Semantic Web: Collaboration and Community

1. Semantic Web: Collaboration and Community

2. Alitora Systems • Semantic Search & Collaboration • Start-Up Software Company, Software-as-a-Service • Premium Semantic Data, Services, Apps • Sector: Biomedical/Pharma – Early Adopters • Memomics: Semantic Application Platform Founders: • Marc Hadfield “Tech Guy” • Peter Berger “Business Guy” http://www.alitora.com NYC, SF

3. Marc Hadfield • Computer Science • Previous: • CTO Financial Services Tech Start-Up • Search, Semantics • Research in NLP & applications to BioMedical / BioInformatics • Developer of kHarmony™ Semantic DB

4. Agenda • Introduction • Enabling Technology • Memomics Presentation • Memomics Web Application Demo • Memomics API Demo • Discussion and Q&A

5. Memomics.com • Memomics • Semantic Web Infrastructure service • Community driven Semantic & Ontology Resource • Accessible via API • Goals: • Community Vocabulary for the Semantic Web • Repository of Semantic Information • Community Process Driven • Concept DNS • Semantic Web “Network Solutions” • google.com  IP 72.14.207.99 • “apple (the fruit)”  ? • Enable Semantic Applications, Embed Semantics in Apps

6. Philosophy • Data Standards: • Bits  ASCII  EDI  XML  {Semantic Web} • More convenient but arbitrary data formats, encapsulate more “value” • Standards are useful because they are standards: • Betamax vs. VHS, TCP/IP, BluRay, … • Provide Overall Economic Advantage, trumps “better” • Semantic Web is at the end of arbitary-ness for data standards • Humans often don’t agree on meaning, are wrong, or inaccurate • No “standard meaning” is possible(i.e. “1984” and unthinkable thoughts) • Meaning must remain fully expressive • A protocol to encode meaning & determine “meaning agreement” is possible, enabling knowledge aggregation

7. Semantic Web • Current gaps and missing pieces: • Data • Technologies • Processes, Infrastructure, Services • Limitations on growth and wide acceptance • Proliferation (unchecked) of ontologies is bad • No better than no ontologies • Reinventing Babel, might as well stick with XML • Point of Ontologies is a shared world-view • Narrow, domain specific Ontologies are typically more useful than general Ontologies • Not one-size-fits-all • Must allow Ontology Interchange

8. Semantic Web sources… • Not Only: • OWL / RDF • But including: • Microformats • Topic Maps • Taxonomies (Species, MeSH, DMOZ) • HTML, XML, … (Wikipedia) • SQL Databases (CRM/SFA: customer data) • Deep Web…

9. Semantic Web – Namespaces • Namespace limitations in OWL / RDF / XML • Fragile dependency chain • Importing files into namespace not useful • Concepts are (pre)determined • No “relative” concepts • Can easily break with changes • Example: Food & Wine Ontology • Need persistence over time • Files as “container” problem • Need finer grain control • Distribute subsets of Ontologies • Externalize version control • Microformats, no namespaces

10. Semantic Web A is A

11. Semantic Web • Must become Easy (well, easier…)

12. Memomics Manifesto (I) • There can be no single ontology. • There can be no single formulism. • There can be no single ontology delivery mechanism.

13. Memomics Manifesto (II) • Concepts should be uniquely identifiable • the “Memes” of Memomics • Don’t URLs do this? (we still have root…) • Concepts should be shared, re-used (when possible) • Webservices must have Semantic Annotations • Mark-Up APIs not just data (Deep Web) • Compatible concepts should be aligned • Allow multiple Ontologies to be used seamlessly together.

14. Memomics Manifesto (III) • The community will use Ontologies in a variety of ways for a variety of purposes, both “formal” and “informal”. • Ontologies should not necessarily be “fragile” (logic), but formally formed Ontologies suitable for inference algorithms should be available wherever possible. • The true developers of Ontologies will be a mixture of Ontology Experts, Domain Experts, Technologists, and End Users. • No one should own an Ontology that is used by the entire Community.

15. Memomics.com • Use Cases: • Competitive Intelligence Platform that’s aware of Companies, Products, Competitors, Suppliers, … • News or Blog that’s aware of your favorite topics, the relationships between topics, and can reorganize information accordingly… • Wine store that’s aware of… • Social Network that’s aware of... • Software Agent that can…

16. Web Services Stack

17. Supporting Tech: Alitora Systems: • UMIS – Concept Identifier; Concept DNS • kHarmony – Semantic Database • ASAPI – Semantic Search and Collaboration API Internet Community: • OWL / RDF • JENA, Parsers, Inference Engines • Microformats / HTML / XML / CSS • REST Webservices, WSDL / SOAP Webservices • Protégé

18. UMIS • URI – directly mapping to a URL • Concept Identifier • Distributed Namespaces • Embedding UMIS • Microformats, OWL/RDF, Webservices • Com.Memomics.AlitoraSystems.upper.876576 • href=“http://memomics.com/umis/<umis>” • href=“http://memomics.com/umis/rdf/<umis>” • Backed by “Concept DNS” • google.com  IP 72.14.207.99 • “apple (the fruit)”  Com.Memomics.AlitoraSystems.upper.876576 • Compare To: • DOI, ISBN • Microformats, RDF

19. UMIS • Use of UMIS • apple Com.Memomics.AlitoraSystems.upper.876876 • Apple Computer Com.Memomics.AlitoraSystems.business.433495 • <service>.<issuer>.<namespace>.<instance> • Concept scheme • concept://Com.Memomics.AlitoraSystems.business.433495

20. kHarmony™ kHarmony™ Semantic Database • Graph Database • Focus on Connections • Graph Topology Algorithms • Semantic Search • Semantic Web Infrastructure Journal Articles

21. kHarmony – Example Query • Subgraph Root = <umis> Distance = * Expand_edge = is_a Expand_edge = has_a Yields Tree Root:Vehicle Car, Boat, Engine, Steering Wheel, …

22. Populating kHarmony • Supports General HyperGraphs Fill with… • Existing Ontologies • Community Built Ontologies • Semantic Instance Data • People, Companies, Places, Websites, … • Semantic Parser

23. Aside: Example Semantic Parse “Suppression of endogenous Bim greatly inhibits Gadd45a induction of apoptosis.” [action, inhibit, [action, suppress, [unknown], [gp, endogenous Bim] ], [action, induce, [gp, Gadd45a], [process, apoptosis] ], ]

24. Aside: Normalization – Entity Extraction Heuristics Bayesian String Similarity Abbreviation Expansion Species Context

25. Aside: Populating kHarmony “Suppression of endogenous Bim greatly inhibits Gadd45a induction of apoptosis.”

26. ASAPI Application Search Annotate Collaborate

27. ASAPI • Alitora Systems API • Search • Memory / Clipboard • Users • Teams • Memes • Relationships • Annotations

28. ASAPI • Access Control • Segments (public / proprietary) • baseline • memomics • proprietary / domain specific • Scope • Private • Public • Team • Namespace – logical domain groupings

29. Memomics • Web Application • API (REST / WSDL) • Client App Plug-In (such as Protégé)

30. Memomics • Tour…

31. Memomics • Search & Navigate Memes

32. Memomics • Collaboration Tools • Teams • Annotations • Voting

33. Memomics • Ontology Editor (micro editing) • “Wiki” Style • Functions: • Add Meme • Add MemeRelation • Add Relationship • Edit with Versioning

34. Memomics • Ontology Repository • Uploads • Downloads • UMIS  Concept Definition

35. Memomics • Embed Semantics via API: UMIS

36. Memomics - Ontology Editing • Change Management – Macro Editing • Versioning • Splitting Concepts • Forwarding to Canonical • Ontology Alignment • Exact (===) • Related…(type of…) • General   Domain Specific

37. Memomics • Community Processes • Ontology Construction Standard(s) • Example: Guidelines for Concept vs. Instance • Example: Guidelines for Domain & Range • Teams as Working Groups • Submit Ontology to Community • Acceptance as “Authoritative”

38. Memomics • Community Roles • Modeler • Ontology Expert • Domain Expert • Adds domain expertise to Ontology • Domain Specialist • Adds individuals / instances, edits, reviews • Technologist • Adds application specific knowledge • Enthusiast • Adds individuals / instances, edits, reviews • Consumer • Read Only

39. Memomics • Usage Scenario: • Domain Selected • Working Group formed from Memomics Community • Upload Existing Owl files, if any • Edit via Plug-in or WebApp • Tweak via Community, Add Instances • Public Review • Available via API for Embedding in Apps • Community voting • Accepted for “Authoritative” Status • Embed in Public-Authoritative Apps

40. Memomics • Demo Community Interaction • Create Teams • Add Members • Add Memes, Relations • Add Annotations • Messages • Access via API

41. Memomics • Demo Application

42. Mash-Up of Semantic Search Pharma, Drug, Chemical, Patent, Gene, and Disease information Select a manufacturer for details about their activity Drill down into chemical or drug detail.

43. Contextual drug/substance information from PubMed

44. Clinical trials, patents Available online. Can filter by disease, gene, keyword, result of semantic lookup Public financial information

45. Clinical Trials…

46. Patent Applications…

47. Memomics API Use • REST client • /khREST/asapi/10/xml/search?query= • Embed in PHP, Java, etc. • Format in XML, JSON, RDF, … • Resources: • Memory / Clipboard, Search, Team, … • WSDL Client

48. Memomics • Discussion Points • How to best engage community? • Organizing Ontology Work Groups? • Community Acceptance processes? • Motivating contributors & editors?

49. Alitora Systems • Contact: • marc@alitora.com • Sign Up for API use • signmeup@alitora.com • Mailing Lists • Community Wiki