Prolonged Fetal Bradycardia as the Presenting Clinical Sign in Congenital Syphilis Complicated by Necrotizing Funisitis: A Case Report

Syphilis remains a serious cause of neonatal morbidity and mortality worldwide. In this paper, we describe a case of congenital syphilis that was fully supported by abnormal fetal heart rate patterns and placental histopathological evidence. A 24-year-old para 4 woman, who did not attend antenatal care, was admitted to our hospital with a complaint of abdominal discomfort at an estimated 31-week gestation. Fetal heart rate monitoring showed prolonged bradycardia. A neonate weighting 1,423 g with severe birth asphyxia was immediately delivered by cesarean section. Following delivery, the mother and the neonate were diagnosed with syphilis. Histopathological examination confirmed severe chorioamnionitis and necrotizing funisitis with numerous Treponema pallidum. Conclusions. Challenges in establishing the diagnosis of necrotizing funisitis are essential for optimal management of a fetus with a systemic inflammatory response in utero

Semantic-JSON: a lightweight web service interface for Semantic Web contents integrating multiple life science databases

Global cloud frameworks for bioinformatics research databases become huge and heterogeneous; solutions face various diametric challenges comprising cross-integration, retrieval, security and openness. To address this, as of March 2011 organizations including RIKEN published 192 mammalian, plant and protein life sciences databases having 8.2 million data records, integrated as Linked Open or Private Data (LOD/LPD) using SciNetS.org, the Scientists' Networking System. The huge quantity of linked data this database integration framework covers is based on the Semantic Web, where researchers collaborate by managing metadata across public and private databases in a secured data space. This outstripped the data query capacity of existing interface tools like SPARQL. Actual research also requires specialized tools for data analysis using raw original data. To solve these challenges, in December 2009 we developed the lightweight Semantic-JSON interface to access each fragment of linked and raw life sciences data securely under the control of programming languages popularly used by bioinformaticians such as Perl and Ruby. Researchers successfully used the interface across 28 million semantic relationships for biological applications including genome design, sequence processing, inference over phenotype databases, full-text search indexing and human-readable contents like ontology and LOD tree viewers. Semantic-JSON services of SciNetS.org are provided at http://semanticjson.org

PosMed: ranking genes and bioresources based on Semantic Web Association Study

ABSTRACT Positional MEDLINE (PosMed; http://biolo

RIKEN MetaDatabase: a database publication platform for RIKENs life-science researchers that promotes research collaborations over different research area

Abstract. To promote data dissemination and integration of life sciences datasets produced by RIKEN, we developed an infrastructure database called "RIKEN MetaDatabase" that enables data publication and integration using the Resource Description Framework. In addition, we implemented a simple workflow for data management and a graphical user interface representing data links across laboratories. Consequently, inter-laboratory collaboration and coordination have been accelerated. Combined with global standardization activities, we expect that this infrastructure will contribute to worldwide data integration

RIKEN MetaDatabase: A Database Platform for Health Care and Life Sciences as a Microcosm of Linked Open Data Cloud

Recently, the number and heterogeneity of life science datasets published on the Web have increased significantly. However, biomedical scientists face numerous serious difficulties finding, using and publishing useful databases. To address these issues, the authors developed a Resource Description Framework-based database platform, called the RIKEN MetaDatabase (http://metadb.riken.jp), that allows biologists to develop, publish and integrate multiple databases easily. The platform manages the metadata of both research and individual data described using standardised vocabularies and ontologies, and has a simple browser-based graphical user interface to view data including tabular and graphical forms. The platform was released in April 2015, and 113 databases, including mammalian, plant, bioresource and image databases, with 26 ontologies have been published using this platform as of January 2017. This paper describes the technical knowledge obtained through the development and operation of the RIKEN MetaDatabase to accelerate life science data distribution.</p

SPARQL Query Construction with Monitoring Service for Endpoints

Abstract. Many databases in life sciences have been provided in Resource Description Framework (RDF) with their SPARQL endpoints. To support a user in constructing SPARQL queries, we developed a service called SPARQL Builder. Although SPARQL Builder makes a user write a query for obtaining data from LOD, empty results or incorrect data might be retrieved by the query if the SPARQL endpoint for the query is not alive or provides out-of-date data. To avoid such queries from SPARQL Builder, YummyData which monitors SPARQL endpoints and gathers information about alive rate, last update, response time, etc. was used. By connecting YummyData to SPARQL Builder, our system can always obtain a SPARQL query for SPARQL endpoints with high usability

SPARQL Builder: Constructing SPARQL Query by Traversing Class-Class Relationships for Life Science Databases

Abstract. Linked Open Data (LOD), a powerful mechanism for linking different datasets published on the World Wide Web, is expected to increase the value of data through mashups of various datasets on the Web. One of the important requirements for LOD is to be able to find a path of resources connecting two given classes. Because each class contains many instances, inspecting all of the paths or combinations of the instances results in an explosive increase of computational complexity. To solve this problem, we have proposed an efficient method that obtains and prioritizes a comprehensive set of connections over resources by traversing class-class relationships of interest. Based on the method, we developed a system for constructing a SPARQL query named SPARQL Builder. We showcase how to generate a SPARQL query according to user&apos;s interest by using the SPARQL Builder system