bars cross

RIKEN Ppen Life Science Platform

JA EN

ACTIVITY/ACHIEVEMENT

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

 

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).

 

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

 

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

 

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

 

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.

 

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/.

 

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.

 

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.

 

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.

 

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