Model tool to describe chemical structures in XML format utilizing structural fragments and chemical ontology

P. Sankar, Alain Krief, G. Aghila

Research output: Contribution to journalArticle


We have developed a model structure-editing tool, ChemEd, programmed in JAVA, which allows drawing chemical structures on a graphical user interface (GUI) by selecting appropriate structural fragments defined in a fragment library. The terms representing the structural fragments are organized in fragment ontology to provide a conceptual support. ChemEd describes the chemical structure in an XML document (ChemFul) with rich semantics explicitly encoding the details of the chemical bonding, the hybridization status, and the electron environment around each atom. The document can be further processed through suitable algorithms and with the support of external chemical ontologies to generate understandable reports about the functional groups present in the structure and their specific environment.
Original languageEnglish
Pages (from-to)755-770
Number of pages16
JournalJournal of chemical information and modeling
Issue number5
Publication statusPublished - 24 May 2010


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