Biochemistry

Metadata Standards

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.

DIF - Directory Interchange Format

An early metadata initiative from the Earth sciences community, intended for the description of scientific data sets. It inlcudes elements focusing on instruments that capture data, temporal and spatial characteristics of the data, and projects with which the dataset is associated.

FGDC/CSDGM - Federal Geographic Data Committee Content Standard for Digital Geospatial Metadata

BGDC policy states that non-Federally authored standards that are endorsed by the FGDC have the same status as FGDC developed standards. Since ISO 19115 and the associated standards are endorsed by the FGDC, federal agencies are encouraged to transition to ISO metadata as their agencies are able to do so.

ISA-Tab

A general purpose framework with which to capture and communicate metadata for data files from 'omics-based' experiments employing combinations of technologies.

MIBBI - Minimum Information for Biological and Biomedical Investigations

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

Repository-Developed Metadata Schemas

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

Extensions

SNRNASM ISA-Tab

An ISA-Tab-based standard for reporting the results of single nucleotide resolution nucleic acid structure mapping experiments.

Tools

ProteoRed Tools

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

Use Cases

BioModels Database

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

BODC - British Oceanographic Data Centre Published Data Library

This national facility for looking after and distributing data concerning the marine environment requires that data sets use a well-documented format such as CF-compliant NetCDF and be accompanied by a Dublin Core record as well as discovery metadata in a recognised standard such as DIF or FGDC/CDGM.

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.

dbEST - Expressed Sequence Tag Database

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

FlowRepository

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

International Molecular Exchange Consortium

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

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

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

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

NCDC - National Climatic Data Center

The world's largest climate data archive, providing climatological services and data worldwide. It currently promotes the FGDC/CSDGM metadata standard for its datasets.

PRIDE - PRoteomics IDEntifications database

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