Adapting the Electronic Laboratory Adapting the Electronic Laboratory Notebook for the Semantic EraNotebook for the Semantic Era

Adapting the Electronic Laboratory Adapting the Electronic Laboratory Notebook for the Semantic EraNotebook for the Semantic Era

Tara Talbott, Michael Peterson, Jens Schwidder, James D. Myers

2005 International Symposium on Collaborative Technologies and Systems May 17th 2005

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PurposePurposePurposePurpose

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.

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Background of the ELNBackground of the ELNBackground of the ELNBackground 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

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Background of SAMBackground of SAMBackground of SAMBackground 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

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SAM ArchitectureSAM ArchitectureSAM ArchitectureSAM Architecture

Notebook Services

Semantic Services

Metadata Services

DataGrid

Database

Web

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Implementation of the ELN on SAMImplementation of the ELN on SAMImplementation of the ELN on SAMImplementation 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.

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Client-Server adaptations for Notebook Client-Server adaptations for Notebook functionalityfunctionality

Client-Server adaptations for Notebook Client-Server adaptations for Notebook functionalityfunctionality

Encapsulation of the ELN’s client-server functionalityDynamic determination of server informationNotebook retrieval and submissionNotebook configurationPage displayNew SAM specific functions

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Features provided through SAMFeatures provided through SAMFeatures provided through SAMFeatures provided through SAM

Translations / data provenanceDASL based SearchJMS services, email notificationsJava Server Pages used for: Notebook creation and configuration Listing available notebooks Generating notebook pages

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DiscussionDiscussionDiscussionDiscussion

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.

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Future work/directionFuture work/directionFuture work/directionFuture work/direction

Implement common server interfaces to allow use of ELN with other applications on SAM server, such as a wiki or ORNL enote clientNext-generation user interface making it easier to incorporate metadata created by other applications.

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AcknowledgementsAcknowledgementsAcknowledgementsAcknowledgements

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 projectMembers of the Collaboratory for Multiscale Chemical Science (CMCS) project

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Questions?Questions?Questions?Questions?

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