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Eureka Research Workbench: A Semantic Approach to an Open Source Electronic Laboratory Notebook
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Eureka Research Workbench: A Semantic Approach to an Open Source Electronic Laboratory Notebook

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Scientists are looking for ways to leverage web 2.0 technologies in the research laboratory and as a consequence a number of approaches to web-based electronic notebooks are being evaluated. In this …

Scientists are looking for ways to leverage web 2.0 technologies in the research laboratory and as a consequence a number of approaches to web-based electronic notebooks are being evaluated. In this presentation I discuss the Eureka Research Workbench, an electronic laboratory notebook built on semantic technology and XML. Using this approach the context of the information recorded in the laboratory can be captured and searched along with the data itself. A discussion of the current system is presented along with the next planned development of the framework and long-term plans relative to linked open data. Presented at the 246th American Chemical Society Meeting in Indianapolis, IN, USA on September 12th, 2013.

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  • 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