Designing'and'Implementing'a'Usable'Interface'for'Test'Databases'

Used'by'Chemoinformatics'Researchers'at'The'University'of'

Sheffield’s'Information'School'

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A'study'submitted'in'partial'fulfilment'

of'the'requirements'for'the''

MSc'Digital'Library'Management'degree'

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at'

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THE'UNIVERSITY'OF'SHEFFIELD'

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by'

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Alex'Williams'

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September'2014

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Acknowledgements.

I'would'like'to'thank'all'of'the'Information'School’s'chemoinformatics'researchers'who'participated'in'the'initial'requirements'gathering'and'user'testing.'Special'thanks'goes'to'my'supervisor,'Dr'John'Holliday,'whose'guidance'and'advice'was'a'continual'source'of'support'throughout'the'project.'Without'the'time'and'effort'he'put'in'this'project'would'not'have'been'possible.'

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Abstract.!

Background:'Chemoinformatics'researchers'at'The'University'of'Sheffield’s'Information'School'use'a'variety'of'test'databases'in'order'to'carry'out'their'research.'At'present,'however,'these'database'lack'any'kind'of'interface'that'would'support'the'tasks'they'typically'conduct.''Aim:'The'aim'of'this'project'is'to'construct'a'frontend'interface'for'the'test'databases'used'by'chemoinformatics'researchers'at'The'University'of'Sheffield’s'Information'School'that'is'specifically'tailored'to'the'individual'needs'of'this'group.'Accordingly,'it'aims'to'identify'the'core'tasks'carried'out'by'this'group,'fulfil'their'requirements'with'the'initial'implemented'interface,'then'use'this'prototype'interface'to'identify'areas'in'which'it'could'be'further'improved'in'the'future.''Methods:'In'order'to'identify'the'initial'core'requirements'of'the'group'a'series'of'informal'interviews'were'conducted.'Following'this,'a'working'interface'was'developed.'After'the'interface'was'complete,'it'underwent'a'process'of'user'testing'in'order'to'gauge'its'success'and'identify'areas'for'future'improvement.''Results:'The'primary'requirement'of'the'interface'was'that'is'enabled'researchers'to'easily'perform'a'compound'or'target'search'on'one'of'the'databases,'add'certain'restrictions'to'the'search,'view'the'results'in'table'form,'and'save'these'results'to'a'tab'delimited'text'file'for'later'use.'The'completed'system'fulfilled'these'requirements,'and'further'user'testing'was'successful'in'identifying'possible'areas'for'future'improvement.''Conclusions:'As'it'stands,'the'completed'interface'will'prove'useful'to'the'researchers'it'was'designed'for.'However,'user'testing'also'uncovered'several'areas'for'future'improvement.'More'research'and'development'is'now'required'in'order'to'further'develop'this'system.

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Table!to!Contents!

1.'Introduction'.....................................................................................................................................'5'1.1.'Background'and'Context'....................................................................................................'5'1.2.'The'Problem'............................................................................................................................'6'1.3.'Aims'and'Objectives'.............................................................................................................'7'

2.'Literature'Review'..........................................................................................................................'9'2.1.'Chemoinformatics'.................................................................................................................'9'2.2.'User'Experience'..................................................................................................................'13'2.3.'Technologies'.........................................................................................................................'16'

3.'Initial'Requirements'Analysis'...............................................................................................'20'3.1.'Methodology'.........................................................................................................................'20'3.2.'Results'.....................................................................................................................................'21'3.2.1.'Basic'User'Requirements'........................................................................................'21'3.2.2.'Advanced'Features'....................................................................................................'24'

4.'Implementation'...........................................................................................................................'26'4.1.'Overall'Design'......................................................................................................................'26'4.2.'Coding'Methodology'.........................................................................................................'38'4.3.'Specific'Features'.................................................................................................................'43'4.3.1.'Searching'.......................................................................................................................'43'4.3.2.'Autosuggest'..................................................................................................................'48'4.3.3.'Displaying'Returned'Results'.................................................................................'51'4.3.4.'Saving'Results'..............................................................................................................'52'4.3.5.'Other'JavaScript'..........................................................................................................'55'

5.'User'Testing'...................................................................................................................................'59'5.1.'Methodology'.........................................................................................................................'59'5.2.'Results'.....................................................................................................................................'59'

6.'Discussion'......................................................................................................................................'63'6.1.'Limitations'and'Weaknesses'.........................................................................................'63'6.2.'Future'Work'..........................................................................................................................'63'

7.'Conclusion'......................................................................................................................................'70'8.'References'......................................................................................................................................'72'9.'Appendices'.....................................................................................................................................'73'Appendix'I:'List'of'Fields'.........................................................................................................'73'Appendix'II:'Overall'File'Structure'......................................................................................'74'Appendix'III:'Adding'a'New'Database'...............................................................................'75'

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1..Introduction.

1.1..Background.and.Context.

The'importance'of'using'computational'methods'to'aid'decision'making,'reduce'costs,'and'accelerate'knowledge'acquisition'in'every'branch'of'the'hard'sciences'is'widely'acknowledged'and'continues'to'increase.'In'the'field'of'chemistry,'one'of'the'most'established'disciplines'in'this'regard'is'chemoinformatics.'' While'the'specific'methods,'processes,'and'problems'within'chemoinformatics'are'complex'and'wide'ranging,'its'ultimate'goal'is'to'support'chemists'in'the'design'and'development'of'new'drugs.'At'the'laboratory'stage,'drug'discovery'and'testing'is'an'expensive,'time'consuming,'and'often'slow'moving'process.'For'this'reason,'work'begins'with'the'mining,'analysis,'and'manipulation,'of'huge'databases'containing'millions'of'chemical'structures'and'related'information.'At'its'core,'the'purpose'of'this'initial'stage'to'reduce'the'actual'number'of'laboratory'tests'required,'and'the'process'of'doing'so'using'computational'methods'is'what'is'known'as'chemoinformatics.'' At'The'University'of'Sheffield’s'Information'School,'chemoinformatics'researchers'work'with'a'number'of'test'databases,'similar'to'those'used'by'pharmaceutical'companies,'in'an'attempt'to'write'and'test'algorithms'for'improving'searches,'speeding'up'the'retrieval'of'compounds'and'related'information,'and'reducing'the'size'of'the'datasets'returned'by'each'search.'Broadly'speaking,'what'these'researchers'aim'to'do'is'improve'the'efficiency'and'effectiveness'of'searches'before'they'are'carried'out'on'real'world'chemical'databases'in'the'initial'stage'of'drug'development.'

In'order'to'carry'out'their'work,'the'chemoinformatics'researchers'interrogate'their'test'databases'with'much'the'same'kinds'of'searches'as'chemists'working'on'real'world'databases.

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1.2..The.Problem.

At'present,'the'only'test'database'accessible'through'any'kind'of'user'interface'at'all'is'the'online'version'of'CHEMBL:'www.ebi.ac.uk/chembl.'Moreover,'CHEMBL'is'the'only'relational'database'and'thus'the'only'one'that'can'be'queried'through'the'structured'query'language'(SQL).'All'other'test'databases'used'by'researchers'at'The'Information'School'exist'only'as'single'flat'files.'As'such,'to'search'these'databases'and'extract'the'results'they'want'researchers'must'write'their'own'programs'using'Pipeline'Pilot'or'another'programming'language.'This'is'quite'an'awkward''process'for'carrying'out'something'that'could'quickly'be'performed'by'an'SQL'query.'' The'CHEMBL'online'database'and'interface,'on'the'other'hand,'is'a'useful'tool'because'it'not'only'allows'users'to'perform'SQL'queries,'but'also'to'carry'out'common'search'tasks'such'as'compound'and'target'searches'at'the'click'of'a'button.'All'users'need'do'is'enter'the'query'term'and'click'either'the'compound,'target,'or'assay'search'button,'in'much'the'same'way'as'with'a'standard'Web'search'engine.'Results'are'then'returned'in'table'form'which,'in'the'case'of'a'compound'search,'lists'the'various'properties'of'that'compound'such'as'its'weight,'number'of'rotatable'bonds,'and'so'on.'' While'the'online'CHEMBL'interface'makes'using'this'database'far'easier'than'any'of'the'others'it'is'nonetheless'unsuitable'for'researchers'at'The'Information'School.'The'reason'for'this'is'that'the'CHEMBL'database'is'regularly'updated'and'the'online'interface'only'accesses'the'latest'version.'The'chemoinformatics'researchers'are'primarily'PhD'students'and,'in'order'for'the'results'of'their'research'to'be'consistent,'it'is'important'that'the'CHEMBL'database'they'are'using'remains'the'same'throughout'the'course'of'their'PhD'(generally'3'to'4'years).'Moreover,'the'CHEMBL'online'interface'has'other'weaknesses'as'far'as'chemoinformatics'researchers'at'The'University'of'Sheffield'are'concerned.'On'the'one'hand,'the'interface'itself'contains'a'host'of'features'that'simply'would'not'be'used'by'these'researchers,'making'it'slower'than'it'could'be'to'navigate'the'system.'On'the'other'hand,'however,'it'is'easy'to'conceive'of'other'possible'features'that'would'be'useful'to'these'researches'that'are'not'available'within'this'interface.'The'same'is'true'of'the'information'

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returned'by'the'searches'because,'on'the'one'hand,'some'of'what'is'returned'is'simply'not'useful'to'these'researchers,'while'on'the'other'hand,'other'useful'information'contained'within'the'databases'is'omitted'from'the'basic'clickcofcacbutton'searches'already'mentioned.'A'final'problem,'which'is'equally'true'of'the'other'test'databases'after'they'have'been'accessed'with'Pipeline'Pilot'or'a'programming'language,'is'that'the'way'returned'information'is'presented'is'not'always'best'suited'to'the'kind'of'analysis'these'researchers'want'to'carry'out'with'the'returned'results.'

1.3..Aims.and.Objectives.

In'light'of'these'problems,'the'aim'of'this'dissertation'project'is'the'creation'of'a'fullycfunctional'interface'for'all'of'the'test'databases'used'by'chemoinformatics'researchers'at'The'University'of'Sheffield.'More'specifically,'this'interface'will'be'tailored'to'the'individual'needs'of'this'group.'As'such,'it'will'include'only'the'features'they'require,'support'the'queries'they'regularly'carry'out,'return'all'the'information'that'is'relevant'to'them'without'including'anything'that'is'not,'and'present'the'results'in'a'way'that'is'most'useful'to'the'kind'of'analysis'they'conduct.'Accordingly,'the'research'objectives'are'to:'

• Identify'the'basic'requirements'of'the'new'system'from'the'users'perspective,'such'as'the'kind'of'searches'they'typically'carry'out,'the'kind'of'information'they'want'returned,'and'how'they'want'that'information'to'be'displayed.''

• Identify'more'advanced'features'and'functionalities'users'would'like'of'the'new'system,'such'as'support'for'query'formulation.'

• Identify'the'basic'requirements'of'the'system'from'the'administrators'perspective,'such'as'maintainability'and'scalability.'

• Identify'the'core'technologies'required'to'implement'the'system'as'well'as'the'best'practices'for'doing'so.'

• Identify'the'core'principles'required'for'providing'users'with'the'best'possible'user'experience.'

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• Identify'areas'in'which'the'system'can'be'expanded'or'improved'in'the'future.'

• Provide'guidelines'for'how'the'administrator'can'expand'and'improve'the'system'in'the'future.

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2..Literature.Review.

2.1..Chemoinformatics.

The'term'chemoinformatics'is'relatively'new,'having'only'been'introduced'in'the'

late'1990s.'However,'early'studies'as'far'back'as'the'1950s'into'the'application'

of'various'computational'methods'for'searching'vast'databases'of'chemical'

molecules'and'predicting'their'properties'demonstrate'that'the'discipline'has'a'

far'longer'history'(Willet,'2011).'

Over'the'years'a'wealth'of'academic'literature'on'chemoinformatics'has'

built'up'and'numerous'commentators'have'attempted'to'define'it.'One'of'the'

most'commonly'cited'and'widespread'definitions'is'that'offered'by'F.'K.'Brown'

in'his'seminal'1998'paper'Chemoinformatics:/What/is/it/and/How/Does/it/Impact/

Drug/Discovery?'Here,'Brown'describes'chemoinformatics'as'follows:''

The'use'of'information'technology'and'management'has'become'a'critical'part'of'the'

drug'discovery'process.'Chemoinformatics'is'the'mixing'of'those'information'resources'

to'transform'data'into'information'and'information'into'knowledge'for'the'intended'

purpose'of'making'better'decisions'faster'in'the'area'of'drug'lead'identification'and'

organization'(Brown,'1998).'

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Two'other'widely'cited'definitions'include'the'far'broader'one'put'forward'by''

Johann'Gasteiger'and'Thomas'Engel'in'Chemoinformatics:/A/Textbook,'and'that'of'

Andrew'R.'Leach'and'Valerie'J.'Gillet'in'their'book'An/Introduction/to/

Chemoinformatics:''

Chemoinformatics'is'the'use'of'informatics'methods'to'solve'chemical'problems'

(Gasteiger'&'Engel,'2003).'

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Chemoinformatics'is'concerned'with'the'application'of'computational'methods'to'tackle'

chemical'problems,'with'a'particular'emphasis'on'the'manipulation'of'chemical'

structural'information'(Leach'&'Gillet,'2003).'

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Finally,'a'definition'that'proves'particularly'useful'for'the'present'study,'and'is'

cited'by'Leach'and'Gillet'on'the'first'page'of'their'book'along'with'Brown’s,'is'

that'of'G.'Paris:''

Chem(o)informatics'is'a'generic'term'that'encompasses'the'design,'creation,'

organisation,'management,'retrieval,'analysis,'dissemination,'visualisation'and'use'of'

chemical'information'(Paris,'1999).'

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What'we'can'see'from'all'these'definitions'is'that'chemoinformatics'is'concerned'

with'the'use'of'information'technology'or'computational'methods'to'help'

manage'chemical'structural'data.'Moreover,'its'objective'is'to'put'this'data'to'use'

in'the'service'of'working'chemists'by'helping'to'transform'it'into'usable'

information,'and'ultimately'knowledge,'that'will'help'them'make'better'

decisions'faster.'

From'this'definition'of'chemoinformatics,'and'an'understanding'of'its'

objectives,'the'question'remains'as'to'how'it'works'in'practice.'Two'of'the'most'

useful'texts'from'this'perspective'are'that'of'Leach'and'Gillet,'and'Gasteiger'and'

Engel.'Both'these'texts'provide'a'comprehensive'overview'of'chemoinformatics'

as'it'is'practiced'today,'including'its'methods,'the'problems'it'addresses,'and'the'

core'technologies'it'employs.'

' While'the'texts'themselves'cover'a'wide'range'of'different'research'areas,'

there'are'two'major'issues'that'dominate'chemoinformatics'for'these'authors.'

Moreover,'these'two'issues'are'equally'dominant'in'the'four'volume'opus,'

Handbook/of/Chemoinformatics,'edited'by'Gasteiger.'These'two'issues'are:'

1. The'representation'and'storage'of'chemical'compounds'and'related'

information'in'chemical'databases.'

2. The'retrieval'of'these'compounds'and'related'information'from'the'

databases.'

To'begin'with'then,'there'is'the'problem'of'how'to'represent'chemical'structures'

so'they'can'be'stored'in'databases'and'later'retrieved.'As'Gasteiger'and'Engel'

point'out,'unlike'other'scientific'disciplines'that'deal'only'with'textual'and'

numerical'data,'chemistry'has'the'problem'of'representing'and'storing'

molecules.'One'of'the'biggest'problems'here'is'that'while'“2D'graphical'

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representation'of'chemical'structures'in'structure'diagrams'can'be'considered'to'

be'the'universal'‘natural'language’'of'chemists”'(Gasteiger'&'Engel,'2003),'such'

image'files'are'not'particularly'useful'for'chemoinformatics'because'although'

they'do'“enable'the'structure'to'be'reproduced,'a'more'appropriate'

representation'is'required'if'the'molecule'is'to'be'stored'in'a'database'for'

subsequent'retrieval'and'search'based'on'its'chemical'structure”'(Leach'&'Gillet,'

2003).1'In'other'words,'we'need'a'way'to'represent'chemical'compounds'or'

structures'in'an'none'imagecbased'way.'Both'texts'point'to'the'same'options'

when'it'comes'to'doing'so:'

• Nomenclature'

• Graph'theoretic'representations'

• Connection'tables'

• Line'notations'

Nomenclature,'as'Gasteiger'and'Engel'point'out,'can'be'either'trivial'or'

systematic.'While'trivial'nomenclature'is'essentially'a'matter'of'the'trivial'names'

of'compounds,'e.g.'Aspirin'or'Heroin,'systematic'nomenclature'uses'rules'such'as'

the'IUPAC'system'to'describe'the'structure'in'detail'and'systematic'order,'e.g.'2c

acetoxycbenzoic'acid'='Aspirin.'With'graph'theoretic'representations,'on'the'

other'hand,'chemical'structures'are'represented'as'a'molecular'graph'that'

“represents'the'topology'of'a'molecule'only,'that'is,'the'way'the'nodes'(or'atoms)'

are'connected”'(Leach'&'Gillet,'2003).'Connection'tables'provide'an'alternative'

way'of'representing'a'molecular'graph.'Here,'lists'of'bonds'and'atoms'are'stored'

in'a'table,'while'hydrogen'atoms'are'omitted.'As'Leach'and'Gillet'point'out,'the'

inclusion'of'the'coordinates'of'atoms'allows'a'standard'2D'diagram'to'be'

reproduced'from'the'table.'Finally,'line'notations'represent'chemical'structures'

as'linear'strings'of'alphanumeric'characters.'The'most'commonly'used'line'

notation'is'SMILES,'which'is'a'highly'compressed'and'simplified'notation.'

However,'there'are'other'examples'of'line'notations'include'Wiswesser'(WLN),'

ROSDAL,'and'Sybl'(SLN).'For'reasons'we'shall'see'in'the'Requirements'Analysis,'

''''''''''''''''''''''''''''''''''''''''''''''''''''''''1'The'topic'of'3D'representations,'now'an'important'area'of'chemoinformatics,'is'beyond'the'scope'of'this'study.'

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line'notations'in'general,'and'SMILES'in'particular,'are'the'most'relevant'form'of'

representation'for'this'project.'

As'Leach'and'Gillet'point'out,'“to'construct'a'SMILES'string'one'needs'to'

‘walk’'through'the'chemical'structure'in'such'a'way'that'all'the'atoms'are'visited'

just'once”'(Leach'&'Gillet,'2003).'The'basic'rules'for'this'are'illustrated'by'

Gasteiger'and'Engel:'

1. Atoms'are'represented'by'their'atomic'symbols.'

2. Hydrogen'atoms'automatically'saturate'free'valences'and'are'omitted'(simple'hydrogen'

connection).'

3. Neighbouring'atoms'stand'next'to'each'other.'

4. Double'and'triple'bonds'are'characterized'by'“=”'and'“#”'respectively.'

5. Branches'are'represented'by'parentheses.'

6. Rings'are'described'by'allocating'digits'to'the'two'“connecting”'ring'atoms.'

(Gasteiger'&'Engel,'2003)'

The'result'in'the'case'of'Aspirin'could'be'OC(=OC)c1ccccc1OC(=O)C.'

As'both'texts'argue,'SMILES'are'easily'handled'by'computers'and'are'

particularly'suited'for'the'representation,'storage,'and'exchange'of'chemical'

structural'information.'One'of'the'major'issues'with'SMILES'however,'as'both'

texts'point'out,'is'that'there'is'generally'more'than'one'valid'way'of'representing'

a'molecule'in'SMILES'form'depending'on'which'atom'one'starts'with'and/or'the'

different'sequence'one'follows'through'the'molecule.'Given'that'these'

representations'should'not'only'be'unambiguous,'i.e.'a'particular'representation'

can'only'indicate'a'single'molecule,'but'also'unique,'i.e.'there'can'only'be'a'one'

representation'for'a'single'molecule'(Gasteiger'&'Engel,'2003),'the'process'of'

canonicalization,'whereby'computer'algorithms'are'used'to'make'noncunique'

representations'unique,'is'required.'As'both'text'point'out,'the'Morgan'algorithm'

is'an'example'that'generates'a'unique'SMILES'for'each'molecule.'

When'it'comes'to'searching,'both'texts'highlight'three'major'forms'of'

search:'

• Full'structure'(or'exact'match)'

• Substructure'

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• Similarity'

Full'structure'is'the'simplest'and'most'widely'used'form'of'search'and'involves'

retrieving'a'single'chemical'structure'from'the'database'along'with'various'

associated'information'such'as'its'boiling'point,'synthetic'roots,'patents,'number'

of'ring'bonds,'and'so'on.'

' Substructure'searching,'on'the'other'hand,'is'the'attempt'to'retrieve'all'

compounds'in'the'database'that'contain'the'substructure'entered'as'the'query.'

As'Gasteiger'and'Engel'put'it,'“substructure'searching'is'the'process'of'

identifying'parts'of''a'given'structure'that'are'equivalent'to'a'specific'query'

substructure”'(Gasteiger'&'Engel,'2003).'An'example'would'be'to'“identify'all'

structures'that'contain'a'particular'functional'group'or'sequence'of'atoms'such'

as'a'carboxylic'acid,'benzene'ring'or'C5'alkyl'chain”'(Leach'&'Gillet,'2003).'

' Finally,'similarity'searching'is'where'a'compound'is'used'as'the'query'

and'the'system'retrieves'all'the'compounds'that'are'similar'to'it'in'order'of'

closest'match'first.'As'Gasteiger'and'Engel'point'out,'this'provides'the'ability'for'

“finding'the'right'chemicals'for'one’s'needs,'even'if'one'does'not'know'exactly'

what'one'is'looking'for”'(Gasteiger'&'Engel,'2003).'

2.2..User.Experience.

One'of'the'most'widely'used'texts'on'user'experience,'at'least'from'a'

practitioners'point'of'view,'is'Jesse'James'Garrett’s'The/Elements/of/User/

Experience:/UserDCentred/Design/for/the/Web/and/Beyond.'In'this'book,'Garrett'

defines'user'experience'as'“the'experience'the'product'creates'for'the'people'

who'use'it'in'the'real'world”'and'identifies'its'two'overall'concerns'as'“how'it'

works”'and'“what'it'is'like'to'use”'(Garrett,'2011).''

While'user'experience'is'certainly'about'how'a'site'behaves'and'looks,'

Garrett'is'quick'to'distinguish'it'from'both'the'features'and'functionality'

themselves,'i.e.'the'site'or'application’s'inner'workings,'and'the'raw'aesthetics.'

In'his'example'of'coffee'maker,'functionality'is'matter'of'making'sure'pressing'

the'button'actually'makes'the'coffee,'while'aesthetics'ensures'the'button'is'an'

appealing'shape'and'texture.'User'experience,'on'the'other'hand,'is'always'a'

matter'of'context,'and'in'this'example'is'about'asking'questions'like:'“Is'the'

button'too'small'for'such'an'important'function?”'and'“Is'the'button'in'the'right'

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place'relative'to'the'other'controls'the'user'would'be'using'at'the'same'time?”'

(Garrett,'2011).'

Garrett'situates'user'experience'in'the'history'of'userccentered'design,'

which'he'defines'as'taking'“the'user'into'account'every'step'of'the'way'as'you'

develop'your'product”'(Garrett,'2011).'Every'design'element'here'should'be'the'

result'of'a'conscious'decision'on'the'part'of'the'designer,'and'the'kinds'of'

question'the'designer'should'be'asking'are:'“Is'it'hard'to'do'simple'things?'Is'it'

easy'to'figure'out?'How'does'it'feel'to'interact'with'the'product?”'(Garrett,'

2011).'This'definition'is'in'accordance'with'other'well'recognised'writers'on'

user'experience'such'as'Jakob'Nielsen,'who'states'that'“user'experience'

encompasses'all'aspects'of'the'end'user’s'interaction'with'the'company”'and'that'

“the'first'requirement'for'an'exemplary'user'experience'is'to'meet'the'exact'

needs'of'the'customer,'without'fuss'or'bother”'(Nielsen'&'Norman,'n.d.).''

More'practically,'Garrett'says'that'in'order'to'achieve'a'successful'user'

experience'we'must'pay'attention'to'the'elements'of'user'experience,'which'he'

formulates'as'the'five'interrelated'planes'of'the'design'process.'These'planes'are:'

The'strategy/plane,'which'is'a'matter'of'user'needs'and'the'objectives'of'

the'site'or'application'and'its'owners.'

The'scope/plane,'which'is'about'defining'the'functionality'of'the'site,'i.e.'it'

is'a'matter'of'what'features'and'functions'are'to'be'included'in'the'site'or'

application.'

The'structure/plane,'which'is'about'how'the'features'and'functions'

determined'in'the'previous'plane'fit'together.'Broadly,'this'plane'is'about'the'

way'options'will'be'presented'to'the'user,'and'includes'both'interaction'design,'

which'is'about'“the'options'involved'in'performing'and'completing'tasks”,'and'

information'architecture,'which'is'about'“the'options'involved'in'conveying'

information'to'the'user”'(Garrett,'2011).'Interaction'design'here'is'particularly'

concerned'with'“understanding'people–the'way'they'think'and'behave”'and'

“building'this'understanding'into'the'structure'of'our'product”'(Garrett,'2011).'

The'skeleton/plane,'which'is'about'interface'and'information'design,'and'

is'broadly'a'matter'of'where'the'features'such'as'button'and'controls,'as'well'as'

information'such'as'blocks'of'text,'are'placed.'Ultimately,'this'is'about'how'the'

arrangement'of'interface'elements'and'information'can'allow'users'to'interact'

' 15'

more'easily'with'the'system.'On'this'plane,'consistency'is'key,'both'in'relation'to'

other'sites'users'are'already'familiar'with'and'the'internal'consistency'of'the'site'

itself.'

The'surface/plane,'which'is'about'the'“sensory'experience'of'the'user”,'

particularly'the'site’s'visual'design'(Garrett,'2011).'What'we'should'be'

concerned'with'here'is'making'clear'distinctions'between'the'features,'functions,'

and'information.'On'this'plane,'uniformity'is'key.'

While'Garratt’s'approach'offers'an'overall'guideline'for'user'experience'

and'the'userccentered'design'process'as'a'whole,'numerous'other'authors,'such'

as'Steve'Krug'in'Don’t/Make/Me/Think:/A/Common/Sense/Approach/to/Web/

Usability/and'Jeff'Johnson'in'Web/Bloopers:/60/Common/Web/Design/Mistakes/and/

How/to/Avoid/Them,'offer'a'far'more'detailed'breakdown'of'the'rules'and'best'

practices'needed'to'achieve'this.'Examples'of'such'practices'include:'how'to'

create'a'visual'hierarchy,'how'to'make'obvious'what'is'clickable,'and'how'to'

design'good'navigation'(Krug,'2006),'as'well'as'how'to'create'site'identity,'

where'to'place'labels'and'buttons,'and'the'right'size'text'and'font'to'use'

(Johnson,'2003).'

' On'the'other'hand,'however,'other'authors'restrict'themselves'to'focusing'

on'the'userccentered'methodology'itself'that'underpins'Garrett’s'entire'

approach,'i.e.'on'how'to'ensure'that'users'are'the'centre'of'the'entire'process'

right'from'the'beginning.'An'interesting'example'of'this'is'put'forward'by'Peter'

Wright'and'John'McCarthy'in'ExperienceDCentered/Design:/Designers,/Users,/and/

Communities/in/Dialogue.'In'their'approach'to'userccentered'design,'Wright'and'

McCarthy'try'to'break'with'the'scientific'approach'to'studying'users'in'favor'of'a'

more'embedded'and'holistic'approach.'This'approach'is'a'concrete,'rather'than'

general'and'abstract'one,'and'they'accordingly'place'a'heavy'emphasis'on'

context,'asking''“what'the'eventual'endcusers'of'the'system'actually'want'the'

system'to'do'for'them'[…]'and'how'those'endcusers'actually'get'their'work'one'

at'present”'(Wright'&'McCarthy,'2010).'What'they'are'aiming'at'here'is'

“capturing'people’s'actual'activity”'within'the'system'(Wright'&'McCarthy,'

2010).'

' The'two'central'components'for'success'according'Wright'and'McCarthy'

are'dialogue'and'an'iterative'design'process.'Dialogue'begins'with'the'

' 16'

interviews,'and'should'be'relatively'unstructured,'thus'allowing'users'to'

describe'the'lived'experience'of'their'current'work'processes'and'thoughts'

about'the'new'system.'The'aim'here'is'for'the'interviewer'to'let'the'users'tell'

their'story'as'much'as'possible,'and'simply'encourage'them'or'ask'a'few'followc

up'questions'for'clarification.'This'dialogue'continues'throughout'the'iterative'

design'and'implementation'process,'during'which'prototypes'are'revised'and'

referred'to'the'users'for'ongoing'feedback.'The'overall'aim'here,'they'claim,'is'“a'

seamless'transition'from'the'formative'evaluation'of'design'concepts'to'the'

summative'evaluation'of'the'finished'product”'(Wright'&'McCarthy,'2010).'

2.3..Technologies.

In'Learning/PHP,/MySQL,/JavaScript/&/CSS,'Robin'Nixon'provides'an'overview'of'

the'core'technologies'needed'for'creating'servercside,'databasecdriven,'dynamic'

websites.'While'there'are'several'options'when'it'comes'to'which'technologies'to'

use,'Nixon'argues'that'one'of'the'most'robust,'scalable,'easy'to'use,'powerful,'

and'commonly'implemented,'is'the'PHP,'MySQL,'and'Apache'combination.''

In'order'to'understand'this'combination'and'how'the'technologies'work'

together,'it'is'necessary'to'understand'the'clientcserver'architecture'and'the'

processes'involved'in'making'a'request'to'a'dynamic'web'page,'which'Nixon'

describes'as'follows:'

1. You'enter'http://server.com/into'your'browser’s'address'bar.'

2. Your'browser'looks'up'the'IP'address'for'server.com.'

3. Your'browser'issues'a'request'to'that'address'for'the'web'server’s'homepage.'

4. The'request'crosses'the'Internet'and'arrives'at'the'server.com'web'page.'

5. The'web'server,'having'received'the'request,'fetches'the'homepage'form'its'hard'disk.'

6. With'the'homepage'now'in'memory,'the'web'server'notices'that'it'is'a'file'incorporating'

PHP'scripting'and'passes'the'page'to'the'PHP'interpreter.'

7. The'PHP'interpreter'executes'the'PHP'code.'

8. Some'of'the'PHP'contains'MySQL'statements,'which'the'PHP'interpreter'now'passes'to'

the'MySQL'database'engine.'

9. The'MySQL'database'returns'the'results'of'the'statement'back'to'the'PHP'interpreter.'

' 17'

10. The'PHP'interpreter'returns'the'results'of'the'executed'code,'along'with'the'results'from'the'MySQL'database,'to'the'web'server.'

11. The'web'server'returns'the'page'to'the'requesting'client,'which'displays'it.'

(Nixon,'2012).'

In'this'combination'then,'MySQL'is'the'relational'database'management'system'(RDMS)'that'manages'the'data'and'“offers'just'about'anything'a'website'might'need'in'order'to'find'and'serve'up'data'to'browsers”'(Nixon,'2012).'As'a'relational'database,'the'data'within'it'is'organised'into'tables,'rows,'and'columns'that'can'be'queried'using'structured'query'language'(SQL).'As'Luke'Welling'and'Laura'Thomson'point'out'in'PHP/and/MySQL/Web/Development,'this'approach'“provides'far'faster'access'to'data'than'flat'files”'and'“can'be'easily'queried'to'extract'data'that'fit'certain'criteria”'(Welling'&'Thomson,'2009).'PHP,'by'contrast,'is'the'servercside'scripting'language'that'handles'all'the'main'work'on'the'server,'such'as'retrieving'the'data'in'the'database,'storing'it,'and'manipulating'it'for'use'in'the'site.'In'fact,'it'can'handle'almost'any'interaction'with'the'databases'that'is'required'for'building'a'dynamic'site.'Finally,'both'these'technologies'run'on'the'popular'opencsource'Apache'web'server.'

In'addition'to'these'core'servercside'technologies,'Nixon'describes'how'CSS'is'used'to'deal'with'the'presentation,'while'JavaScript'adds'dynamic'user'interaction'to'this'presentation'and'is'thus'“the'power'behind'dynamic'web'pages'that'change'in'front'of'your'eyes'rather'than'when'the'server'returns'a'new'page”''(Nixon,'2012).'Moreover,'we'can'also'add'AJAX'to'this'mix.'AJAX'is''a'“development'technique”'that'uses'JavaScript'to'transfer'data'between'the'browser'and'the'server”'behind'the'scenes'(Nixon,'2012).'In'other'words,'it'can'download'data'from'the'server'without'requesting'a'new'page,'as'would'be'required'if'a'servercside'scripting'language'were'doing'the'work.'This'“substantially'reduces'the'amount'of'data'that'must'be'sent'back'and'forth'and'makes'web'pages'seamlessly'dynamic,'allowing'them'to'behave'more'like'self'contained'applications”'(Nixon,'2012).''' Perhaps'more'important'than'the'specific'technologies'themselves,'however,'are'the'methods,'standards,'and'best'practices'that'govern'their'use.'All'programming'is'governed'by'standards'and'best'practices,'and'there'are'

' 18'

many'sites,'blogs,'and'forums'documenting'them,'such'as:'www.php.net,'

www.w3schools.com,'and'www.stackoverflow.com,'to'name'a'few.'To'take'one'

example,'the'www.corephp.com'blog'contains'an'article'listing'the'20'best'

practices'to'follow'when'writing'PHP,'which'includes:'always'documenting'your'

code;'never'using'short'tags'when'including'PHP'code;'always'using'meaningful'

variable'and'function'names,'and'so'on'(Roy,'2013).''

' In'addition'to'such'standards'and'best'practices,'Nixon'also'draws'

attention'to'the'underlying'methodologies'or'approaches'to'writing'PHP'code.'

The'first'choice'to'be'made'is'between'dropping'PHP'code'into'HTML'code'vs.'

writing'everything'in'PHP'and'echoing'the'HTML'from'within'the'PHP'tags.'As'

Nixon'points'out,'this'choice'is'really'down'to'the'preference'of'the'programmer,'

however,'the'modular'approach'that'he'touches'on'next'is'best'practice'and'

should'always'be'used,'especially'for'large'sites.'Nixon'argues'that'while'it'is'

possible'to'create'an'entire'site'using'a'single'PHP'file'it'should'be'avoided'

because'as'the'code'grows'the'file'can'become'incredibly'large'and'complex'

making'it'difficult'to'read'and'maintain.'With'the'modular'approach,'we'instead'

split'the'project'into'“sensible'sections'of'PHP'code,'each'one'selfccontained”'

(Nixon,'2012).'Examples'of'such'sections'could'include'one'file'for'logging'in,'

one'for'the'database'connection,'one'for'dealing'with'sessions,'and'so'on.'What'

this'also'means'is'that'whenever'the'code'in'one'of'these'sections'is'required'

anywhere'else'in'the'project'it'can'simply'be'included'with'one'line'of'code,'thus'

eliminating'duplication.'Welling'and'Thomson'describe'the'importance'of'such'

an'approach'in'more'detail,'arguing'that'this'DRY'(Don’t'Repeat'Yourself)'

approach'leads'to'“more'consistent,'reliable,'maintainable'code,'with'less'effort”'

and'ensures'that'changes'to'one'section'will'automatically'apply'to'every'

instance'it'is'used'(Welling'&'Thomson,'2009).'In'addition,'they'point'out'that'

this'approach'should'also'be'taken'in'regard'to'large'sections'of'HTML'code'that'

appear'on'multiple'pages,'such'as'the'header'and'footer,'so'that'changes'only'

ever'have'to'be'made'once'and'in'one'place.''

' Taking'things'to'the'next'level,'the'next'approach'would'be'to'

functionalise'the'PHP'code.'As'Welling'and'Thomson'aptly'describe'them,'

“functions'exist'in'most'programming'languages'and'separate'code'that'

performs'a'single,'well'defined'task”'(Welling'&'Thomson,'2009).'Examples'

' 19'

could'be'a'particular'query'to'the'database,'checking'the'success'of'any'query,'or'salting'a'password.'The'best'practice'here,'for'both'Welling'and'Thomson,'Nixon,'and'almost'all'the'other'literature,'is'to'place'these'functions'in'a'functions.php'file'and'call'them'when'necessary.'This'approach'also'follows'the'DRY'method'of'programming'and'inherits'all'its'advantages.'As'Nixon'points'out,'functionalising'the'code'also'decreases'the'loading'time'of'files,'and'their'execution'time,'because'each'function'is'only'complied'once'no'matter'how'many'times'it'is'called'(Nixon,'2012).'Moving'on'from'functions,'there'is'the'objectcoriented'approach,'which'takes'the'concept'of'DRY'and'functions'to'the'next'level.'However,'this'methodology'is'beyond'the'scope'of'this'study.'

It'is'important'to'note'that'apart'from'the'optional'choice'of'including'PHP'in'the'HTML'vs.'echoing'the'HTML'from'PHP,'these'approaches'do'not'exclude'each'other'and'should'be'used'in'combination.'''''''''' '''''

' 20'

3..Initial.Requirements.Analysis.

3.1..Methodology.

Interviews'were'the'chosen'methodology'for'gathering'the'initial'user'

requirements.'The'aim'of'these'interviews'was'to'build'up'an'overall'picture'of'

how'chemoinformatics'researchers'currently'work,'the'kinds'of'task'they'carry'

out,'and'what'they'would'like'to'be'able'to'do'with'the'new'system.'

Methods'available'for'acquiring'this'information'were:'questionnaires,'

formal'interviews,'and'informal'interviews.'Given'that'the'first'step'was'to'build'

up'a'general'picture'of'what'researchers'wanted'from'the'new'system,'

questionnaires'were'ruled'out.'It'was'decided'that'asking'specific'questions,'

with'only'limited'knowledge'of'the'working'practices'of'the'group'would'be'of'

little'benefit.'Formal'interviews,'perhaps'involving'recordings'and'

transcriptions,'were'also'ruled'out'on'the'grounds'that'they'would'be'at'odds'

with'the'incremental'method'whereby'the'researchers'could'continue'to'offer'

suggestions'throughout'the'oncgoing'development'of'the'system.'Informal'

interviews'were'therefore'selected.'

This'method'allowed'for'a'dialogue'approach,'however,'a'set'of'basic'

questions'were'also'used'to'guide'the'interviews.'Key'questions'asked'of'each'of'

the'participants'were'as'follows:'

• Which'of'the'test'databases'do'you'commonly'use?'

• What'are'the'main'types'of'search'you'need'to'be'able'to'perform'with'

the'new'system?'

• What'kind'of'restrictions'would'you'like'to'include'in'the'searches'prior'

to'the'results'being'returned?'

• What'data/fields'do'you'want'returned'for'each'of'these'searches?'

• How'do'you'want'the'returned'information'to'be'displayed?'

• What'further'features'would'be'helpful'when'it'comes'to'retrieving'the'

desired'information?'

' 21'

• What'would'you'like'to'be'able'to'do'with'the'returned'data'and'what'

further'features'would'be'helpful'for'doing'this?'

• Are'there'any'other'suggestions'or'features'you'would'like'to'see'

included?'

Throughout'the'interviews,'researchers'were'encouraged'to'demonstrate'how'

they'currently'use'the'test'databases.'They'were'also'informed'that'they'could'

offer'additional'ideas'they'thought'of'later'at'any'time.'

' This'research'has'been'deemed'“low'risk”'by'the'Information'School'

research'panel'of'The'University'of'Sheffield.'The'Certificate'of'Approval'and'

other'documentation'can'be'found'after'the'Appendixes.'

3.2..Results.

3.2.1..Basic.User.Requirements.

The$Databases$

The'test'databases'most'frequently'used'by'researchers'are'CHEMBL,'MDDR,'

Wombat,'and'MUV.'Other'databases'considered'were'Drug'Bank'and'NCI.'In'the'

end,'it'was'decided'that'given'the'time'restrictions'and'lack'of'current'use'of'

these'databases'it'was'best'not'to'include'them'and'spend'the'time'developing'

other'aspects'of'the'system'that'would'be'more'widely'used.'However,'it'became'

evident'that'an'additional'requirement'should'be'that'it'is'easy'for'the'

administrator'to'add'new'databases'to'the'system'if'required'at''later'date'(for'

instructions'on'how'to'add'a'new'database'see'Appendix'III).'

Common$Search$Tasks$

The'two'most'common'search'tasks'performed'by'researchers'were:'

1. The'search'for'a'specific'single'compound'and'its'related'information.'

2. The'search'for'all'compounds'that'have'been'found'to'be'active'against'a'

given'target.'

' 22'

These'two'searches'are'the'most'important'tasks'that'researchers'require'of'the'

new'system'in'general,'and'ultimately'the'primary'purpose'of'the'system'as'a'

whole'should'be'to'support'them.'

' Firstly'then,'the'most'basic'of'the'two'is'the'search'for'a'particular'

compound.'The'main'question'here'was'simply'which'fields'do'researchers'want'

to'use'in'order'to'identify'and'retrieve'the'compounds.'Depending'on'the'given'

database'there'were'several'options'here'because'there'are'several'fields'that'

uniquely'identify'a'compound.'The'most'obvious'examples'included:'common'

names,'such'as'Aspirin;'IUPAC'names,'such'as'5chydroxyc2Hcisoquinolinc1cone;'

and'SMILES.'All'researchers'who'participated'stated'that'the'primary'way'they'

wanted'to'be'able'to'search'for'compounds'was'by'their'SMILES,'and'none'of'

them'needed'to'search'by'their'common'or'IUPAC'name.'SMILES'were'thus'

selected'as'the'sole'means'by'which'users'could'search'for'a'given'compound.'

However,'in'the'case'of'CHEMBL,'several'researchers'stated'they'would'find'it'

useful'to'be'able'to'search'for'a'compound'by'its'CHEMBL'id,'which'was'

therefore'included'as'an'option'for'this'database.'

' Secondly,'the'most'important'of'the'two'searches'from'the'researchers'

perspective'was'the'ability'to'search'for'all'compounds'found'to'be'active'against'

a'given'target'(i.e.'a'given'active'class).'In'short,'what'researchers'need'to'be'able'

to'do'here'is'search'for'a'given'target,'e.g.'thrombin,'and'return'all'the'

compounds'that'have'been'found'to'be'active'against'it.'This'time,'researchers'

simply'wanted'to'be'able'to'search'using'the'name'of'the'specific'target,'expect'

in'the'case'of'CHMEBL'were'a'specific'CHEMBL'id'for'each'target'was'also'

identified'as'a'useful'field'to'be'able'to'search'by.'As'will'be'seen'in'the'section'

on'implementing'the'target'search,'the'field'identifying'the'name'of'a'specific'

target'has'a'different'title'depending'on'the'database'in'question.'

Restricting$the$Search$

In'the'case'of'the'MDDR'and'MUV,'the'information'available'in'the'databases'

meant'the'target'search'would'be'relatively'straightforward:'users'could'simply'

select'the'target'and'search'for'the'compounds'found'to'be'active'against'it.'

However,'the'information'contained'in'the'CHEMBL'and'Wombat'databases'

allowed'for'further'restrictions'prior'to'returning'the'results'from'the'search.'

' 23'

' In'the'case'of'Wombat,'researchers'wanted'to'be'able'to'restrict'their'search'to'a'specific'target'organism,'e.g.'humans,'rats,'mice,'and'so'on.'In'other'words,'they'not'only'wanted'to'select'the'target'and'have'the'compounds'that'had'been'found'active'against'it'retrieved,'but'also'restrict'the'results'to'include'only'those'done'on'a'particular'organism.'Ideally,'they'wanted'to'be'able'to'do'this'prior'to'any'results'being'returned.'' In'the'case'of'CHEMBL,'by'far'the'largest'of'all'the'test'databases'both'in'terms'of'the'number'compounds,'tables,'and'amount'of'related'information,'there'were'several'ways'in'which'researchers'wanted'to'be'able'to'restrict'their'search.'To'begin'with,'they'again'wanted'to'be'able'to'restrict'the'search'to'a'specific'target'organism.'In'addition,'however,'they'also'wanted'to'specify'the'type'of'assay'carried'out,'e.g.'IC50,'MIC,'Ki,'and'so'on.'The'result'of'these'two'restrictions'would'be'that'for'a'particular'target'researchers'could'select'the'type'of'assay'(or'test)'as'well'as'the'target'organism,'and'return'only'the'results'that'matched'these'criteria.'Moreover,'an'assay'has'score,'and'different'researchers'will'count'it'as'a'positive'hit'if'it'is'above'a'certain'threshold.'As'such,'researchers'wanted'to'restrict'the'search'by'specifying'the'threshold'for'each'of'the'assay'types'they'had'already'included'and,'finally,'to'set'the'overall'confidence'score'for'all'the'results.'Again,'they'wanted'to'do'this'prior'to'any'results'being'returned.'

Returned$Information$

When'displaying'the'results,'all'researchers'agreed'that'this'should'be'done'in'table'form,'as'is'typical'of'results'returned'from'a'database.'In'addition,'they'all'wanted'some'way'of'identifying'how'many'entries'had'been'returned'from'the'search'without'having'to'manually'count'the'rows,'which'would'be'impractical'given'the'number'of'results'could'run'into'several'thousand'for'certain'searches.'' When'it'came'to'which'fields'should'be'returned,'there'was'a'huge'difference'in'what'individual'researchers'wanted.'However,'there'were'clearly'many'fields'that'none'of'them'found'necessary.'The'complete'list'of'fields'necessary'to'satisfy'all'researchers'for'each'database'and'type'of'search'can'be'found'in'Appendix'I.'Given'the'large'differences'in'the'fields'individual'researchers'wanted'returned,'the'amount'of'fields'required'to'satisfy'all'

' 24'

researchers,'and'the'fact'that'researchers'did'not'want'to'have'to'work'around'

unnecessary'fields,'it'was'suggested'that'it'may'be'possible'to'include'a'function'

that'allowed'them'to'toggle'off'the'fields'they'did'not'require'after'the'results'

had'been'returned.'All'researchers'agreed'that'this'would'be'the'ideal'situation.'

Moreover,'it'became'evident'that'another'requirement'should'be'that'it'is'easy'

for'the'administrator'to'add'other'fields'if'this'became'necessary.'

3.2.2..Advanced.Features.

Autosuggest$

One'of'the'first'advanced'features'suggested'by'researchers'was'an'autosuggest'

function'when'entering'a'target'search.'Given'the'vast'number'of'possible'targets'

contained'in'the'databases,'which'runs'in'to'the'hundreds'of'thousands'in'some'

cases,'as'well'as'the'length'and'complexity'of'some'of'their'names,'e.g.'tcbox'

transcription'factor'tbx5,'all'of'which'has'to'be'exactly'typed,'it'was'believed'that'

such'a'feature'would'greatly'improved'the'efficiency'of'their'work.'In'addition,'

researchers'also'wanted'this'feature'to'allow'them'to'scroll'down'and'select'a'

particular'autosuggested'result'as'it'appeared.'

' Because'the'compound'searches'are'conducted'using'SMILES,'this'feature'

was'only'though'necessary'for'target'searches,'though'it'was'deemed'necessary'

for'all'databases.'Researchers'do'not'know'which'SMILES'relate'to'which'

compounds,'and'would'almost'exclusively'enter'the'SMILES'in'the'compound'

search'by'copying'and'pasting'them'from'somewhere'else'rather'than'typing'

them.'

Save$Results$

The'advanced'feature'that'researchers'felt'was'most'important'was'the'ability'to'

save'the'results'of'a'given'search.'That'is,'once'a'search'has'returned'a'table'of'

results,'they'wanted'to'be'able'to'save'this'table'and'all'the'results'for'future'use.'

Moreover,'they'wanted'to'be'able'to'use'this'saved'data'with'other'programs'

such'as'Pipeline'Pilot,'Excel,'Access,'and'so'on.'For'this'reason,'they'wanted'it'to'

be'in'a'plain'text'document'and'tab'delimited'format.'

' 25'

Show$Query$

One'researcher'suggested'it'would'be'useful'to'be'able'to'see'the'SQL'of'the'

query'they'had'just'conducted.'When'asked'about'this'feature,'many'other'

researchers'agreed'this'would'be'a'very'useful'function.'However,'given'these'

queries'could'sometimes'be'long,'running'into'several'lines,'it'was'important'

that'these'were'not'displayed'all'the'time'so'they'did'not'in'the'way'of'viewing'

the'results.'

Chembl$Information$

Each'target'in'the'CHEMBL'database'contains'a'host'of'related'information,'such'

as'associated'bioactivities'and'compound'properties.'When'using'the'CHEMBL'

interfaced'itself,'this'can'be'accessed'by'clicking'on'the'chembl_id'for'the'given'

target'and'being'hyperlinked'to'that'target’s'Target'Report'Card'where'this'

information'is'displayed'in'graphical'form.'After'a'target'search'on'the'CHEMBL'

database'had'been'implemented,'one'researcher'suggested'that'a'similar'link'to'

these'pages'would'be'a'useful'feature.'

' 26'

4..Implementation.

4.1..Overall.Design.

The'first'task'users'need'to'be'able'to'perform'after'logging'into'the'system'is'to'select'the'database'they'want'to'use.'Accordingly,'the'welcome'screen'presents'them'with'a'dropdown'menu'at'the'top'left'of'the'page.'Additionally,'the'logout'button'is'clearly'displayed'at'the'top'right'along'the'same'bar'(Figure'1).''

Figure'1''After'selecting'the'database,'users'are'taken'to'its'homepage.'This'page'features'a'coloured'bar'with'a'search'box'and'a'button'for'the'two'kinds'of'search'(Figures'2c5).'So'that'the'user'can'easily'identify'the'database'they'are'using,'a'different'coloured'search'bar'has'been'implemented'for'each.'Further,'to'reinforce'this,'hovering'over'the'name'of'each'database'in'the'dropdown'menu'turns'turn'it'the'same'colour'as'its'search'bar'(Figure'1'and'5).'''

' 27'

Figure'2''

'Figure'3'

' 28'

Figure'4''

'Figure'5'

'As'can'be'seen,'the'main'dropdown'menu'and'login'bar'appear'on'every'page.'This'allows'users'to'select'a'different'database'and'be'taken'to'its'homepage'no'matter'where'they'are'in'the'system.'

In'accordance'with'the'Results'of'the'Initial'Requirements'Analysis,'the'overall'system'is'built'around'two'fundamental'tasks:'a'compound'search,'i.e.'the'search'for'a'specific'compound'and'its'related'information;'and'a'target'search,'i.e.'the'search'for'all'compounds'that'have'been'found'active'against'a'

' 29'

given'target.'In'keeping'with'Nielsen’s'assertion'that'the'aim'of'a'system'is'to'

“meet'the'exact'needs'of'the'customer,'without'fuss'or'bother”'(Nielsen'&'

Norman,'n.d.),'the'homepage'for'each'database'simply'displays'a'search'box'and'

buttons:'one'for'initiating'a'compound'search'and'the'other'for'initiating'a'target'

search'(Figure'2c5).'And,'in'order'to'keep'things'simple,'the'same'search'box'is'

used'for'both'types'of'query.'Additionally,'the'homepage'displays'a'message'in'

the'centre'of'the'screen'telling'users'the'fields'they'can'use'to'perform'each'type'

of'search.'Finally,'the'coloured'search'bar'is'displayed'on'each'page'for'the'given'

database'so'that'no'matter'where'users'are'they'can'initiate'a'new'search'of'the'

database'they'are'currently'using'(Figures'2c5).'

In'accordance'with'the'Results'of'the'Requirements'Analysis,'an'

autosuggest'feature'has'been'implemented'for'the'target'search'(Figure'6).'

'

'Figure'6'

'

This'feature'works'in'such'a'way'that'the'possible'matches'are'refined'as'users'

type'more'characters'into'the'query'box.'At'any'point,'the'user'may'scroll'up'or'

down'the'results'using'the'up'and'down'arrows'on'the'keyboard,'and'a'grey'

highlight'indicates'which'result'they'are'currently'on.'If'the'user'presses'the'

return'key'on'their'keyboard,'the'result'they'are'currently'on'fills'out'the'query'

box.'If'there'are'no'matching'results'corresponding'to'what'the'user'has'entered,'

the'message'“No'target'found”'is'displayed.'

' 30'

' In'order'to'maintain'consistency'across'the'site,'which'was'identified'as'key'in'the'literature'on'user'experience,'all'the'designs'and'feature'so'far'described'are'the'same'across'each'database.'The'only'distinguishing'features'are'the'colour'of'the'search'bar,'the'database'name'in'the'query'box,'and'the'specific'message'stating'which'fields'can'be'used'to'conduct'a'search.''' When'it'comes'to'conducting'a'compound'search,'consistency'has'once'again'been'maintained'across'the'results'pages'of'each'of'the'databases'(Figures'7c10).''

'Figure'7'

'

' 31'

Figure'8''

'Figure'9'

'

' 32'

'

Figure'10'

'

The'only'difference'is'the'specific'columns'displayed'for'each'database'and,'

accordingly,'the'columns'that'can'be'toggled'on'or'off.'

' The'features'on'each'databases'compound'results'page'show'how'the'

displayed'information'meets'the'Results'of'the'Initial'Requirements'Analysis.''

' To'begin'with,'returned'results'are'displayed'table'form.'Because'some'

databases'contained'many'fields'researchers'may'need,'17'for'Wombat'(Figure'

9),'the'tables'were'too'wide'for'most'screen'sizes.'In'order'to'address'this'

problem,'the'ability'to'scroll'horizontally'on'for'all'tables'has'been'implemented'

(Figure'11).'

'

' 33'

'Figure'11'

'Other'features'include'displaying'how'many'results'have'been'returned'(bottom'left'of'the'table),'the'ability'to'select'how'may'results'are'returned'per'page'(top'left'of'the'table),'and'a'tab'for'navigating'from'one'page'of'results'to'the'next'(bottom'right'of'the'table).'Finally,'a'search'box'(top'right'of'the'table)'allows'users'to'narrow'the'results'by'entering'a'query'that'is'applied'across'all'fields,'while'arrows'at'the'top'of'each'column'enable'researchers'to'order'the'results'alphabetically'or'by'highest/lowest'number.'While'some'of'these'features'were'not'specifically'requested,'it'was'again'believed'they'might'prove'useful'in'helping'researchers'narrow'their'results.'' In'addition'to'the'table'itself,'three'other'features'identified'in'the'Initial'Requirements'Analysis'as'important'to'researchers'have'been'implemented.'Firstly,'there'is'the'ability'to'toggle'any'of'the'columns'off'and'on.'As'can'be'seen,'the'fields'that'are'on'are'displayed'blue,'while'deselected'ones'are'greyed'out'(Figure'12).'''

' 34'

'Figure'12'

'Secondly,'there'is'the'ability'to'show'and'hide'the'SQL'of'the'query'that'has'just'been'executed'for'the'search.'As'can'be'seen'(Figure'12),'this'is'displayed'by'default,'however,'it'can'be'hidden'to'allow'more'space'on'the'page'for'viewing'results'(Figure'13).''

'Figure'13'

'Finally,'there'is'the'ability'to'save'the'results,'which'was'a'feature'researchers'identified'as'being'particularly'important.'The'button'to'save'the'results'is'

' 35'

located'at'bottom'left'of'the'table,'just'below'where'the'number'of'returned'

results'are'displayed'(Figure'11).'In'accordance'with'the'Initial'Requirements'

Analysis,'the'results'are'saved'as'a'plain'text'file'in'tab'delimited'format'(Figure'

14).'

'

'Figure'14'

'

As'can'be'seen'from'their'titles,'the'saved'text'siles'are'automatically'named'

according'to'the'date'and'time'they'were'created'(Figure'15).'Moreover,'these'

files'are'automatically'saved'to'a'folder'on'the'server'belonging'to'the'user'who'

is'logged'in.'Naming'and'saving'in'this'way'allows'users'to'quickly'save'results'in'

an'ordered'way'and'continue'their'work'(Figure'15).'

'

'Figure'15'

'

Moving'on'from'the'compound'search,'there'is'the'target'search.'Again,'for'

consistency,'the'results'page'for'a'target'search'is'of'the'same'format'as'the'

compound'search.'Figure'16'shows'the'example'of'a'target'search'on'the'MUV'

database.'Once'again,'the'only'difference'between'databases'is'the'particular'

fields'that'are'returned.'

'

'

'

' 36'

'Figure'16'

'While'the'results'pages'themselves'are'all'consistent'with'each'other,'however,'there'is'an'intermediary'target'refinement'page'for'both'the'Wombat'and'CHEMBL'target'searches'(Figures'17'and'18'respectively).''

'Figure'17'

'

' 37'

'Figure'18'

'These'two'intermediary'pages'are'necessary'in'order'to'allow'for'the'kind'of'search'restrictions'identified'in'the'Initial'Requirements'Analysis'for'these'databases.'Following'a'target'search'then,'these'intermediary'pages'allow'the'researchers'to'makes'various'restrictions.'

In'the'case'of'Wombat,'a'table'and'checkboxes'allow'researchers'to'restrict'the'results'to'a'specific'organism'and'bio_effect'(Figure'17).'A'“Select'All”'checkbox'at'the'bottom'allows'them'quickly'select'all'results.'

For'CHEMBL,'there'is'a'similar'table'allowing'researchers'to'restrict'the'results'to'a'particular'organism'and'target'type,'and'the'same'checkbox'system'is'employed'(Figure'18).'In'addition,'on'the'CHEMBL'intermediary'page'researchers'can'also'restrict'the'search'to'include'only'the'specified'Type'of'assays'and'set'the'threshold'for'that'assay'in'a'text'box.'The'search'will'return'anything'above'and'including'the'entered'threshold,'and'the'units'to'the'side'mark'the'specific'measurements'used'for'that'assay'type.'Finally,'researchers'can'set'the'overall'confidence'score'using'the'dropdown'box.'

For'both'Wombat'and'CHEMBL,'clicking'the'coloured'“Search”'button'at'the'bottom'of'the'intermediary'page'initiates'the'search,'and'results'displayed'in'the'same'way'as'all'other'results'tables.'' One'further'feature'of'the'CHEMBL'intermediary'page,'again'identified'in'the'Initial'Requirements'Analysis,'is'the'link'to'the'target’s'Target'Report'Card.'

' 38'

As'can'bee'seen,'the'chembl_id'field'results'appear'as'standard'web'links'and'open'a'new'window'displaying'the'Target'Report'card'to'the'right'of'the'screen'(Figure'19).''

'Figure'19'

'

4.2..Coding.Methodology.

One'of'the'most'important'considerations'when'it'comes'to'programming'is'how'easy'it'will'be'for'the'final'system'to'be'maintained.'As'identified'in'the'Literature'Review,'one'of'the'key'steps'in'achieving'this'is'to'modularise'the'code,'that'is,'break'it'up'into'selfccontained'coherent'sections/files'that'perform'a'specific'task.'

Appendix'II'shows'the'complete'file'structure'for'this'system,'along'with'a'description'of'each'file.'This'demonstrates'how'the'code'has'been'modularised,'and'we'can'see'there'is'a'file'that'deals'with'all'the'sessions'data'and'nothing'else'(sessions.php),'others'for'managing'the'connections'to'each'database'(e.g.'db_connection_chembl.php'for'CHEMBL),'another'for'handling'all'the'processing'required'for'saving'the'results'(process.php),'and'so'on.'The'same'is'true'for'large'areas'of'HTML'that'are'repeated'across'many'pages,'e.g.'header.php'for'the'header.'Moreover,'it'should'be'noted'that'although'each'database'is'allocated'its'

' 39'

own'page,'e.g.'chembl.php,'this'page'contains'only'that'which'is'essential'to'it'

and'thus'does'not'break'with'this'pattern.'

' As'identified'in'the'Literature'Review,'the'step'beyond'modularisation'is'

to'functionalise'code.'In'line'with'best'practice,'this'has'been'done'by'placing'all'

the'functions'in'their'own'file'(functions.php)'and'granting'access'to'this'file'for'

all'other'pages'that'use'any'of'the'functions'(Figure'28'line'4).'Figures'20c22'

show'a'series'of'examples'from'functions.php.'

'

'

Figure'20'

'

'

' 40'

Figure'21'

'

'Figure'22'

'

As'can'be'seen,'each'function'is'a'piece'of'code'that'performs'a'certain'well'

defined'task,'such'as'checking'the'success'of'a'query'(Figure'20'line'3)'or'

performing'a'target'query'on'CHEMBL'(Figure'21)'or'a'compound'query'on'

MDDR'(Figure'22).'We'can'also'see'how'these'functions,'in'line'with'best'

practice,'have'been'given'names'that'make'their'purpose'easy'to'identify,'e.g.'

mddr_compound_query().'

' Using'one'of'these'function'is'simply'a'matter'of'calling'it'by'name'when'

needed'(Figure'23'line'25'shows'how'this'is'done'for'the'compound'search'in'

mddr.php),'leaving'that'file'itself'to'contain'only'the'code'that'is'essential'to'it.''

'

'Figure'23'

'

In'addition'to'the'overall'methodologies,'it'was'also'mentioned'that'there'are'

many'best'practices'for'programming'in'PHP'and'interacting'with'the'MySQL'

' 41'

database.'One'of'the'most'important'of'these'is'the'use'of'commenting.'In'the'Sublime'Text'editor'used'to'write'the'code'for'this'project,'these'comments'appear'in'grey,'as'can'be'seen'in'Figure'23'line'22.'Here,'the'comment'simply'identifies'that'the'following'code'is'for'the'compound'search.'Later'down'the'page,'there'is'another'comment'indicating'the'code'for'the'target'search'(Figure'24'line'76).''

'Figure'24'

'Such'comments'appear'throughout'most'files'in'the'system'in'order'to'indicate'what'certain'sections'of'code'do'and'explain'code'that'may'not'be'immediately'obvious'(Figures'25c29).'In'the'styles.css'file,'comments'are'again'used'to'separate'the'CSS'code'into'coherent'sections,'e.g.'1.'General'styles,'2.'Login'page'styles,'and'so'on.'These'comments'should'allow'the'administrator'to'easily'navigate'the'code,'thus'speeding'up'maintenance'and'any'future'modifications'to'the'system.''

' 42'

'Figure'25'

'

'Figure'26'

'

'Figure'27'

'

' 43'

'

Figure'28'

'

'

Figure'29'

'

Other'examples'of'best'practice'include'specifically'selecting'the'required'fields'

by'name'in'the'SQL'queries,'as'opposed'to'using'the'select'all'function'(Figure'29'

line'114),'which'speeds'up'the'query'process,'as'well'as'defining'the'variables'

used'for'the'database'connections'as'constants'(Figure'25).'

4.3..Specific.Features.

4.3.1..Searching.

Basic$Search$

Implementing'the'basic'compound'and'target'searches'for'each'database'was'a'

relatively'straightforward'procedure.'Figure'30'shows'the'code'for'the'search'

box'and'submit'buttons'for'the'MDDR'database.'

'

'

Figure'30'

'

' 44'

As'can'be'seen'(line'18),'there'is'one'search'box'for'both'types'of'search,'

(compound'and'target)'and'below'there'is'a'button'for'initiating'a'compound'

search'(line'20)'and'another'for'a'target'search'(line'21).'The'name'identifying'

the'text'box'is'user_query,'while'submit_compound'and'submit_target'identify'

the'compound'and'target'search'buttons'respectively.'As'can'be'seen'in'Figures'

31'and'32,'in'the'main'content'of'the'mddr.php'file'there'is'an'if/elseif/else'

statement'that'sates'that'if'submit_compund'search'is'detected'(i.e.'if'the'user'

has'clicked'the'submit'button)'we'run'the'code'for'the'compound'search'(Figure'

31'line'20),'while'if'submit_target'is'detected'(i.e.'if'the'user'had'clicked'the'

target'button)'we'run'the'code'for'the'target'search'(Figure'32'line'74).'

'

'

Figure'31'

'

'

Figure'32'

'

If'neither'of'these'two'values'are'detected,'the'user'is'on'the'MDDR'homepage'

but'no'search'has'been'initiated.'As'such,'the'welcome'message'is'displayed'

(Figure'33).2'

'

''''''''''''''''''''''''''''''''''''''''''''''''''''''''2'“Detected”'here'means'it'has'come'in'the'POST,'a'particular'method'for'a'requestcresponse'between'client'and'server,'but'a'discussion'of'this'is'beyond'the'scope'of'this'study.'

' 45'

'

Figure'33'

'

The'code'immediately'below'the'submit_compound'or'submit_target'detection'

includes'the'specific'function'for'executing'the'required'search'(Figure'31'line'

24'and'Figure'32'line'78)'and'saves'it'to'the'variable'$query_result.'This'function'

is'called'from'functions.php'as'already'discussed.'Below'this,'the'query'itself'is'

saved'to'a'variable'$query'(Figure'31'line'26'and'Figure'32'line'79)'ready'for'

displaying'to'the'user'in'the'toggle'box,'while'the'result'is'saved'to'the'variable'

$result'(Figure'31'line'27'and'Figure'32'line'80)'ready'for'use'when'it'comes'to'

displaying'the'results'in'a'table.'The'rest'of'the'code'displays'the'table,'making'

use'of'the'$result'array.'The'specific'query'itself,'in'the'functions.php'file'and'

called'by'the'homepage,'can'be'seen'in'Figures'34'(MDDR'compound'query)'and'

35'(MDDR'target'query).'

'

'

Figure'34'

'

' 46'

'Figure'35'

'The'basic'compound'and'target'searches'described'in'this'section'are'the'same'across'all'the'databases.'The'only'exception'is'with'CHEMBL,'where'for'both'types'of'search'users'not'only'have'the'option'of'searching'by'SMILES'(for'the'compound'searches)'and'the'target'name'(target'search),'but'also'by'the'chembl_id'for'the'compound'and'target.3'Figure'36'illustrates'how'this'works'for'the'CHEMBL'compound'search.'Simply'put,'if'the'first'characters'the'user'enters'are'CHEM'a'search'of'the'chembl_id'field'is'initiated'(line'14),'otherwise'a'search'on'the'canonical_smiles'field'is'initiated'(line'23).''

''''''''''''''''''''''''''''''''''''''''''''''''''''''''3'It'should'be'noted'that'depending'on'the'database'the'target'name'filed'had'a'different'name.'These'are'pref_name'for'CHEMBL,'active_class'for'MDDR'and'MUV,'and'target_name'for'Wombat.'

' 47'

'Figure'36'

Refined$Search$

With'CHEMBL'and'Wombat,'the'basic'target'search'is'a'little'more'complicated'

due'to'the'option'of'further'refining'the'search'prior'to'the'results'being'

returned'(Figures'17'and'18).'Without'going'into'the'coding'technicalities'here,'

we'can'see'how'these'refinement'pages'are'used'in'the'code'(Figure'37'line'116).'

Instead'of'going'straight'to'the'target'results'table,'there'is'an'additional'check'to'

see'if'refine_target'(the'name'identifying'the'button'on'the'bottom'of'the'

intermediary'page)'is'detected'(Figure'37'line'140).'

'

' 48'

'

Figure'37'

'

While'the'CHEMBL'refine'search'is'a'little'more'complicated'because'of'the'extra'

criteria'by'which'users'can'restrict'the'search,'the'basic'methodology'is'the'same'

as'in'the'case'of'Wombat.'

4.3.2..Autosuggest.

A'full'explanation'of'how'the'autosuggest'feature'works'is'beyond'the'scope'of'

this'study.'The'brief'explanation'presented'here'demonstrates'the'basic'

workings'and'should'prove'useful'to'the'administrator'should'there'ever'be'the'

need'to'recreate'it'for'another'database.'

' To'begin'with,'each'of'the'database'connection'files,'e.g.'

db_connection_chembl.php,'has'two'additional'lines'of'code'not'normally'

expected'in'such'a'file.'These'lines'specify'the'table'(Figures'38'and'39'lines'7)'

and'column'(Figures'38'and'39'lines'8)'on'which'the'autosuggest'will'operate'for'

each'database'and'saves'them'to'the'constants'DB_TABLE'and'DB_COLUMN'

respectively.'

' 49'

'

'Figure'38'

'

'Figure'39'

'In'addition,'each'database'has'its'own'PHP'file'for'the'autosuggest,'e.g.'

name_fetch_chembl.php,'in'the'main'chem'folder.'When'adding'a'new'database,'a'

new'file,'e.g.'name_fetch_nci.php,'can'be'created'by'copying'the'code'from'

name_fetch_chembl.php.'Only'a'couple'of'changes'need'be'made:'the'database'

connection'include'must'be'changed'to'that'of'the'new'database'(Figure'40'line'

2);'the'SQL'must'specify'the'column'being'selected,'which'may'no'longer'be'

pref_name'(Figure'40'line'7);'the'column'name'must'be'changed'in'the'code'that'

converts'the'user'query'to'lowercase'(Figure'40'line'15)'

'

' 50'

'Figure'40'

'Next,'a'JavaScript'file'for'the'new'database'must'be'created,'which'can'again'be'

done'by'creating,'for'example,'an'autosuggest_nci.js'file'in'the'_js'folder,'based'on'

the'autosuggest_chembl.js'file.'All'that'needs'to'be'changed'is'one'line'of'code'

(Figure'41'line'24)'that'links'to'the'name_fetch'file.'

'

'Figure'41'

''

Finally,'the'link'to'this'new'JavaScript'file'needs'to'be'made'at'the'top'of'the'new'

database’s'homepage.'Figure'42'line'6'shows'how'this'was'done'for'CHEMBL.'

'

' 51'

'Figure'42'

'

For'complete'instructions'on'how'to'add'a'new'database'see'Appendix'III.'

4.3.3..Displaying.Returned.Results.

As'discussed,'all'returned'results'for'both'the'compound'and'target'search'are'

displayed'in'the'same'table'format.'This'has'been'achieved'using'the'popular'

DataTables'plugcin'www.datatables.net,'which'with'a'bit'of'tweaking'makes'

possible'many'of'the'advanced'table'features:'toggling'the'columns'off'and'on;'

selecting'how'many'results'are'displayed'per'page;'page'pagination;'displaying'

the'number'of'results'returned'from'the'search;'searching'the'table;'reordering'

results'by'column;'and'horizontal'scrolling.'

' Unlike'the'autosuggest,'only'one'JavaScript'file'is'needed'for'all'the'tables'

(datatables.js'in'the'_js'folder)'and'it'requires'no'modification.'Moreover,'as'we'

can'see'in'Figure'43,'the'MDDR'homepage'(mddr.php),'lines'29c36'show'how'

easy'it'is'to'add'the'toggle'columns'feature'while'lines'42c62'show'how'easy'it'is'

to'include'the'fields'for'the'main'table.'Adding'a'new'column'is'simply'a'matter'

of'adding'another'line'to'each'of'these'sections'and,'of'course,'making'sure'that'

field'is'selected'in'the'query'in'functions.php'(Figure'34).'

' 52'

'Figure'43'

'

It'should'be'noted'that'the'CSS'for'the'tables'is'quite'lengthy.'However,'it'is'well'

commented'in'sytles.css'and'does'not'require'modification.'

' Finally,'the'DataTables'site'itself'contains'extensive'documentation'on'

modifying'various'features,'modifying'the'way'the'tables'are'displayed,'and'

including'new'addcons.'

4.3.4..Saving.Results.

In'order'to'allow'users'to'save'the'results'of'a'search,'as'discussed'in'the'Overall'

Design'section,'PHP'output'control'functions,'including'object'buffering'(i.e.'the'

ob'functions)'were'used.'

'

' 53'

'

Figure'44'

'

Figure'44'shows'the'code'that'displays'the'results'for'an'MDDR'search.'

As'can'be'seen,'this'is'preceded'by'the'ob_start()'function'(line'40)'and'followed'

by'ob_flush()'(line'68).'ob_start()'turns'internal'buffering'on,'which'tells'the'

server'to'start'remembering'anything'after'it'that'would'normally'be'output.'

That'is,'the'server'does'not'do'anything'with'this'data,'such'a'output'it'to'the'

browser'as'would'normally'be'the'case,'but'simply'remembers'it.'ob_flush(),'on'

the'other'hand,'tells'the'server'to'stop'remembering'any'more'data'and'

discarded'any'data'already'remembered.'

' The'next'important'bit'of'code'is'the'ob_get_content()'function'(Figure'44'

line'64),'which'appears'before'ob_flush()'has'taken'effect.'This'function'gets'the'

content'of'the'internal'buffer'that'is'remembered'by'ob_start().'On'line'64,'we'

see'this'content'(data)'is'now'saved'to'the'variable'$output.'

Next,'the'custom'format_results_for_saving()'function,'called'from'

functions.php'and'created'to'transform'the'data'into'tab'delimited'format'for'

saving'(Figure'45'lines'260c271),'is'run'on'the'$output'variable'and'the'results'

are'saved'to'a'new'variable'called'$formatted_results.''

'

' 54'

'Figure'45'

'

The'$formatted_results'variable'now'contains'the'complete'results'from'the'

internal'buffering'in'the'correct'format'for'saving'and,'because'these'are'saved'

to'a'variable,'they'will'not'be'discarded'when'the'ob_flush()'function'is'executed.'

' Immediately'after'the'ob_flush(),the'button'for'saving'results'is'included'

(Figure'44'line'70).'Because'this'button'is'universal'for'all'tables'it'is'its'own'file:'

save_form.php.'Figure'46'shows'how'the'save_form.php'file'simply'passes'the'

$formatted_results'variable'(line'4)'and'the'specific'users'username'(line'5)'to'

the'process.php'file.'

'

'Figure'46'

'

process.php'then'uses'PHPs'inbuilt'file_put_contents()'function'to'create'a'text'

file'containing'the'formatted'results'in'a'folder'on'the'server'belonging'to'the'

specific'user'who'is'logged'in'(Figure'47'line'11).'

'

' 55'

'Figure'47'

Note'that'at'the'end'of'process.php'there'is'a'script'to'automatically'close'the'

window'this'file'was'loaded'in'(Figure'47'line'16).'

4.3.5..Other.JavaScript.

In'addition'to'the'JavaScript'already'mentioned'–'autosuggest.js'and'its'inclusion'

at'the'top'of'each'database'homepage,'datatables.js,'and'the'process.php'

window.close()'–'several'other'parts'of'the'system'use'JavaScrpt.'All'but'one'of'

these'JavaScripts'are'located'in'the'universal'header.php'file,'and'all'are'well'

commented.'

' First'is'a'script'belonging'to'the'DataTables'plugcin'(Figure'48).'Almost'all'

changes'to'the'way'this'plugcin'behaves'and'displays'data'take'place'in'this'

script,'not'datatables.js.'For'example,'this'is'where'horizontal'scrolling'(line'14)'

and'page'pagination'(line'16)'have'been'added.'A'full'list'of'features'can'be'

found'at'the'DataTables'website,'and'almost'all'would'need'to'be'added'to'this'

location'in'the'code.'

'

' 56'

'

Figure'48'

'

Next'is'another'a'script'belonging'to'DataTables,'this'time'for'adding'the'ability'

to'toggle'columns'off'and'on'(Figure'49).'It'should'be'noted'that'the'HTML'for'

this'is'toggling'is'included'in'the'homepage'of'the'specific'database'in'question.'

'

'

Figure'49'

'

Following'this'are'the'scripts'for'the'“Select'All”'feature'on'the'various'

checkboxes'(Figure'50).'

'

' 57'

'Figure'50'

''Next'is'the'script'required'to'stop'the'return'key,'that'fills'the'search'box'when'

using'autosuggest,'automatically'initiating'a'search'(Figure'51).'This'is'necessary'

because'the'automatic'search'would'always'be'a'compound'search,'which'is'not'

always'what'the'user'wants.'

'

'Figure'51'

'The'final'script'in'header.php'simply'deals'with'the'JavaScript'for'hiding'the'box'

that'displays'the'SQL'of'the'query'just'executed'(Figure'52).'

'

' 58'

'Figure'52'

'Outside'of'header.php,'there'is'a'script'for'the'page'loading'animation'(Figure'53).''

'Figure'53'

'This'feature'has'been'included'because'some'searches'take'a'long'time'to'return'results'and'the'animation'lets'users'know'the'system'is'still'working.'Figure'54'shows'the'code'for'this'feature'in'footer.php.''

'Figure'54'

''

' 59'

5..User.Testing.

5.1..Methodology.

The'methodology'for'the'user'testing'followed'the'same'style'of'informal'interviews'as'used'in'the'Initial'Requirements'Analysis.'This'time,'researchers'were'given'a'quick'demonstration'of'the'system,'then'encouraged'to'use'it'to'try'and'carry'out'the'desired'tasks'while'providing'feedback'throughout.'Once'again,'the'aim'was'to'establish'a'dialogue'with'the'researchers.'This'time,'however,'instead'of'a'list'of'basic'questions,'a'few'core'areas'were'selected'in'order'to'guide'the'interviews.'These'were:'

• Whether'or'not'the'they'felt'the'system'would'be'useful'for'them'at'all.'

• What'they'thought'of'the'main'features'and'functionality.'

• What'they'thought'about'the'information'the'system'returned.'

• How'easy'they'felt'the'system'was'to'understand'and'use.'

• What'they'thought'of'the'system’s'overall'visual'appearance.'

It'should'be'noted'that'each'of'these'areas'is'a'part'of'user'experience'as'it'was'defined'in'the'Literature'Review.'

5.2..Results.

Is$the$system$useful$

All'participants'said'the'system'was'useful'in'general'and,'with'the'exception'of'one'participant,'they'all'said'that'they'would'use'it'throughout'the'normal'course'of'their'work.'The'main'reason'they'felt'it'would'be'so'useful'was'that'it'allowed'them'to'easily'perform'compound'and'target'searches'on'their'test'databases,'and'then'view'the'results'in'a'clearly'laid'out'table,'simply'by'entering'the'query'and'clicking'a'search'button.'The'participant'who'said'he'would'probably'not'use'the'system'added'that'this'was'only'because'he'was'not'carrying'out'these'kinds'of'searches'at'present.'However,'having'previously'been'

' 60'

involved'in'this'kind'of'research,'he'said'the'system'was'useful'for'the'tasks'it'

was'intended'to'carry'out.'

Features$and$functionality$

In'addition'to'meeting'their'basic'requirements,'participants'were'especially'

pleased'with'certain'functional'components'of'the'system:'

• Dropdown'menu'for'selecting'a'database'–'Participants'found'this'very'

intuitive'and'liked'the'fact'that'it'easily'allowed'them'to'select'a'database'

from'anywhere'else'in'the'system'and'immediately'query'it.'

• Basic'search'bar'and'buttons'–'Participants'again'felt'these'were'intuitive'

and'captured'the'main'tasks'they'performed'incredibly'well.'

• Autosuggest'–'Participants'found'this'very'useful'and'particularly'liked'

the'fact'that'they'could'scroll'down'and'select'an'item'using'keyboard'

commands.'

• Toggle'columns'off'and'on'–'All'participants'were'pleased'with'the'way'

this'allowed'them'to'customise'the'results'to'suit'their'individual'needs.'

• Link'to'CHEMBL'Target'Report'Card'–'Those'who'used'this'database'liked'

being'able'to'quickly'view'the'report'card'in'a'separate'window'without'

leaving'the'system.'

Participants'also'had'several'suggestions'for'further'features'and'functions'that'

would'improve'the'system:'

1. The'ability'to'save'search'history.'

2. The'option'to'change'their'own'password.'

3. The'ability'to'search'for'compounds'by'compound'name'using'the'same'

kind'of'autosuggest'feature'available'for'the'target'search.'

4. The'ability'to'set'the'CHEMBL'target'refinement'page'to'retrieve'only'

results'that'are'below'the'specified'threshold.'

5. The'ability'to'click'on'a'compound'name'in'the'results'table'for'a'target'

search'and'automatically'conduct'a'search'for'that'compound.'

' 61'

6. The'ability'to'select'the'name'and'location'of'the'text'file'when'saving'results.'

7. An'advanced'search'button'for'further'restricting'the'results'prior'to'conducting'a'search.'

8. The'inclusion'of'the'PIC50'Type'in'the'CHEMBL'target'refinement'page.'

9. The'ability'to'select'different'versions'of'the'CHEMBL'database.'

10. The'ability'to'click'on'a'SMILES'in'any'of'the'results'tables'and'have'a'diagram'of'that'compound'displayed.'

Returned$information$

Participants'were'for'the'most'part'pleased'with'the'way'the'information'was'returned,'largely'because'they'had'the'ability'to'select'their'own'columns.'In'addition,'participants'who'required'it'were'also'impressed'with'the'way'they'could'view'the'SQL'of'the'query'that'had'just'been'run.'Nevertheless,'there'were'several'comments'that'indicate'areas'for'improvement:'

11. More'fields'relating'to'bio'activities'to'be'returned'in'the'results'table,'particularly'for'CHEMBL'and'Wombat.'

12. Include'the'target_class'field'in'the'MUV'target'search'results'table.'

13. More'information'about'what'the'names'of'the'each'column'mean.'

14. The'ability'to'display'all'compounds'and'active'classes'in'a'given'database'without'having'to'perform'any'kind'of'search.'

15. Making'the'box'that'shows'and'hides'the'SQL'of'the'query'just'run'hidden'by'default.'

Is$the$system$easy$of$use$and$understand$

One'of'the'things'participants'liked'the'most'about'the'system'as'a'whole'was'its'simplicity,'both'in'terms'of'its'appearance'and'easy'of'use,'with'one'participant'commenting'that'it'brought'“Google'like'simplicity”'to'their'search'activities.'Participants'were'pleased'with'how'quickly'they'managed'to'run'through'the'basic'task'of'searching'for'a'target,'restricting'the'search'criteria'(in'the'case'of'CHEMBL'and'Wombat),'and'viewing'the'results.'There'were'no'negative'

' 62'

comments'about'the'position'of'the'buttons,'information,'or'the'way'the'

elements'of'the'system'fit'together.'Moreover,'none'of'the'participants'struggled'

to'operate'the'system'and'all'said'it'was'very'selfcexplanatory.'Ultimately,'

participants'felt'that'while'there'was'room'for'improvement'in'other'areas,'the'

basic'format'and'design'of'the'system'was'solid'and'should'remain'the'same'

even'if'new'features'were'added.'In'fact,'there'was'only'one'negative'indication'

concerning'this'aspect'of'the'system:'

16. The'button'to'save'the'results'had'to'be'pointed'out'to'a'couple'of'the'

participants.'

Visual$design$

In'addition'to'the'ease'of'use,'participants'found'the'overall'minimalistic'design'

visually'pleasing,'and'there'was'only'one'negative'comment'concerning'the'

system’s'appearance:'

17. Columns'in'the'results'table'are'sometimes'wider'than'they'need'to'be'for'

the'information'contained'within'them'(Figure'55).'

'

'Figure'55'

'

' 63'

6..Discussion.

6.1..Limitations.and.Weaknesses..

In'addition'to'the'comments'provided'in'the'Results'section'of'the'User'Testing,'

there'are'several'weaknesses'and'limitation'of'the'system'that'are'worth'

highlighting:'

I. If'a'false'compound'query'is'entered'in'CHEMBL,'for'example'

chembl6824'as'opposed'to'CHEMBL6824,'the'system'takes'far'longer'

than'is'ideal'to'return'the'empty'results'set.'

II. Toggling'certain'columns'off'only'removes'them'from'being'displayed'on'

screen.'The'deselected'columns'and'all'their'content'are'still'saved'to'the'

tab'delimited'text'file'when'the'user'saves'the'results.'

III. The'page'loading'animation'does'not'function'particularly'well.'The'aim'

of'this'animation'was'to'show'users'the'system'was'still'doing'something,'

i.e.'had'not'crashed,'when'waiting'for'large'results'sets'to'be'returned.'

However,'when'returning'large'results'sets'this'loading'animation'itself'

stops,'thus'defeating'its'own'objective.'Worse'still,'when'the'system'

actually'does'crash'the'loading'animation'keeps'spinning'implying'that'

everything'is'fine.'

IV. The'system'works'as'it'should'with'the'Firefox'browser.'However,'it'does'

not'always'look'quite'as'it'should'on'other'browsers.'For'example,'when'

using'Chrome,'the'grey'lines'separating'the'databases'in'the'dropdown'

menu'do'not'appear.'

6.2..Future.Work.

What'follows'is'a'discussion'of'future'work'based'on'the'comments'from'the'

Results'of'the'User'Testing'section'as'well'as'the'Weaknesses'and'Limitations'

section.'The'numbering'used'here'corresponds'to'those'of'the'previous'sections.'

We'start'with'the'Results'of'the'User'Testing:'

1. Saving'search'history'–'Because'sessions'are'already'being'used'to'save'

user'information,'this'should'be'a'relatively'easy'feature'to'include.'

'64'

However,'further'research'would'be'necessary'to'determine'the'depth'of'

the'information'users'wanted'to'be'saved.'

2. Changing'passwords'–'Allowing'users'to'change'their'own'password'is'

very'easy'to'implement,'however,'this'is'down'to'the'discretion'of'the'

administrator.'

3. Search'for'compounds'by'name'–'This'feature'could'have'easily'been'

included'in'the'system'to'begin'with,'and'is'straightforward'to'implement.'

As'identified'in'the'Initial'Requirements'Analysis,'however,'this'was'not'

done'because'participants'did'not'feel'it'was'useful.'What'seems'to'have'

changed'their'minds'is'actually'using'the'autosuggest'feature'for'the'

target'search.'While'researchers'originally'said'they'did'not'know'the'

compound'names,'thus'would'not'search'by'them,'seeing'the'way'the'

autosuggest'allows'them'to'view'the'possible'matches'as'they'type'and'

scroll'through'them'seems'to'have'changed'their'perceptions.'In'fact,'in'

comparison'to'the'target'search,'one'participant'said'that'“searching'for'

compounds'is'little'bit'difficult”.'An'explanation'of'how'to'implement'this'

feature'can'be'found'in'the'Autosuggest'section'of'Implementation.'In'

addition'to'what'is'described'in'that'section,'the'compound'name'field'

should'be'added'to'the'compound'query'functions'in'functions.php.'

4. Set'CHEMBL'target'refinement'page'to'retrieve'results'that'are'below'the'

specified'threshold'–'At'present,'the'system'only'returns'results'that'are'

higher'than'the'threshold'entered'by'the'user.'Modifying'this'to'allow'the'

user'to'return'results'lower'than'the'value'they'enter'is'a'very'important'

feature'to'add'because'at'present'the'system'might'exclude'users'who'

need'this'capability.'The'feature'itself'is'relatively'easy'to'implement'and'

simply'means'slightly'modifying'the'code'for'the'

chembl_target_refinement_query()'function'in'functions.php.'

5. Search'for'a'compound'by'clicking'its'name'in'a'target'results'table'–'At'

present,'compound'names'are'not'a'displayed'field'in'the'target'results'

tables,'nor'can'compounds'be'searched'for'by'their'names.'Making'the'

modification'discussed'in'this'point'would'thus'required'both'of'these'

issues'being'addressed'first.'In'some'ways,'given'that'users'can'already'

' 65'

copy'and'paste'SMILES'from'the'target'return'results'table'into'the'main'

search'box'and'then'click'the'compound'search'button,'it'could'be'argued'

that'enabling'them'to'initiate'a'compound'search'by'clicking'a'compound'

name'in'this'table,'as'opposed'to'simply'enabling'them'to'do'with'the'

compound'name'what'they'can'already'do'with'SMILES,'is'more'about'

better'interactivity'than'necessity.'However,'making'compound'names'in'

the'target'results'table'clickable'in'this'way'would'also'allow'the'

possibility'of'having'the'compound’s'results'displayed'in'a'separate'

window,'much'like'the'CHEMBL'Target'Report'Card.'Further'research'is'

thus'required'in'order'to'determine'how'researchers'might'want'this'

feature'to'work.'

6. Naming'and'setting'the'location'of'the'saved'results'files'–'The'participant'

who'said'they'would'like'to'be'able'to'do'this'felt'that'it'would'make'

organising'and'retrieving'their'text'files'far'easier.'They'also'said'that'the'

current'method'was'a'little'unintuitive'compared'with'using'a'standard'

download'link.'Implementing'this'would'be'a'straightforward'task,'and'

simply'mean'modifying'the'process.php'file'(Figure'47'line'11).'However,'

before'doing'so,'it'would'be'important'to'find'out'if'other'researchers'

would'actually'prefer'this'over'the'current'method.'

7. Advanced'search'feature'–'A'couple'of'participants'mentioned'that'it'

would'be'nice'to'have'an'advanced'search'facility'next'to'the'main'search'

box,'as'is'common'on'many'websites.'However,'when'asked,'these'

participants'did'not'immediately'know'what'kind'of'restrictions'they'

would'want'this'to'include.'It'is'likely'that'as'researchers'get'used'to'

using'the'system'they'will'begin'to'form'stronger'ideas'about'what'they'

want'from'an'advanced'search'feature,'and'that'research'in'this'area'is'

one'of'the'most'promising'areas'of'future'work.'

8. Add'PIC50'to'CHEMBL'target'refinement'page'–'This'is'an'easy'addition'

that'should'be'quickly'implemented.'

9. Different'versions'of'CHEMBL'–'As'mentioned,'one'of'the'reasons'for'

building'this'system'was'to'provide'an'interface'for'a'version'of'CHMEBL'

that'researchers'could'use'throughout'their'studies.'However,'while'still'

' 66'

requiring'a'consistent'version,'new'members'to'the'group'may'want'to'

start'with'different'versions'(the'version'used'in'this'system'is'CHEMBL'

18).'This'requirement'had'already'been'predicted,'and'Appendix'III'

describes'how'a'new'database'can'be'added.'

10. Click'on'a'SMILES'in'any'of'the'results'tables'and'have'a'diagram'of'that'

compound'displayed'–'This'is'a'very'advanced'feature'that'would'

probably'require'using'JavaScript'to'draw'a'2D'diagram'on'the'fly'and'

have'it'pop'up'in'a'new'window'similar'to'the'CHEMBL'Target'Report'

Cards.'The'possibility'of'implementing'of'this'feature'is'beyond'the'scope'

of'this'study,'however,'it'is'worth'noting'that'this'might'be'a'possible'area'

in'which'the'system'could'be'expanded.'

11. More'fields'related'to'bio'activities'in'results'table'–'The'code'has'been'

designed'to'make'it'very'easy'to'add'new'fields'if'required'(see'the'

Displaying'Returned'Results'section'in'Implementation'for'how'to'do'

this).'Further'research'is'thus'needed'to'determine'which'of'the'bio'

activity'fields'are'relevant'to'researchers.'

12. Include'the'target_class'field'in'the'MUV'target'search'results'table'–'As'

with'more'bio'activities'related'fields,'this'is'an'easy'alteration'to'make.'

In'this'case,'however,'no'research'is'needed'and'the'field,'located'in'the'

active_class'table'of'the'MUV'database,'can'easily'be'included'right'away.'

13. More'information'about'column'names'–'At'present,'columns'are'given'

the'same'names'as'they'have'in'the'databases.'These'names'are'generally'

abbreviations'(e.g.'rtb'means'rotatable'bonds).'One'quite'experienced'

participant,'however,'said'they'had'to'guess'what'some'of'these'

abbreviations'meant'and'that,'while'they'agreed'with'the'choice'of'

keeping'the'names'the'same'as'in'the'databases,'they'would'like'the'

system'to'explain'what'these'column'headings'actually'meant.'This'could'

be'achieved'by'with'a'simple'JavaScript'feature'that'displayed'a'popup'

box'with'a'fuller'explanation'when'the'user'hovered'over'the'column'

heading.'

' 67'

14. Display'all'compounds'and'active'classes'in'a'given'database'–'A'participant'who'had'recently'joined'the'group'said'they'would'like'the'ability'to'browse'through'all'the'active'classes'of'a'given'database'without'having'to'conduct'any'kind'of'search.'They'believed'that'such'a'facility'would'enable'them'to'better'understand'the'databases'themselves.'Another'participant,'this'time'an'experienced'researcher'who'had'been'with'the'group'for'many'years,'wanted'to'be'able'to'do'the'same'thing'for'compounds.'Both'of'these'features'would'be'relatively'easy'to'implement,'however,'research'would'need'to'be'conducted'in'order'to'determine'how'to'integrate'this'feature'into'the'current'system.'For'example,'would'users'like'to'be'able'to'generate'this'by'simply'clicking'on'the'compound'and'target'search'buttons'when'the'query'box'was'empty'or'through'some'other'button?'Moreover,'there'are'further'questions'as'to'what'researchers'would'then'want'to'be'able'to'do'with'the'results,'e.g.'how'would'they'like'to'further'restrict'them'once'the'full'list'had'been'generated?'

15. SQL'query'hidden'by'default'–'One'participant'felt'that'setting'the'SQL'of'the'query'just'run'to'be'displayed'by'default,'as'opposed'to'hidden,'was'a'little'confusing'(Figure'7).'Changing'this'is'an'easy'fix'that'simply'requires'modifying'the'show/hide'query'script'in'the'header.php'file'(Figure'52).'

16. Save'button'–'The'fact'that'the'save'button'had'to'be'pointed'out'to'several'participants'suggests'its'is'not'obvious'enough'for'such'an'important'function.'This'problem'would'best'be'addressed'by'making'the'button'larger'and'colour'coded'to'the'database,'such'as'the'target'refinement'search'buttons'(Figures'17'and'18),'and'perhaps'moving'it'closer'to'the'top'of'the'page.'

17. Results'table'columns'–'The'fact'that'some'of'the'columns'are'wider'than'they'need'to'be'is'unfortunately'a'problem'with'the'DataTables'plugcin'itself,'which'is'quite'difficult'to'fine'tune'for'multiple'tables'that'return'different'information.'However,'this'plugcin'is'still'in'development'and'it'is'worth'checking'the'DataTbales'website'from'time'to'time'for'developments'in'this'area.'

' 68'

In'addition'to'future'improvements'based'on'the'Results'of'the'User'Testing,'

several'suggestions'can'also'be'discussed'in'regard'to'the'identified'Weaknesses'

and'Limitations:'

I. CHEMBLE'compound'search'is'slow'to'return'the'empty'results'set'if'the'

user'enters'a'false'query'–'A'CHEMBL'compound'search'using'SMILES'

takes'a'long'time'to'return'results,'and'there'is'nothing'that'can'be'done'

about'this'given'the'complexity'of'the'query'and'number'of'compounds'in'

the'CHEMBL'database.'This'is'why,'as'mentioned,'the'code'for'performing'

a'compound'search'using'the'smiles'field'was'separated'from'a'

compound'search'using'the'chembl_id'field.'This'solution'(Figure'36)'

meant'that'if'the'compound'query'began'with'the'characters'“CHEM”'the'

system'only'ran'a'search'on'the'chembl_id'field,'as'opposed'to'the'smiles'

field.'However,'if'a'false'query,'e.g.'one'beginning'with'the'characters'

“chem”,'is'entered,'the'system'does'not'realise'a'search'on'the'chembl_id'

field'is'being'requested'and'thus'searches'the'smiles'field'as'well.'The'

result'is'a'very'long'wait'to'return'an'empty'results'set.'The'simplest'way'

to'address'this'problem'is'to'automatically'convert'the'entered'query'to'

uppercase'if'it'begins'“chem”,'which'can'be'achieved'using'PHPs'built'in'

strtoupper()'function.'It'should'be'noted,'however,'this'will'only'work'for'

queries'where'the'user'has'made'the'mistake'of'not'capitalising'the'

letters'when'searching'for'a'chembl_id.'Completely'false'queries'will'still'

take'a'long'time'to'return'an'empty'results'set,'and'there'is'nothing'that'

can'be'done'about'this.'Nevertheless,'the'fix'suggested'here'could'

eliminate'the'problem'in'relation'to'one'of'the'ways'users'are'most'likely'

to'make'a'mistake.'

II. Columns'that'have'been'toggled'off'should'not'be'saved'to'the'text'file'–'

This'would'be'difficult'to'achieve'because'it'means'setting'the'output'

buttering'to'remembering'data'that'is'continually'being'changed.'That'is,'

every'time'a'user'toggles'on'or'off'a'column,'that'which'is'remembered'in'

the'output'buffering'would'have'to'be'updated'as'well.'An'alternative'

solution'would'be'to'include'some'kind'of'feature'attached'to'the'save'

button'that'allowed'users'to'eliminate'columns'independently'of'the'

' 69'

current'toggle'feature.'Finding'the'right'solution'to'this'problem'would'

require'further'research'and'is'beyond'the'scope'of'this'study,'however,'it'

is'expected'that'researchers'will'ask'for'this'feature'once'they'have'got'

used'to'using'the'system.'

III. Loading'page'animation'–'If'these'problems'cannot'be'addressed'it'is'best'

to'remove'this'feature'altogether'as'clearly'defeats'its'own'objective.'

However,'given'the'reasons'it'was'included'in'the'first'place,'it'is'worth'

conducting'researching'into'how'a'more'successful'alternative'can'be'

implemented.'

IV. Browser'compatibility'–'The'majority,'if'not'all'of'the'researchers,'use'

Firefox'as'their'browser'of'choice.'However,'it'is'conceivable'that'from'

time'to'time'the'system'will'be'used'on'other'browsers.'Given'that'the'

differences'across'browsers'are'not'major,'do'not'affect'the'system’s'

functionality,'and'that'tweaking'for'crosscbrowser'compatibility'is'a'time'

consuming'process,'it'is'perhaps'best'simply'to'make'users'aware'of'this'

issue.

' 70'

7..Conclusion.

'The'aim'of'this'project'was'to'design'and'implement'a'usable'and'fullyc

functional'frontend'interface'for'the'test'databases'used'by'chemoinformatics'

researchers'at'The'University'of'Sheffield’s'Information'School.'Specifically,'it'aimed'at'creating'a'system'that'was'tailored'to'the'individual'needs'of'this'

group,'and'thus'began'by'identifying'their'core'requirements.'Finally,'user'

testing'of'the'completed'system'was'used'in'order'to'identify'areas'in'which'the'

system'could'be'improved'in'the'future'in'order'to'better'meet'the'needs'of'the'

group.'

The'Initial'Requirements'Analysis'proved'successful'in'identifying'the'

core'requirements'of'the'system.'Ultimately,'researchers'wanted'an'interface'

that'allowed'them'to'easily'perform'a'compound'or'target'search'on'one'of'the'

databases,'add'certain'search'restrictions'where'possible,'view'the'results'in'a'

well'formatted'table,'and'save'the'results'of'their'search'to'a'tab'delimited'text'

file'for'later'use.'

As'evidenced'by'the'User'Testing'section,'the'finished'system'proved'

successful'at'implementing'the'group’s'core'requirements.'Moreover,'as'far'as'

user'experience'is'concerned,'the'implemented'system'exceeded'the'group’s'expectations'and'in'terms'of'how'easy'it'was'to'use'and'how'simply'it'enabled'

them'to'carry'out'their'most'common'tasks.'Further'features'such'as'a'

dropdown'menu'that'allowed'users'to'select'a'new'database'from'anywhere'in'

the'system,'an'autosuggest'for'the'target'search,'and'the'ability'to'deselect'the'

columns'they'did'not'require'and'have'them'removed'from'the'results'table,'all'

added'to'the'overall'user'satisfaction.'

Following'the'completion'of'the'system,'User'Testing'proved'successful'at'

identifying'areas'in'which'the'system'could'be'improved.'Some'of'these'

improvements,'such'as'the'ability'to'set'the'CHEMBL'target'refinement'page'to'

retrieve'results'that'are'below'the'specified'threshold,'the'addition'of'the'PIC50'

assay'type'to'the'CHEMBL'target'refinement'page,'the'inclusion'of'the'

target_class'field'in'the'MUV'target'search'results'table,'the'redesigning'of'the'

save'button,'and'making'the'SQL'of'the'current'query'hidden'by'default,'are'easy'

' 71'

to'implement'right'away.'Other'improvements,'however,'such'as'the'ability'to'

initiate'a'compound'search'by'clicking'on'the'compound'name'in'a'target'results'

table,'adding'different'versions'of'CHEMBL,'adding'the'ability'to'search'for'

compounds'by'name,'adding'more'information'about'column'names,'and'making'

it'so'researchers'can'select'the'results'columns'they'want'to'save'as'well'as'

display,'all'involve'more'difficult'and'time'consuming'technical'solutions'but'are'

nonetheless'perfectly'within'the'bounds'of'the'system.'Finally,'some'suggested'

areas'of'improvement'such'as'the'advanced'search'button,'the'inclusion'of'more'

bio'activities'fields,'and'the'ability'to'view'all'compounds'and'targets'in'a'given'

database'without'conducing'a'specific'search,'the'saving'of'a'user’s'search'

history,'and'altering'the'name'and'location'of'the'saved'files,'all'require'further'

research'in'order'to'determine'what'researchers'really'want'of'these'features.'

In'the'end,'it'is'hoped'that'this'research'project'will'be'taken'up'in'the'

future'and'that'the'system'will'continue'to'be'improved.'Moreover,'we'can'see'

from'the'User'Testing'that'it'is'the'creation'of'this'system'itself'that'has'allowed'

for'a'more'detailed'understanding'of'the'needs'of'chemoinformatics'researchers'

at'The'University'of'Sheffield’s'Information'School,'and'that'any'further'research'

in'this'area'can'now'use'this'system'as'a'starting'point.'

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' 72'

8..References.

Brown,'F.'K.'(1998).'Chemoinformatics:'What'is'it'and'How'Does'it'Impact'Drug'Discovery?'Annual/Reports/in/Medical/Chemistry,'33,'375–384.'

Garrett,'J.'J.'(2011).'The/Elements/of/User/Experience:/UserDCentered/Design/for/the/Web/and/Beyond'(2nd'ed.).'Berkeley:'New'Riders.'

Gasteiger,'J.,'&'Engel,'T.'(Eds.).'(2003).'Chemoinformatics:/A/Textbook.'Dramstradt:'WILEYcVC.'

Johnson,'J.'(2003).'Web/Bloopers:/60/Common/Web/Design/Mistakes/and/How/to/Avoid/Them.'San'Francisco:'Morgan'Kaufmann.'

Krug,'S.'(2006).'Don’t/Make/Me/Think:/A/Common/Sense/Approach/to/Web/Usability'(2nd'ed.).'Berkeley:'New'Riders.'

Leach,'A.,'&'Gillet,'V.'(2003).'An/Introduction/to/Chemoinformatics.'Dordrecht:'Kluwer'Academic'Publishers.'

Nielsen,'J.,'&'Norman,'D.'(n.d.).'The'Definition'of'User'Experience.'Nielsen/Norman/Group.'Retrieved'from'http://www.nngroup.com/articles/definitioncusercexperience/'

Nixon,'R.'(2012).'Learning/PHP,/MySQL,/JavaScript,/&/CSS'(2nd'ed.).'Sebastopol:'O’Reilly'Media.'

Paris,'G.'(1999).'No'Title.'In'August/Meeting/of/the/American/Chemical/Society.'quoted'by'Warr.'Retrieved'from'http://www.warr.com/warrzone.htm'

Roy,'A.'(2013).'20+'Best'PHP'Practices'That'You'Must'Follow.'corephp.com.'Retrieved'from'https://www.corephp.com/blog/phpcbestcpracticescthatcyoucmustcfollow/'

Welling,'L.,'&'Thomson,'L.'(2009).'PHP/and/MySQL/Web/Development'(4th'ed.).'Pearson'Education'Limited.'

Willet,'P.'(2011).'Chemoinformatics:'A'History.'Wiley/Interdisciplinary/Reviews:/Computational/Molecular/Science,'1(1),'46–56.'

Wright,'P.,'&'McCarthy,'J.'(2010).'ExperienceDCentered/Design:/Designers,/Users,/and/Communities/in/Dialogue.'Morgan'&'Claypool'Publishers.'

' 73'

9..Appendices.

Appendix.I:.List.of.Fields.

Compound.Search. Target.Search.CHEMBL. CHEMBL.chembl_id* molregno*molregno* alogp*alogp* rtb*rtb* acd_most_apka*acd_most_apka* acd_logp*acd_logp* acd_logd*acd_logd* aromatic_rings*aromatic_rings* full_mwt*full_mwt* canonical_smiles*compound_name* *canonical_smiles* *. .MDDR* MDDR*name* extreg*molregno* name*molformula* active_class*active_class* molweight*molweight* smiles*smiles* ** *Wombat. Wombat.smiles* smiles*logknow* logknow*logwsol* logwsol*atomcount* atomcount*bondcount* bondcount*ringcount* ringcount*rotbonds* rotbonds*rigbonds* rigbonds*pos_ioniz* pos_ioniz*neg_ioniz* neg_ioniz*lpk_hbd* lpk_hbd*lpk_hba* lpk_hba*lpk_clogp* lpk_clogp*lpk_score* lpk_score*sfa_pol* sfa_pol*sfa_nonpol* sfa_nonpol*

' 74'

isdrug* isdrug** *MUV. MUV.iupac_eo_name* active_class*molformula* target_class*active_class* iupac_eo_name*target_class* molformula*molweight* molweight*canonical_smiles* canonical_smiles*smiles* smiles*'

Appendix.II:.Overall.File.Structure.

FOLDERS.&.FILES. DESCRIPTIONS.chem. Main.folder.for.the.entire.site.*****login.php. Universal*login*page******index.php. Universal*welcome*page******chembl.php. Main*page*for*CHEMBL******mddr.php. Main*page*for*MDDR.*****wombat.php. Main*page*for*Wombat******muv.php. Main*page*for*MUV******name_fetch_chembl.php. PHP*file*for*CHEMBL*target*search*

autosuggest******name_fetch_mddr.php. PHP*file*for*MDDR*target*search*

autosuggest******name_fetch_wombat.php. PHP*file*for*Wombat*target*search*

autosuggest******name_fetch_muv.php. PHP*file*for*MUV*target*search*

autosuggest******process.php. Form*processing*for*saving*results*of*a*

given*search*and*saving*it*to*user*folder******_css. Style.sheets.folder.(CSS).**********style.css. External*style*sheet*....._images. Images.folder.**********logo.jpg. Site*logo***********pageKloader.gif. Page*loading*animation***********sort_asc.png. Up*arrow*for*tables***********sort_both.png. Up*and*down*arrow*for*tables***********sort_desc.png. Down*arrow*for*tables*....._includes. Includes.folder...........functions.php. External*functions*file*..........db_connection_chembl.php. Database*connection*file*for*CHEMBL*..........db_connection_mddr.php. Database*connection*file*for*MDDR*..........db_connection_wombat.php. Database*connection*file*for*Wombat*..........db_connection_muv.php. Database*connection*file*for*MUV*

' 75'

..........db_connection_close.php. Close*database*connection*file*

..........sessions.php. PHP*file*for*sessions*

..........save_form.php. Universal*form*for*saving*results*from*a*given*search*

..........show_hide_query.php. Display*the*user’s*query*in*a*box*and*toggle*it’s*visibility*

.........._layout. Layout.includes.folder.

...............header.php. Header*file****************footer.php. Footer*file****************db_selector_bar.php. Black*bar*and*logout*button****************db_selector_dropdown.php. Database*selection*dropdown*menu****************search_bar.php. Coloured*search*bar*with*search*box*and*

buttons*for*each*database****************welcome_message.php. Welcome*messages*for*the*welcome*

page*and*each*database*homepage*....._js. JavaScript.folder.**********autosuggest_chembl.js. JavaScript*for*CHEMBL*target*search*

autosuggest***********autosuggest_mddr.js. JavaScript*for*MDDR*target*search*

autosuggest***********autosuggest_wombat.js. JavaScript*for*Wombat*target*search*

autosuggest***********autosuggest_muv.js. JavaScript*for*MUV*target*search*

autosuggest***********datatables.js. JavaScript*for*all*tables*

.

Appendix.III:.Adding.a.New.Database.

The'following'presents'a'stepcbycstep'guide'on'how'to'add'a'new'database'to'the'

system'using'the'example'of'the'NCI'database:'

A. Create'a'new'PHP'file'in'the'main'chem'folder'and'name'it'nci.php.'This'

will'be'the'homepage'for'the'new'database.'

B. Copy'all'the'existing'code'from'one'of'the'simple'databases'homepage'

files'(i.e.'mddr.php'or'muv.php)'and'paste'it'into'nci.php.''

C. Change'the'required'connection'at'the'top'of'nci.php'to'

“_includes/db_connection_nci.php”'(see'Autosuggest'section'of'

Implementation).'

D. Change'the'JavaScript'link'at'the'top'of'nci.php'to'“_js/autosuggest_nci.js”'

(see'Autosuggest'section'of'Implementation).'

' 76'

E. Create'a'db_connection_nci.php'file'and'place'it'in'the'_includes'folder''

(see'Autosuggest'section'of'Implementation).'

F. Create'an'autosuggest_nci.js'script'and'place'it'in'the'_js'folder'(see'

Autosuggest'section'of'Implementation).'

G. Create'a'name_fetch_nci.php'file'and'place'it'in'the'main'chem'folder'(see'

Autosuggest'section'of'Implementation).'

H. Write'the'query'functions'for'the'new'compound'and'target'searches'in'

functions.php'file,'remembering'to'include'the'fields'relevant'to'the'new'

database.'

I. Replace'the'function'calls'in'nci.php'that'belonged'to'the'old'database,'e.g.'

mddr_compound_query(),'with'the'ones'that'call'the'functions'written'in'

the'previous'step.'

J. In'nci.php,'replace'the'old'mddr.php'table'heads'and'table'data'entries'

with'the'ones'for'the'NCI'database'(see'Displaying'Returned'Results'in'

Implementation).'

K. Create'a'new'entry'for'the'NCI'database'in'search_bar.php'(see'

Autosuggest'section'of'Implementation).'

L. Create'a'new'entry'for'the'NCI'database'in'welcome_message.php.'

M. Add'a'new'entry'for'the'NCI'database'to'the'db_selector_dropdown.php.'

N. Add'a'new'entry'for'the'NCI'database'to'the'db_selector_bar.php'file.'

O. In'style.css'make'the'necessary'additions'to'section'4.'Database'selection'

bar'(black)'and'section'5.'Search'bar'(coloured).'The'way'the'code'is'laid'

out'in'these'sections'should'make'it'obvious'what'needs'to'be'added.'Note'

that'two'colours'(one'light'and'one'dark)'must'be'chosen'to'identify'the'

new'database.'

If'the'new'database'is'to'include'a'refinement'page,'as'with'Wombat'and'

CHEMBL,'the'procedure'is'a'only'slightly'more'complicated:'

A. Instead'of'using'a'simple'database'homepage'such'as'mddr.php'as'the'

original'template,'use'wombat.php'or'chembl.php'instead.'

' 77'

B. Add'an'extra'query'function'to'the'functions.php'file'to'deal'with'the'refinement.'

C. Add'a'new'section'to'styles.css,'e.g.'15.'NCI'target'refinement'table,'based'on'either'the'10.'Chembl'target'refinement'table'or'11.'Wombat'target'refinement'table.'

'

Ethics'Information'Consent'Form'!!!The'University'of'Sheffield.'Information'School'!

A!UX!Interface!for!the!Chemical!Databases!Used!by!Chemoinformatics!Researchers!at!the!University!of!Sheffield!!

!Researchers'!Alex!Williams!(researcher)!–!awilliams9@sheffield.ac.uk!John!Holliday!(supervisor)!–!j.d.holliday@sheffield.ac.uk!!Purpose'of'the'research'!The!aim!of!this!project!is!the!creation!and!testing!of!single!frontLend!interface!and!point!of!access!to!all!the!test!databases!used!by!Chemoinformatics!researchers!at!The!University!of!Sheffield’s!Information!School.!The!overall!objective!is!the!complete!production!of!a!working!system!to!aid!in!their!retrieval!and!analysis!of!chemical!compounds!and!related!information.!!Who'will'be'participating?'!Participants!will!be!chemoinformatics!researchers!at!The!University!of!Sheffield’s!Information!School.!!What'will'you'be'asked'to'do?'!Participants!will!be!asked!to!take!part!in!an!initial!informal!interview!in!order!to!build!up!a!picture!of!how!the!currently!use!the!databases!and!what!they!would!like!form!the!new!interface.!They!will!then!be!asked!to!incrementally!test!the!new!interface!and!provide!ongoing!feedback.!!What'are'the'potential'risks'of'participating?'!The!risks!of!participating!are!the!same!as!those!experienced!in!everyday!life.!!!What'data'will'we'collect?'!Handwritten!notes!will!be!taken!during!the!interview!and!testing!phases.!!What'will'we'do'with'the'data?'!Data!will!be!used!to!inform!the!development!of!a!single!user!interface!for!accessing!the!test!databases!used!by!chemoinformatics!researchers!at!The!University!of!Sheffield’s!Information!School.!!Will'my'participation'be'confidential?'!

Yes.!There!will!be!no!identifying!information!on!the!notes!other!than!that!participants!are!chemoinformatics!researchers!at!The!University!of!Sheffield’s!Information!School.!!!What'will'happen'to'the'results'of'the'research'project?'!The!results!of!this!project!will!be!a!new!interface!for!the!chemoinformatics!databases!and!a!masters!dissertation!detailing!the!research!involved!in!its!development.!Please!contact!the!Information!School!in!6!months!to!request!access!to!the!dissertation.!!!!I!confirm!that!I!have!read!and!understand!the!description!of!the!research!project,!and!that!I!have!had!an!opportunity!to!ask!questions!about!the!project.!!I!understand!that!my!participation!is!voluntary!and!that!I!am!free!to!withdraw!at!any!time!without!any!negative!consequences.!!I!understand!that!I!may!decline!to!answer!any!particular!question!or!questions,!or!to!do!any!of!the!activities.!If!I!stop!participating!at!all!time,!all!of!my!data!will!be!purged.!!I!understand!that!my!responses!will!be!kept!strictly!confidential,!that!my!name!or!identity!will!not!be!linked!to!any!research!materials,!and!that!I!will!not!be!identified!or!identifiable!in!any!report!or!reports!that!result!from!the!research.!!I!give!permission!for!the!research!team!members!to!have!access!to!my!anonymised!responses.!!I!give!permission!for!the!research!team!to!reLuse!my!data!for!future!research!as!specified!above.!!I!agree!to!take!part!in!the!research!project!as!described!above.!!! ! !Participant!Name!(Please!print)! ! Participant!Signature!!!!Alex!Williams!

! !

Researcher!Name!(Please!print)! ! Researcher!Signature!!!Date!!!Note:''If'you'have'any'difficulties'with,'or'wish'to'voice'concern'about,'any'aspect'of'your'participation'in'this'study,'please'contact'Dr.'Angela'Lin,'Research'Ethics'Coordinator,'Information'School,'The'University'of'Sheffield'(ischool_ethics@sheffield.ac.uk),'or'to'the'University'Registrar'and'Secretary.'!

Information School Research Committee – Research Ethics Application Form, version 1.1, 2012

The$University$of$Sheffield.$Information$School$

$

Proposal$for$$Research$Ethics$Review$

!

Students$ Staff$This$proposal$submitted$by:$! This$proposal$is$for:$$! Undergraduate! ! Specific!research!project!X! Postgraduate!(Taught)!–!PGT! ! Generic!research!project!! Postgraduate!(Research)!–!PGR! This!project!is!funded!by:!

Project$Title:! A!UX!Interface!for!the!Chemical!Databases!Used!by!Chemoinformatics!Researchers!at!the!

University!of!Sheffield!!!

Start$Date:! 25/06/14! End$Date:$ 01/09/2014! Principal$Investigator$(PI):$$

(student(for(supervised(UG/PGT/PGR(research)(

Alex!Williams!!

Email:$ awilliams9@sheffield.ac.uk!!Supervisor:$$

(if$PI$is$a$student)$John!Holliday!!

Email:$ j.d.holliday@sheffield.ac.uk!!Indicate$if$the$research:$$$$$$$$$$$$$$(put$an$X$in$front$of$all$that$apply)$

$ Involves!adults!with!mental!incapacity!or!mental!illness,!or!those!unable!to!make!a!personal!decision$

$ Involves!prisoners!or!others!in!custodial!care!(e.g.!young!offenders)$

$ Involves!children!or!young!people!aged!under!18!years!of!age!

$ Involves!highly!sensitive!topics!such!as!‘race’!or!ethnicity;!political!opinion;!religious,!spiritual!or!other!beliefs;!physical!or!mental!health!conditions;!sexuality;!abuse!(child,!adult);!nudity!and!the!body;!criminal!activities;!political!asylum;!conflict!situations;!and!personal!violence.$

Please$indicate$by$inserting$an$“X”$in$the$left$hand$box$that$you$are$conversant$with$the$University’s$policy$

on$the$handling$of$human$participants$and$their$data.$

X

We$confirm$that$we$have$read$the$current$version$of$the$University$of$Sheffield$Ethics$Policy$Governing$Research$Involving$Human$Participants,$Personal$Data$and$Human$Tissue,$as$shown$on$the$University’s$research$ethics$website$at:$www.sheffield.ac.uk/ris/other/govMethics/ethicspolicy

Information School Research Committee – Research Ethics Application Form, version 1.1, 2012

Part$B.$$Summary$of$the$Research$!B1.$ Briefly$summarise$the$project’s$aims$and$objectives:$(This!must!be!in!language!comprehensible!to!a!layperson!and!should!take!no!more!than!one[half!page.!Provide!enough!information!so!that!the!reviewer!can!understand!the!intent!of!the!research)!$Summary:$!The!aim!of!this!project!is!the!creation!and!testing!of!single!front[end!interface!and!point!of!access!to!all!the!test!databases!used!by!Chemoinformatics!researchers!at!The!University!of!Sheffield’s!Information!School.!The!overall!objective!is!the!complete!production!of!a!working!system!to!aid!in!their!retrieval!and!analysis!of!chemical!compounds!and!related!information.!Research!will!allow!this!interface!to!be!usable!and!specifically!tailored!to!user!needs,!including!the!features!and!functionalities!they!require!and!supporting!the!typical!tasks!they!carry!out.!$$B2.$ Methodology:$Provide!a!broad!overview!of!the!methodology!in!no!more!than!one[half!page.!$Overview$of$Methods:$$Research!will!involve!exploring!the!specific!needs!of!researchers!in!regard!to!the!proposed!system.!This!research!will!be!combined!with!the!basic!principles!of!user[experience!and!chemical!information!retrieval!as!identified!in!the!literature.!Overall,!two!specific!research!methodologies!will!be!used!throughout!this!project.!Firstly,!initial!informal!interviews!with!participants!will!be!used!to!build!up!a!picture!of!how!they!currently!use!the!databases,!what!they!would!like!to!be!able!to!do!with!the!new!interface,!the!kinds!of!tasks!they!commonly!perform,!the!essential!features!to!be!included!in!the!new!interface,!and!the!information!they!want!returned!when!conducting!a!search.!Secondly,!an!incremental!design!and!development!process,!beginning!with!an!initial!mock[up,!will!be!used!to!test!and!refine!the!system.!!$!If$more$than$one$method,$e.g.,$survey,$interview,$etc.$is$used,$please$respond$to$the$questions$in$Section$C$for$each$method.$That$is,$if$you$are$using$both$a$survey$and$interviews,$duplicate$the$page$and$answer$the$questions$for$each$method;$you$need$not$duplicate$the$information,$and$may$simply$indicate,$“see$previous$section.”!!! !

Information School Research Committee – Research Ethics Application Form, version 1.1, 2012

C1.$ Briefly$describe$how$each$method$will$be$applied Method$(e.g.,$survey,$interview,$observation,$experiment):$Informal!Interviews$$Description$–$how$will$you$apply$the$method?$Participants!will!be!asked!to!discuss!the!kinds!of!research!they!currently!use!the!databases!for,!including!the!kind!of!information!they!typically!want!returned!and!the!most!common!tasks,!as!well!as!indicate!why!they!would!like!to!be!able!to!do!with!the!new!interface.!These!will!not!be!recorded,!but!notes!will!be!taken.$$Method$(e.g.,$survey,$interview,$observation,$experiment):$Incremental!Design!and!Development$$Description$–$how$will$you$apply$the$method?$Participants!will!be!asked!to!repeatedly!test!the!system!interface!and!provide!on[going!feedback.!This!will!not!be!recorded,!but!notes!will!be!taken.$! About$your$Participants$$C2.$ Who$ will$ be$ potential$ participants?$ Participants! will! be! chemoinformatics! researchers! at! The!University!of!Sheffield’s!Information!School$$C3.$ How$ will$ the$ potential$ participants$ be$ identified$ and$ recruited?$ Potential! participants! will! be!contacted!by!email!and!asked!if!they!wish!to!take!part.$!C4.$$ What$ is$ the$ potential$ for$ physical$ and/or$ psychological$ harm$ /$ distress$ to$ participants?$ The! risks!involved!are!the!same!as!those!encountered!in!everyday!life.$!C5.$ Will$informed$consent$be$obtained$from$the$participants?$ $$

X! Yes$$ No$

$If$Yes,$please$explain$how$informed$consent$will$be$obtained?$Participants!will!be!asked!to!read!and!agree!to!the!Information!Consent!Form$$If$No,$please$explain$why$you$need$to$do$this,$and$how$the$participants$will$be$deMbriefed?$!$C6.$ Will$financial$/$in$kind$payments$(other$than$reasonable$expenses$and$compensation$for$time)$be$offered$to$participants?!No!!About$the$Data$!C7.$What$data$will$be$collected?$(Tick$all$that$apply)$$

$ Print$ Digital$Participant$observation$$ $ $Audio$recording$ $ $Video$recording$ $ $Computer$logs$ $ $Questionnaires/Surveys$$ $ !Other:$ ! Interview!

notes!Other:$ $ User!

Information School Research Committee – Research Ethics Application Form, version 1.1, 2012

testing!notes!

$$C8.$What$measures$will$be$put$in$place$to$ensure$confidentiality$of$personal$data,$where$appropriate?$$There! will! be! no! identifying! information! in! the! notes! or! questionnaires! other! than! that! participants! are!chemoinformatics!researchers!at!The!University!of!Sheffield’s!Information!School.!$C9.$How/Where$will$the$data$be$stored?$$Data!will!be!stored!on!my!own!machine!and!deleted!at!the!end!of!the!study.!$C10.$Will$the$data$be$stored$for$future$reMuse?$If$so,$please$explain$$No!$$About$the$Procedure$ C11.$ Does$ your$ research$ raise$ any$ issues$ of$ personal$ safety$ for$ you$ or$ other$ researchers$ involved$ in$ the$project$ (especially$ if$ taking$ place$ outside$working$ hours$ or$ off$University$ premises)?$ If$ so,$ please$ explain$how$it$will$be$managed.$$ $

Information School Research Committee – Research Ethics Application Form, version 1.1, 2012

The$University$of$Sheffield.$Information$School$$

Research$Ethics$Review$Declaration$

Title$of$Research$Project:$A!UX!Interface!for!the!Chemical!Databases!Used!by!Chemoinformatics!Researchers!at!the!

University!of!Sheffield!

!

We!confirm!our!responsibility!to!deliver!the!research!project!in!accordance!with!the!University!of!Sheffield’s!

policies!and!procedures,!which!include!the!University’s!‘Financial(Regulations’,!‘Good(Research(Practice(Standards’!and!the!‘Ethics(Policy(Governing(Research(Involving(Human(Participants,(Personal(Data(and(Human(Tissue’!(Ethics!Policy)!and,!where!externally!funded,!with!the!terms!and!conditions!of!the!research!funder.!

!

In$submitting$this$research$ethics$application$form$I$am$also$confirming$that:$• The!form!is!accurate!to!the!best!of!our!knowledge!and!belief.$!• The!project!will!abide!by!the!University’s!Ethics!Policy.(• There!is!no!potential!material!interest!that!may,!or!may!appear!to,!impair!the!independence!and!

objectivity!of!researchers!conducting!this!project.!

• Subject!to!the!research!being!approved,!we!undertake!to!adhere!to!the!project!protocol!without!

unagreed!deviation!and!to!comply!with!any!conditions!set!out!in!the!letter!from!the!University!ethics!

reviewers!notifying!me!of!this.!

• We!undertake!to!inform!the!ethics!reviewers!of!significant!changes!to!the!protocol!(by!contacting!our!

academic!department’s!Ethics!Coordinator!in!the!first!instance).!

• we!are!aware!of!our!responsibility!to!be!up!to!date!and!comply!with!the!requirements!of!the!law!and!

relevant!guidelines!relating!to!security!and!confidentiality!of!personal!data,!including!the!need!to!

register!when!necessary!with!the!appropriate!Data!Protection!Officer!(within!the!University!the!Data!

Protection!Officer!is!based!in!CiCS).!

• We!understand!that!the!project,!including!research!records!and!data,!may!be!subject!to!inspection!for!

audit!purposes,!if!required!in!future.!

• We!understand!that!personal!data!about!us!as!researchers!in!this!form!will!be!held!by!those!involved!

in!the!ethics!review!procedure!(e.g.!the!Ethics!Administrator!and/or!ethics!reviewers)!and!that!this!

will!be!managed!according!to!Data!Protection!Act!principles.!

• If!this!is!an!application!for!a!‘generic’!project!all!the!individual!projects!that!fit!under!the!generic!

project!are!compatible!with!this!application.!

• We$understand$that$this$project$cannot$be$submitted$for$ethics$approval$in$more$than$one$department,$and$that$if$I$wish$to$appeal$against$the$decision$made,$this$must$be$done$through$the$original$department.$

!

Name$of$the$Student$(if$applicable):$Alex(Williams($Name$of$Principal$Investigator$(or$the$Supervisor):$$John(Holliday($Date:$$25/06/2014(

Information School Research Committee – Research Ethics Application Form, version 1.1, 2012

Information School Research Ethics Panel Letter of Approval Date: 2nd July 2014 TO: Alex Williams The Information School Research Ethics Panel has examined the following application: Title: A UX Interface for the Chemical Databases Used by Chemoinformatics Researchers at the University of Sheffield Submitted by: Alex Williams And found the proposed research involving human participants to be in accordance with the University of Sheffield’s policies and procedures, which include the University’s ‘Financial Regulations’, ‘Good Research Practice Standards’ and the ‘Ethics Policy Governing Research Involving Human Participants, Personal Data and Human Tissue’ (Ethics Policy). This letter is the official record of ethics approval by the School, and should accompany any formal requests for evidence of research ethics approval. Effective Date: 1st July 2014

Dr Angela Lin Research Ethics Coordinator

Information School.

Access to Dissertation A Dissertation submitted to the University may be held by the Department (or School) within which the Dissertation was undertaken and made available for borrowing or consultation in accordance with University Regulations. Requests for the loan of dissertations may be received from libraries in the UK and overseas. The Department may also receive requests from other organisations, as well as individuals. The conservation of the original dissertation is better assured if the Department and/or Library can fulfill such requests by sending a copy. The Department may also make your dissertation available via its web pages. In certain cases where confidentiality of information is concerned, if either the author or the supervisor so requests, the Department will withhold the dissertation from loan or consultation for the period specified below. Where no such restriction is in force, the Department may also deposit the Dissertation in the University of Sheffield Library. To be completed by the Author – Select (a) or (b) by placing a tick in the appropriate box If you are willing to give permission for the Information School to make your dissertation available in these ways, please complete the following:

√ (a) Subject to the General Regulation on Intellectual Property, I, the author, agree to this dissertation being made immediately available through the Department and/or University Library for consultation, and for the Department and/or Library to reproduce this dissertation in whole or part in order to supply single copies for the purpose of research or private study

(b) Subject to the General Regulation on Intellectual Property, I, the author, request that this dissertation be withheld from loan, consultation or reproduction for a period of [ ] years from the date of its submission. Subsequent to this period, I agree to this dissertation being made available through the Department and/or University Library for consultation, and for the Department and/or Library to reproduce this dissertation in whole or part in order to supply single copies for the purpose of research or private study

Name: Alex Williams

Department : Information School

Signed Date: 31/08/14

To be completed by the Supervisor – Select (a) or (b) by placing a tick in the appropriate box

(a) I, the supervisor, agree to this dissertation being made immediately available through the Department and/or University Library for loan or consultation, subject to any special restrictions (*) agreed with external organisations as part of a collaborative project.

*Special restrictions

(b) I, the supervisor, request that this dissertation be withheld from loan, consultation or reproduction for a period of [ ] years from the date of its submission. Subsequent to this period, I, agree to this dissertation being made available through the Department and/or University Library for loan or consultation, subject to any special restrictions (*) agreed with external organisations as part of a collaborative project

Name

Department

Signed Date

THIS SHEET MUST BE SUBMITTED WITH DISSERTATIONS BY DEPARTMENTAL REQUIREMENTS.