Academic scientists need a tool to capture the science they do so that it can be shared in open science, integrated with linked data, and shared/searched. Eureka is an evolving platform to do this.

1. Eureka Research Workbench:
An Open Source eScience
Laboratory Notebook
Stuart J. Chalk
Department of Chemistry
University of North Florida
schalk@unf.edu
2014 Spring ACS Meeting – CINF Paper 38

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/)
 “Research Data Sharing without barriers”
 Fran Berman at RPI is NSF funded co-chair of RDA
Big Data

4.  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
 We need more than an electronic version of a notebook
 We need a science version of “Second Life” (SciLife?)
Electronic Notebooks

5.  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

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

7. ExptML Chemical Schema

8. ExptML
Chemical
Schema

9. ExptML Chemical (Instance)

10.  Data are connected to other data – ‘Linked Data’
(http://www.w3.org/standards/semanticweb/data)
 The ‘Semantic Web’ approach to contextualize data
 Proposed storage of ‘relationships’ between data is the
Resource Description Format (RDF - http://www.w3.org/RDF/)
Semantic Data

11.  Digital repository software http://fedora-commons.org/
 Creation and management of online digital libraries
 Fedora ‘Digital Object’ consists of metadata + streams
 Metadata stored as Dublin Core (DC stream)
 ExptML file stored as EXPTML stream
 Other files (PDFs, Images, Word etc.) stored as streams
 Relationships stored as RDF (RELS-EXT stream)
 Features: Version control, Checksumming, Archiving
 Built-in search of objects and relationships
 Add-on for file content search (Fedora GSearch)
Fedora Commons

12.  Fedora-Commons defines and works on digital objects
 In the definition of a Fedora object an ExptML 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,
binary file formats (if a conversion has been done)
 Video, audio, RDF, anything…
 You can export individual streams or the whole Fedora
object with streams binary encoded (Sharing/archiving)
Fedora for File Storage

13. Fedora Object Storage

14.  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://example.com/chemicals/view/exptml:chm1
 Creation of ExptML via interface
 Provides search via Fedora and Gsearch
 Can extract data out of XML files
 Can gather data from other websites (via API controller)
and integrate into ExptML files
Eureka Web Application

15. Eureka Website – Group View
Only data types related to the research group show up on left

16. Eureka Website – Bench View
Clicking on the “Add” menu on the right
allows you add a comment or link to data

17. Eureka Website – Notebook View

18. Eureka Website – Laboratory View
The “Rel” menu shows you the information related to this instrument

19. Eureka Website – Library View
You can add the PDF of the paper to the citation. The contents of the PDF are searchable in the system

20. Eureka Website – Stockroom View

21.  Web Application
 Server: Fedora 4, JSON-LD, ElasticSearch
 Client: CakePHP 3/HTML5, Recline.js, Annotator, JQuery
 Standards
 Linked Data Platform (http://www.w3.org/TR/ldp/)
 Datapackage/Simple Data Format (http://dataprotocols.org/)
 Markup Languages: AnIML, UnitsML, CML
 Other Molecular File Formats: MOL/SDF/CDX/CIF/PDB etc.
 Open Framework for Laboratory Data (Allotrope Foundation)
 Datasources
 ChemSpider, CIR, PubChem, Google Scholar, CrossRef, VIVO
 ExchangeNetwork (EPA), NIST, SDBS (no API’s yet)
 Tools
 Marvin for JS, JSXGraph, JSpecView, Chemicalize.org
Eureka Technology Stack

22.  Implement ingest of all data types, file (if appropriate) and web based
 In browser processing of data -> dataset -> result, report writing
 Extraction of file based legacy data -> ExptML format data
 Open access to data/spectra, ‘available data’ page (browser only)
 Access to data/spectra via linked data server (discovery/indexing)
 Publishing of packaged datasets with authenticated download option
 Automated ingestion of data from instruments/sensors
 Collaborative research: authentication and data exchange
 Timeframe? Depends on securing funding
Eureka Roadmap

23.  Eureka: Web application to create ExptML files
 Built on ExptML to capture data/resources/workflows
 Reliable storage/archiving system for ExptML files (Fedora)
 Storage of relationships between data (RDF)
 TODO
 Provide mechanism for sharing of data (different levels)
 Add tools to find, visualize and work on science data
 Integration into the RDA model for sharing research data
 Get the word out and test system with many users
Conclusion

24. References
 Eureka – http://sourceforge.net/projects/eureka
 Fedora-Commons – http://fedora-commons.org
 XML – http://www.w3.org/standards/xml
 AnIML – http://animl.sourceforge.net
 ExptML – http://exptml.sourceforge.net/
 UnitsML – http://unitsml.nist.gov/
 CML – http://www.xml-cml.org/
 JSON-LD – http://www.w3.org/TR/json-ld/
 RDF – http://www.w3.org/RDF/
 CIR – http://cactus.nci.nih.gov/chemical/structure
 RDA – http://rd-alliance.org
 ChemSpider – http://www.chemspider.com/
 Allotrope Foundation – http://allotrope.org