A5042299793- Biomedical Text Mining and Ontologies
- Bioinformatics and Genomic Networks
- Scientific Computing and Data Management
- Gene expression and cancer classification
- Cell Image Analysis Techniques
- Natural Language Processing Techniques
- Semantic Web and Ontologies
- Genomics and Phylogenetic Studies
- Genomics and Rare Diseases
- Genetics, Bioinformatics, and Biomedical Research
- Topic Modeling
- Cancer Genomics and Diagnostics
- Biomedical and Engineering Education
- linguistics and terminology studies
- Glycosylation and Glycoproteins Research
- Research Data Management Practices
Research Organization of Information and Systems
2020-2025
RIKEN BioResource Research Center
2013-2020
RIKEN Center for Brain Science
2016
Cell lines have been widely used in biomedical research. The community-based Line Ontology (CLO) is a member of the OBO Foundry library that covers domain cell lines. Since its publication two years ago, significant updates made, including new groups joining CLO consortium, line cells, upper level alignment with (CL) and for Biomedical Investigation, logical extensions. Collaboration among CLO, CL, OBI has established consensus definitions line-specific terms such as ‘cell line’, cell’,...
TogoID ( https://togoid.dbcls.jp/ ) is an identifier (ID) conversion service designed to link IDs across diverse categories of life science databases. With its ability obtain related in different semantic relationships, a user-friendly web interface, and regular automatic data update system, has been valuable tool for bioinformatics. We have recently expanded TogoID's represent semantics between datasets, enabling it handle multiple relationships within dataset pairs. This enhancement...
Positional MEDLINE (PosMed; http://biolod.org/PosMed) is a powerful Semantic Web Association Study engine that ranks biomedical resources such as genes, metabolites, diseases and drugs, based on the statistical significance of associations between user-specified phenotypic keywords connected directly or inferentially through biological databases MEDLINE, OMIM, pathways, co-expressions, molecular interactions ontology terms. Since 2005, PosMed has long been used for in silico positional...
Ontologies play a crucial role in data management and especially life science, they have been indispensable for decades as the complexity of science requires rigor. Biomedical ontologies often undergo change improvement, e.g. disease phenotype develop constantly along with our scientific understanding. In order to bridge gap between annotated datasets thus semantically enable applications retrieve insights improve interoperability, ontology mapping plays key role.To implement sophisticated...
<ns3:p>We report on the activities of 2015 edition BioHackathon, an annual event that brings together researchers and developers from around world to develop tools technologies promote reusability biological data. We discuss issues surrounding representation, publication, integration, mining reuse data metadata across a wide range biomedical types relevance for life sciences, including chemistry, genotypes phenotypes, orthology phylogeny, proteomics, genomics, glycomics, metabolomics....
One of the recurring questions when it comes to BioHackathons is how measure their impact, especially funded and/or supported by public purse (e.g., research agencies, infrastructures, grants). In order do so, we first need understand outcomes from a BioHackathon, which can include software, code, publications, new or strengthened collaborations, along with more intangible effects such as accelerated progress and professional personal outcomes. this manuscript, report on three complementary...
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...
The Human Phenotype Ontology (HPO) is the de facto standard ontology to describe human phenotypes in detail, and it actively used, particularly field of rare disease diagnoses. For clinicians who are not fluent English, HPO has been translated into many languages, there have four initiatives develop Japanese translations. At Biomedical Linked Annotation Hackathon 6 (BLAH6), a rule-based approach was attempted determine preferable translation for each term among candidates developed by...
Previous approaches to create a controlled vocabulary for Japanese have resorted existing bilingual dictionary and transformation rules allow such mappings. However, given the possible new terms introduced due coronavirus disease 2019 (COVID-19) emphasis on respiratory infection-related terms, coverage might not be guaranteed. We propose creating based MeSH assigned COVID-19 related publications in this work. For such, we manual curation of several dictionaries computational approach machine...
The coronavirus disease 2019 (COVID-19) pandemic has led to a flood of research papers and the information been updated with considerable frequency. For society derive benefits from this research, it is necessary promote sharing up-to-date knowledge these papers. However, because most are written in English, difficult for people who not familiar English medical terms obtain them. To facilitate COVID-19 Japanese speakers, we tried construct dictionary an open license by assigning MeSH unique...