Development and Application of XyM2Mol System for Converting Structural Data by XyM Notation into Connection Tables

Ito, Kei; Tanaka, Nobuya; Fujita, Shinsaku

doi:10.2477/jccj.4.79

Cited by 1 publication

(1 citation statement)

References 12 publications

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“…In the present trend of transforming the WWW into a new wave of the semantic Web, − the storage, retrieval, and communication of chemical contents are heading toward new technology completely based on markup procedures. Thus a communication oriented representation methodology based on a markup procedure is gaining importance in both representing and rendering chemical information. − The progress of WWW based on XML syntax resulted in the evolution of SVG to describe the two-dimensional graphics in XML to be communicated via the Internet with the advantages of lesser storage and shorter download time. The SVG is a W3C endorsed XML specification capable of capturing rich graphical content with a group of XML elements.…”

Section: Introductionmentioning

confidence: 99%

Ontology Aided Modeling of Organic Reaction Mechanisms with Flexible and Fragment Based XML Markup Procedures

Sankar

Aghila

2007

J. Chem. Inf. Model.

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The mechanism models for primary organic reactions encoding the structural fragments undergoing substitution, addition, elimination, and rearrangements are developed. In the proposed models, each and every structural component of mechanistic pathways is represented with flexible and fragment based markup technique in XML syntax. A significant feature of the system is the encoding of the electron movements along with the other components like charges, partial charges, half bonded species, lone pair electrons, free radicals, reaction arrows, etc. needed for a complete representation of reaction mechanism. The rendering of reaction schemes described with the proposed methodology is achieved with a concise XML extension language interoperating with the structure markup. The reaction scheme is visualized as 2D graphics in a browser by converting them into SVG documents enabling the desired layouts normally perceived by the chemists conventionally. An automatic representation of the complex patterns of the reaction mechanism is achieved by reusing the knowledge in chemical ontologies and developing artificial intelligence components in terms of axioms.

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Section: Introductionmentioning

confidence: 99%

Ontology Aided Modeling of Organic Reaction Mechanisms with Flexible and Fragment Based XML Markup Procedures

Sankar

Aghila

2007

J. Chem. Inf. Model.

View full text Add to dashboard Cite

show abstract

Development and Application of XyM2Mol System for Converting Structural Data by XyM Notation into Connection Tables

Abstract: The XyM2Mol system, which consists of the XyM2Mol application and the XyM2Mol applet, is developed to convert XyM-notation codes into connection tables. Thereby, the structural data by XyM Notation become applicable to a wide variety of chemical applications through such connection tables.

Cited by 1 publication

References 12 publications

Ontology Aided Modeling of Organic Reaction Mechanisms with Flexible and Fragment Based XML Markup Procedures

Ontology Aided Modeling of Organic Reaction Mechanisms with Flexible and Fragment Based XML Markup Procedures

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