DIGITAL SCIENCE LIBRARY FOR DIGITAL SCIENCE LIBRARY FOR NUCLEAR MAGNETIC NUCLEAR MAGNETIC

RESONANCE SPECTROSCOPYRESONANCE SPECTROSCOPY

Przemysław Rek, Mirosław Kopeć,

Zofia Gdaniec, Łukasz Popenda, Ryszard W. Adamiak,

Marcin Wolski, Marcin Lawenda, Norbert Meyer, Maciej Stroiński

Agenda

• Introduction• Nuclear Magnetic Resonance

Spectroscopy• Data stored in NMR database• Digital Science Library• Project design issues

Digital Science Library

• Category – the ability to group the related publications

• Catalogue description –detailed information about digital entries in the library

• Searching – library content lookup by the user-defined criteria

• Browsing – visualization of the searched out data in the user-friendly interface

DSL Features

• Widespread access to the published papers

• Durability

• Version Management

• Access Management

• Copying Protection

• Notifications

• Credibility

DSL – Characteristics

• The Data Management System (DMS) is a distributed system featuring data access and delivery

• Data Archiving System built on DMS enables:– Storing huge files on the magnetic tape drives– Access to the particular parts of file– Automatic file replication

DMS Architecture

NMR Spectroscopy

• Application Domain– identification of organic compounds– determination of the threedimensional

structures of small molecules and biomolecules

– analysis of conformation equilibria– analysis of intra- and intermolecular

interactions– study of molecular dynamics– study of chemical reaction kinetics

Data Stored in NMR Database• 56 attributes stored in NMR database

– Information about the compound

– Information about NMR experiment

– Information about spectral data

– Information about the author

– Bibliography– Experimental data– Structural analysis– Other information

Project design - functionality

• Data gathering and updating – storing and updating information about compounds and experiment data

• Querying/viewing – getting information on chemical compounds, experiments, results and analysis– Query for compound info– Query for experiment data– Query for post-experimental analyses– Query for post-experimental additional data

Project design – use case diagram

NMR Interface

• Web application letting user handle NMR through the web browser

• Primary module– File-Directory Panel– Panel for file upload: transport over GSIFTP protocol

• NMR database module– Search data– Deposit data– Update data

File-Directory Panel

• Navigate over the hierarchy of directories and files

• Add, modify, move and remove directories and files

NMR Deposit Data

Literature Publications

• Storing publications, documents, notes

connected with results of the experiment

Exploring Panel - Compound

• Let the user create search profile, including– Information about compound

– Number of atoms– Reference and literature

Security within DSL

Digital ScienceLibrary

Identity serverRAD

authorizationsystem

Logon

Authentication

Request

Method invocation

Proxy certificate

Resource access

authorization

PortalPortal

DSL Storing data

Repository

Data Container

RADData

Broker

Data ContainerData

Container

Data Broker

Creating the file location

AuthorizationData Broker

Creating the Site URL (SURL)

Space reservation

Return Transfer URL (TURL)

Under negotiationsFile uploading

ftp://server/path/4601393919636291836

PortalPortal

Virtual Laboratory Architecture

Summary

• Digital libraries become more and more popular among users

• Digital libraries have different profiles• It is very important to use open standards in

information recording• Compared with the other NMR databases DSL:

– Flexible and opened architecture

– Is more suitable for teaching

Thank you for your attention

http://vlab.psnc.pl/vlab@psnc.pl

http://dms.progress.psnc.plszd@man.poznan.pl