• The Journal of Korean Institute of Communications and Information Sciences
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• v.36 no.11B
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• pp.1269-1276
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• 2011

In the Proxy Mobile IPv6 (PMIPv6), the data transmission performance may be degraded when the two communicating hosts are located within the same mobile domain, since all the data packet shall be delivered by way of Local Mobility Anchor (LMA). In this paper we propose an extensional scheme of PMIPv6 using binding query. In the proposed Query-based PMIPv6 (Q-PMIPv6) scheme, the Mobile Access Gateway (NAG) of Correspondent Node (CN) sends a binding query to LMA to obtain the Proxy Care-of-Address of Mobile Node (MN). Since then, CN and MN can communicate with each other by using an optimized data path. For comparison, we performed the numerical analysis and the ns-2 simulations for the proposed Q-PMIPv6 scheme and the existing PMIPv6 and PMIPv6 Localized Routing (PMIPv6-LR). From the results, we can see that the proposed scheme outperforms the existing PMIPv6 and PMIPv6-LR schemes in terms of the signaling control and data delivery costs.

• The Transactions of the Korea Information Processing Society
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• v.6 no.6
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• pp.1447-1457
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• 1999

Visual Object Query language(VOQL) proposed recently is a visual object-oriented database query language which can effectively represent queries on complex structured data, since schema information is visually included in query expressions. VOQL, which is a graph-based query language with inductively defined semantics, can concisely represent various text-based path expressions by graph, and clearly convey the semantics of complex path expressions. however, the existing VOQL assumes that all the attributes are multi-valued, and cannot visualize the concept of binding of object variables. therefore, VPAL query expressions are not intuitive, so that it is difficult to extend the existing VOQL theoretically. In this paper, we propose VOQL that improved on these problems. The improved VOQL visualizes the result of a single-valued attribute and that of a multi-valued attribute as a visual element and a subblob, respectively, and specifies the binding of object variables by introducing visual variables, so that the improved VOQL intuitively and clearly represents the semantics of queries.

• Database Research
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• v.34 no.3
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• pp.69-85
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• 2018

Many researches proposed federated query engines to perform query on several homogeneous or heterogeneous datasets simultaneously that significantly improve the quality of query results. The existing techniques allow querying only over a few heterogeneous datasets considering the static binding using the non-standard query. However, we observe that a simultaneous system considering the integration of heterogeneous metadata standards can offer better opportunity to generalize the query over any homogeneous and heterogeneous datasets. In this paper, we propose a transparent federated engine (DRAZ) to query over multiple data sources using SPARQL. In our system, we first develop the ontology for a non-RDF metadata standard based on the metadata kernel dictionary elements, which are standardized by the metadata provider. For a given SPARQL query, we translate any triple pattern into an API call to access the dataset of corresponding non-RDF metadata standard. We convert the results of every API call to N-triples and summarize the final results considering all triple patterns. We evaluated our proposed DRAZ using modified Fedbench benchmark queries over heterogeneous metadata standards, such as DCAT and DOI. We observed that DRAZ can achieve 70 to 100 percent correctness of the results despite the unavailability of the JOIN operations.

• Journal of KIISE
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• v.42 no.9
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• pp.1109-1116
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• 2015

In this paper, we propose a query processing approach that uses the Spark functional programming and distributed memory system to solve the computational overhead of SPARQL. In the semantic web, RDF ontology data is produced at large scale, and the main challenge for the semantic web is to query and manipulate such a large ontology with a high throughput. The most existing studies on SPARQL have focused on deploying the Hadoop MapReduce framework, and although approaches based on Hadoop MapReduce have shown promising results, they achieve a low level of throughput due to the underlying distributed file processes. Therefore, in order to speed up the query processes, we suggest query- processing methods that are based on memory caching in distributed memory system. Our approach is also integrated with a clause unification method for propagating between the clauses that exploits Spark join, map and filter methods along with caching. In our experiments, we have achieved a high level of performance relative to other approaches. In particular, our performance was nearly similar to that of Sempala, which has been considered to be the fastest query processing system.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.9
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• pp.3759-3765
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• 2015

Background: Approaches in disruption of MDM2-p53 interactions have now emerged as an important therapeutic strategy in resurrecting wild type p53 functional status. The present study highlights virtual screening strategies in identification of high affinity small molecule non-peptidic inhibitors. Nutlin3A and RG7112 belonging to compound class of Cis-imidazoline, MI219 of Spiro-oxindole class and Benzodiazepine derived TDP 665759 served as query small molecules for similarity search with a threshold of 95%. The query molecules and the similar molecules corresponding to each query were docked at the transactivation binding cleft of MDM2 protein. Aided by MolDock algorithm, high affinity compound against MDM2 was retrieved. Patch Dock supervised Protein-Protein interactions were established between MDM2 and ligand (query and similar) bound and free states of p53. Compounds with PubCid 68870345, 77819398, 71132874, and 11952782 respectively structurally similar to Nutlin3A, RG7112, Mi219 and TDP 665759 demonstrated higher affinity to MDM2 in comparison to their parent compounds. Evident from the protein-protein interaction studies, all the similar compounds except for 77819398 (similar to RG 7112) showed appreciable inhibitory potential. Of particular relevance, compound 68870345 akin to Nutlin 3A had highest inhibitory potential that respectively showed 1.3, 1.2, 1.16 and 1.26 folds higher inhibitory potential than Nutilin 3A, MI 219, RG 7112 and TDP 1665759. Compound 68870345 was further mapped for structure based pharamacophoric features. In the study, we report Cis-imidazoline derivative compound; Pubcid: 68870345 to have highest inhibitory potential in blocking MDM2-p53 interactions hitherto discovered.

• Bulletin of the Korean Chemical Society
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• v.35 no.7
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• pp.2097-2108
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• 2014

Chemical feature based quantitative pharmacophore models were generated using the HypoGen module implemented in DS2.5. The best hypothesis, Hypo1, which was characterized by the highest correlation coefficient (0.96), the highest cost difference (61.60) and the lowest RMSD (0.74), consisted of one hydrogen bond acceptor, one hydrogen bond donor, one hydrophobic and one ring aromatic. The reliability of Hypo1 was validated on the basis of cost analysis, test set, Fischer's randomization method and GH test method. The validated Hypo1 was used as a 3D search query to identify novel inhibitors. The screened molecules were further refined by employing ADMET, docking studies and visual inspection. Three compounds with novel scaffolds were selected as the most promising candidates for the designing of Mcl-1 antagonists. Finally, a 10 ns molecular dynamics simulation was carried out on the complex of receptor and the retrieved ligand to demonstrate that the binding mode was stable during the MD simulation.

• Journal of KIISE:Computing Practices and Letters
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• v.7 no.5
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• pp.383-391
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• 2001

The value of XML as electronic documents is increasing nowadays. The XML document has properties of semistructured data. It can be modeled as object-oriented model which can be easily adapted by object-oriented database. For storing XML documents to conventional database system, extracting schema information from the DTD of a XML document has been studied for several years. In this paper we store XML documents into object-oriented database, which preserve the semantics of the documents. We can store and query by OQL and make applications by C++ and make applications by C++ binding which is the access method of object-oriented database. Therefore, existing database applications can be used without modification.

• Asian Pacific Journal of Cancer Prevention
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• v.16 no.18
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• pp.8191-8196
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• 2016

Inhibition of EGFR-EGF interactions forms an important therapeutic rationale in treatment of non-small cell lung carcinoma. Established inhibitors have been successful in reducing proliferative processes observed in NSCLC, however patients suffer serious side effects. Considering the narrow therapeutic window of present EGFR inhibitors, the present study centred on identifying high efficacy EGFR inhibitors through structure based virtual screening strategies. Established inhibitors - Afatinib, Dacomitinib, Erlotinib, Lapatinib, Rociletinib formed parent compounds to retrieve similar compounds by linear fingerprint based tanimoto search with a threshold of 90%. The compounds (parents and respective similars) were docked at the EGF binding cleft of EGFR. Patch dock supervised protein-protein interactions were established between EGF and ligand (query and similar) bound and free states of EGFR. Compounds ADS103317, AKOS024836912, AGN-PC-0MXVWT, GNF-Pf-3539, SCHEMBL15205939 were retrieved respectively similar to Afatinib, Dacomitinib, Erlotinib, Lapatinib, Rociletinib. Compound-AGN-PC-0MXVWT akin to Erlotinib showed highest affinity against EGFR amongst all the compounds (parent and similar) assessed in the study. Further, AGN-PC-0MXVWT brought about significant blocking of EGFR-EGF interactions in addition showed appreciable ADMET properties and pharmacophoric features. In the study, we report AGN-PC-0MXVWT to be an efficient and high efficacy inhibitor of EGFR-EGF interactions identified through computational approaches.

• Proceedings of the Korean Society for Bioinformatics Conference
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• 2000.11a
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• pp.53-55
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• 2000

Xenie is the JAVA application software that integrates and represents 'gene to function'information of human gene. Xenie extracts data from several heterogeneous molecular biology databases and provides integrated information in human readable and machine usable way. We defined 7 semantic frame classes (Gene, Transcript, Polypeptide, Protein_complex, Isotype, Functional_object, and Cell) as a common schema for storing and integrating gene to function information and relationship. Each of 7 semantic frame classes has data fields that are supposed to store biological data like gene symbol, disease information, cofactors, and inhibitors, etc. By using these semantic classes, Xenie can show how many transcripts and polypeptide has been known and what the function of gene products is in General. In detail, Xenie provides functional information of given human gene in the fields of semantic objects that are storing integrated data from several databases (Brenda, GDB, Genecards, HGMD, HUGO, LocusLink, OMIM, PIR, and SWISS-PROT). Although Xenie provide fully readable form of XML document for human researchers, the main goal of Xenie system is providing integrated data for other bioinformatic application softwares. Technically, Xenie provides two kinds of output format. One is JAVA persistent object, the other is XML document, both of them have been known as the most favorite solution for data exchange. Additionally, UML designs of Xenie and DTD for 7 semantic frame classes are available for easy data binding to other bioinformatic application systems. Hopefully, Xenie's output can provide more detailed and integrated information in several bioinformatic systems like Gene chip, 2D gel, biopathway related systems. Furthermore, through data integration, Xenie can also make a way for other bioiformatic systems to ask 'function based query'that was originally impossible to be answered because of separatly stored data in heterogeneous databases.