Molecular biology

Standards Add

ISA-Tab Edit

The Investigation/Study/Assay (ISA) tab-delimited (TAB) format is a general purpose framework with which to collect and communicate complex metadata (i.e. sample characteristics, technologies used, type of measurements made) from 'omics-based' experiments employing a combination of technologies.

Created by core developers from the University of Oxford, ISA-TAB v1.0 was released in November 2008.

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.

Repository-Developed Metadata Schemas Edit

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

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.

ProteoRed Tools Edit

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

Use Cases Add

Chem-BLAST Edit

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 Edit

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

International Molecular Exchange Consortium Edit

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 Edit

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 Edit

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 Edit

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

PRIDE - PRoteomics IDEntifications database Edit

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

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.

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