Designing Universal Chemical Markup (UCM) through the reusable methodology based on analyzing existing related formats
Author and article information
Abstract
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.
Cite this as
2015. Designing Universal Chemical Markup (UCM) through the reusable methodology based on analyzing existing related formats. PeerJ PrePrints 3:e1335v1 https://doi.org/10.7287/peerj.preprints.1335v1Author comment
This is a preprint submission to PeerJ Computer Science.
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Supplemental Information
Designing Universal Chemical Markup - Supplemental information
Supplemental information for the article "Designing Universal Chemical Markup (UCM) through the reusable methodology based on analyzing existing related formats" includes additional file 1 (Interactive references), 2 (Formats excluded from second stage) and 3 (UCM tree structure).
Additional Information
Competing Interests
The authors declare that they have no competing interests.
Author Contributions
Jan Mokrý analyzed the data, contributed reagents/materials/analysis tools, wrote the paper, prepared figures and/or tables, performed the computation work, reviewed drafts of the paper.
Miloslav Nič analyzed the data, reviewed drafts of the paper.
Data Deposition
The following information was supplied regarding data availability:
All materials related to the project are available at "http://www.universalchemicalmarkup.org".
Funding
There was no external funding for this project. All financial resources needed to carry out this research were contributed by one of the authors, Jan Mokrý.
