The document discusses the Eureka Research Workbench, an electronic laboratory notebook that utilizes a semantic approach to facilitate the management and sharing of scientific data through the Experiment Markup Language (ExptML) and RDF protocols. It emphasizes the challenges faced by academics in data sharing and the necessity for a user-friendly electronic notebook to properly document scientific workflows. The workbench integrates multiple data types and offers a web interface for efficient data retrieval and management, promoting collaboration and enhancement of research processes.

1. Eureka Research Workbench:
A Semantic Approach
to an Open Source
Electronic Laboratory Notebook
Stuart J. Chalk
Department of Chemistry
University of North Florida
schalk@unf.edu
2013 Fall ACS Meeting – CINF Paper 116

2. Big Data
Electronic Notebooks
The Eureka Research Workbench
Experiment Markup Language
ExptML Schema and Files
Semantic Data and Ontologies
File Storage
Eureka Interface
Web Interface
Conclusion
Outline

3. Current buzz word for “this bring together lots of data and
build tools on top to extract knowledge”
This is great, except…
How do we do that for science?
Platform, data structures, and exchange protocols to
capture, identify, and disseminate scientific information
Research Data Alliance (https://rd-alliance.org/)
http://www.nytimes.com/2013/08/13/science/how-to-share-scientific-data.html
Big Data

4. Electronic Notebooks (ELNs) very common in industry
Not appropriate for academics doing science
Expensive
Overly complicated (regulations)
Data sharing not easy
We need an electronic notebook for faculty/students
LabArchives http://www.labarchives.com
eCAT http://www.researchspace.com/electronic-lab-notebook/
LabTrove http://www.labtrove.org/
Dryad data publishing http://datadryad.org/
Electronic Notebooks

5. Started in 2006 as an offshoot of getting involved in the
Analytical Information Markup Language (AnIML) project
through ASTM
No way to store all research notes in a digital format
No way to capture the workflow of scientists
Realized writing in a lab notebook is equivalent to “multi-
type” blogging in the digital world
How to capture information? Many datatypes -> ExptML
How to store files and make them available through web
interface? (Fedora-Commons)
How to link data together? RDF (in Fedora-Commons)
Eureka Research Workbench

6. A specification (written in XML) that describes
different types of information recorded during the
scientific process (http://exptml.sourceforge.net)
Many datatypes (will expand…)
Experiment Markup Language (ExptML)
 Sample
 Solution
 Space
 Specimen
 Substance
 Task
 Template
 Timeline
 User
 Vendor
 Annotation
 Api
 Calculation
 Chemical
 Citation
 Communication
 Customer
 Data
 Dataset
 Definition
 Element
 Equipment
 Event
 Experiment
 Group
 Project
 Protocol
 Quote
 Report
 Result

7. ExptML Chemical Schema

8. ExptML Chemical Schema

9. ExptML Chemical Instance

10. ExptML Chemical Instance

11. Files that represent the data need to be ‘linked’ together to
allow the user to see the context of the data
The ‘Semantic Web’ is a big push to contextualize data
Proposed storage of ‘relationships’ between data is the
Resource Description Format (RDF - http://www.w3.org/RDF/)
Semantic Data
From http://www.w3.org/TR/2004/REC-rdf-primer-20040210/

12. In computer science and ontology
“formally represents knowledge as a set of concepts within
a domain, and the relationships between those concepts. It
can be used to model a domain and support reasoning about
concepts.”*
In essence, an ontology allows us to define the
relationships and assertions about concepts
For substances represented in ExptML we define
isSubstance (assertion)
hasSubstance
isSubstanceOf
ExptML Ontology
*https://en.wikipedia.org/wiki/Ontology_(information_science)

13. ExptML Ontology

14. Digital repository software for creating and managing
online digital libraries
Stores the ExptML files
Stores any other files (PDFs, Images, Word etc.)
Stores relationships as RDF
Version control
Checksumming
Built in search of content and relationships
Fedora Commons

15. Fedora-Commons treats each ExptML file as an object
In the definition of a fedora object the file is just one
stream of many. By default each object also has a “DC”
stream of metadata and an “RELS-EXT” stream of
relationships
Each Fedora object can have any number of additional
streams for
Paper PDFs, product/sample pictures, original file formats (if a
conversion has been done)
Video, audio, anything
You can export individual streams or the whole Fedora
object with streams binary encoded (Sharing/archiving)
File Storage

16. File Storage

17. So, finally to the Eureka Research Workbench!
Web interface written in PHP using the CakePHP Framework
Communicates with Fedora-Commons API to create,
retrieve, update and delete (CRUD) ExptML and other files
Representational State Transfer (REST) format for URLs
E.g. http://web.server/chemicals/view/exptml:chm1
Allows for searching of all files in Fedora
Can also search based on relationships
Can extract data out of XML files
Can gather data from other websites (via API controller) and
add it to ExptML files
Eureka Interface

18. Eureka Website - Group
Onlydatatypesrelatedtothe
researchgroupshowuponleft


19. Eureka Website – Lab Bench
Typesofinformationthatarethingsyou
wouldhaveonyourlabbenchareonleft

Clicking on the “Add” menu on the right
Allows you add a comment to this solution

20. Eureka Website – Notebook
Typicalthingswerecord
inournotebook


21. Eureka Website - Laboratory
Informationaboutresourcesthat
youuseinyourlaboratory

The “Rel” menu shows you the information related to this instrument

22. Eureka Website - Library
Papersandprotocols
relatedtoyourwork

You can add the PDF
of the paper to the
citation.
The contents of the
PDF is searchable in
the system

23. Eureka Website - StockroomChemicalandSubstance
Informationisrelatedtogether


24. Robust markup language for representing science data
(ExptML)
Reliable storage system for ExptML files (Fedora)
Method for storage of relationships (RDF in Fedora)
Web application to create ExptML files (Eureka)
TODO
Provide web functionality to process data
Provide mechanism for sharing of data (different levels)
Integration into the RDA model for sharing research data
Get the word out and test system with many users
Conclusion

25. References
Eureka – http://sourceforge.net/projects/eureka
Fedora-Commons – http://fedora-commons.org
XML – http://www.w3.org/standards/xml
ExptML – http://exptml.sourceforge.net/
JSON – http://www.json.org/
UnitsML – http://unitsml.nist.gov/
RDF – http://www.w3.org/RDF/
CIR – http://cactus.nci.nih.gov/chemical/structure
RDA – http://rd-alliance.org