Molecular 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.

PDBx/mmCIF – Protein Data Bank Exchange Dictionary and the Macromolecular Crystallographic Information Framework

PDBx/mmCIF is the standard archive format used by the Protein Data Bank (PDB). It provides both metadata and data according to properties defined in the PDB Exchange Dictionary and the Macromolecular Crystallographic Information Framework (mmCIF).

Repository-Developed Metadata Schemas

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

Tools

PDBx/mmCIF Software Resources

Parsing, validation, and visualization tools and libraries supporting PDBx/mmCIF, the data standard used by the Worldwide Protein Data Bank.

ProteoRed Tools

Bioinformatics tools to create and extract metadata compliant with the MIBBI-registered MIAPE minimum requirements.

Use Cases

Chem-BLAST

A Web-based service for searching for and visualizing chemical structures. It uses data from the Protein Data Bank that has been transformed to RDF.

dbEST - Expressed Sequence Tag Database

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

International Molecular Exchange Consortium

An international collaboration to provide access to a non-redundant set of protein-protein interaction data from a broad taxonomic range of organisms. IMEx partner databases require data to be MIMIx (a MIBBI-registered standard) compatible.

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.

MetaboLights

A database for metabolomics experiments and derived information in ISA-Tab format.

PRIDE - PRoteomics IDEntifications database

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

Worldwide Protein Data Bank

The Protein Data Bank archive (PDB) is a worldwide archival repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies. The Worldwide PDB (wwPDB) organization manages the PDB archive and ensures that the PDB is freely and publicly available to the global community.