| Publication | Symposium/Workshop | Database/Resource |
[Publication]
Preprint Published (Jan. 23, 2024)
Led by the Allen Institute, a global community has published white papers on arXiv for realize the added value of and infrastructure requirements for global image data sharing in the life sciences primarily for the USA.
https://doi.org/10.48550/arXiv.2401.13023
https://doi.org/10.48550/arXiv.2401.13022
Paper Punlished (Jul. 10, 2023)
The international community for OME-NGFF published a paper on a cloud-optimized bioimaging file format named OME-Zarr. We contribute to promoting the development of analysis tools for bioimaging data by providing OME-Zarr filesets for selected datasets stored in SSBD:database.
https://doi.org/10.1007/s00418-023-02209-1
Paper Punlished (Mar. 8, 2023)
A global community, which DR Arita (CSRS Metabolome Information Research Team) joins, proposed recommendations on the annotation of compound names for the establishment of international standards for metabolomics.
https://doi.org/10.1038/s42255-023-00757-3
Paper Published (Dec. 29, 2022)
A joint research group by Team leader Kikuchi (Environmental Metabolic Analysis Research Team, RIKEN CSRS), Team Leader Ono and Visiting scientist Miyamoto (Laboratory for Intestinal Ecosystem, RIKEN IMS, respectively), Director Masuya (Integrated Bioresource Information Division, RIKEN BRC) and Assistant Professor Satoh (School of Medicine, Kitasato University) et al. succeeded in finding an evaluation index for growth characteristics related to the flourishing of seagrass (eelgrass) downstream of fish land-based aquaculture facilities with using machine learning, structural equations, and causal inference. To understand this research more, please refer to the RIKEN press release* (dated Jan 12, 2023). * The article is written in Japanse only.
https://doi.org/10.1016/j.envres.2022.115130
Paper Published (Aug. 8, 2022)
The global community of lipidomics researchers has been working hard to establish international guidelines for lipidomics and standard indicators for publishing lipidome data. They have published recommendations in Nature Metabolism. The creation of a dynamic checklist of key details of lipidome analysis in a common language is expected to harmonise the field by improving both traceability and reproducibility.
https://doi.org/10.1038/s42255-022-00628-3
Related Publication (May 23, 2022. Paper published: Sep. 29, 2021)
Dr Torigoe (CBS Decision Circuit Dynamics Research Team), who joined the research project of OLSP (2020) , published a paper on the further elucidation of common vertebrate decision-making mechanisms using zebrafish brains. He worked on making the data generated publicly available in the project, and some sample data and analysis codes generated in this paper are available on Zenodo.
https://www.nature.com/articles/s41467-021-26010-7
Paper Published (Jan. 22, 2022)
As a part of the achievements of the RIKEN Hackathon 2021, Dr Suzuki (BRC Integrated Bioresource Information Division), Dr Masuya (BRC Integrated Bioresource Information Division) et al. published a paper on the detectability of microbial interactions.
https://doi.org/10.3390/ijerph19031228
Paper Published (Jan. 14, 2022)
DR Kasukawa (IMS Laboratory for Large-Scale Biomedical Data Technology) et al. have developed a new quality assessment method applicable to single-cell RNA-Seq data, SkewC. SkewC identifies skewed cells by comparing coverage patterns of gene regions. SkweC is capable of processing any type of scRNA-seq data set, regardless of protocol.
https://doi.org/10.1016/j.isci.2022.103777
Paper Published (Dec. 17, 2021)
DR Fukushima, DR Arita (CSRS Metabolome Information Research Team, respectively) and DR Kobayashi (R-IH Data Knowledge Development Unit) et al. published a paper on the RIKEN Plant Metabolome MetaDatabase (RIKEN PMM), which is a database developed to facilitate the sharing and reuse of plant metabolome data by mass spectrometry.
https://doi.org/10.1093/pcp/pcab173
Paper Published (May. 24, 2021)
DR Tohsato and DR Itoga (BDR Laboratory for Developmental Dynamics, respectively) , together with Prof. Tatsumi Hirata (NIG) and colleagues, developed the “NeuroGT database,” which contains whole-brain image data of tagged neurons based on time of neurogenesis. Through NeuroGT, researchers can find suitable neurogenic tagging driver lines for their research. For more details, please visit the National Institute of Genetics website.
https://doi.org/10.1016/j.crmeth.2021.100012
Paper Published (May. 21, 2021)
DR Onami (BDR Laboratory for Developmental Dynamics) joined discussions on metadata standards in biological image data sharing with an international bioimaging community lead by EMBL-EBI. They propose global metadata guidelines, REMBI: Recommended Metadata for Biological Images.
https://doi.org/10.1038/s41592-021-01166-8
Paper Published (May. 12, 2021)
DR Suzuki (BRC Integrated Bioresource Information Division), Dr Masuya (BRC Integrated Bioresource Information Division) and their collaborative research group have developed a data analysis method to capture comprehensively changes in the stability of ecosystems in multispecies communities. This method can lead to new utilization of bioresources in various fields such as disease treatment, health maintenance, and agricultural technology development.
https://doi.org/10.1002/ecm.1469
Paper Published (May. 4, 2021)
Dr Onami (BDR Laboratory for Developmental Dynamics) and Prof. Jason Swedlow (University of Dundee, UK) along with Global Bioimaging, an international consortium of the leading experts in bioimaging communities, released recommendations for bioimage data format standards and open access image data repositories. These recommendations contribute to accelerating the development of the bioimaging field through data sharing.
https://doi.org/10.1038/s41592-021-01113-7
Paper Published (Apr. 26, 2021)
A paper on the gene expression database from the brain of the common marmoset Dr Shimogori (CBS Laboratory for Molecular Mechanisms of Brain Development) et al. was published in Proceedings of the National Academy of Sciences of the United States of America (PNAS). Marmosets have recently attracted much attention as a novel animal model for brain science. This research is expected to lead to the identification of brain regions that cause mental and neurological disorders as well as the investigation of the causes of neural circuit dysfunction in the human brain.
https://doi.org/10.1073/pnas.2020125118
Paper Published (Jan. 18, 2021)
A review paper by Dr Masuya (BRC Integrated Bioresource Information Division) on RIKEN Bioresource was published on Laboratory Animal Research. This review summarizes the features of the current version of databases related to mouse strain resources in RIKEN BioResource Research Center and discusses future views.
https://doi.org/10.1186/s42826-020-00068-8
Paper Published (Nov. 19, 2020)
A paper by Dr Kasukawa (IMS Lab for Large-Scale Biomedical Data Technology) et al. on the latest updates of the FANTOM (The Functional ANnoTation Of the Mammalian genome) web resources was published is in Nucleic Acids Research. This paper reports the latest updates of the FANTOM mainly the updates of viewers and interfaces regarding new non-coding RNA datasets which the FANTOM5 and FANTO6 produced the enhancement and expansion.
https://doi.org/10.1093/nar/gkaa1054
Paper Published (Sep. 3, 2020)
Dr Yamagata (BDR Lab for Developmental Dynamics) et al. published a paper on the toxic process ontology (TXPO) for decreasing potential risks in drug safety management in Scientific Reports. The TXPO systematizes knowledge concerning hepatotoxic courses with consistency and no ambiguity. In their application work, a toxic process interpretable knowledge system (TOXPILOT) was developed. Using semantic web technology, TOXPILOT supports the interpretation of toxicity mechanisms and provides visualizations of toxic courses with useful information based on ontology.
https://doi.org/10.1038/s41598-020-71370-7
Paper Published (Aug. 12, 2020)
A paper by Dr. Koji Kyoda (BDR Lab for Developmental Dynamics) et al. on developing the BD5, a new open data format based on HDF5, was published in PLOS ONE. It can be used to represent quantitative data of biological dynamics obtained from bioimage informatics techniques and mechanobiological simulations. BD5 enables fast access to quantitative data and fast transfer of files containing large quantitative data.
https://doi.org/10.1371/journal.pone.023746
Paper Presented at SWAT4HCLS (Dec. 9 – 12, 2019 UK)
Dr. Kobayashi (ISC Data Knowledge Organization Unit) and Open Microscopy Environment (OME) presented a paper at an international conference, SWAT4HCLS.
A new method for standardization of microscopy imaging data and utilization of imaging data was proposed. It enables the integration of metadata of bio-imaging projects around the world and the integrative analysis with other types of data. The full paper is available on the SWAT4HCLS website.
Paper Published in Nature Metabolism (July 29, 2019)
As a member of the Lipidomics Standards Initiative (LSI), Dr. Arita (CSRS Metabolome Informatics Research Team) co-authored a paper on positioning in lipidomics was published in Nature Metabolism. International abbreviations for 130 lipid classes were standardized and standard data on lipids identified by lipidomics was open.
https://doi.org/10.1038/s42255-019-0094-z
[Symposium/Workshop]
Honored with the 28th Miyadi Award of the Ecological Society of Japan (Mar. 18, 2024 Kannnai Hall)
We are pleased to announce that Dr. Suzuki ((BRC Integrated Information Development Office) has received the 28th Miyadi Award from the Ecological Society of Japan (ESJ). He gave a commemorative lecture in the 71st ESJ annual meeting.
- Lecture title: Ecosystems, Dynamical Systems, and Complex Systems: Toward an Ecology of Predictive Control
- Abstract (in Japanese)
OLSP research project (2023)
We selected proposals, two in research proposal type, as FY2023 Call for proposals for OLSP Research Project. Each proposal will be conducted for one year and terminate in December 2024. See details of accepted proposals.
Symposium of Database Togo (Integration) (Oct. 5, 2023 Miraikan)
Team Leader Kasukawa(IMS Lab for Large-Scale Biomedical Data Technology) ‘s oral presentation on the construction of the INTRARED at the Symposium of Database Togo (Integration) 2023, hosted by JST is available on the TOGO TV.
ABiS-GBI 2023 course – Image data: image analysis, data management and reuse (Jul. 3 – Jul. 7, 2023 NIBB Conference Centre and RIKEN Kobe）
Jointly organized by Global BioImaging (GBI) and Advanced Bioimaging Support (ABiS), we held the ABiS-GBI 2023 course – Image data: image analysis, data management and reuse. Researchers from all over the world who acquire images in microscopy facilities, researchers who analyse images, microscopy facility managers and data managers gathered to learn and exchange comprehensive topics on image data, including image analysis, data management and image data repositories.
BioHackathon 2023 (Jun. 25 – Jul. 1, 2023 Kagawa International Conference Hall and Olivean Shodoshima）
Members of OLSP joine the DBCLS BioHackathon 2023. THALHATH Nishad (IMS Lab for Large-Scale Biomedical Data Technology) published their achievements on BioHackrXiv.
- Yokochi, M., & Thalhath, N. (2023, July 1). Evaluating Oxigraph Server as a triple store for small and medium-sized datasets.
- Labra-Gayo, J. E., Waagmeester, A., Yamamoto, Y., Iglesias-Préstamo, Á., Katayama, T., Liener, T., … Thalhath, N. (2023, July 3). RDF Data integration using Shape Expressions.
OLSP Workshop 2023（Jun. 15-16, 2023 RIKEN Wako Campus and Online)
We held the OLSP Workshop 2023. This year, we had not only members of OLSP labs but also researchers selected for the 2020 to 2022 OLSP research project. On day 1, researchers form the OLSP research project 2022 introduced their ongoing project. Past OLSP research project members presented the subsequent development of their projects. On day 2, each working group in the OLSP project discussed topics such as ontology, open science activity evaluation criteria, and TRIP (Transformative Research Innovation Platform of RIKEN platforms) concept and their prospects.
The 37th Annual Conference of the Japanese Society for Artificial Intelligence, 2023 (Jun. 6-9, 2023 Kumamoto-jo Hall and Online)
A oral presentation “Ontological modeling of cellular senescence for aging regulation” by Dr Yamagata (R-IH Life Science Data Sharing Development Unit and BRC Integrated Information Development Office) awarded the JSAI Annual Conference Award at the 37th Annual Conference of the Japanese Society for Artificial Intelligence.
NII Open Forum 2023（May 29-31, 2023 Hitotsubashi Univ. & Online)
Dr Kushida (BRC Integrated Information Development Office) was invited to the NII Open Forum 2023 and introduced RIKEN’S activity for improving and monitoring the semantics of research data in the life sciences. His speech is open on YouTube as well as slides are available on the Open forum’s website (in Japanese).
OLSP research project (2022)
We selected proposals, two in research proposal type, as FY2022 Call for proposals for OLSP Research Project. Each proposal will be conducted for one year and terminate in December 2023. See details of accepted proposals.
IMGC2023 (Mar.28-31, 2023 Tsukuba International Congress Center and Online)
36th International Mammalian Genome Conference (IMGC2023) was held at Tsukuba International Congress Center, Tsukuba, Ibaraki, Japan, from March 28 to 31, 2023. 246 participants (205 on-site and 41 online) joined this hybrid conference, 129 participants from outside Japan, exceeding the number of domestic participants. In addition to the 61 oral presentations and 96 poster presentations, three experimental technology workshops were held, and on the second and third days, the RIKEN Symposium “Developmental Epigenetics and Advanced phenotyping Technology” was held in collaboration with RIKEN. On the final day, 13 researchers, including Japanese, received awards for young honor reseachers.
AJACS online 15 (Jan. 26, 2023 Online)
Dr Morioka(IMS Lab for Large-Scale Biomedical Data Technology), who is also working on the OLSP research project, gave a lecture on the UCSC Genome Browser at the Integrated Database Training Course: AJACS Online 15, hosted by the NBDC. The lecture is now available on YouTube. You can learn about rich tools on the UCSC Genome Browser and their utilisation.
MBSJ2022 Forum (Nov. 30 – Dec. 2, 2022 Makuhari Messe, Chiba and Online)
The NBDC hosted a forum “Life Science Database introduction” at MBSJ 2022. Lectres by Dr Onami (BDR Lab for Developmental Dynamics Research Team) and Dr Arita (CSRS Metabolome Informatics Research Team) at MBSJ2022 went pulic at the NBDC website.
AJACS online 13 (Nov. 24, 2022 Online)
Dr Suzuki (BRC Integrated Bioresource Information Division) gave a lecture on public chemical database at the Integrated Database Training Course: AJACS Online 13, hosted by the NBDC. The lecture is now available on YouTube. You can learn how to use commonly used chemical databases such as PubChem and ChEMBL and undestand each features and differences between them.
Symposium of Database Togo (Integration) (Oct. 5, 2022 Online)
Team Leader Onami (BDR Lab for Developmental Dynamics Research Team) and Team Leader Kasukawa(IMS Lab for Large-Scale Biomedical Data Technology) ‘s oral presentations at the Symposium of Database Togo (Integration), hosted by JST to introduce project activities and exchange research and development on databases. Presentation slides and video clips, both in Japanase, are available on the Symposium 2022 website.
Bio”Pack”athon 2022 #9 (Sep. 2, 2022 Online)
Dr Kasukawa (IMS Lab for Large-Scale Biomedical Data Technology)’s talk at Bio “Pack “athon 2022 #9, “Development of the database of cis-regulatory elements for transcriptional regulatory data infrastructure,” is now available on Togo TV. The talk is about FANTOM5 data and his DICP projects adopted for FY2022, the development of the database of cis-regulatory elements.
AJACS online 12 (Aug. 25, 2022 Online)
Drs Itoga and Kyoda (BDR Lab for Developmental Dynamics Research Team, respectively) lectured on the overview and usage of bio-imaging databases, including SSBD and the latest status of bio-imaging at the Integrated Database Training Course: AJACS Online 12, hosted by the NBDC. The lecture is now available on YouTube.
Reports of OLSP research project (2020)
We have updated reports of FY2020 Call for proposals for OLSP Research Project. See reports of each proposals (in Japanese).
OLSP Workshop 2022 (May 12, 2022 Online)
The internal workshop, OLSP Workshop 2022, was took place online. The ongoing OLSP reseach projects in FY2021 were presented. Each working group in the OLSP project, such as the Open Science Evaluation Working Group, Ontology Working Group, International Collaboration, and Human Resource Development, reported on their activities and discussed their future prospects with participants.
OLSP research project (2021)
We selected proposals, two in research proposal type, as FY2021 Call for proposals for OLSP Research Project. Each proposals will be conducted for one year and terminate in December, 2022. See details of accepted proposals.
OLSP Workshop 2021（Apr. 20 and 22, 2021 Online)
An online workshop, OLSP Workshop 2021, took place on the 20th and 22nd April 2021 as an online event with the participation of researchers from each center in RIKEN which joined OLSP. On Day 1, each research proposal accepted in FY2020 gave a presentation on their research. On Day2, each working group in the OLSP project, including the Ontology Working Group, reported on their activities and discussed future prospects.
RIKEN Symposia: RIKEN Hackathon Open Symposium (Mar. 22, 2021 Online)
An open symposium co-hosted by RIKEN Open Life Science Platform (OLSP) was held online. See the announcement page.
OLSP research project (2020)
We selected proposals, four in research proposal type and 2 in data provision type, as FY2020 Call for proposals for OLSP Research Project. Each proposals will be conducted for one year from October, 2020. See details of accepted proposals.
Invited Speech: Open Symposium by Science Council Japan (Oct. 14, 2020)
Dr. Yokota (RAP Image Processing Research Team) and Dr. Onami (BDR Laboratory for Developmental Dynamics) respectively gave a speech regarding ” Prospects for next-generation integrated bioimaging and mathematical collaboration at an online open symposium organized by Science Council Japan. For more information please visit the symposium website ( in Japanese only).
RIKEN Symposia: RIKEN Hackathon Open Symposium (Feb. 17, 2020 RIKEN Kobe Campus)
On February 17, 2020, an open symposium co-hosted by RIKEN Open Life Science Platform (OLSP) was held at RIKEN Kobe Campus. See the announcement page.
RIKEN Open Life Science Platform Data Collection Workshop (Jan. 20 – 21, 2020 RIKEN Kobe Campus)
The RIKEN Open Life Science Platform held the Data Collection Workshop (Project members only) at RIKEN Kobe Campus. In this workshop, we discussed on the types and management of public databases and published data, and activities for the future.
The 6th RIKEN-KI-SciLifeLab Symposium (Nov. 6, 2019 RIKEN Yokohama Campus)
RIKEN, Karolinska Institute and SciLifeLab in Sweden organized the 6th RIKEN-KI-SciLifeLab Symposium. Dr. Onami (BDR Lab for Developmental Dynamics) and Dr. Kasukawa (IMS Lab for Large-Scale Biomedical Data Technology) participated in the symposium and joined discussions on strengthening cooperation between the two organizations in data science and contributed future developments in the life sciences in both countries. See the symposium website.
BioImage Archive Metadata Workshop (Oct. 14 – 15, 2019 UK)
Dr. Onami (BDR Lab for Developmental Dynamics) was invited to the BioImage Archive Metadata Workshop organized by EMBL-EBI. In this workshop, experts in Bio-image Data Repositories from Europe, the US, and Japan established the first version of global metadata standards for Bio-image Data Repositories and discussed a global collaboration of Bioimaging Data Repositories.
Global BioImaging Exchange of Experience IV (Sep. 13, 2019 Singapore)
Dr. Onami (BDR Lab for Developmental Dynamics) participated in the Global BioImaging Exchange of Experience IV to discuss bio-imaging data sharing with leading-scientists in this fieled mainly from Europe, the US, and Japan. This community can be a major data collaboration that promotes open life sciences on a global scale. For more information, please see the meeting website.
[Database/Resource]
QTBD5Viewer – a visualizer for BD5-format files – (May 18, 2023)
QTBD5Viewer – a visualizer for BD5-format files – is now available. It runs on Windows, macOS, and Ubuntu Linux. BD5-format is a unified file format for quantitative biodynamics data and SSBD:database provides various types of such data in BD5-format.
Chronic cellular senescence course – Homeostasis imbalance process ontology (HoIP) (Mar. 9, 2023)
Dr Yamagata (R-IH Life Science Data Sharing Unit) et al. are developing an ontology on cellular senescence and have published ontology-based visualization data on cellular senescence mechanisms on NDEx (Network Data Exchange), an open-platform for the publication of biological network data.
https://doi.org/10.18119/N9KS4H
INSDC spatiotemporal metadata – minimum standards update (Mar. 3, 2023)
The International Nucleotide Sequence Database Collaboration (INSDC), a consortium operated by DDBJ, EMBL-EBI, and NCBI, has published standards for the listing of genetic resources in the Convention on Biological Diversity. For details, please visit the article on IBSDC website: INSDC spatiotemporal metadata – minimum standards update (03-03-2023). You may be interested in a lecture on “Policy of INSDC and Response to the Convention on Biological Diversity” given by Dr. Arita in October 2022. The video is available on the Youtube channel of National Institute of Technology and Evaluation (NITE).
Decomposing predictability to identify dominant causal drivers in complex ecosystems (Oct. 17, 2022)
Drs Suzuki and Masuya(BRC Integrated Bioresource Information Division) and Dr Matsuzaki (Biodiversity Division, NIES) have developed a method to estimate the relationships among elements in an ecosystem from temporal data through the collaboration of a large number of AI processes. By applying this method to a long-term lake monitoring dataset, the team clarified some factors behind the large cyanobacterial blooms linked to water quality degradation. This approach, EcohNet, could be used to analyze complex and hybrid multivariate time series in many scientific areas not limited to ecosystems. For more research details, please read RIKEN BRC Press Release, dated Oct. 17, 2022.
Developed the RIKEN Plant Metabolome MetaDatabase (Dec. 17, 2021)
The plant metabolome is complex and diverse, and contains useful substances that can be used for energy supply and medicine not only for plants themselves but also for other species on the earth, including humans.Although major public repositories for general metabolome data have been established, the community still has shortcomings in terms of reanalysis, reusability, and reproducibility of the open data. CSRS Metabolome Information Research Team developed a database of plant metabolome datathe RIKEN Plant Metabolome MetaDatabase (PMM). The database stores plant metabolome data obtained by mass spectrometry (e.g., GC-MS) and facilitate the sharing and reuse of plant metabolome data from mass spectrometers (e.g., GC-MS). PMM publishes experimental metadata and raw data from plant metabolome studies in a structured, machine-readable format (compliant with international standards for the Web).
Released NeuroGT database (May. 24, 2021)
Drs Tohsato and Itoga (BDR Developmental Dynamics Research Team, respectively) collaborated with Prof. Hirata (National Institute of Genetics) launched “NeuroGT database”, a brain atlas of neurogenic tagging mouse lines. Currently, the database consists of 84 datasets containing 13,538 images and is available at https://ssbd.riken.jp/neurogt/.
Development of HoIP Ontology (2020)
Dr Yamagata (BDR Lab for Developmental Dynamics) et al. have developed Homeostasis imbalance process ontology (HoIP) ontology. HoIP is available at the NCBO BioPortal (http://bioportal.bioontology.org/ontologies/HOIP). HoIP systematizes a wide variety of terms involving homeostasis imbalance processes by manual annotation. HoIP contains information about SARS-CoV-2 infectious processes and biological defense processes such as immune response, related molecules, and chemical compounds in COVID-19.
Updated Metadata on Bioresouces (Mar. 23, 2020)
BRC Integrated Bioresource Information Division worked on the development of metadata for the data on RIKEN Bioresource. This improvement established a system for linking individuals (phylogenies) and cells across species and provided the ability to utilize data in varied fields of life science.
Resource Catalogs by Biomaterial
Mouse resource catalog in RIKEN BRC
Plant resources catalog in RIKEN BRC
Cell resource catalog in RIKEN BRC
DNA resource catalog in RIKEN BRC
Microbial resource catalog in RIKEN BRC
SSBD: database Update (Nov. 20, 2019)
SSBD is an integrated biological database of quantitative data and microscopy images developed by BDR Lab for Developmental Dynamics. The former SSBD was divided into SSBD:database and SSBD:repository to enhance its feature and additional data was published on them. For more information, visit http://ssbd.qbic.riken.jp/.
Development of metadata items for metabolomic data (2019)
CSRS Metabolome Informatics Research Team has developed ontology in plant data accumulated by RIKEN PSC and CSRS. This allowed 53 studies and approximately 7,000 measurement data open in the database. Accordingly, 131 studies have been available including the data from Kazusa DNA Research Institute. These data are available at http://metabobank.riken.jp/. In the future, the database will have a wider range of areas such as mice, human organs, food, and the environment.
