The semantic architecture of the World-Wide Molecular Matrix (WWMM)

RIGHTS : This article is licensed under the BioMed Central licence at http://www.biomedcentral.com/about/license which is similar to the 'Creative Commons Attribution Licence'. In brief you may : copy, distribute, and display the work; make derivative works; or make commercial use of the work - under the following conditions: the original author must be given credit; for any reuse or distribution, it must be made clear to others what the license terms of this work are.Abstract The World-Wide Molecular Matrix (WWMM) is a ten year project to create a peer-to-peer (P2P) system for the publication and collection of chemical objects, including over 250, 000 molecules. It has now been instantiated in a number of repositories which include data encoded in Chemical Markup Language (CML) and linked by URIs and RDF. The technical specification and implementation is now complete. We discuss the types of architecture required to implement nodes in the WWMM and consider the social issues involved in adoption.Peer Reviewe

Resource description framework technologies in chemistry

ISSN:1758-294

Automated analysis and validation of open chemical data

Methods to automatically extract Open Data from the chemical literature, validate it, and use it to validate theory are examined. Chemical identifiers which assist the automatic location of chemical structures using commercial Web search engines are investigated. The IUPAC International Chemical Idenfitifer (InChI) gives almost 100% recall and precision, though is shown to be too long for present search engines. A combination of InChI and InChIKey, a shorter, fixed-length hash of the InChI string, is concluded to be the best current method of identifying structures. The proportion of published, Open Crystallographic Information Files (CIFs) that are valid with respect to the specification is shown to be improving, and is around 99% in 2007. The error rate in the conversion of valid CIFs to Chemical Markup Language (CML) is less than 0.2%. The machine generation of connection tables from CIFs requires many heuristics, and in some cases it is impossible to deduce the exact connection table. CrystalEye, a fully-automated system for the reformulation of the fragmented crystallographic Web into a structured XML-based repository is described. Published, Open CIFs can be located and aggregated programmatically with almost 100% recall. It is shown that, by converting CIF data to CML, software can be created to use the latest Web standards and technologies to enhance the ability of Web users to browse, find, keep updated, download and reuse the latest published crystallography. A workflow for the high-throughput calculation of solid-state geometry using a semi-empirical method is described. A wide-range of organic and inorganic systems provided by CrystalEye are used to test both the data and the method. Several errors in the method are discovered, many of which can be attributed to the parameterization process. An Open NMR experiment to perform high-throughput prediction of 13C chemical shifts using a GIAO protocol is described. The data and analysis were provided on publicly-available webpages to enable crowdsourcing, which assisted in discovering an error rate of 6.1% in the starting data. The protocol was refined during the work and shown to have an average unsigned error of 2.24ppm for 13C nuclei of small, rigid molecules; comparable to the errors observed elsewhere for general structures using HOSE and Neural Network methods

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

Emerging technologies for learning (volume 1)

Collection of 5 articles on emerging technologies and trend

XML: aplicações e tecnologias associadas: 6th National Conference

This volume contains the papers presented at the Sixth Portuguese XML Conference, called XATA (XML, Aplicações e Tecnologias Associadas), held in Évora, Portugal, 14-15 February, 2008. The conference followed on from a successful series held throughout Portugal in the last years: XATA2003 was held in Braga, XATA2004 was held in Porto, XATA2005 was held in Braga, XATA2006 was held in Portalegre and XATA2007 was held in Lisboa. Dued to research evaluation criteria that are being used to evaluate researchers and research centers national conferences are becoming deserted. Many did not manage to gather enough submissions to proceed in this scenario. XATA made it through. However with a large decrease in the number of submissions. In this edition a special meeting will join the steering committee with some interested attendees to discuss XATA's future: internationalization, conference model, ... We think XATA is important in the national context. It has succeeded in gathering and identifying a comunity that shares the same research interests and has promoted some colaborations. We want to keep "the wheel spinning"... This edition has its program distributed by first day's afternoon and next day's morning. This way we are facilitating travel arrangements and we will have one night to meet