The Analytical Information
Markup Language (AnIML) for
instrument data storage and access
Stuart J. Chalk
Department of Ch...
Liberating Laboratory Data
What does this mean?
In a vendor, platform, and language independent format
Archivable, Authent...
AnIML History
AnIML is an activity under ASTM subcommittee E13.15 on
Analytical Data (http://animl.sourceforge.net/)
Work ...
AnIML Schema Structure
AnIML Structure
AnIML Data Structures
The “Series” element is used to store arrays of data
Can contain many x/y spectra in one data file
(...
AnIML Data
Example
AnIML Data
Example
AnIML Data
Example
Embedding AnIML
in Other XML Specifications
Publishing AnIML Stored Data
AnIML being XML leverages a variety of tools and
technologies
Making data in AnIML files acce...
XSLT
eXensible Stylesheet Language (XSL) is an XML
standard for conversion of XML encode data to other
formats
E.g. HTML, ...
XSLT
An XML file that extracts data from another
XML document and formats its based on
specifications
Returning data in JS...
XSLT
An XML file that extracts data from another XML
document and formats its based on specifications
Returning data in JS...
XSLT: AnIML -> SVG
XPath

https://eureka.coas.unf.edu/data/source/exptml:dat1/data/xml
XPath

https://eureka.coas.unf.edu/data/source/exptml:dat1/a:AnIML/xml
XPath

https://eureka.coas.unf.edu/data/source/exptml:dat1/a:Result[@name=‘Spectrum’]/xml
XPath

https://eureka.coas.unf.edu/data/source/exptml:dat1/a:Series[@name=‘Absorbance’]_a:IndividualValueSet_a:F[3]/xml
XQuery
Conclusion
AnIML being an XML specification makes it easily
readable, archivable, and searchable
The data within an AnIML ...
References
AnIML – http://animl.sourceforge.net
XML – http://www.w3.org/standards/xml/coreXpath
SVG – http://www.w3.org/TR...
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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 (http://www.dial-a-molecule.org/wp/events-listing/liberating-laboratory-data/)

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Liberating Laboratory Data - AnIML

  1. 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. 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. 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. 4. AnIML Schema Structure
  5. 5. AnIML Structure
  6. 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. 7. AnIML Data Example
  8. 8. AnIML Data Example
  9. 9. AnIML Data Example
  10. 10. Embedding AnIML in Other XML Specifications
  11. 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. 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. 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. 14. XSLT An XML file that extracts data from another XML document and formats its based on specifications Returning data in JSON format
  15. 15. XSLT: AnIML -> SVG
  16. 16. XPath https://eureka.coas.unf.edu/data/source/exptml:dat1/data/xml
  17. 17. XPath https://eureka.coas.unf.edu/data/source/exptml:dat1/a:AnIML/xml
  18. 18. XPath https://eureka.coas.unf.edu/data/source/exptml:dat1/a:Result[@name=‘Spectrum’]/xml
  19. 19. XPath https://eureka.coas.unf.edu/data/source/exptml:dat1/a:Series[@name=‘Absorbance’]_a:IndividualValueSet_a:F[3]/xml
  20. 20. XQuery
  21. 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. 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/
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