integrating animl files in electronic laboratory notebooks - pittcon 2015
TRANSCRIPT
Integrating AnIML Files in Electronic Laboratory
NotebooksStuart J. Chalk, Department of Chemistry, University of North
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
[email protected] 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?