The semantics of Chemical Markup Language (CML): dictionaries and conventions

Murray‐Rust, Peter; Townsend, J.E.; Adams, Sam; Phadungsukanan, Weerapong; Thomas, Jens M. H.

doi:10.1186/1758-2946-3-43

Cited by 36 publications

(38 citation statements)

References 11 publications

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“…Avogadro has used CML [19,20] as its default file format from a very early stage; this was chosen over other file formats because of the extensible, semantic structure provided by CML, and the support available in Open Babel [51]. The CML format offers a number of advantages over others in common use, including the ability to extend the format.…”

Section: Resultsmentioning

confidence: 99%

“…The creation of an open and extensible framework that implements many of the necessary foundations for a molecular builder and visualizer would facilitate more effective research in this area. Further, the open, standardized Chemical Markup Language (CML) file format [19,20] would be used, to secure semantic and chemical data and allow easy interoperability with other chemistry software.…”

Section: Introductionmentioning

confidence: 99%

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Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

et al. 2012

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BackgroundThe Avogadro project has developed an advanced molecule editor and visualizer designed for cross-platform use in computational chemistry, molecular modeling, bioinformatics, materials science, and related areas. It offers flexible, high quality rendering, and a powerful plugin architecture. Typical uses include building molecular structures, formatting input files, and analyzing output of a wide variety of computational chemistry packages. By using the CML file format as its native document type, Avogadro seeks to enhance the semantic accessibility of chemical data types.ResultsThe work presented here details the Avogadro library, which is a framework providing a code library and application programming interface (API) with three-dimensional visualization capabilities; and has direct applications to research and education in the fields of chemistry, physics, materials science, and biology. The Avogadro application provides a rich graphical interface using dynamically loaded plugins through the library itself. The application and library can each be extended by implementing a plugin module in C++ or Python to explore different visualization techniques, build/manipulate molecular structures, and interact with other programs. We describe some example extensions, one which uses a genetic algorithm to find stable crystal structures, and one which interfaces with the PackMol program to create packed, solvated structures for molecular dynamics simulations. The 1.0 release series of Avogadro is the main focus of the results discussed here.ConclusionsAvogadro offers a semantic chemical builder and platform for visualization and analysis. For users, it offers an easy-to-use builder, integrated support for downloading from common databases such as PubChem and the Protein Data Bank, extracting chemical data from a wide variety of formats, including computational chemistry output, and native, semantic support for the CML file format. For developers, it can be easily extended via a powerful plugin mechanism to support new features in organic chemistry, inorganic complexes, drug design, materials, biomolecules, and simulations. Avogadro is freely available under an open-source license from http://avogadro.openmolecules.net.

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Section: Resultsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

et al. 2012

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“…Detailed discussions have already been published in Murray-Rust et al [13] and Townsend et al [11]. The latest information of the ongoing developments are also publicly available online at http://www.xml-cml.org.…”

Section: Introductionmentioning

confidence: 99%

The semantics of Chemical Markup Language (CML) for computational chemistry : CompChem

et al. 2012

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This paper introduces a subdomain chemistry format for storing computational chemistry data called CompChem. It has been developed based on the design, concepts and methodologies of Chemical Markup Language (CML) by adding computational chemistry semantics on top of the CML Schema. The format allows a wide range of ab initio quantum chemistry calculations of individual molecules to be stored. These calculations include, for example, single point energy calculation, molecular geometry optimization, and vibrational frequency analysis. The paper also describes the supporting infrastructure, such as processing software, dictionaries, validation tools and database repositories. In addition, some of the challenges and difficulties in developing common computational chemistry dictionaries are discussed. The uses of CompChem are illustrated by two practical applications.

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“…As 51 a result the format structure can be highly variable and usually there is more than one way of PrePrints more complicated (see ISSUES 10 and 13). Although there is an ongoing effort to avoid these 1 problems (also to address external suggestions 85,86 ) using a mechanism for denoting standard 2 conventions, 22,28,81,87 the mechanism is still not fully implemented to address all complex problems 3 stemming from the highly unrestricted and variable structure of the format. Initially in version 1 the 4 usage of convention attribute was limited to certain elements.…”

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confidence: 99%

“…87 With version 2, when the format 5 was redefined using XSD instead of DTD, 28 the convention attribute started to be used on more 6 elements as various communities adapted the format in their domains of chemistry. 87 In version 7 3 schema it is enabled for nearly all elements. The main issue is that until version 3 no official between appropriate attributes or elements.…”

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Designing Universal Chemical Markup (UCM) through the reusable methodology based on analyzing existing related formats

Mokrý

Nic

2015

Preprint

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Background: In order to design concepts for a new general-purpose chemical format we analyzed the strengths and weaknesses of current formats for common chemical data.While the new format is discussed more in the next article, here we describe our software tools and two stage analysis procedure that supplied the necessary information for the development. The chemical formats analyzed in both stages were: CDX, CDXML, CML, CTfile and XDfile. In addition the following formats were included in the first stage only: CIF, InChI, NCBI ASN.1, NCBI XML, PDB, PDBx/mmCIF, PDBML, SMILES, SLN and Mol2. Results:A two stage analysis process devised for both XML (Extensible Markup Language) and non-XML formats enabled us to verify if and how potential advantages of XML are utilized in the widely used general-purpose chemical formats. In the first stage we accumulated information about analyzed formats and selected the formats with the most general-purpose chemical functionality for the second stage. During the second stage our set of software quality requirements was used to assess the benefits and issues of selected formats. Additionally, the detailed analysis of XML formats structure in the second stage helped us to identify concepts in those formats. Using these concepts we came up with the concise structure for a new chemical format, which is designed to provide precise built-in validation capabilities and aims to avoid the potential issues of analyzed formats. Conclusions:We believe our analysis methodology is potentially highly reusable and could be easily adapted even for domains outside the chemistry area. It is because the methodology and software tools will need only few changes, although analyzed formats and software quality requirements for a format will differ according to the given domain. ABSTRACT BackgroundIn order to design concepts for a new general-purpose chemical format we analyzed the strengths and weaknesses of current formats for common chemical data. While the new format is discussed more in the next article, here we describe our software tools and two stage analysis procedure that supplied the necessary information for the development. The chemical formats analyzed in both stages were: CDX, CDXML, CML, CTfile and XDfile. In addition the following formats were included in the first stage only: CIF, InChI, NCBI ASN.1, NCBI XML, PDB, PDBx/mmCIF, PDBML, SMILES, SLN and Mol2.

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The semantics of Chemical Markup Language (CML): dictionaries and conventions

Cited by 36 publications

References 11 publications

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

Avogadro: an advanced semantic chemical editor, visualization, and analysis platform

The semantics of Chemical Markup Language (CML) for computational chemistry : CompChem

Designing Universal Chemical Markup (UCM) through the reusable methodology based on analyzing existing related formats

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