Cell Biology

Metadata Standards

ISA-Tab

A general purpose framework with which to capture and communicate metadata for data files from 'omics-based' experiments employing combinations of technologies.

MIBBI - Minimum Information for Biological and Biomedical Investigations

A common portal to a group of checklists of Minimum Information in nearly 40 biological disciplines.

OME-XML - Open Microscopy Environment XML

A metadata standard and data file format for biological light microscopy data.

Extensions

OME-TIFF - Open Microscopy Environment TIFF

A specification of how to embed OME-XML metadata within a TIFF or BigTIFF image file.

SNRNASM ISA-Tab

An ISA-Tab-based standard for reporting the results of single nucleotide resolution nucleic acid structure mapping experiments.

Tools

Bio-Formats

Bio-Formats reads proprietary microscopy image data and metadata, and converts them to OME-TIFF, a combination of TIFF and OME-XML.

Fiji

Fiji is an image processing package that supports the OME data model for images

ISA Software Suite

The open source ISA metadata tracking tools facilitate ISA-TAB-compliant collection, curation, local management and reuse of datasets in an increasingly diverse set of life science domains.

OMERO

Repository software for organising, viewing, analysing and sharing biological microscopy images. It supports proprietary file formats but normalises to OME-TIFF/OME-XML.

Use Cases

FlowRepository

A database of flow cytometry experiments where you can query and download data collected and annotated according to the MIBBI-registered MIFlowCyt standard.

Harvard Medical School LINCS Database

One of two research centers in the US creating libraries of signatures that describe how cells respond to perturbation, it uses the ISA-TAB standard to describe its data.

ISA Commons

A network of systems and projects that use the ISA-Tab file format, and/or are powered by components of the ISA software suite.

ISA Commons

A network of systems and projects that use the ISA-Tab file format, and/or are powered by components of the ISA software suite.

JCB Data Viewer

A repository for viewing and analysing multi-dimensional image data associated with articles published in The Journal of Cell Biology. Its native metadata format is OME-XML.

The Cell: An Image Library

A resource database of images, videos, and animations of cells, capturing a wide diversity of organisms, cell types, and cellular processes. Its native metadata format for images is OME-XML.