CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 1 CrystalGrid 2004...

1 CSE Computational Science & Engineering Department

CHEMICAL DATABASE CHEMICAL DATABASE SERVICESERVICE

CrystalGrid 2004

• Aspects of Current CDS Service

• Interactions with e-Science



CDS Overview• Grant funded by EPSRC• Based at Daresbury Lab (CCLRC)• Present Service started 1993• 4 staff• Provide access to data, support and training• Service free of charge to users• Currently 3300+ users from 100+ sites



Database coverage

• Crystallography

• Synthetic Organic Chemistry

• Spectroscopy

• Physical Chemistry



Help/support• Website - http://cds.dl.ac.uk/cds

• Phone/email us

• Manuals - mostly online

• Online help

• Online tutorials

• Flash movies



Registration• Online system

• Individual ids required

• Current Rep



CDS RefundingLatest 3 years Refunding Grant began 1/4/04

• CDS continues to be supported by four staff members

• Boost to Physical Chemistry holding with successful application for funding for DETHERM thermophysical properties database

• Starting major publicity iniative with ambitious site visits programme

• Interim review of Service in 2005



Physical Chemistry

• DETHERM One of the world's largest thermophysical

property databases of pure compounds and compound mixtures

Contains 4.9 Million data sets for around 130,000 systems

(about 24,000 pure substances and 106,000 mixtures)

covering more than 500 property fields.



Physical Chemistry

The recent CDS renewal grant included funding to acquire a full set of datasets from the supplier (DECHEMA e.V.) for use by the UK academic community

For instance in the field of vapour-liquid-equilibrium data, it contains more than 95% of data published worldwide.

Further details are available at the DETHERM pages on the CDS web site.



Publicity Initiatives• In the light of discussions with the EPSRC following

on from the meeting with the CDS Grant Review Panel

training plans have been modified and enhanced:

• Our Roadshow ideas have been refined and expanded. At each site will

now give a CDS Overview lecture/seminar which takes place after a

manned CDS poster and discussion session in the departmental foyer.

• The planned schedule of visits is advertised on the CDS web

• Fuller details of these and other aspects are given in the CDS 2003/4 Annual and Interim Reports



CrystalGrid 2004

• Interactions with e-Science

• Some Aims for the Future



1. Current - What CDS has at the moment

2. Future - Interactions with e-ScienceExample – DLVExample – Linking Databases - Crystal Web

• Metadata

• Collaboration Tools

• Archiving /Data Curation



PRESENT

A. Search individual database using proprietary Search individual database using proprietary software to see if compound, crystal, spectrum, software to see if compound, crystal, spectrum, data exists.data exists.

B.B. Save/download/convert specific data for use Save/download/convert specific data for use with packages on their desktop machine.with packages on their desktop machine.

Or Conduct simple search of CDS databases using Or Conduct simple search of CDS databases using desktop package (currently only one )and then desktop package (currently only one )and then making use of some of that data in the package.making use of some of that data in the package.



IssuesIssues

• Proprietary databases, different systems,

different front-ends – no direct control by CDS.

• Data is different in each database.

• Cannot query ALL databases using one query.



e-Science - Experience

• Integration into Problem Solving Environments (PSEs)

• Database access over the Grid (OGSA-DAI; IBM & Oracle)

• Data and metadata technologies for storage (XML

etc)

• Authorisation and authentication.



Example: DL Visualise (DLV)

Simple search of databases

Takes crystal co-ordinates and produces displays

Fires up computational packages



DL VisualiseCurrent

1. It is a ‘kludged’ system.

2. Requires on going interactions between CDS and CSE

to set up and maintain - sensitive to future modifications.

Future - Input from e-Science

1. Use standard protocols and definitions

2. Publicised to community

3. “Web services” - e-Science concept should do the job better.





Linking DatabasesPresent - Crystal Web - (miniGRID) able to search different crystallography Crystal Web - (miniGRID) able to search different crystallography

databases (databases (cannotcannot as yet use drawn structure as query) as yet use drawn structure as query)



Linking Databases - Future - Input from e-Science

MetadataMetadata – taken – taken from disparate databases and merged

into one database (e.g. Compound Locator idea

[MDL])

• Creates a meta data layer• Transparently passes queries to the meta layer• Transparently translates queries through metadata to different formats and different query types• Transparently searches multi-data sources with different

query formats/types• Present results to the user



Linking Databases - Future

StructuresStructures

May contain large amount of binary data. - Use Metadata but with links to full data.

Requires generic chemistry format.• XML? • INChI? (IUPAC-NIST Chemical Identifier)



CDS and e-ScienceCDS and e-Science

Collaboration Tools

e.g. Examining and manipulating datasets over the network (e.g. rotating structure on colleagues machine)

Review data and add comments.

[Similar technology to video conferencing and remote experiments]




Archiving /Data Curation

Data deposited and saved in one location or distributed Data deposited and saved in one location or distributed around linked locations.around linked locations.

• Established e-Science aspirationEstablished e-Science aspiration• Local DL expertiseocal DL expertise• JISC Integrated Information EnvironmentJISC Integrated Information Environment initiative initiative

Would also require incentive to users to add data!Would also require incentive to users to add data![e.g. Spectral data – mandatory for those with government grant to [e.g. Spectral data – mandatory for those with government grant to archive data]archive data]




Archiving /Data Curation

Some tools already present at CDS (e.g. ISIS - Screening Some tools already present at CDS (e.g. ISIS - Screening

Compound Database) – data can be input if users send it.Compound Database) – data can be input if users send it.

Data entry tools required if users enter data directly to Data entry tools required if users enter data directly to

local database. local database.

Could then use batch entry to main database or data Could then use batch entry to main database or data

could be harvested (whole or meta data?)could be harvested (whole or meta data?)

e.g. CrystalGrid – elemental composition and reduced cell e.g. CrystalGrid – elemental composition and reduced cell

data.data.





CDSCDS CommercialCommercialdatabasesdatabases

Legacy formatsLegacy formats

Added value from Added value from cross database cross database

integrationintegration

Communities

Computational codes

Site Visits / PR

Internationalisation?

Training/infrastructure

Extensible data representations

Project databasesExpert systems

Hardware/software infrastructure

New mechanisms for authentication, authorisation, eventually payment

Grid modalities for search / delivery

Testbed projects

Serving structures to GUIs

Comp Results Libraries

building up additional data?

Integrated delivery of data & compute

services

CCPsCCPs

E-ScienceE-Science

Integrated delivery of data & compute

services

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CSE Computational Science & Engineering Department CHEMICAL DATABASE SERVICE 1 CrystalGrid 2004...

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