Universal Chemical Markup (UCM)


UCM Overview And Examples

UCM is an open source format for common chemical data. It is based on XML (Extensible Markup Language) and aims to utilize the advantages provided by XML technology. The first version of UCM, developed by Jan Mokrý and Miloslav Nič, focuses on the recording of chemical structures and their properties. Further information is available in our detailed preprint articles published in PeerJ Computer Science. The first article discusses the process of UCM development while the second describes the UCM format. In addition you can browse all supplementary materials offered on this website.

The practical UCM examples below are a good starting point. Most modern web browsers should successfully run UCM VIEWER, as it only only uses XSLT (Extensible Stylesheet Language Transformations) and JavaScript (or other ECMAScript implementation). Note that for some simple examples no 3-dimensional visualization is rendered, because these examples do not have 3-dimensional coordinates. However, UCM VIEWER will still display other data found in the examples and you can also view their source code. The following figure provides a brief overview of the UCM VIEWER user interface and its usage.

UCM VIEWER User Interface Overview
UCM VIEWER User Interface Overview
* Uses UCM VIEWER 1-1-1 – Online version GNU General Public License Version 3

UCM Specifications

UCM 1-1-1

Here we offer the complete UCM 1-1-1 software package with specifications as well as the corresponding online version of the documentation.

UCM Software Tools


The complete UCM VIEWER 1-1-1 software package may be downloaded below. After downloading and extracting the package you can open the "Ucmv.html" file in a web browser. This should load UCM VIEWER 1-1-1 interface, which is slightly adapted for offline usage (i.e. UCM files are opened using a file chooser dialog). Of course another possibility is to directly open the XML files with UCM examples in your web browser (it will load UCM VIEWER 1-1-1 online interface without the file chooser dialog).

Both versions of UCM VIEWER 1-1-1 interface require that your web browser has enabled JavaScript (or other ECMAScript implementation) support, while the online interface also needs XSLT support. Note that if your web browser uses a very strict "same origin" policy and blocks the access to local files, UCM VIEWER 1-1-1 interface will not open when run directly from your local device instead of a web server (e.g. Google Chrome does this without even showing a noticeable message to the user). There are at least three solutions: use a different web browser (e.g. Mozilla Firefox), find the web browser option for overriding the "same origin" security feature, or serve UCM VIEWER 1-1-1 directory with UCM files using a local web server. For example, in the third case, with Python installed you can serve the directory by executing a single command "python -m SimpleHTTPServer" (from that directory) and then just open "" in your web browser to access UCM VIEWER 1-1-1 interface.


Chemical Formats Analysis

UCM design is based on examining other formats for common chemical data using a two stage analysis procedure devised for both XML and non-XML formats. To effectively handle the processing, updating and storage of all information about various chemical formats we utilized DATA FORMATS ANALYZER and a specific work-flow (it combined Google Spreadsheets for collaborative editing and custom XML files for data storage). Because similar work-flow could be used for analyzing other data formats, we offer DATA FORMATS ANALYZER for download as open source software.

While in the first stage the focus was mostly on gathering information about analyzed formats, during the second stage we performed the detailed analysis of selected formats with the most general-purpose chemical functionality. The obtained knowledge about the benefits, issues and concepts of analyzed formats was utilized in designing the concise structure for UCM.

* Marked formats were included in the second stage of our analysis.

Interactive References

Below are provided the interactive XHTML (Extensible HyperText Markup Language) references generated with DATA FORMATS ANALYZER 1-1-1 during the first stage of our chemical formats analysis. In the case of NCBI XML schema files, we generated references specifically for chosen modules describing XML formats for chemical data.

* Marked abbreviations are non-official and were used only for the consistent naming of generated materials.


The complete DATA FORMATS ANALYZER 1-1-1 software package can be downloaded below. In addition it is also possible to browse the corresponding online version of the documentation.