The Molecular Information File (MIF): Core Specifications of a New Standard Format for Chemical Data

Abstract

The initial core data definitions of a universal data exchange format for chemical information is proposed. The Molecular Information File (MIF) represents a coalescence of two major format developments: the Standard Molecular Data Format (SMD) and the Crystallographic Information File that conforms to the STAR (Self-Defining Text Archive and Retrieval) syntax. Essentially, the MIF is a re-expression of the major SMD concepts using STAR syntax. The core data items, defined here, cover chemical connectivity representations, stereochemistry, and associated data for complete 2D and 3D molecules and for 2D substructural queries. INTRODUCTIONEach advance in computer technology, database design, and network capability contributes to the need for a universal method of exchanging data electronically. Nevertheless, specialized formats continue to proliferate for specific applications. This diversity of formats represents a serious obstacle to the global exchange of data and to the development of general access methods for databases.The need for flexible, extensible, and universal methods for exchanging scientific data is recognized.1-4 The most important attributes for chemical data files are machine independence and portability; the suitability of a format for long term archiving; the ability to add new data without corrupting existing archives; and a simple robust mechanism for moving data between software packages. In short, a common data file structure is needed to provide a general communication link that can be used by researchers, journals, and databases.Chemical software packages offer a wide variety of tools for acquiring structural knowledge and for applying this knowledge to problems in the structural domain. Machinereadable representations of two-dimensional (2D) molecular structures are central to these applications. The dissemina-' tion, searching, and manipulation of large collections of these representations are basic requirements of modem computational chemistry. Further, molecular modeling, via force field, semiempirical and ab initio techniques, is used routinely to predict and categorize the three-dimensional (3D) aspects of molecular structure from this basic 2D information. Other more rapid processes now employ rule-based and artificial intelligence methodologies to generate 3D structural models from 2D representations.

An automated system designed for large scale NMR data deposition and annotation: application to over 600 assigned chemical shift data entries to the BioMagResBank from the Riken Structural Genomics/Proteomics Initiative internal database

“…The NMR-STAR format (Ulrich et al 2008; www.bmrb.wisc.edu/formats.html) is based on the STAR (Self Defining Text Archival and Retrieval) format developed by Hall and coworkers (Hall 1991; Hall and Spadaccini 1994; Allen et al 1995) and is commonly used for the exchange and deposition of NMR data. The NMR-STAR format has a systematically curated data structure based on the NMR-STAR data model (http://www.bmrb.wisc.edu/formats.html).…”

Metabolomics standards initiative: ontology working group work in progress

“…The CVs for the Chromatography sub-component, shared by both proteomics and metabolomics domains, will be developed in close collaboration with the PSI Sample Processing Ontology WG. Every effort will be made to cover as many components as possible and similarly to evaluate and leverage on existing public sources of terms (Allen et al 1995;Bodenreider 2004;de Matos et al 2006;Jenkins et al 2004;Kanehisa et al 2006;Lindon et al 2005;Soldatova and King 2006;Spasic et al 2006;Vranken et al 2005;Wishart et al 2007). …”

CIF: the computer language of crystallography

“…These included the creation of a Dictionary De®nition Language which was subsequently used to build the CIF dictionaries, the use of the complete set of syntactic constructs permitted by STAR for encapsulating and nesting data, and the possible use of STAR as a query language. A subset of this material was published as the Molecular Information File (MIF; Allen et al, 1995), but there has been no subsequent development of MIF tools or applications, despite its potential as an open and non-proprietary standard. The reasons for this must remain speculative, but the crystallography community, being both smaller and more homogeneous than the larger community of chemists, has been better placed to adopt new solutions.…”