Notebook for the Semantic Era

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28 Οκτ 2013 (πριν από 3 χρόνια και 7 μήνες)

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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


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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.


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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

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




5


SAM Architecture

Notebook Services

Semantic Services

Metadata Services

DataGrid

Database

Web

DAV, DASL, JMS, SAM Extensions

DAV, JDBC, GridFTP

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.

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


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

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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.


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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.

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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


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Questions?

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