Minimal Standards Initiatives

Standards are necessary to improve data quality and facilitate their management, annotation and exchange.
Several initiatives, which have been deployed to establish standards are listed below.
Developing and maintaining community standards is one of the core tasks of BBMRI WP4.

How to standardize your experiments and data:
1) Use Standard Operating Procedures (SOPs)
2) Use software facilitating the use of standard data formats to store your data
3) Use ontologies and controlled vocabularies to describe your data

Biobanking guidelines:
The P3G-consortium has prepared a Comparison Chart of Guidelines, which cover all biobanking steps, i.e. biological sample collection, labelling, processing, and storage applied to a wide range of sample types.

General standards:

The International System of Units is the recommended practical system of units of measurement.

NIST Standard Reference Materials can be used to calibrate equipment in clinical laboratories.

Minimum Information for Biological and Biomedical Investigations
MIBBI - Minimum Information for Biological and Biomedical Investigations maintains a portal to checklists specifying the key information to include in reports of experimental data. Some of these are listed below.

The MGED Society has defined the following standards:
MIAME Minimum Information About a Microarray Experiment. See MIAME 2.0 for a detailed description of the required information elements. MIAME compliant microarray data can be submitted to and obtained from public repositories: ArrayExpress (EBI, UK), GEO (NCBI, US) and CIBEX (DDBJ, Japan) .
MAGE-TAB The recommended spreadsheet-based format for microarray data.
MINSEQE Minimum Information about a high-throughput SeQuencing Experiment

The HUPO Proteomics Standards Initiative has defined the following standards:
MIAPAR Minimum Information About a Protein Affinity Reagent
PSI-PAR A community standard format for the representation of protein affinity reagents. (Gloriam et al., 2009)

Database standards:

CASIMIR Database Description Framework Criteria This formal framework aims to capture key technical data about a database which can provide potential users with the required information about its quality, interoperability and standards. Widespread uptake of this standard is expected to support the development of on-line resource discovery, uptake and full utilisation of databases.

Specific standards:

Nomenclature for the description of sequence variations Human Genome Variation Society

Guidelines for human gene nomenclature Human Gene Nomenclature Committee

Ontologies and controlled vocabularies :

The Open Biological and Biomedical Ontologies website provides access to ontologies for different purposes.

National Center for Biomedical Ontology (NCBO) Bioportal(NCBI)

Ontology Lookup Service (OLS)(EBI)