Integrating AnIML Files in Electronic Laboratory Notebooks - PittCon 2015
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This document discusses integrating AnIML files, an XML data standard for analytical instrument data, into electronic laboratory notebooks. It describes what AnIML files contain, how they can be used to store and reference instrument data in ELNs, and how that data can be viewed, published, and used for calculations. Integrating AnIML allows scientists to capture instrument data digitally along with the experimental context and workflow in their notebooks.
![ 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](https://image.slidesharecdn.com/animlandelnspittcon2015-150708134232-lva1-app6891/85/Integrating-AnIML-Files-in-Electronic-Laboratory-Notebooks-PittCon-2015-14-320.jpg)
Integrating AnIML Files in Electronic Laboratory Notebooks - PittCon 2015
- 1. Integrating AnIML Files in Electronic Laboratory Notebooks Stuart J. Chalk, Department of Chemistry, University of North Florida [email protected] 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
- 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. [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?