When we think about search there are essentially two activities we wish to perform 1) Search to find a known thing and 2) Search to explore/research around a thing. When we search to find returning hits in a list format works well. However when we want to explore a list is a poor way to visualise the returned hits. This presentation looks at how semantics can be used to develop solutions that allow people to explore information space rather than just search it.

1. From Search to Semantics
Ben Gardner
Collaboration & Information Consultant
Ben at differentiatedthinking.com
http://www.linkedin.com/in/bengardner135

2. From Search to Semantics
Looking for Information
Exploring Connections
meet Jessica – A vision of working in a
Semantic enabled organisation
Ben Gardner

3. We live in exponential times
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4. Many Places for Lots of Bits
? Targetpedia
TOU
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5. Clay Shirky http://www.youtube.com/watch?v=LabqeJEOQyI or Filter Failure

6. Search – Quick & Dirty
The problem The first step
GDMS
ECF
BioBook CeN
Multiple repositories x Multiple Search tools
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7. Search 101
On the Web content is networked
In the organisation content is disconnected
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8. Navigators
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9. Refine Results
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10. Steps in Developing Search
Validate UI
Index Content
Identify Navigators
Identify the Sources
Understand your
Community
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11. What is the community looking for?
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12. Target Relevancy
Regulatory Document
Management System
IND/NDA
Filter Investigator Brochure
Clinical Study Report
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13. Building Navigators
Metadata Vocabularies/Taxonomies/Ontologies
• Intracellular Signalling P&P
– Protein Kinase
• Serine Kinase
• Tyrosine Kinase
– ……
– JAK2
– JAK3
» JAK-3
» LJAK
» L-JAK
» ……
– KDR
– …..
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14. Indexing
Target
Author Disease
Doc
Project Drug
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15. Networked Information
Disconnected
Networked
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16. User Interface
• Synonym expansion
• Tune vocabularies
• Promote recommended hits
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17. Showing Value
How long does it take to find a Clinical Study Report?
• Clinical Study Report for Maraviroc (UK-427857) Clinical Protocol A5002345
GDMS SEEK Research Edition
Navigate to 1:43 Min NA
Basic Search 8:24 Min & 4950 hits <1 second & 7 hits
(3rd document)
Advanced 20 Sec & 519 hits Not Needed
Search (8th document)*
Complex UI that requires
significant GDMS SME
SEEK Research Edition – simple, fast and focused
* It took 3 attempts to correctly construct the GDMS Adv. Search query, the first 2 attempts returned no documents
& took 8 minutes each to complete
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18. Search to Find

19. Semantics to Explore

20. Things have Properties
Jessica
Expertise Projects Targets Location
Molecular Pharmacology D3 Agonist for FSD 5HT1a&b Sandwich
Molecular Biology Nav1.7 for Pain G-Proteins
Receptor Theory CB2 for Obesity CB1&2
G-Protein Coupled Receptors D2 for Schizophrenia P38
Modelling Arrestin’s
Data Visualisation
Receptor Regulation
In Vitro Assay Development
Ben Gardner

21. Semantics: Exploring Connections
Jessica Cannabinoid Receptor 2 Migraine
[+] Expertise [+] Structure [-] Targets
[+] Projects [+] Isoforms CGRP
[-] Targets [+] Pharmacological tools 5HT1D
CBR2 [-] Implicated in CB2
5HT1A&C Migraine PDE3
G-Proteins Obesity Ras
P38 Schizophrenia [+] Competitive Intelligence
Arrestin’s ….. [+] Treatments
[+] Location [+] ……
Vocabularies
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22. Resource Description Framework (RDF)
Subject Predicate Object
<Jessica> <hasExpertise> <CB2>
RDF Triple
Combining Triples creates a directed, labelled graph
<Molecular
Biology>
hasSkill <Nav1.7 for
hasWorkedOn Pain>
Graph
<Jessica> hasLocation
<Sandwich>
hasExpertise
<CB2>
Inspired by J Phil Brooks
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23. Graphs can be joined together ……
<Molecular
Biology>
hasSkill <Nav1.7 for
hasWorkedOn Pain>
<Jessica> hasLocation
<Sandwich>
hasExpertise
<CB2>
<CB2> Implicated_in
<Migraine>
subClassOf hasTool
<PF-334,765>
<GPCR>
Inspired by J Phil Brooks
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24. Graphs can be joined together ……
<Molecular
Biology>
hasSkill <Nav1.7 for
hasWorkedOn Pain>
<Jessica> hasLocation
<CGRP>
<Sandwich>
Associated target
hasExpertise
<CB2> Implicated_in
Associated target
<Migraine> <5HT1D>
subClassOf hasTool
hasTreatmentClass
<PF-334,765>
<GPCR>
<Tryptan>
…... to traverse the knowledge space Inspired by J Phil Brooks
Ben Gardner

25. Linked Open Data
http://richard.cyganiak.de/2007/10/lod/ Ben Gardner

26. Targetpedia: Building Nodes
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27. Simplifying Access to Target Information
What’s Know About My Target?
Where is My Target Expressed?
Can I Better Understand the Pathway?
Is There Relevant Compound Information ?
What Can I Learn About Pfizer Projects and Portfolio Information?
What Safety Tools Might Be Available?
Ben Gardner

28. Simplifying Access to Target Information
What’s Know About My Target?
TKR2 (tkr2.pfizer.com)Ensembl (http://uswest.ensembl.org/index.html) Provides information on gene knowledge,OMIM
(http://www.ncbi.nlm.nih.gov/entrez/query.fcgi?db=OMIM) Association the genes with genetic disorders,NCBI
(www.ncbi.nlm.nih.gov/Sitemap/index.html) Broad source of genomic information,NextBio (https://pfizer.nextbio.com ) Comprehensive
literature search on the target; also body atlas,GEMM phenotype finder (http://phenotypepfinder.pfizer.com/gemmi/),JAX Lab Mouse
Phenome (http://phenome.jax.org/) Mouse phenotype database,Kinase Safety Knowledgebase (Kinase Safety Knowledgebase) for kinase
targets
Where is My Target Expressed?
Protein: Lifespan (http://www.lsbio.com/) login is “pfizer”; password is “phish”, Human Protein Atlas (http://www.proteinatlas.org/ Human
IHC Tissue staining , mRNA: Body map (http://bodymap.pfizer.com/) Use this to access Rat Map, Dog Map, Mouse Map, Eye Map
,etc, BioGPS (http://biogps.gnf.org/#goto=welcome) affymetrix chip information, Expression Portal
(http://sanlnx33.uk.pfizer.com:8777/ExpressionPortal/) Internal and external data sets for target queries, including a variety of species, cell
lines and disease conditions ,Gene Expression Atlas (http://www.ebi.ac.uk/gxa/) External data; version with internal Pfizer data added is
available at http://amrgrol002.pfizer.com:8888/gxa/ , Allen Brain Atlas (http://www.brain-map.org/welcome.do) Mouse Brain ISH staining
Transgenic mouse), BGEM (http://www.gensat.org/index.html) Brain staining in transgenic mice
Can I Better Understand the Pathway?
Ingenuity (http://www.ingenuity.com/) Explore networks involving genes of interest. Links to known pathways, GeneGo MetaCore
(http://www.genego.com/metacore.php/) Curated pathways, metabolic and signaling networks
Is There Relevant Compound Information ?
RGate (http://rgate.pfizer.com/portal/) Compound structure, similar compounds, compound properties, assay results
What Can I Learn About Pfizer Projects and Portfolio Information?
PMI (http://pmi.pfizer.com) Link to Pfizer Portfolio information,Competitor Information –Prous database
(http://integrity.prous.com/integrity/servlet/xmlxsl/pk_home.util_home)
What Safety Tools Might Be Available?
Toxicomatrix (http://pfizerpedia.pfizer.com/index.php/Toxicomatrix), DSRD Safety Road Maps (http://ecf.pfizer.com/sites/DSRD-
ERTS/default.aspx?RootFolder=%2fsites%2fDSRD%2dERTS%2fShared%20Documents%2fRoad%20Maps&FolderCTID=&View=%7b640BA3E6%2d
ECEE%2d4A0F%2d99D4%2d6000FE11798C%7d) Ben Gardner

29. Targetpedia a One Stop Shop
What safety tools
What’s to might be available?
know about
Where is my
my target?
target Expressed?
What can I
learn about
Pfizer Projects
and Portfolio
Information?
Is there
Relevant
Compound Can I better
Information? Understand the
Pathway?
29
Ben Gardner

30. Targetpedia is a Node
http://richard.cyganiak.de/2007/10/lod/ Ben Gardner

31. Exploring
Connections
with Jessica
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32. Jessica works here………..
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33. and here………..
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34. Jessica’s needs to connect with people
and information across the globe
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35. so Jessica needs tools that help her to
find the connections between people
and information inside and outside
of the firewall ….
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36. Jessica uses SEEK to search for the documents
she needs
SEEK also
suggests
colleagues,
papers and
projects that
may be relevant
based on her
search
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37. Jessica likes SEEK because it is
easy to use
She no longer needs to
know where a document is
stored
One place to Search
for everything
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38. Jessica likes targetpedia as it provides a one stop shop
for all her target information
Being able to tag and annotate targets lets Jessica
share insights and expertise

39. Targetpedia is just one of a suite of pedias that
Jessica uses
drugbook
Each pedia contains
contextually relevant
projectpedia
information in an easy
to consume format
diseasepedia
Having all this information available in theright place
makes it easy to find
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40. projectpedia provides Jessica with more than just a
snapshot of a projects status ….
….. it also
connects her
to the
team, their
notebook, Sha
rePoint
site, referen
ces ….
.... and alerts her if new content is available
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41. Jessica switch's to the Grid Explorer…….
…… to navigate the connections between the pedias
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42. The reflect plug-in lets Jessica light up the
documents she reads …..
drugbook
CENSORDED
projectpedia
diseasepedia
…… providing links that connect to people and information
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43. Now the information and people
Jessica needs are just
one click away
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44. 18 months ago Jessica’s did not know what she
was missing
She needed to know where information was
before she could use it
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45. Today because of Semantics…..
…… information finds Jessica’s
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46. ..ask Jessica what
Semantics means to
her………..?
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47. ..she’d say she
hates buzz
words………
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48. ..but it’s most
definitely about
Making
Connections
Matter
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49. Semantics Provides Context and
Enables Exploration
Web 2.0: People 2 People Linked Data: Data 2 Data
Contextualised Connections Ben Gardner

50. Invest in Language

51. Profile
Ben Gardner
Collaboration and Information Consultant
Contact via:
http://www.linkedin.com/in/bengardner135
Blog http://dif-fer-en-ti-ate.blogspot.com/
http://www.slideshare.net/bengardner135
email Ben at Differentiatedthinking.com