Connecting and Expanding RIKEN's Systems Science of Biological Dynamics and OME's Image Data Resource Databases
Lead Research Organisation:
University of Dundee
Department Name: School of Life Sciences
Abstract
Japan
Publications
Sarkans U
(2021)
REMBI: Recommended Metadata for Biological Images-enabling reuse of microscopy data in biology.
in Nature methods
Swedlow JR
(2021)
A global view of standards for open image data formats and repositories.
in Nature methods
| Description | The Swedlow group has led the OME Consrotium for many years and developed and released Bio-Formats and OMERO software platforms and the Image Data Resource (IDR; https://idr.openmicroscopy.org), the world's open, comprehensive public resource for reference imaging datasets in the life and biomedical sciences. The Onami Group (RIKEN, Japan) has developed the Systems Science of Biological Dynamics Database (SSBD; http://ssbd.qbic.riken.jp/), public image data resource based on OME's OMERO and Bio-Formats software. The funding allowed the two groups to spend 10 days together, reviewing each other's progress and identifying avenues for future collaboration. |
| Exploitation Route | Both IDR and SSBD are publishing imaging data on the scale fof 10s to 100s of TBytes, and these datasets can be re-used by others for benchmarks and re-analysis. The cited preprint reflects our views of requirements for public image data formats and resources. The preprint is now in press at Nature Methods. |
| Sectors | Digital/Communication/Information Technologies (including Software) Pharmaceuticals and Medical Biotechnology |
| URL | https://arxiv.org/abs/2010.10107 |
| Description | They have informed a discussion in Global BioImaging, leading to the preprint cited above. |
| First Year Of Impact | 2020 |
| Sector | Digital/Communication/Information Technologies (including Software) |
| Impact Types | Policy & public services |
| Title | Image Data Repository (IDR) |
| Description | A collection of image data and metadata, including all experimental, acquisition, and analytic metadata. |
| Type Of Material | Database/Collection of data |
| Year Produced | 2015 |
| Provided To Others? | Yes |
| Impact | The scripts used for importing datasets into the IDR form the basis of proposed standards for experimental and analytic metadata image-based phenotypic studies. A proposal to fund the full development of these standards has been submitted. |
| URL | http://idr-demo.openmicroscopy.org |
| Description | IDR |
| Organisation | EMBL European Bioinformatics Institute (EMBL - EBI) |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have built the OMERO and Bio-Formats technology that forms the basis of the IDR. |
| Collaborator Contribution | Alvis Brazma is a collaborator on our BBSRC IDR award (BB/M018423/1). |
| Impact | The IDR is the major current output. Publications are now in prep. |
| Start Year | 2015 |