Bioinformatics

Metadata Standards

MIBBI - Minimum Information for Biological and Biomedical Investigations

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

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).

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.

Use Cases

BioModels Database

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

CHD7 Database
An open access database that contains anonymised data on both published and unpublished CHD7 variations and phenotype.
dbEST - Expressed Sequence Tag Database

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

International dystrophic eb Patient Registry
The international registry of dystrophic epidermolysis bullosa (DEB) patients and associated COL7A1 mutations.
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.

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.