DeepNitro: Prediction of Protein Nitration and Nitrosylation Sites by Deep Learning / 基因组蛋白质组与生物信息学报·英文版

Protein nitration and nitrosylation are essential post-translational modifications (PTMs) involved in many fundamental cellular processes. Recent studies have revealed that excessive levels of nitration and nitrosylation in some critical proteins are linked to numerous chronic diseases. Therefore, the identification of substrates that undergo such modifications in a site-specific manner is an important research topic in the community and will provide candidates for targeted therapy. In this study, we aimed to develop a computational tool for predicting nitration and nitrosylation sites in proteins. We first constructed four types of encoding features, including positional amino acid distributions, sequence contextual dependencies, physicochemical properties, and position-specific scoring features, to represent the modified residues. Based on these encoding features, we established a predictor called DeepNitro using deep learning methods for predicting protein nitration and nitrosylation. Using n-fold cross-validation, our evaluation shows great AUC values for DeepNitro, 0.65 for tyrosine nitration, 0.80 for tryptophan nitration, and 0.70 for cysteine nitrosylation, respectively, demonstrating the robustness and reliability of our tool. Also, when tested in the independent dataset, DeepNitro is substantially superior to other similar tools with a 7%-42% improvement in the prediction performance. Taken together, the application of deep learning method and novel encoding schemes, especially the position-specific scoring feature, greatly improves the accuracy of nitration and nitrosylation site prediction and may facilitate the prediction of other PTM sites. DeepNitro is implemented in JAVA and PHP and is freely available for academic research at http://deepnitro.renlab.org.

Functional design of patient App in internet + era / 医疗卫生装备

Objective To explore the functional framework design and scheme of the patient App with the thought combining internet+ medicine.Methods The system structure design was executed based on the patient App requirements analysis.WeX5 was used to develop the App,and Web Service was applied to calling the external interface and generating internal interface to realize system integration and data exchange.Results Internet+ mode had high efficiency,easy maintenance and management when used for patient treatment,and thus is worthy promoting practically.

Integration of Traditional Chinese Medicine and Western Medicine Information Resources Based on Distributed Technology / 世界科学技术-中医药现代化

In order to solve difficulties in traditional Chinese medicine (TCM) and western medicine integration of information resources, based on the research of distributed technology, this article used Web service technology based on SOA architecture associated TCM and western medicine treatment of the same disease. It finally put forward the integrated model of TCM and western medicine information resources based on distributed technology and in-depth design. It solved the problem of professional TCM or western medicine doctors who cannot use combined TCM and western medicine scheme. It realized the integration, reusability and expansibility of TCM and western medicine information resources. It provided important reference for the development of modern medicine.

Research on system integration technology for hospital information construction based on Web Service / 中国医学装备

Objective:In view of the current existing in the construction of hospital information system, poor compatibility between the software, data sharing difficult shortcomings, puts forward the solution based on Web service to realize the hospital information resources integration and sharing. Methods: Using medical digital image communication standard (DICOM), medical layer 7 (HL7) and Web service technology, through constructing a unified hospital information integration platform to integrate hospital information system (HIS), medical imaging system (PACS) and radiology information system (RIS). Results: Based on Web service integration platform can apply complex heterogeneous system, support custom adapter connection, reduce the coupling between modules, improve the commonality of data, system have strong extensibility. Conclusion:The application of integration technology will greatly improve the hospital the system stability, security, compatibility and efficiency, and the hospital running maintenance costs were reduced.

An Information-based Model for an Interactive Web Service with Agricultural Biotechnology

The National Agricultural Biotechnology Information Center (NABIC) constructed an agricultural biology-based infrastructure and developed a biological information-based database. The major functions of the NABIC are focused on biotechnological developments for agricultural bioinformatics and providing a web-based service to construct bioinformatics workflows easily, such as protein function prediction and genome systems biology programs. The NABIC has concentrated on the functional genomics of major crops, building an integrated biotechnology database for agro-biotech information that focuses on the proteomics of major agricultural resources, such as rice, Chinese cabbage, rice Ds-tagging lines, and microorganisms.

Design and implementation of disease notification system based on HL7 standards / 国际生物医学工程杂志

Objective According to the lack of timeliness in the current domestic disease notification system,an effective solution is proposed to solve the problem.Methods Based on research and analysis of the health information exchange standards HL7 (Health Level 7),which is widely used in the world,a solution on the base of HL7 standards is proposed in this study,to store,transfer,analyze and publish data.Results The solution allows medical institutions and the centers for disease control connect seamlessly,ensuring the data transfer in time,and publishing the data through Web service.Conclusion The solution can keep the people abreast of the latest status of the epidemic,and do their own protection as well as promote social stability.

Implementation of Medical Information Exchange System Based on EHR Standard / 대한의료정보학회지

OBJECTIVES: To develop effective ways of sharing patients' medical information, we developed a new medical information exchange system (MIES) based on a registry server, which enabled us to exchange different types of data generated by various systems. METHODS: To assure that patient's medical information can be effectively exchanged under different system environments, we adopted the standardized data transfer methods and terminologies suggested by the Center for Interoperable Electronic Healthcare Record (CIEHR) of Korea in order to guarantee interoperability. Regarding information security, MIES followed the security guidelines suggested by the CIEHR of Korea. This study aimed to develop essential security systems for the implementation of online services, such as encryption of communication, server security, database security, protection against hacking, contents, and network security. RESULTS: The registry server managed information exchange as well as the registration information of the clinical document architecture (CDA) documents, and the CDA Transfer Server was used to locate and transmit the proper CDA document from the relevant repository. The CDA viewer showed the CDA documents via connection with the information systems of related hospitals. CONCLUSIONS: This research chooses transfer items and defines document standards that follow CDA standards, such that exchange of CDA documents between different systems became possible through ebXML. The proposed MIES was designed as an independent central registry server model in order to guarantee the essential security of patients' medical information.

D-MaPs - DNA-microarray projects: web-based software for multi-platform microarray analysis

The web application D-Maps provides a user-friendly interface to researchers performing studies based on microarrays. The program was developed to manage and process one- or two-color microarray data obtained from several platforms (currently, GeneTAC, ScanArray, CodeLink, NimbleGen and Affymetrix). Despite the availability of many algorithms and many software programs designed to perform microarray analysis on the internet, these usually require sophisticated knowledge of mathematics, statistics and computation. D-maps was developed to overcome the requirement of high performance computers or programming experience. D-Maps performs raw data processing, normalization and statistical analysis, allowing access to the analyzed data in text or graphical format. An original feature presented by D-Maps is GEO (Gene Expression Omnibus) submission format service. The D-MaPs application was already used for analysis of oligonucleotide microarrays and PCR-spotted arrays (one- and two-color, laser and light scanner). In conclusion, D-Maps is a valuable tool for microarray research community, especially in the case of groups without a bioinformatic core.

Patome: Database of Patented Bio-sequences

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 components-the 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.

Design of Wired/Wireless Integrated Medical Information Management System Based on Web Service / 대한의료정보학회지

OBJECTIVE: According to development of web service technology and mobile device supply, mobile web service becomes an essential element of ubiquitous healthcare. But there are many constraints for offering mobile web services on mobile devices. Hence, this paper propose optimal system supplying web services about medical information in wired /wireless network according to resources of device. METHODS: Proposed system consists of web server, database, desktop subscriber, mobile device and mobile context server. When a mobile device requires the web service, a mobile context server rewrites and offers the equivalent contents provided from web server to suit the requiring device's resource. Our proposed system services the same medical information after its recomposition as the network and devices of user. RESULTS: The medical staff may require patient information in wired/wireless environment, web server and mobile context server supports their correct judgment and expeditious response by servicing optimized data of the patient according to the requiring device. CONCLUSION: Proposed system designed the wired/wireless integrated medical information system using web service and mobile web service as the bases of ubiquitous healthcare system. Not only for web service in wired network, to provide the optimal web service in wireless network, we should know the limited resource of mobile devices and appropriately divide the web contents of wired network to fit the mobile device's screen. The future research needs dynamic division of screen according to extension of medical information data.

Design and Implementation of an Effective Hospital System Based on an RFID and Web Service Technology / 대한의료정보학회지

OBJECTIVE: Currently hospitals are working hard to make their hospital stand out from the rest in the medical market. The government is trying to hard to resolve the problem in regards to false claims for treatment expenses through issued medical prescriptions. There is a known limit to 1:1 service which needs much improvement. This proposed system will help prevent fake medical prescriptions from being issued. METHODS: In order to provide distinguished medical services for the next generation, we have designed and implemented a system that applies the Radio Frequency Identification standard, web services and mobile technology. RESULTS: In the proposed system, the Radio Frequency Identification card is issued to the patient and the hospital system can automatically recognize the patient and a simple SMS message will be sent. Through this method of communication 1:1 customer service can be accomplished. By applying the web services technology, any pharmacy can use the saved medical prescription code contained in the Radio Frequency Identification tag. This in turn resolves the systematic problems with illegal usage. CONCLUSION: Through this proposed system, we offer the functionality of easily applying the Radio Frequency Identification technology to various medical fields. By using a mobile device, it is possible to collect bio data remotely about a patient.

A framework based on Web service orchestration for bioinformatics workflow management

Bioinformatics activities are growing all over the world, with proliferation of data and tools. This brings new challenges: how to understand and organize these resources and how to provide interoperability among tools to achieve a given goal. We defined and implemented a framework to help meet some of these challenges. Four issues were considered: the use of Web services as a basic unit, the notion of a Semantic Web to improve interoperability at the syntactic and semantic levels, and the use of scientific workflows to coordinate services to be executed, including their interdependencies and service orchestration.

RESEARCH ON REUSE-BASED WEB SERVICES COMPOSITION / 药物分析学报

Objective To solve the three principal problems for reusing the software components, i.e., existence, discovery and availability principles, web services provided a new solution for reusing and assembling web software or components under distributed environment with a series of XML-based protocols. Methods A 4+1 meta-model between atomic services, such as Sequence, Parallelism, Alternation, Substitute and Iteration, and a kind of service composition description language in composition process are investigated. Furthermore, an architecture-based service composition model with Ontology Engine is proposed, which is based on the software architecture life-cycle model and provides a mechanism for services composition with dynamic management and deployment. Results The results of the prototype system development show that the service-composed application not only reused the web service components, but also reused the data resources located in distributed databases. Conclusion The method of reused-based web services composition observably decreases the period and cost of development and greatly improves the programming efficiency.

Construction of Sanatorium Data Center and Implementation of Key Technologies / 医疗卫生装备

Objective Sanatoriums have many complex business systems,so there is an urgent need for safe,reliable and stable operation of data centers to provide uninterrupted data services for its business systems. Methods Based on Web service heterogeneous system integration technology,data crawling robot technology,data center core technologies related to the data center,data center of sanatoriums was built. Results Sanatorim data center is the foundation on the integration platform of information,it is an effective solution to application integration and data sharing to achieve data consistency,timeliness,completeness,safety,effectiveness and accuracy. Conclusion The relative concentration of data center in the building of sanatorium is necessary in the development of sanatorium.

Development of a Measurement Tool System in Health and Medical Areas via the World Wide Web / 대한의료정보학회지

Scientific information databases produce insufficient and unsatisfactory levels of data for the specialized needs of researchers. Especially in the health and medical areas, researchers are looking for a measurement tool on the web that allows interaction between the database and the researcher for the production of new information through searching, accumulating, modifying, and deleting data. In this research paper, first a concrete explanation of the informational items in databases such as the types of measurement tool in the health and medical areas, their usage methods, their reliability and validity. Secondly, this report developed the service system of the measurement tool in the health and medical areas including functions of searching and answers of measurement information, functions in writing up information measurements from the web, and the user's friendly system according to their accessing levels. This measurement tool system can be applied for digital data collection and analysis rapidly via the web.

An Experimental Trial of Web-based Problem Based Learning / 한국의학교육

In this paper, we present some results from an experimental web-based Problem-Based Learning(PBL) course, which was offered to 64 medical students in the first grade at Konkuk university for 7 weeks. For the course, we developed a web-based PBL module, which is composed of three sections. The first section includes the 8 stages of problem probing and solving in patient's care. In every stage, the students can browse all the data for the problem solving. The second section contains some problems for evaluating the academic achievement of the students who successfully passed in the first section. In the third section, some questionnaires are presented to survey the students response. The followings are the results. 1. Average score of the first section was 64.1+/-13.2. Most students participated in the course with integrity, and especially seven students(11%) were remarkable in their clinical reasoning. 2.The student's computer skill did not largely affect their academic achievements. However, it is desirable for the students to learn basic computer usage in advance. 3.A few students attended to the discussion through bulletin board facilities. Considering the importance of discussion in PBL, we need to devise a new way of attracting students in the discussion. 4. The survey showed that sixty five percent of the students thought that the lecture was effective and ninety one percent of them that it would be better if it is offered as a regular course during summer or winter vacations. Seventy five percent of students became to realize the importance of basic sciences such as biochemistry and physiology after this course. 5. There were many students who complained about the malfunctioning of the system. The system should be modified to be more reliable and robust. In conclusion, the web-based PBL course provided an effective way of learning in medical education. It also turned out to be used as an alternative of traditional PBL and especially useful for self study.