increasing in Korea. We present biological features of Korean patented sequences though bioinformatic analysis. The analysis is divided into two steps. The first is an annotation step in which the patented sequences were annotated with the Reference Sequence (RefSeq) database. The second is an association step in which the patented sequences were linked to genes, diseases, pathway, and biological functions. We used Entrez Gene, Online Mendelian Inheritance in Man (OMIM), Kyoto Encyclopedia of Genes and Genomes (KEGG), and Gene Ontology (GO) databases. Through the association analysis, we found that nearly 2.6% of human genes were associated with Korean patenting, compared to 20% of human genes in the U.S. patent. The association between the biological functions and the patented sequences indicated that genes whose products act as hormones on defense responses in the extra-cellular environments were the most highly targeted for patenting. The analysis data are available at http://www.patome.net