This document provides an overview of the Analytical Information Markup Language (AnIML), which is an XML standard for storing analytical instrumentation data. It discusses the goals of AnIML, including being extensible, flexible, and human-readable. The document outlines the sections of an AnIML file and how AnIML defines techniques. It also covers using AnIML for publishing, referencing, and performing calculations on instrumentation data. Future developments mentioned include finalizing the AnIML 1.0 specification and creating additional technique definitions.

1. Overview of the Analytical
Information Markup Language
Stuart J. Chalk, Department of Chemistry, University of North Florida
schalk@unf.edu
ACS Meeting Denver 2015

2.  Data Formats
 Goals for Data Handling
 Introduction to AnIML
 Sections of an AnIML file
 AnIML Schemas and Files
 AnIML Technique Definitions
 Publishing Instrument Data
 Referencing Data Elements
 Calculations on Data
 Future Developments
 Conclusion
Overview

3.  Native Data Formats
 Proprietary formats
 "Metadata" separated from result data
 Metadata and data in multiple files
 Metadata not available electronically
 No way to link metadata with result data
 Interchange Data Formats
 Available for only a few techniques
 ANDI — GC, LC, MS
 JCAMP-DX — IR/FTIR, NMR, UV/Vis, IMS
 Fixed order, fixed syntax, immutable formats
 Content limitations
 Inconsistent implementations
Data Formats

4.  Extensible
 Easy to add new elements without breaking existing
applications
 Flexible
 Useful for diverse needs: Interchange, Interconversion,
Archiving...
 Useable & Maintainable
 Easy to create, use, adapt, maintain...
 Readily available tools
 Acceptable
 Use standard mechanisms accepted by mainstream
computing
 Human readable
 eXtensible Markup Language
Goals for Data Handling

5.  Extensible Markup Language (XML) specification
 Development under ASTM E13.15 ‘AnIML Task Group’
 Data standard to:
“Develop an analytical data standard that can
be used to store data from any analytical instrument”
Introduction to AnIML
http://animl.sourceforge.net

6.  JCAMP-DX
 http://www.jcamp-dx.org/
 ANDI (netCDF)
 ThermoML (NIST)
 SpectroML
 Nguyen, A. D. T., Arslan, A., Travis, J., Smith, M., Schafer, R., &
Kramer, G. W. (2004) ‘Molecular Spectrometry Data
Interchange Applications for NIST's SpectroML’, JALA 9 (6),
346-354. doi:10.1016/j.jala.2004.09.001
 Generalized Analytical Markup Language (GAML)
 http://www.gaml.org/
 First official meeting March 23, 2003 @ ASTM
Brief History of Time AnIML

7.  Broad scope
 Different types of data
 Size of data sets
 Everyone calls ‘widgit’ something different
 Need for metadata dictionaries
 One size does not fit all
 Getting broad community involvement
 Domain experts
 User communities
 What format?
Challenges for AnIML

8.  AnIML XML elements are ‘pigeon holes’ for metadata
 Minimal ‘required’ information
 If it’s not required you don’t have to include the element
 Extensible
 Store raw data not processed data
(except for FT techniques)
 Support for legacy data
 Record of changes
 Validatable
 Signable (digital sense)
AnIML Design Philosophy

9. AnIML Schemas and Files

10. Sections of an AnIML File

11. AnIML Technique Definitions

12. AnIML - Sample

13. AnIML - Sample

14. AnIML
-
Experiment

15. AnIML - Result

16.  Access
 Reference
 Search
 Visualize
 Export
 Manipulate
 Process
 Contextualize
 Leverage XML
tools/formats
AnIML in an ELN

17.  AnIML Viewer -> Jmol/JSpecView (http://jmol.sourceforge.net)
Viewing Instrument Data

18.  Conversion of AnIML data to SVG using XSLT
Publishing Instrument Data

19.  Expose an AnIML file at a URL
 Optional: Define a DOI for that URL
 Use XPath to reference a specific data point in an AnIML file
 //ExperimentStepSet[1]/ExperimentStep[1]/Method[1]/Auth
or[1]/Name[1]
 Encode the XPath expression so it can be part of the URL
Referencing Instrument Data

20. Calculations with Instrument Data
 Extract data from files using XPath
 XML data to JSON conversion using XSLT*
 Browser based JavaScript functions to
 Smooth: moving window, Savitsky-Golay
 Integrate: summation
 Conversion: Absorbance <-> %T
 Linear regression
*http://www.bramstein.com/projects/xsltjson/

21.  AnIML 1.0 Deliverables
 Core Schema - Fundamental framework for AnIML documents
 Technique Schema - Fundamental framework for technique definition and
extension documents
 AnIML Technique Definition Documents (ATDD) - Rules for content of
specific technique file
 AnIML Naming and Design Rules - Specifies rules about data element
structure for interoperability
 Standard Practice for AnIML Files - Describes how the specification is
supposed to work
 How to Create a Technique Definition Document - Guidelines for creating
new technique definition documents
 Other documents
 Draft Requirements Specification for AnIML Version 1.0
 Requirements and Goals of the Analytical Information Markup Language
AnIML Specification
http://animl.sourceforge.net

22.  Documentation
 Core specification
 Technique and extension specification
 Naming and design rules
 Annotated technique definitions
(UV/Vis, IR, 1D NMR, MS, Chromatography)
 Balloting through ASTM (end of 2015)
 Vendor, User, Developer extensions
 Semantic extension
 Ontological reference to AnIML metadata items
Future Developments

23. Conclusion
 AnIML is a great solution for storing instrument data
 Human readable (plain text - UTF-8)
 Platform neutral
 Archivable
 Validatable
 Being XML based leverages the extensive XML
ecosystem of tools that are mostly free
 Software designers are familiar with dealing with XML
due to its well defined and stable architecture

24.  schalk@unf.edu
 Phone: 904-620-1938
 Skype: stuartchalk
 LinkedIn/Slidehare: https://www.linkedin.com/in/stuchalk
 ORCID: http://orcid.org/0000-0002-0703-7776
 ResearcherID: http://www.researcherid.com/rid/D-8577-2013
Questions?