This presentation one approach to integrating AnIML XMlLfiles into an ELN.

1. Integrating AnIML Files in
Electronic Laboratory Notebooks
Stuart J. Chalk, Department of Chemistry, University of North Florida
schalk@unf.edu
Paper 2670-1 Pittcon 2015

2.  Introduction to AnIML
 Sections of an AnIML file
 AnIML Schemas and Files
 AnIML Technique Definitions
 Electronic Laboratory Notebooks
 Viewing Instrument Data
 Publishing Instrument Data
 Referencing Data Elements
 Calculations on Data
 Future Developments
 Conclusion
Overview

3.  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”
 Website http://animl.sourceforge.net
Introduction to AnIML

4. Sections of an AnIML File

5. AnIML Schemas and Files

6. AnIML Technique Definitions

7. Electronic Laboratory Notebooks
 Scientists need to move to
digital notebooks…
 ...and record not just the data
but the flow and context
 How science is done is
important for searching,
aggregation, meta-analysis
 Writing in a scientific notebook is about telling the
of what a scientist has learned by gathering using
the available in their laboratory*
* Concept: Tony Williams

8.  Started in 2006 after getting involved in the
Analytical Information Markup Language (AnIML) project
 Store all research notes/data in a digital format
 Capture the workflow of scientists
 Writing in a lab notebook is equivalent to
“multi-type” blogging in the digital world
 How to capture information? Many data types! (ExptML)
 How to store files “online”? (Fedora-Commons)
 How to access files in the browser? (CakePHP)
 How to represent laboratory resources? (ExptML)
 How to link data together? RDF (in Fedora-Commons)
Eureka Research Workbench (ERW)

10.  Comes in many different forms…
 Instrument data (lots of numbers)
 Readings (a few numbers)
 Observations (strings)
 …and types
 Binary (proprietary – vendor specific)
 Text (unstructured/unidentified)
 Text (structured/identified - JCAMP)
 Text (structured and programmatically accessible - AnIML)
Laboratory Data

11.  Access
 Reference
 Search
 Visualize
 Export
 Manipulate
 Process
 Contextualize
 Leverage XML
tools/formats
Laboratory Data in an ELN

12.  AnIML Viewer application or browser plugin
 Jmol/jSpecView
 Jquery/flot viewer (inspired by NIST JCAMP viewer*)
 Many others…
Viewing Instrument Data
* http://webbook.nist.gov/chemistry

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

14.  Expose AnIML file at a URL
 Define a DOI for that URL
 Use xpath to reference a specific data value in the AnIML
file
 //ExperimentStepSet[1]/ExperimentStep[1]/Method[1]/Auth
or[1]/Name[1]
Referencing Instrument Data

15. Calculations with Instrument Data
 Extract data from files using xpath
 Browser based Javascript functions to
 Smooth
 Integrate
 Absorbance <-> %T
 Linear regression

16.  Promulgated as an ASTM Standard
 Documentation
 Core specification
 Technique and extension specification
 Naming and design rules
 Annotated technique definitions
 Ontological reference to AnIML metadata items
 Semantic search of AnIML documents
Future Developments

17. Conclusion
 AnIML is a perfect solution to the storage of
instrument data within ELNs
 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

18.  schalk@unf.edu
 Phone: 904-210-5311
 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?