Liberating Laboratory Data - AnIML
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The document discusses the Analytical Information Markup Language (AnIML), which is an XML standard for storing and sharing instrument data. AnIML allows data to be stored in a vendor-neutral, sharable format. It has been in development since 2003 as a replacement for JCAMP-DX. The schema structure and data structures of AnIML allow arrays of data from multiple instruments to be stored together. AnIML data can be transformed and accessed using XML technologies like XSLT, XPath, and XQuery to convert or extract the data in different formats.
![XSLT
An XML file that extracts data from another
XML document and formats its based on
specifications
Returning data in JSON format
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![XPath
https://eureka.coas.unf.edu/data/source/exptml:dat1/a:Result[@name=‘Spectrum’]/xml](https://image.slidesharecdn.com/liblabdata-animl-140122124203-phpapp01/85/Liberating-Laboratory-Data-AnIML-18-320.jpg)
![XPath
https://eureka.coas.unf.edu/data/source/exptml:dat1/a:Series[@name=‘Absorbance’]_a:IndividualValueSet_a:F[3]/xml](https://image.slidesharecdn.com/liblabdata-animl-140122124203-phpapp01/85/Liberating-Laboratory-Data-AnIML-19-320.jpg)
Liberating Laboratory Data - AnIML
- 1. The Analytical Information Markup Language (AnIML) for instrument data storage and access Stuart J. Chalk Department of Chemistry University of North Florida Jacksonville, FL USA [email protected] Liberating Laboratory Data – Day 1
- 2. Liberating Laboratory Data What does this mean? In a vendor, platform, and language independent format Archivable, Authenticated, Provenanced Datatyped, Qualified (accuracy/precision for numeric data) Contextualized – annotated with descriptive metadata Uniquely Referenceable – URI, DOI Shareable, Searchable, Readable by computers and human
- 3. AnIML History AnIML is an activity under ASTM subcommittee E13.15 on Analytical Data (http://animl.sourceforge.net/) Work on AnIML began in 2003 Designed as a replacement for JCAMP-DX (backwards compatible). Charter: "Develop an analytical data standard that can be used to store data from any analytical instrument" Task group holds virtual meetings on a monthly basis to develop the specification Targeted to through ASTM balloting in 2014
- 6. AnIML Data Structures The “Series” element is used to store arrays of data Can contain many x/y spectra in one data file (good for LC-UV/MS data for instance) Also used for the chromatogram (time slice) data Autoincrement Value Set Typically used for evenly distributed data (e.g. x-axis) Individual Value Set Typically used for y-axis data Encoded Value Set Base64 encoded binary data (per XML specification)
- 10. Embedding AnIML in Other XML Specifications
- 11. Publishing AnIML Stored Data AnIML being XML leverages a variety of tools and technologies Making data in AnIML files accessible can be achieved by using eXtensible Stylesheet Language (XSL) transformations -> to convert data into different formats -> to process data into results XPath -> provide unique identifiers/references to data points or data sets XQuery -> search for particular data with a dataset
- 12. XSLT eXensible Stylesheet Language (XSL) is an XML standard for conversion of XML encode data to other formats E.g. HTML, PDF, Javascript Object Notation (JSON) , or even graphics Scaled Vector Graphics (SVG) is (another!) XML specification for vector graphics So we can use and XSL Transformation (XSLT) processor (e.g. Saxon) to convert data stored in the AnIML to a graphic representation of the data
- 13. XSLT An XML file that extracts data from another XML document and formats its based on specifications Returning data in JSON format {"data":[200.0:.3720,200.5:.3503,201.0:.5042,201.5:.0130, …]}
- 14. XSLT An XML file that extracts data from another XML document and formats its based on specifications Returning data in JSON format
- 15. XSLT: AnIML -> SVG
- 16. XPath https://eureka.coas.unf.edu/data/source/exptml:dat1/data/xml
- 17. XPath https://eureka.coas.unf.edu/data/source/exptml:dat1/a:AnIML/xml
- 20. XQuery
- 21. Conclusion AnIML being an XML specification makes it easily readable, archivable, and searchable The data within an AnIML file can easily be extracted, manipulated and repurposed With the development of additional XML technologies the options for using and sharing AnIML data will only increase over time
- 22. References AnIML – http://animl.sourceforge.net XML – http://www.w3.org/standards/xml/coreXpath SVG – http://www.w3.org/TR/2011/REC-SVG11-20110816/ XSL – http://www.w3.org/standards/xml/transformation.html Saxon (XSLT) – http://saxonica.com ExptML – http://exptml.sourceforge.net/ JSON – http://www.json.org/ UnitsML – http://unitsml.nist.gov/ RDF – http://www.w3.org/RDF/