Less is More Lightweight Ontologies and User Interfaces for Smart Labs J. G. Frey, G. V. Hughes, H....

Less is MoreLightweight Ontologies and User Interfaces for Smart Labs

J. G. Frey, G. V. Hughes, H. R. Mills, m. c. schraefel, G. M. Smith, David De Roure

CombeChem Project

Electronics and Computer Science / School of Chemistry

University of Southampton

Combechem Aims

Support end-to-end collection & sharing of data and metadata for chemistry experiments.

Publish@SourceAccessible (online) publication of results

Make data and records available

Accessible to humans and computers

The Chemistry Experiment

Plan

Perform

Ponder

Publish

Planner

Experiment planning tool:Basic metadata (short description, etc.)IngredientsPlanned quantitiesProcesses

Based on COSHH formSimple web application in PHP

COSHH

critical data entry

A digital lab book replacement that

chemists were able to use, and liked.

1 1 2 2 1 3 1 4

Sample of 4-flourinatedbiphenyl

Add CoolReflux

Butanone Sample ofK2CO3Powder

Weigh

grammes0.9031

Measure

40 ml

Add

Weigh

2.0719 g

text

3 5

Add

g

Sample ofBr11OCB

2 6

Reflux

2 7

Cool

Water

Measure

30 ml

9

Liquid-liquid

extraction

DCM

Measure

3 of 40 ml

10

Dry

MgSO4

11

Filter(Buchner)

12

RemoveSolvent

by RotaryEvaporation

13

Fuse

Silica

14

ColumnChromatography

Ether/PetrolRatio

Butanone dried via silica column andmeasured into 100ml RB flask.

Used 1ml extra solvent to wash outcontainer.

Started reflux at 13.30. (Had tochange heater stirrer) Only reflux

for 45min, next step 14:15.

Inorganics dissolve 2layers. Added brine

~20ml.

Organics are yellowsolution

Washed MgSO4 withDCM ~ 50ml

Measure

excess

Observation Types

weight - grammes

measure - ml, drops

annotate - text

temperature - K, °C

Key

Process

Input

Literal

Observation

Add CoolRefluxAddAdd Reflux Cool Dry Filter Remove

Solventby Rotary

Evaporation

Fuse ColumnChromatography

Dissolve 4-flourinatedbiphenyl inbutanone

Add K2CO3powder

Heat at refluxfor 1.5 hours

Cool and addBr11OCB

Heat atreflux untilcompletion

Cool and addwater (30ml)

Combine organics,dry over MgSO4 &filter

Removesolvent invacuo

Liquid-liquid

extraction

Extract withDCM(3x40ml)

Fuse compound to silica &column in ether/petrol

4 8

Add

Add

text

Annotate

Annotate

text

Weigh

Annotate

g

Annotate Annotate

text text

Future Questions

Whether to have many subclasses of processes or fewer with annotations

How to depict destructive processes

How to depict taking lots of samples

What is the observation/process boundary? e.g. MRI scan

1.5918

Combechem

30 January 2004gvh, hrm, gms

Ingredient List

Fluorinated biphenyl 0.9 gBr11OCB 1.59 gPotassium Carbonate 2.07 gButanone 40 ml

image

To

Do

Lis

tP

lan

Pro

ce

ss

Re

co

rd

1 1 2 2 1 3


Add Reflux


Weigh

grammes0.9031

Measure

40 ml

Add

Weigh

2.0719 g

text





Add RefluxAdd


Add K2CO3powder


text

Annotate

Annotate

Ingredient List


1 1 2 2 1 3


Add Reflux


Weigh

grammes0.9031

Measure

40 ml

Add

Weigh

2.0719 g

text





Add RefluxAdd


Add K2CO3powder


text

Annotate

Annotate

Ingredient List


1 1 2 2 1 3


Add Reflux


Weigh

grammes0.9031

Measure

40 ml

Add

Weigh

2.0719 g

text





Add RefluxAdd


Add K2CO3powder


text

Annotate

Annotate

Ingredient List


1 1 2 2 1 3


Add Reflux


Weigh

grammes0.9031

Measure

40 ml

Add

Weigh

2.0719 g

text





Add RefluxAdd


Add K2CO3powder


text

Annotate

Annotate

Ingredient List


1 1 2 2 1 3


Add Reflux


Weigh

grammes0.9031

Measure

40 ml

Add

Weigh

2.0719 g

text





Add RefluxAdd


Add K2CO3powder


text

Annotate

Annotate

Ingredient List


1 1 2 2 1 3


Add Reflux


Weigh

grammes0.9031

Measure

40 ml

Add

Weigh

2.0719 g

text





Add RefluxAdd


Add K2CO3powder


text

Annotate

Annotate

Ingredient List


Architecture

ViewingTools

Sem. WebApps

ServicesServicesServicesServicesServicesResults

Data

SemanticData

Computeservices

Weights &Measures

Bench

Planner

RDF over SOAP

Key

Process

Input

Literal

Observation

pla

n-t

o-

hea

t_te

a_in

_wat

er

plan-to-add_tea_to_water

Add tea to hotwater

Heat tea for5 minutes

Filter off tealeaves

File: combechem/process/tea.rdfOntology: combechem/process/process-record.rdfs

13:41:36 14 July 2004© 2004 University of Southampton

Ste

ps

Pla

nP

roc

ess R

ec

ord

planned-weight_of_tea_leaves

5

planned_tea_leaves

plan-to-weigh_tea_leaves

processed-by-iv

material-observed-by

produces-observation

has-unitvalue

produces-substance

pla

n-t

o-f

ilter

_tea

produces-substance

300

has-unitvalue

processed-by-iv


planned_some_water

plan-to-measure_some_water


planned-volume_of_some_water

processed-by

processed-by

next-step next-step

hea

t_te

a_in

_wa

ter

add_tea_to_water

weight_of_tea_leaves

5.021

tea_leaves

weighing_tea_leaves

processed-by-iv



has-unitvalue

produces-

substance

filt

er_

tea

produces-substance

&cec;volumeunit-millilitre310

has-unitvalue

processed-by-iv


some_water

measuring_some_water


volume_of_some_water

processed-by

processed-by

pla

n-t

o-t

ea_i

n_w

ater

pla

n-t

o-h

ot_

tea

tea_

in_w

ate

r

ho

t_te

a

step-text step-text step-text

experiment-pretty-name

The basic teaexperiment

experiment-description

Add tea leaves tohot water, refluxing,

filtering, drinking(maybe)

experimenter

starting-process

MakingTea

http://www.ecs.soton.ac.uk/info/#person-00389

process-record-of

material-record-of

process-record-of

produces-substance

pla

n-t

o-f

inis

he

d_t

ea

produces-substance

fin

ish

ed_t

ea

<tabletscribble>

value

process-observed-by

watching_tea_boil


heat_tea_notes

&cec;massunit-gramme

&cec;volumeunit-millilitre


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/corecec http://www.combechem.org/ontology/process/0.1#st http://smarttea.org/#

part-of-step

part-of-step

part-of-step

step1 step2 step3

experiment-goal

material-is-ingredient-of


material-record-of

process-record-of

process-record-of

process-record-of

material-record-of

material-record-of

starting-step

Key

Process

Input

Literal

Observation

pla

n-t

o-

hea

t_te

a_i

n_w

ate

r


Add tea to hotwater





Ste

ps

Pla

nP

roc

ess R

ec

ord


5

planned_tea_leaves


processed-by-iv



has-unitvalue

produces-substance

pla

n-t

o-f

ilte

r_te

a

produces-substance

300

has-unitvalue

processed-by-iv


planned_some_water




processed-by

processed-by

next-step next-step

hea

t_te

a_in

_wa

ter

add_tea_to_water


5.021

tea_leaves

weighing_tea_leaves

processed-by-iv



has-unitvalue

produces-

substance

filt

er_

tea

produces-substance


has-unitvalue

processed-by-iv


some_water




processed-by

processed-by

pla

n-t

o-t

ea_i

n_

wat

er

pla

n-t

o-h

ot_

tea

tea_

in_

wat

er

ho

t_te

a







experimenter

starting-process

MakingTea


process-record-of

material-record-of

process-record-of

produces-substance

pla

n-t

o-f

inis

he

d_

tea

produces-substance

fin

ish

ed

_te

a

<tabletscribble>

value

process-observed-by

watching_tea_boil


heat_tea_notes




Smarttea.org

Making Tea

Namespaces


part-of-step

part-of-step

part-of-step

step1 step2 step3

experiment-goal



material-record-of

process-record-of

process-record-of

process-record-of

material-record-of

material-record-of

starting-step

getRecord()

Key

Process

Input

Literal

Observation

pla

n-t

o-

hea

t_te

a_i

n_w

ate

r


Add tea to hotwater





Ste

ps

Pla

nP

roc

ess R

ec

ord


5

planned_tea_leaves


processed-by-iv



has-unitvalue

produces-substance

pla

n-t

o-f

ilte

r_te

a

produces-substance

300

has-unitvalue

processed-by-iv


planned_some_water




processed-by

processed-by

next-step next-step

hea

t_te

a_in

_wa

ter

add_tea_to_water


5.021

tea_leaves

weighing_tea_leaves

processed-by-iv



has-unitvalue

produces-

substance

filt

er_

tea

produces-substance


has-unitvalue

processed-by-iv


some_water




processed-by

processed-by

pla

n-t

o-t

ea_i

n_

wat

er

pla

n-t

o-h

ot_

tea

tea_

in_

wat

er

ho

t_te

a







experimenter

starting-process

MakingTea


process-record-of

material-record-of

process-record-of

produces-substance

pla

n-t

o-f

inis

he

d_

tea

produces-substance

fin

ish

ed

_te

a

<tabletscribble>

value

process-observed-by

watching_tea_boil


heat_tea_notes




Smarttea.org

Making Tea

Namespaces


part-of-step

part-of-step

part-of-step

step1 step2 step3

experiment-goal



material-record-of

process-record-of

process-record-of

process-record-of

material-record-of

material-record-of

starting-step

getObservation()

Design discussion

Handling RDF both ends – tricky

Structure to data:good: clients can add what they want

Ontology extensions: Uncertainty to measurements

bad: clients can add what they wantIs the structure you’re given navigable in the way you expect?

Design Discussion

We have an ontology (shared understanding)

But... experiment structure is a higher-level entity

Must be created and maintained by good programming, not simply by adherence to rules of the ontology

Current & Future Work

Publish@SourceGenerating an experiment report for publication

“Natural” language generation considered, but rejected by chemists

Standard language for papers is dense, cryptic, and frequently unhelpful

Culture change

Different methods of publicationOn-line

Electronic data sent to print journals for peer review and publication

Different form for procedure description

Summary

System to support end-to-end capture of experimental work in chemistry

Light-weight in-lab systems

Desktop

Credits & More Information

Jeremy Frey, David De Roure, Gareth Hughes, Hugo Mills, monica schraefel, Graham Smith.

www.combechem.org

www.smarttea.org

Process record notation

Analyse a real experimentWhat information do chemists record?

What should they record?

What do they want to record?

How does this differ from their experiment plan?

Evolved our own graph of plan and record

Information collection

Process record

Provenance record

MeasurementsProcesses

Annotations

Service invocationsSecure time-stamps

etc…

Incr

easi

ng

deta

il

Data model

Process record

Provenance record

MeasurementsProcesses

Annotations

Service invocationsSecure time-stamps

etc…

Incr

easi

ng

deta

il

PlanIntended actions:guide to chemist,or [later] workflow

Date post:	28-Mar-2015
Category:	Documents
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Less is More Lightweight Ontologies and User Interfaces for Smart Labs J. G. Frey, G. V. Hughes, H....

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