CombeChem

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The CombeChem Project

Semantic Support for the Chemistry Life cycle

Jeremy Frey Dave De Roure

Schools of Chemistry and

(2)

The Comb

e

Chem Project

 End to End linking of data and information: Laboratory

to publication and back again

 The exponential world of combinatorial synthesis and

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Plan &

COSHH

Digital Model

Information

Integration

Report

Knowledge

Goal

Literature

Synthesis

not just one laboratory but many co-laboratories

working together

Analysis

Smart Laboratory

Smart Storage Smart Dissemination

Smart HCI

(4)

The Stretches of CombeChem

Interdisciplinary

Chemistry

Computer

Science

Methodologies

Deployment

Research

Holistic

(5)

CombeChem Smart Tea



Ethnography



Electronic Lab

Notebook



Capture in RDF

(6)

Observations are never collected on note pads,

filter paper or other temporary paper for

later transfer into a notebook

(7)

PLANS

 Make use of Plans to

inform the digital context - metadata in advance

 Have concern for the

“End-to-End life cycle” of chemistry information

from the start

 Understanding Usability

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National Crystallography Service

Grid Service Architecture

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Statistics

 Collect information about

ligands and their (transition metal) complexes

 Calculate descriptors with

standard computational approach (DFT)

 Robustness

(computational,

chemical, statistical)

 Overlap with available

experimental data

Map of Ligand Space for

Monodentate Phosphorus(III) Ligands

(12)

Dave’s Chemistry

Experiment

1. Take a building full of

chemists

2. Add RDF tools

3. Stir occasionally

4. See what’s been made

 A very big chunk of

Semantic Web

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Semantic DataGrid



CombeChem uses

Semantic Web for

Enhanced (annotated)

DataGrid over multiple diverse stores

Some Data Storage

Storage of Provenance

Information

Annotated multimedia

(14)

Triplestores

 Started with the data

hoarding approach of CSAKTive Space, using 3store from the AKT IRC

 Scalability, lifecycle and the

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Workflow Execution And Monitoring

Instrument Tracking And utilisation Resource

+ Floor Management

Run-time tracking and control

Action Realisation + Rationale Feedback

Comb-Comb-e-Cheme-Chem: Facility e-Science in Action: Facility e-Science in Action

Presence Awareness

(16)

Autonomic e-Science

 Built simulator of a

future combechem in which 1000s of services are negotiating and self-organising

 Informed by combechem

experience

 Article in IEEE Intelligent

Systems on the

Self-Organising Semantic Grid

 Raises questions about

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Access to the

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SVG “active” graphics

Link to data, follow links back to the raw data

Take Homes

 Making sure other people can find, understand

and re-use your data easily and with confidence (even when there is a huge amount of it!)

 Whole lifecycle approach from lab to publication

 Significant rollout of next generation Web

technologies – Semantic DataGrid

 Distinctive in e-Science for focusing on

laboratory, usability and collaboration

 Agent of culture shift in publishing and open

access to data

 Outreach including schools

 Platform and agenda for future research in the

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Grid Innovation



CombeChem has focused on

accelerating science by accelerating the

process and not necessarily the

computation

Uses existing cluster and grid techniques

Early focus on security for National

Crystallographic Service

Adopted Web Services from the outset

Uses asynchronous message passing for

integration

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Middleware Outputs



Security and access control developed

for NCS



Software written by IT Innovation for

CombeChem fed into the software

distribution for the EU Grid for

Industrial Applications (GRIA) Project



It forked!

GRIA now on release 5, good adoption by

industrials in EU projects (e.g. SIMDAT)

Solutions evolved with current Grid

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Other Outputs



Security and Access Control in GRIA 5



Statistics software:

Design search algorithms for Generalized

Linear Models

Design of experiments eLearning module

Elicitation in Chemistry Investigations

(EliCIT)

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Staffing



Deploy-then-research strategy



Core team persisted through most

of project and developed

interdisciplinary knowledge



Brought in additional staff for

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Key Process Input Literal Observation p la n -t o -h ea t_ te a_ in _w at er plan-to-add_tea_to_water

Add tea to hot water

Heat tea for

5 minutes Filter off tealeaves File: combechem/process/tea.rdf

Ontology: combechem/process/process-record.rdfs 13:41:36 14 July 2004

S te ps P la n P ro ce ss R ec or d planned-weight_of_tea_leaves 5 planned_tea_leaves plan-to-weigh_tea_leaves processed-by-iv material-observed-by produces-observation has-unit value p r o d u c e s -s u b s t a n c e p la n -t o -f ilt er _t ea p r o d u c e s -s u b s t a n c e 300 has-unit value processed-by-iv material-observed-by planned_some_water plan-to-measure_some_water produces-observation planned-volume_of_some_water p r o c e s s e d -b y p r o c e s s e d -b y next-step next-step h ea t_ te a_ in _w at er add_tea_to_water weight_of_tea_leaves 5.021 tea_leaves weighing_tea_leaves processed-by-iv material-observed-by produces-observation has-unit value p r o d u c e s -s u b s t a n c e fi lt er _t ea p r o d u c e s -s u b s t a n c e &cec;volumeunit-millilitre 310 has-unit value processed-by-iv material-observed-by some_water measuring_some_water produces-observation volume_of_some_water p r o c e s s e d -b y p r o c e s s e d -b y p la n -t o -t ea _i n _w at er p la n -t o -h o t_ te a te a_ in _w at er h o t_ te a

step-text step-text step-text

experiment-pretty-name

The basic tea experiment

experiment-description

Add tea leaves to hot water, refluxing, filtering, drinking (maybe) experimenter starting-p_rocess MakingTea http://www.ecs.soton.ac.uk/ info/#person-00389 p r o c e s s -r e c o r d -o f m a t e r i a l -r e c o r d -o f p r o c e s s -r e c o r d -o f p r o d u c e s -s u b s t a n c e p la n -t o -f in is h ed _t ea p r o d u c e s -s u b s t a n c e fi n is h ed _t ea <tablet scribble> value process-observed-by watching_tea_boil produces-observation heat_tea_notes &cec;massunit-gramme &cec;volumeunit-millilitre &cec;massunit-gramme Smarttea.org Making Tea Namespaces rdf http://www.w3.org/1999/02/22-rdf-syntax-ns# rdfs http://www.w3.org/2000/01/rdf-schema# xsd http://www.w3.org/2001/XMLSchema# akt http://www.aktors.org/ontology/portal# cml http://www.xml-cml.org/schema/cml2/core cec http://www.combechem.org/ontology/process/0.1# st http://smarttea.org/# p a r t -o f -s t e p p a r t -o f -s t e p p a r t -o f -s t e p

step1 step2 step3

experiment-goal material-is-ingredient-of mater_ial-i s-ing_redie nt-of m a t e r i a l -r e c o r d -o f p r o c e s s -r e c o r d -o f p r o c e s s -r e c o r d -o f p r o c e s s -r e c o r d -o f m a t e r i a l -r e c o r d -o f m a t e r i a l -r e c o r d -o f star ting -ste p getRecord()

There is a potential

containment

problem in pulling

back partial RDF

graphs from the

triple store.

Solved by using

multiple triple

stores but

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15 Sept 06 31

Potential applications of ligand maps

1. Identify and screen new catalysts

in silico –prediction of desirable properties.

2. Direct experimental screening

(high-throughput).

3. Detect and quantify ligand

similarities/differences.

4. Add to chemical knowledge –

interpret ligand contributions to experimental observations.

2050 2060 2070 2080 2090 2100 2110 2120

2050 2070 2090 2110

experimental

p

re

d

ic

te

d

Tolman Electronic Parameter (cm-1₎

(νCO in Ni(CO)3L)

Descriptors: PA, %s, Q(Pt fragm.), He₈_steric, P-B, P-Pt, ΔR-P-R(Pd)

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15 Sept 06 32

Portlet API

Portal Layout Engine

Core Services G ri d S p h e re S e rv le t HTP Services Core Portlets HTP Portlets Core Portlets Core Portlets HTP Portlets HTP Portlets Browser HTP Database Data Unpack Script Hibernate

(-> JDBC ) CLI / Perl /_{Python ?} HTP Server

Tomcat Servlet Container

HTP Architecture (First Prototype )

Lab Server

Results Data Pack Script Filesystem Upload ZIP file

Launches

CLI / Perl / Python ?

Experiment PC

Experiment Driver (e. g. XAFS )

Filesystem Drives XAFS Manual Copy User Drives

Using ideas from the NCS Grid Service we have produced a prototype for a high throughput catalyst experiment involving array samples

investigated by

Raman, MS, EXAFS with the samples

manufactured at one site and tested at

several others

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15 Sept 06 33

 The edge with the attribute name set_attr_1 is an attribute of a nodeset.

 The edge with the attribute name triple_prop is an attribute of the above

edge.

13

20

temperature

an gle

set_attr_1 trip

le_ pro_p

Nodeset

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15 Sept 06 34