# Presentation: 268831

## 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

## 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.

## 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

## 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

## SAM Architecture

- Notebook Services

- Semantic Services

- Metadata Services

- DataGrid

**DAV, DASL, JMS, SAM Extensions**

**DAV, JDBC, GridFTP**

## 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.

## 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

## 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

## 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.

## 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.

## 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

## Questions?

- For additional information: http://collaboratory.pnl.gov/sam