Chemistry

Metadata Standards

CIF - Crystallographic Information Framework

An extensible standard file format and set of protocols for the exchange of crystallographic and related structured data.

CSMD-CCLRC Core Scientific Metadata Model

A study-data oriented model that captures high-level information about scientific studies and the data that they produce, primarily tailored for the physical sciences.

NeXus

NeXus is an international standard for the storage and exchange of neutron, x-ray, and muon experiment data.

Observations and Measurements

This standard specifies an XML implementation for the OGC and ISO Observations and Measurements (O&M) conceptual model, including a schema for Sampling Features.

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

CIF2Cell

A tool to generate the geometrical setup for various electronic structure codes from a CIF file.

ICATLite

A sister project of ICAT, consisting of a suite of CSMD-based software tools designed to support derived data management in the scientific research process.

IUCr checkCIF

A tool used to check the integrity and cosistency of crystal structure encodings in CIF format.

PDBx/mmCIF Software Resources

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

Software for CIF

The International Union of Crystallography's list of programs and libraries available for use with CIF files.

SOS -Sensor Observation Service

This tool uses the Observations and Measurements standard to define a Web service interface which allows querying observations, sensor metadata, as well as representations of observed features.

Use Cases

American Mineralogist Crystal Structure Database

A CIF crystal structure database that includes every structure published in the American Mineralogist, The Canadian Mineralogist, European Journal of Mineralogy and Physics and Chemistry of Minerals, as well as selected datasets from other journals.

Cambridge Structural Database

A repository of small molecule crystal structures, many with accompanying CIF files.

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.

Crystallography Open Database

An open-access collection of crystal structures of organic, inorganic, metal-organic compounds and minerals, many of which are in CIF form.

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.