title: Ontology aided modeling of organic reaction mechanisms with flexible and fragment based XML markup procedures.
abstract: 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.
authors: Department of Chemistry and Computer Science & Engineering and Information Technology, Pondicherry Engineering College, Puducherry - 605 014, India.
authors: Punnaivanam
authors: P
authors: Sankar
authors: Gnanasekaran
authors: G
authors: Aghila
mesh_terms: D001185:Artificial Intelligence; D002625:Chemistry, Organic / Q000706:statistics & numerical data*; D003658:Decision Making, Computer-Assisted; D004583:Electrons; D005609:Free Radicals; D006841:Hydrocarbons, Aromatic / Q000737:chemistry; D051188:Knowledge Bases; D009930:Organic Chemicals / Q000737:chemistry*; D011381:Programming Languages; D013329:Structure-Activity Relationship
chemical_list: D005609:Free Radicals; D006841:Hydrocarbons, Aromatic; D009930:Organic Chemicals