A5073025090- Biomedical Text Mining and Ontologies
- Genomics and Rare Diseases
- Semantic Web and Ontologies
- Scientific Computing and Data Management
- Genomics and Phylogenetic Studies
- Gene expression and cancer classification
- Bioinformatics and Genomic Networks
- Natural Language Processing Techniques
- Pregnancy and preeclampsia studies
- Topic Modeling
- Biomedical and Engineering Education
- Genetics, Bioinformatics, and Biomedical Research
- Genetics and Neurodevelopmental Disorders
- MicroRNA in disease regulation
- Cancer Genomics and Diagnostics
- RNA Research and Splicing
- Pancreatic function and diabetes
- Cancer-related gene regulation
- Web Data Mining and Analysis
- Genetic Associations and Epidemiology
- Birth, Development, and Health
- RNA modifications and cancer
- Cancer, Hypoxia, and Metabolism
Research Organization of Information and Systems
2018-2025
The University of Tokyo
2018
The application of semantic technologies to the integration biological data and interoperability bioinformatics analysis visualization tools has been common theme a series annual BioHackathons hosted in Japan for past five years. Here we provide review activities outcomes from held 2011 Kyoto 2012 Toyama. In order efficiently implement life sciences, participants formed various sub-groups worked on following topics: Resource Description Framework (RDF) models specific domains, text mining...
Abstract Background Virtual Gene Panels (VGP) comprising disease-associated causal genes are utilized in the diagnosis of rare genetic diseases to evaluate candidate identified by whole-genome and whole-exome sequencing. VGPs generated PanelApp software were a UK 100,000 Genome Project pilot study filter genes, thus enhancing diagnostic efficiency for diseases. However, also filtered out disease-causing nearly 50% cases. Methods Here, we propose various methods optimized approach design that...
Biological databases vary enormously in size and data complexity, from small that contain a few million Resource Description Framework (RDF) triples to large billions of triples. In this paper, we evaluate whether RDF native stores can be used meet the needs biological database provider. Prior evaluations have synthetic with limited size. For example, largest BSBM benchmark uses 1 billion e-commerce knowledge on single node. However, real world differs simple much. It is difficult determine...
Most currently available text mining tools share two characteristics that make them less than optimal for use by biomedical researchers: they require extensive specialist skills in natural language processing and were built on the assumption should optimize global performance metrics representative datasets. This is a problem because most end-users are not specialists researchers often care about like F-measure or datasets do more granular such as precision recall their own specialized Thus,...
To promote research activities in a particular area, it is important to efficiently identify current trends, advances, and issues that area. Although review papers the area can suffice for this purpose general, researchers are not necessarily able obtain these from aspects of their interests at time they required. Therefore, utilization citation contexts has been considered as another approach. However, there few search services retrieve life sciences domain; furthermore, obtaining becoming...
microRNAs (miRNAs) are tiny endogenous RNAs that have been discovered in animals and plants, direct the post-transcriptional regulation of target mRNAs for degradation or translational repression via binding to 3'UTRs coding exons. To gain insight into biological role miRNAs, it is essential identify full repertoire mRNA targets (target genes). A number computer programs developed miRNA-target prediction. These essentially focus on potential sites 3'UTRs, which recognized by miRNAs according...
Over 10,000 rare genetic diseases have been identified, and millions of newborns are affected by severe each year. A variety Human Phenotype Ontology (HPO)-based clinical decision support systems (CDSS) patient repositories developed to clinicians in diagnosing patients with suspected diseases. In September 2017, we released PubCaseFinder (https://pubcasefinder.dbcls.jp), a web-based CDSS that provides ranked lists using HPO-based phenotypic similarities, where top-listed represent the most...
Abstract Background Virtual Gene Panels (VGP) comprising disease-associated causal genes are utilized in the diagnosis of rare genetic diseases to evaluate candidate identified by whole-genome and whole-exome sequencing. VGPs generated PanelApp software were a UK 100,000 Genome Project pilot study filter genes, thus enhancing diagnostic efficiency for diseases. However, also filtered out disease-causing nearly 50% cases. Methods Here, we propose various methods optimized approach design that...
Abstract The Human Phenotype Ontology (HPO) is widely used for annotating clinical text data, and sufficient annotation crucial the effective utilization of texts. It was known that use LLMs can successfully extract symptoms findings, but cannot annotate them with HPO. We hypothesized one potential issue this lack appropriate terms in Therefore, during Biomedical Linked Annotation Hackathon 8 (BLAH8), we attempted following two tasks order to grasp overall picture (1) Extract all HPO each 23...
Whole exome sequencing has been widely used to make a diagnosis of genetic disease efficiently, especially for rare diseases. To support the identification gene that causes disease, ranking system from symptoms is essential narrow down many genes obtained analysis. Therefore, this paper proposed method by based on paths phenotypes knowledge graph. First, we constructed graph resources about phenotypes, diseases, and genes. Then, designed an algorithm rank following Furthermore, evaluated...
<ns3:p>Publishing databases in the Resource Description Framework (RDF) model is becoming widely accepted to maximize syntactic and semantic interoperability of open data life sciences. Here we report advancements made 6th 7th annual BioHackathons which were held Tokyo Miyagi respectively. This review consists two major sections covering: 1) improvement utilization RDF various domains sciences 2) meta-data about these data, resources that store them, service quality SPARQL Protocol Query...
For researchers, writing a paper is an essential task, and it crucial for them to have environment facilitate the process. In addition, in English more difficult many non-native speakers. The Database Center Life Science (DBCLS) provides researchers life sciences with several text-mining related services, such as Allie inMeXes, which were developed writing. abbreviation database that shows expanded forms relevant data, papers contain abbreviations their corresponding forms. Since large...
Over 7,000 rare genetic diseases have been identified, and millions of newborns are affected by severe each year. A variety Human Phenotype Ontology (HPO)-based clinical decision support systems (CDSS) patient repositories developed to clinicians in diagnosing patients with suspected diseases. In September 2017, we released PubCaseFinder (https://pubcasefinder.dbcls.jp), a web-based CDSS that provides ranked lists using HPO-based phenotypic similarities, where top-listed represent the most...