Towards a semantic model to enhance knowledge sharing and discovery in organic chemistry

4 pagesInternational audienceThis paper presents the project of an electronic encyclopaedia of organic Chemistry. The goal of the EnCOrE (Encyclopédie de la Chimie Organique Electronique) encyclopaedia is twofold: first, it aims at enhancing knowledge sharing in organic Chemistry, by providing a unified access to the increasing amount of domain resources; second, it aims at improving knowledge discovery in the field of organic Chemistry, by revealing unknown connections between those resources. EnCOrE encyclopaedia is designed for a broad category of users such as students, researchers, and teachers. The paper introduces our vision of the EnCOrE encyclopaedia as an information system. It presents its architecture and describes the semantic model sustaining this architecture. Critical points and challenges related to the EnCOrE project are also discussed

ChEBI: a database and ontology for chemical entities of biological interest

Chemical Entities of Biological Interest (ChEBI) is a freely available dictionary of molecular entities focused on ‘small’ chemical compounds. The molecular entities in question are either natural products or synthetic products used to intervene in the processes of living organisms. Genome-encoded macromolecules (nucleic acids, proteins and peptides derived from proteins by cleavage) are not as a rule included in ChEBI. In addition to molecular entities, ChEBI contains groups (parts of molecular entities) and classes of entities. ChEBI includes an ontological classification, whereby the relationships between molecular entities or classes of entities and their parents and/or children are specified. ChEBI is available online at http://www.ebi.ac.uk/chebi

Luscus: molecular viewer and editor for MOLCAS

The novel program for graphical display and editing of molecular systems, luscus, is described. The program allows fast and easy building and/or editing different molecular structures, up to several thousands of atoms large. Luscus is able to visualise dipole moments, normal modes, molecular orbitals, electron densities and electrostatic potentials. In addition, simple geometrical objects can be rendered in order to reveal a geometrical feature or a physical quantity. The program is developed as a graphical interface for the MOLCAS program package, however its adaptive nature makes possible to use luscus with other computational program packages and chemical formats. All data files are opened via simple plug-ins which makes easy to implement a new file format in luscus. The easiness of editing molecular geometries makes luscus suitable for teaching students chemical concepts and molecular modelling

The Declaratron: Semantic specification for scientific computation using MathML

Abstract. We introduce the Declaratron, a system which takes a declarative approach to specifying mathematically based scientific computation. This uses displayable mathematical notation (Content MathML) and is both executable and semantically well defined. We combine domain specific representations of physical science (e.g. CML, Chemical Markup Language), MathML formulae and computational specifications (DeXML) to create executable documents which include scientific data and mathematical formulae. These documents preserve the provenance of the data used, and build tight semantic links between components of mathematical formulae and domain objects—in effect grounding the mathematical semantics in the scientific domain. The Declaratron takes these specifications and i) carries out entity resolution and decoration to prepare for computation ii) uses a MathML execution engine to run calculations over the revised tree iii) outputs domain objects and the complete document to give both results and an encapsulated history of the computation. A short description of a case study is given to illustrate how the system can be used. Many scientific problems require frequent change of the mathematical functional form and the Declaratron provides this without requiring changes to code. Additionally, it supports reproducible science, machine indexing and semantic search of computations, makes implicit assumptions visible, and separates domain knowledge from computational techniques. We believe that the Declaratron could replace much conventional procedural code in science.

Open Babel: An open chemical toolbox

Background: A frequent problem in computational modeling is the interconversion of chemical structures between different formats. While standard interchange formats exist (for example, Chemical Markup Language) and de facto standards have arisen (for example, SMILES format), the need to interconvert formats is a continuing problem due to the multitude of different application areas for chemistry data, differences in the data stored by different formats (0D versus 3D, for example), and competition between software along with a lack of vendorneutral formats. Results: We discuss, for the first time, Open Babel, an open-source chemical toolbox that speaks the many languages of chemical data. Open Babel version 2.3 interconverts over 110 formats. The need to represent such a wide variety of chemical and molecular data requires a library that implements a wide range of cheminformatics algorithms, from partial charge assignment and aromaticity detection, to bond order perception and canonicalization. We detail the implementation of Open Babel, describe key advances in the 2.3 release, and outline a variety of uses both in terms of software products and scientific research, including applications far beyond simple format interconversion. Conclusions: Open Babel presents a solution to the proliferation of multiple chemical file formats. In addition, it provides a variety of useful utilities from conformer searching and 2D depiction, to filtering, batch conversion, and substructure and similarity searching. For developers, it can be used as a programming library to handle chemical data in areas such as organic chemistry, drug design, materials science, and computational chemistry. It is freely available under an open-source license fro

Языки разметки семантического веба: практические аспекты: [учебно-методическое пособие по направлению "Электронные образовательные ресурсы"]

Основной целью руководства является описание специализированных языков разметки, построенных на основе XML. Дано краткое описание XML, DTD, XML Schema, XML Namespace, XSL, приведены примеры, иллюстрирующие назначение и особенности указанных технологий. Показано, как начать проектирование собственного языка разметки на основе XML. Знакомство с уже созданными специализированными языками разметки, описанными в руководстве, призвано помочь читателю ориентироваться в постоянно расширяющемся множестве языков разметки семантического веба. Для научных работников, преподавателей, аспирантов и студентов, специализирующихся в области естественных наукЭлектронные образовательные ресурсыбакалавриа