przemysław rek, mirosław kopeć, zofia gdaniec, Łukasz popenda, ryszard w. adamiak, marcin...
TRANSCRIPT
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
