KRGDB: the large-scale variant database of 1722 Koreans based on whole genome sequencing

Since 2012, the Center for Genome Science of the Korea National Institute of Health (KNIH) has been sequencing complete genomes of 1722 Korean individuals. As a result, more than 32 million variant sites have been identified, and a large proportion of the variant sites have been detected for the first time. In this article, we describe the Korean Reference Genome Database (KRGDB) and its genome browser. The current version of our database contains both single nucleotide and short insertion/deletion variants. The DNA samples were obtained from four different origins and sequenced in different sequencing depths (10× coverage of 63 individuals, 20× coverage of 194 individuals, combined 10× and 20× coverage of 135 individuals, 30× coverage of 230 individuals and 30× coverage of 1100 individuals). The major features of the KRGDB are that it contains information on the Korean genomic variant frequency, frequency difference between the Korean and other populations and the variant functional annotation (such as regulatory elements in ENCODE regions and coding variant functions) of the variant sites. Additionally, we performed the genome-wide association study (GWAS) between Korean genome variant sites for the 30×230 individuals and three major common diseases (diabetes, hypertension and metabolic syndrome). The association results are displayed on our browser. The KRGDB uses the MySQL database and Apache-Tomcat web server adopted with Java Server Page (JSP) and is freely available at http://coda.nih.go.kr/coda/KRGDB/index.jsp. Availability: http://coda.nih.go.kr/coda/KRGDB/index.jsp

REPRESENTASI PENGETAHUAN DALAM SEMANTIK ONTOLOGI PADA DOMAIN KRIMINALITAS KEPOLISIAN SEKTOR DEPOK TIMUR DAERAH ISTIMEWA YOGYAKARTA

The performance of an agency is very dependent on the data and quality of information obtained, not least in the police agency. The Criminal Investigation Unit (SatResKrim) is one of the most important units in the police force. One form of handling SatResKrim is to manage crime data. Crime data is managed because it contains information to support the investigation process. The information used in the investigation process is included in the crime data, so it is necessary to search for documents of criminal data relevant to the investigation process. Currently, data on SatResKrim unit at East Sector Police Dept. of Yogyakarta Special Region still use Microsoft Excel application, so the process of searching data is still based on text not based on knowledge, consequently if the search keyword is not in accordance with the text contained in the data, then the data is not will appear, if the data does not appear it will slightly hamper the investigation process. From these problems raised the idea to represent police crime data into the form of knowledge as an effort in providing references to the police agencies against the form of development of data processing crime-based semantic ontology. Knowledge of crime data is limited to criminal data by category of theft. Knowledge related to theft criminal data is then stored or represented in an ontology-based semantic model. In representing knowledge using language Ontology Web Language (OWL) and SPARQL as its query. Software used to build systems in this study include protégé 3.5, NetBeans and Jena API as its library. The programming language used is Java Server Page (JSP). Based on the results of research that has been done, by representing crime data into the form of semantic ontology-based knowledge and tested into the form of search-based applications, can generate semantic-based search or search that is able to understand the meaning. It is also supported by test results using recall and precision methods, each of which results in a value of more than 90%. Abstrak:Kinerja suatu instansi sangat bergantung pada data dan mutu informasi yang diperoleh, tak terkecuali pada instansi kepolisian. Satuan Reserse Kriminal (SatResKrim) merupakan salah satu unit terpenting dalam kepolisian. Salah satu bentuk penanganan SatResKrim adalah dengan mengelola data kriminalitas. Data kriminalitas dikelola karena mengandung informasi guna menunjang proses investigasi. Informasi yang digunakan dalam proses investigasi diantaranya terdapat pada data kriminalitas, sehingga diperlukan adanya pencarian terhadap dokumen data kriminalitas yang relevan dengan proses investigasi. Saat ini data yang berada pada unit SatResKrim pada Kepolisian Sektor Depok Timur Daerah Istimewa Yogyakarta masih menggunakan aplikasi Microsoft Excel, sehingga proses pencarian data masih berdasarkan teks bukan berdasarkan pengetahuan, akibatnya apabila kata kunci pencarian tidak sesuai dengan teks yang terdapat pada data, maka data tidak akan muncul, jika data tidak muncul maka akan sedikit menghambat proses investigasi. Dari permasalahan tersebut memunculkan gagasan untuk merepresentasikan data kriminalitas kepolisian kedalam bentuk pengetahuan sebagai upaya dalam memberikan referensi kepada instansi kepolisian terhadap bentuk pengembangan pengolahan data kriminalitas berbasis semantik ontologi. Pengetahuan-pengetahuan mengenai data kriminalitas dibatasi pada data kriminalitas dengan kategori pencurian. Pengetahuan-pengetahuan terkait data kriminalitas pencurian kemudian disimpan atau di representasikan dalam model semantik berbasis ontologi. Dalam merepresentasikan pengetahuan menggunakan bahasa Ontology Web Language (OWL) serta SPARQL sebagai query-nya. Software yang digunakan untuk membangun sistem dalam penelitian ini meliputi protégé 3.5 ,NetBeans serta Jena API sebagai library-nya. Bahasa pemrograman yang digunakan adalah Java Server Page (JSP). Berdasarkan hasil penelitian yang telah dilakukan, dengan merepresentasikan data kriminalitas kedalam bentuk pengetahuan berbasis semantik ontologi dan di ujikan ke dalam bentuk aplikasi berbasis pencarian, dapat menghasilkan pencarian berbasis semantik atau pencarian yang mampu memahami makna. Hal tersebut juga didukung oleh hasil uji dengan menggunakan metode recall dan precision yang masing-masing hasilnya menunjukkan nilai lebih dari 90%.

Web-Based Collaborative Concurrent Engineering for Product Design and Manufacturing

We present a developed Web-based product design and manufacturing system that supports collaborative Concurrent Engineering. It models distributed systems and databases using Web technologies, so that these distributed system and databases can be accessed anywhere in the world. In such system, product developers can exchange and share product data, communicate with other team members, modify geometry data on particular aspects of the design and maintain operations consistency in all the distributed cooperative sites on a wide variety of platforms. The new system is a Client/Server architecture. The server manages the sharing of the common model, as well as the coordination among multiple users, in which different users can modify different parts of the shared model. In addition, the server supports many client through the Internet, and it also allows peer to peer negotiation, sharing different databases located in different machines, establishing relations between them at run time. A group of users can work together in a common single write mode, which continuously synchronized with the master copy on the central server. The proposal model is producing a new manner and has many algorithms for viewing, editing, synchronizing, and collaboration coordination. It utilizes Java 3D to view 3D CAD files in interactive manner. It introduces an intelligent user interface for editing and modification. STEP, which is international standard introduced by the International Standards Organization (ISO), is used to exchange engineering information. Java Server Page (JSP) is used for Collaboration coordination and semantic-based coordination.