integrating animl files in electronic laboratory notebooks - pittcon 2015

Integrating AnIML Files in Electronic Laboratory

NotebooksStuart J. Chalk, Department of Chemistry, University of North

Floridaschalk@unf.edu

Paper 2670-1 Pittcon 2015

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

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

Sections of an AnIML File

AnIML Schemas and Files

AnIML Technique Definitions

Electronic Laboratory Notebooks

Scientists need to move todigital notebooks…

...and record not just the databut the flow and context

How science is done isimportant for searching,aggregation, meta-analysis

Writing in a scientific notebook is about telling the story of what a scientist has learned by gathering data using the resources available in their laboratory*

* Concept: Tony Williams

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)

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

Access Reference Search

Visualize Export Manipulate Process Contextualize

Leverage XMLtools/formats

Laboratory Data in an ELN

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

Conversion of AnIML data to SVG using XSLT

Publishing Instrument Data

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]/Author[1]/Name[1]

Referencing Instrument Data

Calculations with Instrument Data

Extract data from files using xpath

Browser based Javascript functions to Smooth Integrate Absorbance <-> %T

Linear regression

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

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

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?