IUPAC PROJECT MEETINGS: EXTENSIBLE MARKUP LANGUAGE (XML) DATA DICTIONARIES AND CHEMICAL IDENTIFIER NOVEMBER 12-14, 2003, NATIONAL INSTITUTE OF STANDARDS AND TECHNOLOGY, (NIST), GAITHERSBURG, MARYLAND, USA A report by Dr. Wendy A. Warr Wendy Warr & Associates June 2004 Dr Wendy A Warr Wendy Warr & Associates, 6 Berwick Court Holmes Chapel, Cheshire CW4 7HZ, England Tel/fax +44 (0)1477 533837 [email protected] http://www.warr.com Introduction and Overview............................................................................................................... 1 Stephen Stein, NIST.................................................................................................................... 1 Report on IUPAC and XML in Chemistry ........................................................................................ 2 Tony Davies, Creon Lab Control AG, Germany (Secretary, IUPAC Committee on Printed and Electronic Publications)............................................................................................................... 2 Discussion ................................................................................................................................... 6 IUPAC and the Gold Book............................................................................................................... 6 Alan McNaught, Royal Society of Chemistry (RSC) ................................................................... 6 Discussion ................................................................................................................................... 6 Units Markup Language .................................................................................................................. 7 Bob Dragoset, NIST .................................................................................................................... 7 Discussion ................................................................................................................................... 9 Chemistry and the Crystallographic Information File (CIF) ............................................................. 9 David Brown, McMaster University, Hamilton, Ontario, Canada ................................................ 9 Discussion ................................................................................................................................. 10 SpectroML and AnIML for molecular spectroscopy and chromatography data ............................ 10 Gary W. Kramer, NIST .............................................................................................................. 10 Capturing chemical information..................................................................................................... 11 Miloslav Nič and Jiřī Jirát, Institute of Chemical Technology, Prague, Czech Republic........... 11 Discussion ................................................................................................................................. 21 ThermoML and IUPAC Activities in Standardizing Thermodynamic Data Communications ........ 22 Michael Frenkel, Thermodynamics Research Center (TRC), National Institute of Standards and Technology (NIST), Boulder, Colorado.............................................................................. 22 Discussion ................................................................................................................................. 25 Protein Data Bank (PDB) and Chemical Compound Data Annotation and Query........................ 25 T. N. Bhat, NIST ........................................................................................................................ 25 ToxML: Controlled Vocabulary for Toxicity Data Integration and Data Mining ............................. 26 Chihae Yang, LeadScope Inc. .................................................................................................. 26 The Green Book “Quantities, Units and Symbols” ........................................................................ 28 Jeremy Frey, University of Southampton.................................................................................. 28 The Gold and Green Books: Day Two Introduction....................................................................... 28 Stephen Stein, NIST.................................................................................................................. 28 Discussion ................................................................................................................................. 29 Standards and Conventions for Electronic Interchange of Chemical Data ................................... 29 Peter J. Linstrom, NIST............................................................................................................. 29 The Gold Book: Progress Report ..................................................................................................31 Stephen Stein, NIST.................................................................................................................. 31 Discussion ................................................................................................................................. 31 The Use of Graph Theory to Describe Chemical Structures......................................................... 32 David Brown, McMaster University, Hamilton, Ontario, Canada .............................................. 32 Discussion ................................................................................................................................. 32 The Green Book: Progress Report................................................................................................ 32 Jeremy Frey, University of Southampton.................................................................................. 32 Discussion ................................................................................................................................. 33 Discussion Item One. Is This the Right Time to Encourage Data Dictionary Development?........ 33 Discussion Item Two. Is Multiplicity of XMLs a Real Problem that has Real Solutions? .............. 34 Discussion Item Three. Will XML Authoring Tools Ever be Available?......................................... 34 Discussion Item Four. How do we Deliver and Maintain the Namespace?................................... 35 Discussion Item Five. How do we Raise Awareness and Interactions?........................................ 36 Discussion Item Six. What about Subdividing the Glossary?........................................................ 36 The IChI Project: Background and Overview ................................................................................ 36 Alan McNaught, RSC ................................................................................................................ 36 The IUPAC Chemical Identifier (IChI): Project Objectives ............................................................ 37 Steve Stein, NIST...................................................................................................................... 37 IChI in Action ................................................................................................................... 37 Peter Murray-Rust, University of Cambridge ............................................................................ 37 Chemical Databases, Identifiers, and Web Services .................................................................... 38 Marc C. Nicklaus, Laboratory of Medicinal Chemistry (LMC), National Cancer Institute (NCI), National Institutes of Health (NIH).............................................................................................38 Chemical Markup Language (CML)............................................................................................... 40 Peter Murray-Rust, University of Cambridge ............................................................................ 40 Chemical Data Handling in the NIST Chemistry WebBook: a Brief Overview .............................. 41 Peter J. Linstrom, NIST............................................................................................................. 41 Discussion ................................................................................................................................. 41 An Identifier for Crystal Phases..................................................................................................... 41 I. David Brown, McMaster University, Hamilton, Ontario, Canada ........................................... 41 Discussion ................................................................................................................................. 42 Proposed IUPAC Project: Graphical Representation Standards for Chemical Structure Diagrams ................................................................................................................... 42 Bill Town, Kilmorie Consulting................................................................................................... 42 ChEBI. A Reference Database of Biochemical Compounds......................................................... 44 Paula de Matos, European Molecular Biology Laboratory-European Bioinformatics Institute, EMBL-EBI.................................................................................................................................. 44 Discussion ................................................................................................................................