Topic
Chemical Markup Language
About: Chemical Markup Language is a research topic. Over the lifetime, 55 publications have been published within this topic receiving 5662 citations. The topic is also known as: .cml & ChemicalML.
Papers published on a yearly basis
Papers
More filters
TL;DR: The implementation of Open Babel is detailed, key advances in the 2.3 release are described, and a variety of uses are outlined both in terms of software products and scientific research, including applications far beyond simple format interconversion.
Abstract: 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 vendor-neutral formats. 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. 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 from http://openbabel.org
.
6,040 citations
TL;DR: Chemical markup language (CML) is an application of XML, the extensible markup language, developed for containing chemical information components within documents and provides a base functionality for atomic, molecular, and crystallographic information.
Abstract: Chemical markup language (CML) is an application of XML, the extensible markup language, developed for containing chemical information components within documents. Its design supports interoperability with the XML family of tools and protocols. It provides a base functionality for atomic, molecular, and crystallographic information and allows extensibility for other chemical applications. Legacy files can be imported into CML without information loss and can carry any desired chemical ontology. Some applications of CML (Markush structures, chemical searching) will be discussed in later articles. An XML document type declaration (DTD) for CML is included as a Chart.
228 citations
TL;DR: A revision to Chemical Markup Language is presented as a XML Schema compliant form, modularized into nonchemical and chemical components, which allows much greater control over datatyping, document validation, and structure.
Abstract: A revision to Chemical Markup Language (CML) is presented as a XML Schema compliant form, modularized into nonchemical and chemical components. STMML contains generic concepts for numeric data and scientific units, while CMLCore retains most of the chemical functionality of the original CML 1.0 and extends it by adding handlers for chemical substances, extended bonding models and names. We propose extension via new namespaced components for chemical queries, reactions, spectra, and computational chemistry. The conformance with XML schemas allows much greater control over datatyping, document validation, and structure.
188 citations
TL;DR: It is shown how a document object model (DOM) for chemistry can be constructed using as its basis Chemical Markup Language (CML).
Abstract: We describe the development of a structured method of representing chemistry on the World-Wide Web using an object-oriented approach to information objects. We show how a document object model (DOM) for chemistry can be constructed using as its basis Chemical Markup Language (CML). Application of the CMLDOM to the development of chemical tools is described.
99 citations
TL;DR: The first fully operational system for managing complex chemical content entirely in interoperating XML-based markup languages is reported, resulting in electronic documents with the significant advantages of data retrieval and flexibility over existing HTML/plugin solutions.
Abstract: We report the first fully operational system for managing complex chemical content entirely in interoperating XML-based markup languages. This involves the application of version 1.0 of chemical markup language (CML
1.0) and the development of mechanisms allowing the display of CML marked up molecules within a standard
web browser (Internet Explorer 5). We demonstrate how an extension to include spectra and reactions could be
achieved. Integrating these techniques with existing XML compliant languages (e.g. XHTML and SVG) results in electronic documents with the significant advantages of data retrieval and flexibility over existing HTML/plugin solutions. These documents can be optimised for a variety of purposes (e.g. screen display or printing) by single XSL stylesheet transformations. An XML schema has been developed from the CML 1.0 DTD to allow document validation and the use of data links. A working online demonstration of these concepts, termed ChiMeraL, containing a range of online demonstrations, examples and CML resources such as the CML DTD and schema has been associated with this article ia the supplementary material.
92 citations