Becoming familiar with Life Sciences metadata and data standards

By the turn of 20th century, the questions were about: what are data standards? do we need data standards? and so on.
Today, the core issue is to make the right choice within the mess of standards when more than 500 standards are currently available in Life Sciences. With this respect, the alternative seems to be either to finely relate the standard selection to interests/needs or to waste all or parts of further data processing.
To get used to the main initiatives, tables below present main features of more important standards in use (a maximum of 3 examples is given when several standards are developped within the same organization).

Health standards

Visual Identification Organisation URL Model(s) Model feature(s)
# Health Level Seven (HL7)
Reference Information Model (RIM) RIM represents the clinical and administrative content of health care
Domain Messaging Information Model (DMIM) DMIM allows modeling information requirements of a particular problem domain
Refined Message Information Model (RMIM) RMIM defines the information content for sets of messages
# Clinical Data Interchange Standards Consortium (CDISC)
Study Data Tabulation Model/ Submission Data Domain Models (STDM) SDTM allows specifying clinical trial data tabulations that are to be submitted to FDA
Analysis Dataset Model(ADAM) ADAM describes the data attributes that are typically found in clinical trial analysis datasets
Clinical Data Acquisition Standards Harmonization (CDASH) CDASH for standard case report forms
# Cancer Biomedical Information Grid (caBIG) Business Architecture Model (BAM) BAM describes the activities, goals, and people involved in biomedical research, including clinical trials
# National Electrical Manufacturers Association Digital Imaging and Communication In Medicine (Dicom) DICOM is the standard for medical images and related information (ISO 12052)
# Regenstrief Institute (RI) Logical Observation Identifiers Names and Codes (LOINC) LOINC is a universal code system for identifying laboratory and clinical observations
# International Health Terminology Standards Development Organisation (IHTSDO) Systematized Nomenclature of Medicine (SNOMED) SNOMED is the main used clinical healthcare terminology i
# U.S. National Library of Medicine National Institutes of Health
Unified Medical Language System (UMLS) UMLS is a metathesaurus that contains more than 100 source vocabularies

Standards in Functional Genomics

Visual Identification Organisation URL Model(s) Model feature(s)
# Functional Genomics Data Society (FGED SOCIETY)
Minimum Information About Micro-array Experiment (MIAME) MIAME describes the required information for enabling the interpretation of the results of the experiment unambiguously
Minimum Information about a high-throughput SeQuencing Experiment (MINSEQE) MINSEQE is a draft proposal for information to be reported about HTS experiments to enable unambiguous interpretation
MicroArray and Gene Expression TABular format (MAGE-TAB) MAGE-TAB a simple tab-delimited, spreadsheet-based representation of microarray expression data (it avoids using XML (MAGE-ML) or OM (MAGE-OM) formats)
# Human Proteome Society
Proteomics Standard Initiative
Sample Processing Markup Language (spML) spML represents the modeling of sample processing, other than using gels, prior to mass spectrometric protein identification in an experimental pipeline.
Mass Spectrometry Markup Language (mzML) mzML represents the description of mass spectrometry data output and its experimental context
Molecular Interaction XML format (PSI-MI XML) is a data exchange format modeling molecular interactions.
# Gene Ontology Consortium Gene Ontology (GO) GO provides an ontology of defined terms representing gene product properties .
# AR Jones, University of Manchester (UK) and others... Functional Genomics Experiment (FuGE) FuGE provides a foundation for describing entire laboratory workflows and for the development of new data formats.
# Sansonne'Group, University of Oxford (UK) Investigation/Study/Assay-TABular model (ISA-TAB) ISA-TAB is an umbrella model that allows linking biological (omics) experiments and resulting data files

Web portals on standards in Life Sciences

Visual Identification Organisation URL Content Content feature)
# BioSharing Biosharing provides a catalogue of standards The catalogue classifies standards into three types: (i)reporting requirements, (ii) terminological artifacts, (iii) exchange formats
# OBO Foundry Open Biological and Biomedical Ontologies (OBO) OBO is a suite of orthogonal interoperable reference ontologies in the biomedical domain, which operate under a set of principles for ontology development.