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Adapting the Electronic Laboratory Notebook for the Semantic Era

Adapting the Electronic Laboratory Notebook for the Semantic Era. Tara Talbott, Michael Peterson, Jens Schwidder, James D. Myers 2005 International Symposium on Collaborative Technologies and Systems May 17 th 2005. Purpose. Allow scientists to work in distributed teams

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Adapting the Electronic Laboratory Notebook for the Semantic Era

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  1. Adapting the Electronic Laboratory Notebook for the Semantic Era Tara Talbott, Michael Peterson, Jens Schwidder, James D. Myers 2005 International Symposium on Collaborative Technologies and Systems May 17th 2005

  2. Purpose • Allow scientists to work in distributed teams • Eliminate need for manual transcription of electronic data • Automate searching, indexing, and metadata generation • Can serve as records with digital signatures • Stand-alone EN’s may be limited in their ability to interact with other producers and consumers of data. • Enable the sharing of this information among portals and problem solving environments, software agents, scientific applications, and electronic notebooks • With different levels of sophistication • Without global schema • Improve the completeness, accuracy, and availability of the scientific record. 2

  3. Background of the ELN • Hierarchical Chapters/Pages/Notes • Editors including file upload, sketch, text, equations, forms, image capture • Interactive views of data • Add/View/Search Notes • Editor/Viewer APIs • Digital Signatures/Timestamps 3

  4. Background of SAM • A layered middleware designed to manage data annotations and semantic relationships. • Built on the Jakarta Slide content management system which uses the webDAV protocol for managing data and metadata. • Semantic Services Layer • RDF/GXL Pedigree Generation • Metadata Services Layer • Property Generation from binary/ASCII/xml files • Dynamic Virtual Translations • Server generated Properties and Relationships • Notebook Services Layer • Notebook Management, Page Display 4

  5. Database Web SAM Architecture Notebook Services DAV, DASL, JMS, SAM Extensions Semantic Services DAV, JDBC, GridFTP Metadata Services DataGrid 5

  6. Implementation of the ELN on SAM • Client-Server communications • Dynamically select appropriate communications classes for server • Mapping the ELN client model to the webDAV protocol • Mapping to existing DAV properties • Additional properties such as samns:children • Mapping specific client methods to atomic server calls • webDAV PUT, GET, PROPPATCH, etc… • Higher level server interface to ease integration. 6

  7. Client-Server adaptations for Notebook functionality • Encapsulation of the ELN’s client-server functionality • Dynamic determination of server information • Notebook retrieval and submission • Notebook configuration • Page display • New SAM specific functions 7

  8. Features provided through SAM • Translations / data provenance • DASL based Search • JMS services, email notifications • Java Server Pages used for: • Notebook creation and configuration • Listing available notebooks • Generating notebook pages 8

  9. Discussion • Benefits • Flexibility of new implementation. • Ability to reference data created through external tools. • Integrations with portals such as CMCS. • Reduction of ELN Specific server code. • Drawbacks/Considerations • Lack of support in webDAV for multi-valued properties. • Possible interference with ELN data by third party clients. 9

  10. Future work/direction • Implement common server interfaces to allow use of ELN with other applications on SAM server, such as a wiki or ORNL enote client • Next-generation user interface making it easier to incorporate metadata created by other applications. 10

  11. Acknowledgements • Pacific Northwest National Lab • Pacific Northwest National Laboratory is a multi-program national laboratory operated by Battelle Memorial Institute for the U.S. Department of Energy under Contract DE-AC06-76RL0 1830 • Oak Ridge National Lab • Oak Ridge National Laboratory is a multi-program national laboratory operated by UT-Battelle, LLC for the U.S. Department of Energy under Contract DE-AC05-00OR22725 • Prasad Saripalli, who contributed to an early draft of this paper. • Past and Present members of the SAM project • Members of the Collaboratory for Multiscale Chemical Science (CMCS) project 11

  12. Questions? For additional information: http://collaboratory.pnl.gov/sam 12

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