Chemical Information Sources/SIRCh/Cheminformatics/Data Standards and Standards Groups

SIRCh: Selected Internet Resources for Chemistry

Molecular Data Standards

• InChI the IUPAC International Chemical Identifier
• inchi.info
• SMILES
• Structure Data Format (SDF) Files
• CT File (MDL)
• CML (Chemical Markup Language) at SourceForge
• Chemical Markup Language (CML) (original site)
• Chemical Markup Language (CML) (original poster)
• The Chemical MIME Home Page
• CambridgeSoft CDX for ChemDraw [See the Software Developer's Kit]
• CXF : chemical eXchange format, version 1.0 / (Chemical Abstracts Service book available from the Indiana University Chemistry Library: QD8.3 .C97 1994)
• Crystallographic Information File Format (CIF)
• macromolecular Crystallographic Information File (mmCIF)
• Encoded Archival Description (EAD)
• EPrints
• Glossolalia: a common language for MS data (mzXML: Institute for Systems Biology)

• MDL's CTfile Formats (See "Download Products")
• Minimum information about a microarry experiment (MIAME) (MGED Society)
• MIRIAM - a standard for computational models in biology (Biomodels.net)
• The NCBI C++ Toolkit
• netCDF (network Common Data Form)

• The Open Archives Initiative Protocol for Metadata Harvesting
• PDB - Protein Data Bank
  • PDB Dictionary Resources
  • PDB File Format
• SBML - Systems Biology Markup Language
• SMRS: The Standard Metabolic Reporting Structure
• Tripos Mol2 file format
• UniProtKB/Swiss-Prot Documentation
• VOTable Format Definition

Molecular Standards Groups

• The Blue Obelisk
• caBIG Compatibility and Certification

• CiDX: Chemical Industry Data Exchange
• ERCC - External RNA Control Consortium (National Institute of Standards and Technology)
• Guidance Documents for NARSTO and U.S. EPA Supersites Program
• HUPO Proteomics Standard Initiative (Human Proteome Organisation)
• PSI-MS: Mass Spectromety Standards Working Group (The mzData Standard)
• IUPAC CPEP Subcommittee on Electronic Data Standards (Successor to JCAMP-DX)
• littleb.org
• LSIT Global Institute
• MicroArray and Gene Expression (MAGE)(MGED Society)
• MAQC - MicroArray Quality Control Project (US Food and Drug Administration)

• NISO (National Information Standards Organization)
• OAIster
• OMG Life Sciences Research Group
• Open Archives Initiative

Converters of Chemical Structure Formats

• Open Babel
• Mol2Mol
• CLiDE (chemical literature data extraction tool from SimBioSys)
• ACD/ChemSketch
• Corina (Molecular Networks)