Standards Add

MIBBI (Minimum Information for Biological and Biomedical Investigations) Edit

A common portal to a group of nearly 40 checklists of Minimum Information for various biological disciplines. The MIBBI Foundry is developing a cross-analysis of these guidelines to create an intercompatible, extensible community of standards.

The concept was realized initially through the joint efforts of the Proteomics Standards Initiative, the Genomic Standards Consortium and the MGED RSBI Working Groups. The latest project to register with MIBBI is the MIABie guidelines for reporting biofilm research, as of January 2012.

Open Standard for Particle-Mesh Data (openPMD) Edit

The openPMD standard provides naming and attribute conventions that allow the exchange of particle and mesh based data from scientific simulations and experiments. The primary goal is to define a minimal set/kernel of meta information that enables the sharing and exchange of data to achieve.

  • portability between various applications and differing algorithms;
  • a unified open-access description for scientific data (publishing and archiving);
  • a unified description for post-processing, visualization and analysis.

The standard suits any kind of hierarchical, self-describing data format, such as, but not limited to ADIOS1 (BP3), ADIOS2 (BP4), HDF5, JSON, and XML.

PDBx/mmCIF (Protein Data Bank Exchange Dictionary and the Macromolecular Crystallographic Information Framework) Edit

Protein Data Bank archive (PDB) is the single worldwide archival repository of information about the 3D structures of proteins, nucleic acids, and complex assemblies, managed by the Worldwide PDB (wwPDB). The PDB Exchange Dictionary (PDBx) is used by the wwPDB to define data content for deposition, annotation and archiving of PDB entries. PDBx incorporates the community standard metadata representation, the Macromolecular Crystallographic Information Framework (mmCIF), orginally developed under the auspices of the International Union of Crystallography (IUCr). PDBx has been extended by the wwPDB to include descriptions of other experimental methods that produce 3D macromolecular structure models such as Nuclear Magnetic Resonance Spectroscopy, 3D Electron Microscopy and Tomography.

Extensions Add

Tools Add

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

Use Cases Add

BioModels Database Edit

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

CHD7 Database Edit
dbEST (Expressed Sequence Tag Database) Edit

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

International dystrophic eb Patient Registry Edit
MVID Patient Registry Edit
NEBC ISA Network BioInvestigationIndex Edit

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

wwPDB (Worldwide Protein Data Bank) Edit

Protein Data Bank archive (PDB) is the single 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.