UCM MATERIALS
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
- Browse the examples*:
- UCM 1-1-1 EXAMPLE 1 – simple structures and structure fragments
- Contains 8 UCM structure elements without 3-dimensional coordinates.
- Without 3-dimensional coordinates no visualization will be rendered, but you can instead:
- See descriptions for the currently loaded UCM structure element (click the "Descriptions" button).
- Load the next UCM structure element using available controls (click the "Controls" button).
- View the source code of the whole example (select the "View Page Source" or similar menu item offered by your web browser).
- UCM 1-1-1 EXAMPLE 2 – urea
- Contains 1 UCM structure element with 3-dimensional coordinates.
- The visualization should be rendered and adjustable using available controls (click the "Controls" button).
- Loaded descriptions and identifiers may be viewed (click the "Descriptions" or "Identifiers" button) as well as the source code of the example (select the "View Page Source" or similar menu item offered by your web browser).
- UCM 1-1-1 EXAMPLE 3 – ethane
- Contains 1 UCM structure element with 3-dimensional coordinates and 1 UCM structure element without 3-dimensional coordinates.
- The visualization of the first UCM structure element should be rendered and adjustable using available controls (click the "Controls" button).
- The second UCM structure element does not support any visualization, because it contains a structure of ethane recorded using SMILES format (without 3-dimensional coordinates).
- Loaded descriptions, identifiers and properties of the first UCM structure element may be viewed (click the "Descriptions", "Identifiers" or "Properties" button) as well as the source code of the whole example (select the "View Page Source" or similar menu item offered by your web browser).
- UCM 1-1-1 EXAMPLE 4 – diborane
- Contains 1 UCM structure element with 3-dimensional coordinates.
- The visualization should be rendered and adjustable using available controls (click the "Controls" button).
- Loaded descriptions and identifiers may be viewed (click the "Descriptions" or "Identifiers" button) as well as the source code of the example (select the "View Page Source" or similar menu item offered by your web browser).
- UCM 1-1-1 EXAMPLE 5 – ferrocene
- Contains 1 UCM structure element with 3-dimensional coordinates.
- The visualization should be rendered and adjustable using available controls (click the "Controls" button).
- Loaded descriptions and identifiers may be viewed (click the "Descriptions" or "Identifiers" button) as well as the source code of the example (select the "View Page Source" or similar menu item offered by your web browser).
- UCM 1-1-1 EXAMPLE 6 – trichloro(ethene)platinate(II) anion
- Contains 2 UCM structure elements with 3-dimensional coordinates.
- The visualizations of both UCM structure elements should be rendered and adjustable using available controls (click the "Controls" button).
- Loaded descriptions of both UCM structure elements may be viewed (click the "Descriptions" button) as well as the source code of the whole example (select the "View Page Source" or similar menu item offered by your web browser).
- UCM 1-1-1 EXAMPLE 7 – serine amino acid
- Contains 1 UCM structure element with 3-dimensional coordinates.
- The visualization should be rendered and adjustable using available controls (click the "Controls" button).
- Loaded descriptions and identifiers may be viewed (click the "Descriptions" or "Identifiers" button) as well as the source code of the example (select the "View Page Source" or similar menu item offered by your web browser).
- UCM 1-1-1 EXAMPLE 8 – 1-bromo-1,2-dichloroethene
- Contains 1 UCM structure element with 3-dimensional coordinates.
- The visualization should be rendered and adjustable using available controls (click the "Controls" button).
- Loaded descriptions may be viewed (click the "Descriptions" button) as well as the source code of the example (select the "View Page Source" or similar menu item offered by your web browser).
- UCM 1-1-1 EXAMPLE 9 – Lambda tris(catecholato)ferrate(III) anion
- Contains 1 UCM structure element with 3-dimensional coordinates.
- The visualization should be rendered and adjustable using available controls (click the "Controls" button).
- Loaded descriptions may be viewed (click the "Descriptions" button) as well as the source code of the example (select the "View Page Source" or similar menu item offered by your web browser).
- UCM 1-1-1 EXAMPLE 10 – Lambda tris(1-hydroxy-2-aminoethane)cobalt(III)
- Contains 1 UCM structure element with 3-dimensional coordinates.
- The visualization should be rendered and adjustable using available controls (click the "Controls" button).
- Loaded descriptions may be viewed (click the "Descriptions" button) as well as the source code of the example (select the "View Page Source" or similar menu item offered by your web browser).
- UCM 1-1-1 EXAMPLE 11 – all examples in one file
- Contains 11 UCM structure elements with 3-dimensional coordinates and 9 UCM structure elements without 3-dimensional coordinates.
- For all UCM structure elements with 3-dimensional coordinates the visualization should be rendered and adjustable using available controls (click the "Controls" button).
- Remaining UCM structure elements without 3-dimensional coordinates do not support any visualization.
- Loaded descriptions, identifiers and properties of the current UCM structure element may be viewed (click the "Descriptions", "Identifiers" or "Properties" button) as well as the source code of the whole example (select the "View Page Source" or similar menu item offered by your web browser).
- UCM 1-1-1 EXAMPLE 1 – simple structures and structure fragments
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 1-1-1 SPECIFICATIONS – ZIP archive
- UCM 1-1-1 ONLINE DOCUMENTATION
UCM Software Tools
UCM VIEWER 1-1-1
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 "http://0.0.0.0:8000/Ucmv.html" in your web browser to access UCM VIEWER 1-1-1 interface.
- UCM VIEWER 1-1-1 – ZIP archive
HOW WAS UCM DESIGNED
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.
- The following formats were included in our analysis:
- CDXML (ChemDraw Exchange Markup Language)* and CDX (ChemDraw Exchange)*
- CIF (Crystallographic Information File)
- CML (Chemical Markup Language)*
- InChI (International Chemical Identifier)
- NCBI XML (National Center for Biotechnology Information XML) and NCBI ASN.1 (NCBI Abstract Syntax Notation 1)
- PDBML (Protein Data Bank Markup Language), PDBx/mmCIF (Protein Data Bank Exchange Dictionary Macromolecular Crystallographic Information File) and PDB (Protein Data Bank)
- SMILES (Simplified Molecular Input Line Entry System)
- SLN (SYBYL Line Notation)
- Mol2 (Tripos Mol 2 File)
- XDfile (XML Data File)* and CTfile (Chemical Table File)*
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.
- CDXML 4-8 Reference
- CML 3 Reference
- NCBI XML 20141117 References:
- PDBML 4-0 Reference
- PDBML 4-2 Reference
- XDFILE* (XML Data File) 20110328 Reference
DATA FORMATS ANALYZER 1-1-1
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.
