Genomics

Metadata Standards

ABCD - Access to Biological Collection Data

A standard for the access to and exchange of primary biodiversity data, including specimens and observations.

Genome Metadata

Descriptive data about single genomes within the Pathosystems Resource Integration Center.

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.

Repository-Developed Metadata Schemas

Some repositories have decided that current standards do not fit their metadata needs, and so have created their own requirements.

Extensions

ABCDDNA

An extension of the ABCD standard for DNA data.

isaconfig-diXa
An extension of ISA-TAB for representing and sharing metadata about toxicogenomics experiments.
MIBBI Portal

A list of nearly 40 Minimum Information standards projects registered with the MIBBI initiative.

Tools

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.

PATRIC Download Tool

Tool for downloading data from PATRIC.

Use Cases

BioModels Database

A repository hosting computational models of biological systems, using the MIBBI-registered MIRIAM and MIASE minimal metadata requirements.

dbEST - Expressed Sequence Tag Database

A repository-developed metadata schema for EST data in Genbank.

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.

MVID Patient Registry
The international registry of Microvillus Inclusion Disease (MVID) patients and associated MYO5B mutations.
NEBC ISA Network BioInvestigationIndex

The NERC Environmental Bioinformatics Centre ISA Network's index of ISA-Tab and MIBBI-compliant environmental 'omics data.

PRIDE - PRoteomics IDEntifications database

A centralized, MIBBI standards compliant, public data repository for proteomics data, post-translational modifications and supporting spectral evidence.

WormQTL-HD
A comprehensive web database for linking human disease to natural variation data in Caenorhabditis elegans