CIF MSOS type system
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This document provides a formal description of the type system of a modeling language called Compositional Interchange Format (CIF).Cite
The Crystallographic Information File (CIF) has for over a decade been the standard mechanism for electronic information interchange in crystallography.Its success is due partly to the specialized nature of the information exchanged by the coherent community of crystallographers.By contrast, chemistry in general embraces a much larger community with many different requirements; several initiatives in chemical information representation and exchange have been unsuccessful.Increasingly, however, the chemical community sees eXtensible Markup Language (XML) as a suitable vehicle for information exchange.A Task Group of the International Union of Pure and Applied Chemistry (IUPAC) is currently charged with making effective use of XML.It proposes to acquire from the body supervising XML development the authority to define markup tags with chemical content, and to identify specific topic areas in which suitable tags are to be defined.Chemical Markup Language (CML) is an example of a chemical XML document type definition.The format of XML is different from the CIF syntax, but mechanistic transformation between file formats is becoming more common as abstract data models are increasingly refined.The creation of suitably meaningful tags will however be a formidable challenge.Defining the tags in a new data dictionary for a CIF extension can occupy a group of experts for several years and result in a few dozen new identifiers.Existing CIF and related molecular information file (MIF) dictionaries provide a source for identifiers that, if adopted in a general chemical context, could form a bridge between crystallographic and chemical information exchange standards.
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Prostaglandin (PG) D 2 is a natural somnogen inducing non-rapid eye moving (NREM) sleep and an immuno-modulator.PGD synthase (PGDS) is responsible for the production of PGD 2 .We determined the crystal structures of lipocalin-type PGDS (L-PGDS) as the first enzymatic lipocalin by using SeMet-MAD phasing at 2.1 Å resolution [1].L-PGDS has a catalytic architecture similar to the phylogenetically independent PGDS, hematopoietic PGDS, which belongs to a sigma class glutathione S-transferase [2].L-PGDS is a multi-functional protein which also acts as a hydrophobic ligandbinding protein.The structures with different conformations in two crystal forms suggest the structural basis of the multi-functionalities as well as the mode of the catalytic action [3].These proposed mechanisms were consistent with the extended site-directed mutagenesis.We present the structural and functional basis of L-PGDS as a multi-functional protein relevant to the biological actions including NREM sleep promotion in the prostanoid cascade [4].
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The eXtensible Markup Language (XML) is a language developed for the exchange of information over the Internet independent of particular application domains.XML has been adopted by most software vendors as a preferred exchange medium and is well supported with parsers and editing tools.However, XML and its schema have significant limitations compared to Star File dictionaries [1] in the precise specification of data and particularly in the retention of semantic information, such as the relationships between data items [2].There are also concerns that the syntax of XML, which is driven largely by commercial pressures, will evolve significantly, and is therefore unsuitable as a long-term archival medium.The Star File offers established archives (including those in the taxanomic sciences) advantages in interoperability because its syntax is simple, extensible and stable, and its dictionaries are capable of a much higher level of semantic definition.Even so, exchange activities over disparate data collections are likely to need access to, or generation of, XML files at some stage, even if its only for communication purposes.This paper will describe generic processes for converting Star Files into XML instance documents, and the reverse, and the automatic translation of Star dictionaries into an XML schema (XSD).Such approaches are also useful for gaining access to commercial browser/editors such as XmlSPY.
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CIFXML applies the XML strategies and technologies to create a general interface for processing CIF documents that conform to the CIF syntax and DDL1. Both a DTD and an XML schema for CIFs are presented. CIFs can be read, edited, validated syntactically, sorted, normalized, filtered, stored as an XML document object model, transformed and output. CIFXOM provides an easy way of converting CIFs to XML and vice versa using Java.
XML Schema (W3C)
RELAX NG
XPath
Schema (genetic algorithms)
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