AnIML:
A New Analytical Data Standard
Stuart J. Chalk, Department of Chemistry, University of North Florida
schalk@unf.edu
ACS Meeting Boston 2015

 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

 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 — UV-Vis, IR, NMR, UV/Vis, IMS
 Fixed order, fixed syntax, immutable formats
 Content limitations
 Inconsistent implementations
Current Data Formats

 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

 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

 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

 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

 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

AnIML Schemas and Files

Sections of an AnIML File

AnIML Technique Definitions

AnIML - Sample

AnIML - Sample

AnIML
-
Experiment

AnIML - Result

 Data storage
format
 Not just for
spectral data
 Access
 Data
 Metadata
 Manipulate
using XSLT
 Validate
 Signable
AnIML in an ELN

 AnIML Viewer -> Jmol/JSpecView (http://jmol.sourceforge.net)
Publish Supplementary Data

 Conversion of AnIML data to SVG using XSLT
Convert to Image File for Publication

 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
Open Instrument Data

Part of a Data Management Plan
 Federal agencies are mandating data be made available
 Long term archive format for research data
 Referenceable if available online
 Searchable with Xquery
 Publish data processing algorithms (XSLT)
 Future proof data -> conversion to future data formats

 The Healthcare and Life Science (HCLS) Community Profile
is a Note from the Semantic Web HCLS Interest Group
 Access to consistent, high-quality metadata is critical to finding,
understanding, and reusing scientific data. This document
describes a consensus among participating stakeholders in the
Health Care and the Life Sciences domain on the description of
datasets using the Resource Description Framework (RDF). This
specification meets key functional requirements, reuses existing
vocabularies to the extent that it is possible, and addresses
elements of data description, versioning, provenance,
discovery, exchange, query, and retrieval.
Data Descriptions:
HCLS Community Profile
http://www.w3.org/TR/hcls-dataset/

 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

 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 of AnIML metadata items
Future Developments

Conclusion
 AnIML is a great solution
for storing instrument data
 Human readable (UTF-8)
 Platform neutral
 Archivable
 Validatable
 AnIML leverages the extensive
XML ecosystem of tools
 Software engineers know XML

 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?