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Liberating Laboratory Data - AnIML

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Presentation on the use of the Analytical Information Markup Language (AnIML) to store and access scientific data. Presented online as part of the Dial-a-molecule 'Liberating Laboratory Data' event …

Presentation on the use of the Analytical Information Markup Language (AnIML) to store and access scientific data. Presented online as part of the Dial-a-molecule 'Liberating Laboratory Data' event (http://www.dial-a-molecule.org/wp/events-listing/liberating-laboratory-data/)

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  • 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 schalk@unf.edu 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
  • 4. AnIML Schema Structure
  • 5. AnIML Structure
  • 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)
  • 7. AnIML Data Example
  • 8. AnIML Data Example
  • 9. AnIML Data Example
  • 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
  • 18. XPath https://eureka.coas.unf.edu/data/source/exptml:dat1/a:Result[@name=‘Spectrum’]/xml
  • 19. XPath https://eureka.coas.unf.edu/data/source/exptml:dat1/a:Series[@name=‘Absorbance’]_a:IndividualValueSet_a:F[3]/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/