title: Encoding of Fundamental Chemical Entities of Organic Reactivity Interest using chemical ontology and XML.
abstract: Fundamental chemical entities are identified in the context of organic reactivity and classified as appropriate concept classes namely ElectronEntity, AtomEntity, AtomGroupEntity, FunctionalGroupEntity and MolecularEntity. The entity classes and their subclasses are organized into a chemical ontology named "ChemEnt" for the purpose of assertion, restriction and modification of properties through entity relations. Individual instances of entity classes are defined and encoded as a library of chemical entities in XML. The instances of entity classes are distinguished with a unique notation and identification values in order to map them with the ontology definitions. A model GUI named Entity Table is created to view graphical representations of all the entity instances. The detection of chemical entities in chemical structures is achieved through suitable algorithms. The possibility of asserting properties to the entities at different levels and the mechanism of property flow within the hierarchical entity levels is outlined.
authors.affiliation: Department of Chemistry, Kanchi Mamunivar Centre for Post Graduate Studies, Puducherry 605 008, India.
authors.forename: Vijayasarathi
authors.initials: V
authors.lastname: Durairaj
authors.affiliation: Department of Chemistry, Pondicherry Engineering College, Puducherry 605 014, India. Electronic address: gapspec@gmail.com.
authors.forename: Sankar
authors.initials: S
authors.lastname: Punnaivanam
mesh_terms: D000465:Algorithms; D003196:Computer Graphics; D015394:Molecular Structure; D011381:Programming Languages; D012985:Software Design; D014584:User-Computer Interface
keywords: Chemical entity; Chemical ontology; Chemical structure; Notation; Organic reactivity; XML