This project collects and maintains minimum information metadata templates designed and used in the National NL-Bioimaging initiative. The templates are based on the REMBI standards and contribute to FAIR bioimaging data in the Netherlands, together with data management in the OMERO database.
Programme: NL-Bioimaging: FAIR-DM
SEEK ID: https://fairdomhub.org/projects/303
Public web page: http://eurobioimaging.nl/
Organisms: No Organisms specified
FAIRDOM PALs: No PALs for this Project
Project created: 10th Oct 2022
Related items
- People (2)
- Programmes (1)
- Institutions (1)
- Investigations (1)
- Studies (1)
- Assays (5+1)
- Data files (7)
- SOPs (3)
- Documents (1)
Projects: NL-Bioimaging FAIR Metadata Templates
Institutions: University of Leiden
https://orcid.org/0000-0002-3704-3675Projects: SysMO DB, HUMET Startup, FAIRDOM, Consensus Hallmark Annotation, NL-Bioimaging FAIR Metadata Templates, FAIR Functional Enrichment, Benefit for All FAIR Data
Institutions: University of Leiden, LIACS
https://orcid.org/0000-0002-1279-5133Expertise: Biochemistry, Bioinformatics, Data Management
Tools: Data Management, Transcriptomics, Databases, Workflows, Web services, Taverna, Ontologies, semantic web
I am an Assistant Professor at Leiden University in the Leiden Institute of Advanced Computer Science. I am a bioinformatician and my research interests are in data integration. I use scientific workflows and semantic web technologies to integrate and analyse data in systems biology and functional genomics.
NL-BioImaging AM is a distributed research infrastructure aimed at promoting progress in the most cutting edge microscopy technologies and providing open access to these technologies to a broad community of academic and industrial users. All Netherlands bio(medical) microscopy centers participate.
FAIR (Findable Accessible, Interoperable and Reusable) data management is a challenge for the optical microscopy community due to a high diversity in participating research fields and methodologies, ...
Projects: NL-Bioimaging FAIR Metadata Templates
Web page: http://eurobioimaging.nl/
User metadata is an essential part of experimental data. Scientists need to understand underlying conditions and experimental procedures in order to model or investigate relevant biological questions. Currently, only a small fraction of the High Content SCreening (HCS) investigations are deposited for reuse by the community, and an even smaller fraction of that data is standards-compliant. For reusing data, scientists need to be able to understand how data was generated, under which experimental ...
Submitter: Katy Wolstencroft
Studies: MIHCSME templates
Assays: General MIHCSME template, MIHCSME template example for "Integration of biological data by kernels ..., MIHCSME template example for "Uncovering the signaling landscape control..., MIHCSME template example for compound screen on HepG2 CHOP-GFP reporter ..., MIHCSME template example for “Temporal single cell cellular stress respo...
Snapshots: No snapshots
A minimal metadata template for high content screening experiments in microscopy. The template is compliant with REMBI (Recommended Metadata for Biological Images) and the ISA framework (Investigations, Studies and Assays).
Here you will find guidelines for filling in MIHCSME metadata templates, as well as examples of published HCS studies that use MIHCSME.
Submitter: Rohola Hosseini
Investigation: Minimal Information for High Content Screening ...
Assays: General MIHCSME template, MIHCSME template example for "Integration of biological data by kernels ..., MIHCSME template example for "Uncovering the signaling landscape control..., MIHCSME template example for compound screen on HepG2 CHOP-GFP reporter ..., MIHCSME template example for “Temporal single cell cellular stress respo...
Snapshots: No snapshots
Generic metadata template describing High Content Screening data that conform to the REMBI and ISA specification. LEI-MIHCSME empty template that can serve as basis for filling in metadata. This template was created and modified from templates produced by Leiden University.
Submitter: Rohola Hosseini
Assay type: high content screening
Technology type: Imaging
Investigation: Minimal Information for High Content Screening ...
Study: MIHCSME templates
Organisms: No organisms
SOPs: LEI-MIHCSME Template guidlines
Data files: LEI-MIHCSME - empty template
Snapshots: No snapshots
Compound screen on 13 HepG2 -GFP reporter lines, to measure GFP protein induction, and cell death induction. Template and associated files describe High Content Screening experimental data that conform to the MIHCSME specification.
Submitter: Rohola Hosseini
Assay type: high content screening
Technology type: Confocal Laser Scanning Microscopy (CLSM)
Investigation: Minimal Information for High Content Screening ...
Study: MIHCSME templates
Organisms: No organisms
SOPs: Protocols file
Data files: Example MIHCSME live cell imaging, Example MIHCSME live cell imaging
Snapshots: No snapshots
MIHCSME template example for IDR0022 dataset. Primary and validation RNAi screen using smartpool and single siRNAs to identify cell migratory regulators in Hs578T and MDA-MB-231 triple-negative breast cancer cells.
Submitter: Rohola Hosseini
Assay type: high content screen of cells treated with library of siRNAs
Technology type: bright-field microscopy
Investigation: Minimal Information for High Content Screening ...
Study: MIHCSME templates
Organisms: No organisms
SOPs: No SOPs
Data files: Example MIHCSME screenA, Example MIHCSME screenB
Snapshots: No snapshots
RNAi Screen of 100 candidate genes predicted to be involved in mitotic chromosome condensation. MIHCSME template example for IDR0002 dataset.
Submitter: Rohola Hosseini
Assay type: high content screen of cells treated with library of siRNAs
Technology type: fluorescence microscopy
Investigation: Minimal Information for High Content Screening ...
Study: MIHCSME templates
Organisms: No organisms
SOPs: No SOPs
Data files: Example MIHCSME screenA idr0002
Snapshots: No snapshots
Compound screen on HepG2 CHOP-GFP reporter, to measure CHOP-GFP protein induction upon treatment with compounds. Template and associated files describe High Content Screening experimental data that conform to the MIHCSME specification.
Submitter: Rohola Hosseini
Assay type: high content screen of cells in treated with a compound library
Technology type: Confocal microscopy
Investigation: Minimal Information for High Content Screening ...
Study: MIHCSME templates
Organisms: No organisms
SOPs: SOP Library file
Data files: Example template HepG2 CHOP-GFP
Snapshots: No snapshots
An example template for screen published in IDR (idr0022, screenA).
Creator: Rohola Hosseini
Submitter: Rohola Hosseini
Investigations: Minimal Information for High Content Screening ...
Studies: MIHCSME templates
An example template for screen published in IDR (idr0022, screenB).
Creator: Rohola Hosseini
Submitter: Rohola Hosseini
Investigations: Minimal Information for High Content Screening ...
Studies: MIHCSME templates
An example template describing compound screen on HepG2 CHOP-GFP reporter .
Creator: Rohola Hosseini
Submitter: Rohola Hosseini
Investigations: Minimal Information for High Content Screening ...
Studies: MIHCSME templates
An example template for screen published in IDR (idr0002, screenA).
Creator: Rohola Hosseini
Submitter: Rohola Hosseini
Investigations: Minimal Information for High Content Screening ...
Studies: MIHCSME templates
This excel template is for use of describing HCS microscopy data. It was created based on ISA methodology and modified to conform REMBI recomandations.
Creator: Rohola Hosseini
Submitter: Rohola Hosseini
Investigations: Minimal Information for High Content Screening ...
Studies: MIHCSME templates
Assays: General MIHCSME template
An example of MIHCSME describing live cell imaging HepG2 -GFP reporter line.
Creator: Rohola Hosseini
Submitter: Rohola Hosseini
Investigations: Minimal Information for High Content Screening ...
Studies: MIHCSME templates
An example of MIHCSME describing live cell imaging HepG2 -GFP reporter line, describing assay with cell death staining.
Creator: Rohola Hosseini
Submitter: Rohola Hosseini
Investigations: Minimal Information for High Content Screening ...
Studies: MIHCSME templates
An overview of MIHCSME template components.
Creator: Rohola Hosseini
Submitter: Rohola Hosseini
Investigations: Minimal Information for High Content Screening ...
Studies: MIHCSME templates
Assays: General MIHCSME template
This file is associated with performed study and describes protocols used.
Creator: Rohola Hosseini
Submitter: Rohola Hosseini
Investigations: Minimal Information for High Content Screening ...
Studies: MIHCSME templates
Associated library SOP file with metadata template.
Creator: Rohola Hosseini
Submitter: Rohola Hosseini
Investigations: Minimal Information for High Content Screening ...
Studies: MIHCSME templates
This document is associated with metadata file and describes compounds used in this study.
Creator: Rohola Hosseini
Submitter: Rohola Hosseini
Investigations: Minimal Information for High Content Screening ...
Studies: MIHCSME templates