Engineering

Standards Add

CIF (Crystallographic Information Framework) Edit

A well-established standard file structure for the archiving and distribution of crystallographic information, CIF is in regular use for reporting crystal structure determinations to Acta Crystallographica and other journals.

Sponsored by the International Union of Crystallography, the current standard dates from 1997. As of July 2011, a new version of the CIF standard is under consideration.

CSMD (Core Scientific Metadata Model) Edit

A study-data oriented model, primarily in support of the ICAT data managment infrastructure software. The CSMD is designed to support data collected within a large-scale facility’s scientific workflow; however the model is also designed to be generic across scientific disciplines.

Sponsored by the Science and Technologies Facilities Council, the latest full specification available is v 4.0, from 2013.

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.

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.

NeXus Edit

NeXus is an international standard for the storage and exchange of neutron, x-ray, and muon experiment data. The structure of NeXus files is extremely flexible, allowing the storage of both simple data sets, such as a single data array and its axes, and highly complex data and their associated metadata, such as measurements on a multi-component instrument or numerical simulations. NeXus is built on top of the container format HDF5, and adds domain-specific rules for organizing data within HDF5 files in addition to a dictionary of well-defined domain-specific field names.

Extensions Add

ISA-TAB Nano Edit

An extension of ISA-TAB specifying the format for representing and sharing information about nanomaterials, small molecules and biological specimens along with their assay characterization data.

Tools Add

CIF2Cell Edit

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

ICATLite Edit

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 Edit

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

Software for CIF Edit

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

Use Cases Add

American Mineralogist Crystal Structure Database Edit

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 Edit

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

Crystallography Open Database Edit

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

FlowRepository Edit

A database of flow cytometry experiments where you can query and download data collected and annotated according to the MIBBI-registered MIFlowCyt standard.