CML: Evolution and design

Murray‐Rust, Peter; S., Rzepa Henry

doi:10.1186/1758-2946-3-44

Cited by 46 publications

(47 citation statements)

References 12 publications

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“…(Formats supported by multiple software tools preferably from different vendors 23 were favored.) 24 • Both format and software tools, which support it, should not be obsolete.…”

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confidence: 99%

“…Consequently, the usability 48 requirements are as follows: 12. The format should be publicly available under a clearly indicated license, which permits the 26 free usage and implementation of the format in software tools and also grants the freedom to 27 further develop the format.…”

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confidence: 99%

“…• MODIFIABILITY -We think a chemical format should be flexible and easily extensible to facilitate 27 efficient interaction with modern online environment and other data formats. Because of that we 28 investigated if data stored in the given format could be transformed into a form suitable for web 29 browsers and if any modifications are necessary to make the format inter-operable.…”

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confidence: 99%

“…Adequate annotation possibilities should be included in the format (i.e. highly compact 24 formats can rely on external annotations, while less compact formats should support both 25 plain text and some widely used markup for additional formatting inside the annotations).…”

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confidence: 99%

“…27 To design concepts for the new format, the selected chemical formats were analyzed to discover 28 their benefits and issues together with the main currently implemented concepts for common chemical 29 data. Both XML and non-XML formats were analyzed, as we wanted to verify whether XML offers real 30 benefits for chemical formats.…”

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confidence: 99%

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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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“…(Formats supported by multiple software tools preferably from different vendors 23 were favored.) 24 • Both format and software tools, which support it, should not be obsolete.…”

mentioning

confidence: 99%

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confidence: 99%

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confidence: 99%

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confidence: 99%

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confidence: 99%

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