Chemical Markup, XML, and the World Wide Web. 7. CMLSpect, an XML Vocabulary for Spectral Data

Kühn, Stefan; Helmus, Tobias; Lancashire, Robert J.; Murray‐Rust, Peter; Rzepa, Henry; Steinbeck, Christoph; Willighagen, Egon

doi:10.1021/ci600531a

Cited by 27 publications

(25 citation statements)

References 15 publications

Supporting

Mentioning

Contrasting

Order By: Relevance

“…Here node names are written in italic. Data persistence is guaranteed via the Chemical Markup Language (CML) [14] serializing the molecule when necessary. The underlying CDK molecules are handled and stored within data cells in standardized form, i.e., with implicit hydrogen atoms added, atom types perceived, and aromaticity detected.…”

Section: Methodsmentioning

confidence: 99%

KNIME-CDK: Workflow-driven cheminformatics

Beisken

Meinl

Wiswedel³

et al. 2013

BMC Bioinformatics

Self Cite

130

102

View full text Add to dashboard Cite

BackgroundCheminformaticians have to routinely process and analyse libraries of small molecules. Among other things, that includes the standardization of molecules, calculation of various descriptors, visualisation of molecular structures, and downstream analysis. For this purpose, scientific workflow platforms such as the Konstanz Information Miner can be used if provided with the right plug-in. A workflow-based cheminformatics tool provides the advantage of ease-of-use and interoperability between complementary cheminformatics packages within the same framework, hence facilitating the analysis process.ResultsKNIME-CDK comprises functions for molecule conversion to/from common formats, generation of signatures, fingerprints, and molecular properties. It is based on the Chemistry Development Toolkit and uses the Chemical Markup Language for persistence. A comparison with the cheminformatics plug-in RDKit shows that KNIME-CDK supports a similar range of chemical classes and adds new functionality to the framework. We describe the design and integration of the plug-in, and demonstrate the usage of the nodes on ChEBI, a library of small molecules of biological interest.ConclusionsKNIME-CDK is an open-source plug-in for the Konstanz Information Miner, a free workflow platform. KNIME-CDK is build on top of the open-source Chemistry Development Toolkit and allows for efficient cross-vendor structural cheminformatics. Its ease-of-use and modularity enables researchers to automate routine tasks and data analysis, bringing complimentary cheminformatics functionality to the workflow environment.

show abstract

Section: Methodsmentioning

confidence: 99%

KNIME-CDK: Workflow-driven cheminformatics

Beisken

Meinl

Wiswedel³

et al. 2013

BMC Bioinformatics

Self Cite

130

102

View full text Add to dashboard Cite

show abstract

“…It emerged from these exercises that the elements and attributes of CML were sufficient to support the sub-community but that additional semantics in their use and constraints was necessary. Thus, for example, the CMLSpect [10] community decided that a spectrum must have a child representing the data in the spectrum (it is still possible to have an empty spectrum in CML but it would be used by a different community for a different purpose).…”

Section: Semantic Elements Of CMLmentioning

confidence: 99%

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

et al. 2011

Self Cite

View full text Add to dashboard Cite

The semantic architecture of CML consists of conventions, dictionaries and units. The conventions conform to a top-level specification and each convention can constrain compliant documents through machine-processing (validation). Dictionaries conform to a dictionary specification which also imposes machine validation on the dictionaries. Each dictionary can also be used to validate data in a CML document, and provide human-readable descriptions. An additional set of conventions and dictionaries are used to support scientific units. All conventions, dictionaries and dictionary elements are identifiable and addressable through unique URIs.

show abstract

“…Both XML and non-XML formats were analyzed, as we wanted to verify whether XML offers real 30 benefits for chemical formats. It was important for main design decisions concerning the new format in 31 our mind, since the usage of XML technology theoretically brings various advantages. 4 For example the 32 basic built-in validation should be offered automatically by XML, because a schema, which defines the 33 structure of some XML format, can be used to validate that data conform to such a format.…”

mentioning

confidence: 99%

“…Extensibility 30 of the format was evaluated too. This means our modifiability requirements mostly focus on how 31 difficult it is to modify either the given format as such (i.e. extend it) or its instance containing data 32 (i.e.…”

mentioning

confidence: 99%

See 1 more Smart Citation

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

Mokrý

Nic

2015

Preprint

View full text Add to dashboard Cite

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.

show abstract

Chemical Markup, XML, and the World Wide Web. 7. CMLSpect, an XML Vocabulary for Spectral Data

Cited by 27 publications

References 15 publications

KNIME-CDK: Workflow-driven cheminformatics

KNIME-CDK: Workflow-driven cheminformatics

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

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

Contact Info

Product

Resources

About