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From Search to SemanticsBen GardnerCollaboration & Information ConsultantBen at differentiatedthinking.comhttp://www.linke...
From Search to Semantics Looking for Information Exploring Connections  meet Jessica – A vision of working in a  Semantic ...
We live in exponential times                               Ben Gardner
Many Places for Lots of Bits        ?               Targetpedia        TOU                                      Ben Gardner
Clay Shirky   http://www.youtube.com/watch?v=LabqeJEOQyI   or Filter Failure
Search – Quick & Dirty            The problem                         The first step               GDMS                   ...
Search 101On the Web content is networked                      In the organisation content is disconnected                ...
Navigators             Ben Gardner
Refine Results                 Ben Gardner
Steps in Developing Search                                              Validate UI                                   Inde...
What is the community looking for?                                     Ben Gardner
Target RelevancyRegulatory DocumentManagement System                               IND/NDA                      Filter   I...
Building NavigatorsMetadata            Vocabularies/Taxonomies/Ontologies                    • Intracellular Signalling P&...
Indexing              TargetAuthor                    Disease              Doc    Project            Drug                 ...
Networked InformationDisconnected                            Networked                                   Ben Gardner
User Interface• Synonym expansion• Tune vocabularies• Promote recommended hits                             Ben Gardner
Showing Value   How long does it take to find a Clinical Study Report?         •   Clinical Study Report for Maraviroc (UK...
Search to Find
Semantics to Explore
Things have Properties                                        JessicaExpertise                     Projects               ...
Semantics: Exploring ConnectionsJessica                 Cannabinoid Receptor 2      Migraine[+] Expertise           [+] St...
Resource Description Framework (RDF)                              Subject                   Predicate                     ...
Graphs can be joined together ……                           <Molecular                            Biology>         hasSkill...
Graphs can be joined together ……                            <Molecular                             Biology>         hasSki...
Linked Open Datahttp://richard.cyganiak.de/2007/10/lod/                  Ben Gardner
Targetpedia: Building Nodes                              Ben Gardner
Simplifying Access to Target InformationWhat’s Know About My Target?Where is My Target Expressed?Can I Better Understand t...
Simplifying Access to Target Information What’s Know About My Target? TKR2 (tkr2.pfizer.com)Ensembl (http://uswest.ensembl...
Targetpedia a One Stop Shop                                      What safety toolsWhat’s to                             mi...
Targetpedia is a Nodehttp://richard.cyganiak.de/2007/10/lod/                Ben Gardner
Exploring   Connectionswith   Jessica                 Ben Gardner
Jessica   works here………..                            Ben Gardner
and here………..                Ben Gardner
Jessica’s needs to connect with peopleand information across the globe                                         Ben Gardner
so Jessica needs tools that help her tofind the connections between peopleand information inside and outsideof the firewal...
Jessica uses   SEEK   to   search   for the documentsshe needs                                              SEEK also     ...
Jessica likes   SEEK   because it iseasy to use She   no longer needs to know where a document is stored     One place to ...
Jessica likes targetpedia as it provides a     one stop shopfor all her target information                 Being able to  ...
Targetpedia           is just one of a   suite of pedias thatJessica uses                                                 ...
projectpedia provides Jessica with more than just asnapshot    of a projects status ….                                    ...
Jessica switchs to the   Grid Explorer…….          …… to   navigate   the   connections   between the pedias              ...
The reflect plug-in lets Jessica                        light up   thedocuments she reads …..                             ...
Now the   information and people          Jessica needs are just                        one click away                    ...
18 months ago Jessica’s did not know what shewas missing        She needed to know where information was                  ...
Today because of Semantics…..                 …… information finds Jessica’s                                          Ben ...
..ask Jessica whatSemantics means toher………..?                     Ben Gardner
..she’d say shehates buzzwords………             Ben Gardner
..but it’s mostdefinitely about             Making               Connections                      Matter                  ...
Semantics Provides Context and            Enables ExplorationWeb 2.0: People 2 People                        Linked Data: ...
Invest in Language
ProfileBen GardnerCollaboration and Information Consultant                        Contact via:                            ...
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From Search to Semantics

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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.

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From Search to Semantics

  1. 1. From Search to SemanticsBen GardnerCollaboration & Information ConsultantBen at differentiatedthinking.comhttp://www.linkedin.com/in/bengardner135
  2. 2. From Search to Semantics Looking for Information Exploring Connections meet Jessica – A vision of working in a Semantic enabled organisation Ben Gardner
  3. 3. We live in exponential times Ben Gardner
  4. 4. Many Places for Lots of Bits ? Targetpedia TOU Ben Gardner
  5. 5. Clay Shirky http://www.youtube.com/watch?v=LabqeJEOQyI or Filter Failure
  6. 6. Search – Quick & Dirty The problem The first step GDMS ECF BioBook CeNMultiple repositories x Multiple Search tools Ben Gardner
  7. 7. Search 101On the Web content is networked In the organisation content is disconnected Ben Gardner
  8. 8. Navigators Ben Gardner
  9. 9. Refine Results Ben Gardner
  10. 10. Steps in Developing Search Validate UI Index Content Identify Navigators Identify the SourcesUnderstand yourCommunity Ben Gardner
  11. 11. What is the community looking for? Ben Gardner
  12. 12. Target RelevancyRegulatory DocumentManagement System IND/NDA Filter Investigator Brochure Clinical Study Report Ben Gardner
  13. 13. Building NavigatorsMetadata Vocabularies/Taxonomies/Ontologies • Intracellular Signalling P&P – Protein Kinase • Serine Kinase • Tyrosine Kinase – …… – JAK2 – JAK3 » JAK-3 » LJAK » L-JAK » …… – KDR – ….. Ben Gardner
  14. 14. Indexing TargetAuthor Disease Doc Project Drug Ben Gardner
  15. 15. Networked InformationDisconnected Networked Ben Gardner
  16. 16. User Interface• Synonym expansion• Tune vocabularies• Promote recommended hits Ben Gardner
  17. 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 Ben Gardner
  18. 18. Search to Find
  19. 19. Semantics to Explore
  20. 20. Things have Properties JessicaExpertise Projects Targets LocationMolecular Pharmacology D3 Agonist for FSD 5HT1a&b SandwichMolecular Biology Nav1.7 for Pain G-ProteinsReceptor Theory CB2 for Obesity CB1&2G-Protein Coupled Receptors D2 for Schizophrenia P38Modelling Arrestin’sData VisualisationReceptor RegulationIn Vitro Assay Development Ben Gardner
  21. 21. Semantics: Exploring ConnectionsJessica 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 Ben Gardner
  22. 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 Ben Gardner
  23. 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 Ben Gardner
  24. 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. 25. Linked Open Datahttp://richard.cyganiak.de/2007/10/lod/ Ben Gardner
  26. 26. Targetpedia: Building Nodes Ben Gardner
  27. 27. Simplifying Access to Target InformationWhat’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. 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 targetsWhere is My Target Expressed?Protein: Lifespan (http://www.lsbio.com/) login is “pfizer”; password is “phish”, Human Protein Atlas (http://www.proteinatlas.org/ HumanIHC 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, celllines and disease conditions ,Gene Expression Atlas (http://www.ebi.ac.uk/gxa/) External data; version with internal Pfizer data added isavailable at http://amrgrol002.pfizer.com:8888/gxa/ , Allen Brain Atlas (http://www.brain-map.org/welcome.do) Mouse Brain ISH stainingTransgenic 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 networksIs There Relevant Compound Information ?RGate (http://rgate.pfizer.com/portal/) Compound structure, similar compounds, compound properties, assay resultsWhat 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%2dECEE%2d4A0F%2d99D4%2d6000FE11798C%7d) Ben Gardner
  29. 29. Targetpedia a One Stop Shop What safety toolsWhat’s to might be available?know about Where is mymy target? target Expressed? What can I learn about Pfizer Projects and Portfolio Information?Is thereRelevantCompound Can I betterInformation? Understand the Pathway? 29 Ben Gardner
  30. 30. Targetpedia is a Nodehttp://richard.cyganiak.de/2007/10/lod/ Ben Gardner
  31. 31. Exploring Connectionswith Jessica Ben Gardner
  32. 32. Jessica works here……….. Ben Gardner
  33. 33. and here……….. Ben Gardner
  34. 34. Jessica’s needs to connect with peopleand information across the globe Ben Gardner
  35. 35. so Jessica needs tools that help her tofind the connections between peopleand information inside and outsideof the firewall …. Ben Gardner
  36. 36. Jessica uses SEEK to search for the documentsshe needs SEEK also suggests colleagues, papers and projects that may be relevant based on her search Ben Gardner
  37. 37. Jessica likes SEEK because it iseasy to use She no longer needs to know where a document is stored One place to Search for everything Ben Gardner
  38. 38. Jessica likes targetpedia as it provides a one stop shopfor all her target information Being able to tag and annotate targets lets Jessica share insights and expertise
  39. 39. Targetpedia is just one of a suite of pedias thatJessica 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 Ben Gardner
  40. 40. projectpedia provides Jessica with more than just asnapshot 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 Ben Gardner
  41. 41. Jessica switchs to the Grid Explorer……. …… to navigate the connections between the pedias Ben Gardner
  42. 42. The reflect plug-in lets Jessica light up thedocuments she reads ….. drugbook CENSORDED projectpedia diseasepedia …… providing links that connect to people and information Ben Gardner
  43. 43. Now the information and people Jessica needs are just one click away Ben Gardner
  44. 44. 18 months ago Jessica’s did not know what shewas missing She needed to know where information was before she could use it Ben Gardner
  45. 45. Today because of Semantics….. …… information finds Jessica’s Ben Gardner
  46. 46. ..ask Jessica whatSemantics means toher………..? Ben Gardner
  47. 47. ..she’d say shehates buzzwords……… Ben Gardner
  48. 48. ..but it’s mostdefinitely about Making Connections Matter Ben Gardner
  49. 49. Semantics Provides Context and Enables ExplorationWeb 2.0: People 2 People Linked Data: Data 2 Data Contextualised Connections Ben Gardner
  50. 50. Invest in Language
  51. 51. ProfileBen GardnerCollaboration 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

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