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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.
Citation preview
Ben GardnerCollaboration & Information Consultant
Ben at differentiatedthinking.comhttp://www.linkedin.com/in/bengardner135
From Search to Semantics
From Search to Semantics
Looking for Information
Exploring Connections
Ben Gardner
meet Jessica – A vision of working in a Semantic enabled organisation
We live in exponential times
Ben Gardner
http://www.youtube.com/watch?v=LabqeJEOQyI or Filter FailureClay Shirky
Search – Quick & Dirty
GDMSECF
BioBook CeN
The problem The first step
Multiple repositories x Multiple Search tools
Ben Gardner
On the Web content is networked
In the organisation content is disconnected
Search 101
Ben Gardner
Navigators
Ben Gardner
Refine Results
Ben Gardner
Steps in Developing Search
Understand your Community
Identify the Sources
Identify Navigators
Index ContentValidate UI
Ben Gardner
What is the community looking for?
Ben Gardner
FilterIND/NDAInvestigator BrochureClinical Study Report
Target Relevancy
Regulatory Document Management System
Ben Gardner
Building Navigators
Metadata Vocabularies/Taxonomies/Ontologies
• Intracellular Signalling P&P– Protein Kinase
• Serine Kinase• Tyrosine Kinase
– ……– JAK2– JAK3
» JAK-3» LJAK» L-JAK» ……
– KDR– …..
Ben Gardner
Indexing
Doc
Target
Disease
DrugProject
Author
Ben Gardner
Networked Information
Disconnected
NetworkedBen Gardner
User Interface
• Synonym expansion• Tune vocabularies• Promote recommended hits
Ben Gardner
Showing Value
GDMS SEEK Research Edition
Navigate to 1:43 Min NA
Basic Search 8:24 Min & 4950 hits <1 second & 7 hits(3rd document)
Advanced Search
20 Sec & 519 hits(8th document)*Complex UI that requires significant GDMS SME
Not Needed
How long does it take to find a Clinical Study Report?• Clinical Study Report for Maraviroc (UK-427857) Clinical Protocol A5002345
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
Ben Gardner
Search to Find
Semantics to Explore
Things have Properties
Jessica
ExpertiseMolecular PharmacologyMolecular BiologyReceptor TheoryG-Protein Coupled ReceptorsModellingData VisualisationReceptor RegulationIn Vitro Assay Development
ProjectsD3 Agonist for FSDNav1.7 for PainCB2 for ObesityD2 for Schizophrenia
Targets5HT1a&bG-ProteinsCB1&2P38Arrestin’s
LocationSandwich
Ben Gardner
Semantics: Exploring Connections
Jessica[+] Expertise[+] Projects[-] Targets
CBR25HT1A&CG-ProteinsP38Arrestin’s
[+] Location
Cannabinoid Receptor 2[+] Structure[+] Isoforms[+] Pharmacological tools[-] Implicated in
MigraineObesitySchizophrenia…..
Migraine[-] Targets
CGRP5HT1DCB2PDE3Ras
[+] Competitive Intelligence[+] Treatments[+] ……
Vocabularies
Ben Gardner
Resource Description Framework (RDF)
Subject
<Jessica>
Predicate
<hasExpertise>
Object
<CB2>
RDF Triple
<Jessica>
<CB2>
<Sandwich>
<Nav1.7 forPain>
<MolecularBiology>
hasExpertise
hasLocation
hasWorkedOn
hasSkill
Graph
Combining Triples creates a directed, labelled graph
Ben GardnerInspired by J Phil Brooks
Graphs can be joined together ……
Inspired by J Phil Brooks
<Jessica>
<CB2>
<Sandwich>
<Nav1.7 forPain>
<MolecularBiology>
hasExpertise
hasLocation
hasWorkedOn
hasSkill
<CB2>
<PF-334,765>
<Migraine>
<GPCR>
hasTool
Implicated_in
subClassOf
Ben Gardner
<Jessica>
<CB2>
<Sandwich>
<Nav1.7 forPain>
<MolecularBiology>
hasExpertise
hasLocation
hasWorkedOn
hasSkill
<CB2>
<PF-334,765>
<GPCR>
hasTool
Implicated_in
subClassOf
<Migraine>
<Tryptan>
<5HT1D>
<CGRP>
hasTreatmentClass
Associated target
Associated target
…... to traverse the knowledge spaceBen Gardner
Graphs can be joined together ……
Inspired by J Phil Brooks
Linked Open Data
http://richard.cyganiak.de/2007/10/lod/ Ben Gardner
Targetpedia: Building Nodes
Ben Gardner
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 Safety Tools Might Be Available?
What Can I Learn About Pfizer Projects and Portfolio Information?
Ben Gardner
Simplifying Access to Target Information
28
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 targetsWhere 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 miceCan 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 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%2dECEE%2d4A0F%2d99D4%2d6000FE11798C%7d)
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)
Ben Gardner
Targetpedia a One Stop Shop
29
What’s to know about my target?
Where is my target Expressed?
Can I better Understand the Pathway?
Is there Relevant Compound Information?
What safety tools might be available?
What can I learn about Pfizer Projects and Portfolio Information?
Ben Gardner
Targetpedia is a Node
http://richard.cyganiak.de/2007/10/lod/ Ben Gardner
Exploring
Connections
with Jessica
Ben Gardner
Jessica works here………..
Ben Gardner
and here………..
Ben Gardner
Jessica’s needs to connect with people and information across the globe
Ben Gardner
so Jessica needs tools that help her to find the connections between people and information inside and outside of the firewall ….
Ben Gardner
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
Ben Gardner
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 Ben Gardner
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
projectpedia
drugbook
diseasepedia
Targetpedia is just one of a suite of pedias that Jessica uses
Having all this information available in the right place makes it easy to find
Each pedia contains contextually relevant information in an
easy to consume format
Ben Gardner
projectpedia provides Jessica with more than
just a snapshot of a projects status ….
.... and alerts her if new content is available
….. it also
connects her to the
team, their
notebook, SharePoint site,
references ….
Ben Gardner
Jessica switch's to the Grid Explorer…….
…… to navigate the connections between the pedias
Ben Gardner
projectpedia
drugbook
diseasepedia
The reflect plug-in lets Jessica light up the documents she reads …..
…… providing links that connect to people and information
CENSORDED
Ben Gardner
Now the information and people
Jessica needs are just
one click away
Ben Gardner
18 months ago Jessica’s did not know what she was missing
She needed to know where information was before she could use it
Ben Gardner
Today because of Semantics…..
…… information finds Jessica’sBen Gardner
..ask Jessica what
Semantics means to her………..?
Ben Gardner
..she’d say she hates
buzz words………
Ben Gardner
..but it’s most definitely about
Making
Connections
Matter
Ben Gardner
Semantics Provides Context and Enables Exploration
Web 2.0: People 2 People Linked Data: Data 2 Data
Contextualised Connections Ben Gardner
Invest in Language
Ben GardnerCollaboration and Information Consultant
http://www.linkedin.com/in/bengardner135
http://dif-fer-en-ti-ate.blogspot.com/ Bloghttp://www.slideshare.net/bengardner135
Contact via:
Profile
Ben at Differentiatedthinking.com
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