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RIKEN Open Life Science Platform

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ACTIVITY/ACHIEVEMENT

| Publication | Symposium/WorkshopDatabase/Resource |


[Publication]

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]

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 Hackathon FY2019

 

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.

photo of the data collection workshop

 

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]

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.