• Genomics & Informatics
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• v.18 no.2
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• pp.19.1-19.6
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• 2020

In semantic annotation, semantic concepts are linked to natural language. Semantic annotation helps in boosting the ability to search and access resources and can be used in information retrieval systems to augment the queries from the user. In the research described in this paper, we aimed to identify ontological concepts in scientific text contained in spreadsheets. We developed a tool that can handle various types of spreadsheets. Furthermore, we used the NCBO Annotator API provided by BioPortal to enhance the semantic annotation functionality to cover spreadsheet data. Table2Annotation has strengths in certain criteria such as speed, error handling, and complex concept matching.

• Journal of Digital Contents Society
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• v.12 no.4
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• pp.429-436
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• 2011

Various documents, images, videos and other materials on the web has been increasing rapidly. Efficient search of those things has become an important topic. From keyword-based search, internet search has been transformed to semantic search which finds the implications and the relations between data elements. Many annotation processing systems manipulating the metadata for semantic search have been proposed. However, annotation data generated by different methods and forms are difficult to process integrated search between those systems. In this study, in order to resolve this problem, we categorized levels of many annotation documents, and we proposed the method to measure the similarity between the annotation documents. Similarity measure between annotation documents can be used for searching similar or related documents, images, and videos regardless of the forms of the source data.

• Genomics & Informatics
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• v.12 no.2
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• pp.76-78
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• 2014

Owing to the generation of vast amounts of sequencing data by using cost-effective, high-throughput sequencing technologies with improved computational approaches, many putative proteins have been discovered after assembly and structural annotation. Putative proteins are typically annotated using a functional annotation system that uses extant databases, but the expansive size of these databases often causes a bottleneck for rapid functional annotation. We developed SFannotation, a simple and fast functional annotation system that rapidly annotates putative proteins against four extant databases, Swiss-Prot, TIGRFAMs, Pfam, and the non-redundant sequence database, by using a best-hit approach with BLASTP and HMMSEARCH.

• Journal of Korea Multimedia Society
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• v.7 no.9
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• pp.1321-1328
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• 2004

In this article, we present a new DICOM object able to create image-based annotations in DICOM image. Since the proposed image-based annotation uses images themselves of annotation, various types like character, sketch, and scanning image, etc., can be imported into annotation easily. The proposed annotation is inserted into DICOM image directly but they do not influence original DICOM image quality by using independent data channel. The proposed annotation is expected to be very useful to medium and small clinics that cannot afford picture archiving and communication systems or electronic medical record.

• Journal of the Korea Academia-Industrial cooperation Society
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• v.7 no.6
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• pp.1129-1133
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• 2006

In this thesis, we propose a semantics-based video retrieval system which supports semantics-retrieval for various users of massive video data. Proposed system automatically processes the extraction of contents information which video data has and retrieval process using agent which integrate annotation-based retrieval and feature-based retrieval. From experiment, the designed and implemented system shows increase of recall rate and precision rate for video data scene retrieval in performance assessment.

• The Journal of Korea Robotics Society
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• v.14 no.2
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• pp.139-149
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• 2019

In this paper, we present auto-annotation tool and synthetic dataset using 3D CAD model for deep learning based object detection. To be used as training data for deep learning methods, class, segmentation, bounding-box, contour, and pose annotations of the object are needed. We propose an automated annotation tool and synthetic image generation. Our resulting synthetic dataset reflects occlusion between objects and applicable for both underwater and in-air environments. To verify our synthetic dataset, we use MASK R-CNN as a state-of-the-art method among object detection model using deep learning. For experiment, we make the experimental environment reflecting the actual underwater environment. We show that object detection model trained via our dataset show significantly accurate results and robustness for the underwater environment. Lastly, we verify that our synthetic dataset is suitable for deep learning model for the underwater environments.

• Journal of Korea Multimedia Society
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• v.21 no.2
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• pp.158-165
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• 2018

Since a large amount of multimedia image has dramatically increased, it is important to search semantically relevant image. Thus, several semantic image annotation methods using RDF(Resource Description Framework) model in mobile environment are introduced. Earlier studies on annotating image semantically focused on both the image tag and the context-aware information such as temporal and spatial data. However, in order to fully express their semantics of image, we need more annotations which are described in RDF model. In this paper, we propose an annotation method inferencing with RDFS entailment rules and user defined rules. Our approach implemented in Moment system shows that it can more fully represent the semantics of image with more annotation triples.

• 한국균학회소식:학술대회논문집
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• 2018.05a
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• pp.22-22
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• 2018

Fungal genome sequencing and assembly have been trivial in these days. Genome analysis relies on high quality of gene prediction and annotation. Automatic fungal genome annotation pipeline is essential for handling genomic sequence data accumulated exponentially. However, building an automatic annotation procedure for fungal genomes is not an easy task. FunGAP (Fungal Genome Annotation Pipeline) is developed for precise and accurate prediction of gene models from any fungal genome assembly. To make high-quality gene models, this pipeline employs multiple gene prediction programs encompassing ab initio, evidence-, and homology-based evaluation. FunGAP aims to evaluate all predicted genes by filtering gene models. To make a successful filtering guide for removal of false-positive genes, we used a scoring function that seeks for a consensus by estimating each gene model based on homology to the known proteins or domains. FunGAP is freely available for non-commercial users at the GitHub site (https://github.com/CompSynBioLab-KoreaUniv/FunGAP).

• Journal of Korea Multimedia Society
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• v.19 no.8
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• pp.1498-1504
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• 2016

The progress of mobile computing technology is bringing a large amount of multimedia contents such as image. Thus, we need an image retrieval system which searches semantically relevant image. In this paper, we propose a semantic image annotation and retrieval in mobile environments. Previous mobile-based annotation approaches cannot fully express the semantics of image due to the limitation of current form (i.e., keyword tagging). Our approach allows mobile devices to annotate the image automatically using the context-aware information such as temporal and spatial data. In addition, since we annotate the image using RDF(Resource Description Framework) model, we are able to query SPARQL for semantic image retrieval. Our system implemented in android environment shows that it can more fully represent the semantics of image and retrieve the images semantically comparing with other image annotation systems.

• Genomics & Informatics
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• v.19 no.3
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• pp.21.1-21.5
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• 2021

The use of social media data, like Twitter, for biomedical research has been gradually increasing over the years. With the coronavirus disease 2019 (COVID-19) pandemic, researchers have turned to more non-traditional sources of clinical data to characterize the disease in near-real time, study the societal implications of interventions, as well as the sequelae that recovered COVID-19 cases present. However, manually curated social media datasets are difficult to come by due to the expensive costs of manual annotation and the efforts needed to identify the correct texts. When datasets are available, they are usually very small and their annotations don't generalize well over time or to larger sets of documents. As part of the 2021 Biomedical Linked Annotation Hackathon, we release our dataset of over 120 million automatically annotated tweets for biomedical research purposes. Incorporating best-practices, we identify tweets with potentially high clinical relevance. We evaluated our work by comparing several SpaCy-based annotation frameworks against a manually annotated gold-standard dataset. Selecting the best method to use for automatic annotation, we then annotated 120 million tweets and released them publicly for future downstream usage within the biomedical domain.