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Websites

Websites. http://mor.nlm.nih.gov/download/rxnav/ http://www.stccmop.org/quarry. Charting a Dataspace: Lessons from Lewis and Clark. David Maier Department of Computer Science Portland State University & Microsoft Research. With Much Support. Dataspaces: Alon Halevy, Mike Franklin

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  1. Websites • http://mor.nlm.nih.gov/download/rxnav/ • http://www.stccmop.org/quarry NEDS 2008

  2. Charting a Dataspace:Lessons from Lewis and Clark David Maier Department of Computer Science Portland State University & Microsoft Research

  3. With Much Support Dataspaces: Alon Halevy, Mike Franklin RxSafe: Paul Gorman, Karl Ordelheide, Judy Logan, Nick Rayner (InfoSonde) SACO: Shannon McWeeney, Ranjani Ramakrishnan Quarry: Bill Howe, James Rucker DIESEL: Lois Delcambre, David Archer, Susan Price, Scott Fletcher, John McCall Funding: NSF ACI 0121475, IIS-0534762AHRQ 1 UC1 HS014928-01, DARPA NEDS 2008

  4. Dataspaces* • Deal with all the data from an enterprise – in whatever models • Data co-existence Might not be fully integrated, especially early on • Pay-as-you-go services • I’m interested in understanding sources and their relationships * “From Databases to Dataspaces: A New Abstraction for Information Management”, Michael Franklin, Alon Halevy, David Maier, SIGMOD Record, December 2005. NEDS 2008

  5. Example Dataspace: RxSafe Consolidated medication list for rural elders Points in lifetime of a prescription • Order (clinic, hospital) • Dispensing (pharmacy) • Approval (insurer) • Administration (rehabilitation facility) Relevant Standards NDCD, RxNorm, NDF-RT NEDS 2008

  6. listings firms packages f_seq_no lblcode firm_name l_seq_no pkgcode pkgsize l_seq_no lblcode prodcode tradename f_seq_no formulation l_seq_no strength unit ingredient_name NDCD: National Drug Code Directory Codes for drug packages NEDS 2008

  7. Sample NDC: 62584-023-00 NEDS 2008

  8. RxNorm: Drug Nomenclature RxNav from National Library of Medicine NEDS 2008

  9. NDF-RT National Drug File – Reference Terminology From Veterans Affairs • Drug class • Chemical class • Effects and actions NEDS 2008

  10. NDF-RT (Blue) NEDS 2008

  11. People Who Would Benefit • Physician – what is the patient actually getting • Pharmacist – interaction, duplication • Assisted-living-facility (ALF) nurse – monthly reconciliation • Emergency Department – what might be in the patient’s body • Patient – what should I be taking? NEDS 2008

  12. Lewis and Clark Expedition* • Explore western US • Corps of Volunteers for North Western Discovery  “Corps of Discovery” • 1804-1806 William Clark Meriwether Lewis *Note: Largely based on Lewis and Clark: The Bicentennial Exhibition and the accompanying book Lewis and Clark—Across the Divide by Carol Gilman, 2003 NEDS 2008

  13. Their Route Source: www.sd4history.com NEDS 2008

  14. Charting the Country,Charting a Dataspace • Diversity of purposes • Myths and legends • Evaluating maps • Alternative models of the world • Translating between languages • Surveying the countryside • Generic description languages • Changing landscape NEDS 2008

  15. Lewis & Clark:Different Purposes • Thomas Jefferson claimed different purposes to different audiences • Congress: Customers for trade • Cabinet: Settlement by US, keep Great Britain out • British, French: Purely scientific Source: www.thecemeteryproject.com Observation vs. Evaluation vs. Diplomacy NEDS 2008

  16. Louisiana Purchase US bought territory from France in 1803-4 Additional purpose: Inform people of new sovereignty Source: NOAA NEDS 2008

  17. RxSafe:Different Purposes • Grouping similar medications • Connecting possible incarnations of same prescription Generic – Brand Name • Combining medication information for a given patient Must be error preserving NEDS 2008

  18. Lewis & Clark:Myths and Legends Northwest passage sea, inland sea, river + short portage “symmetrical geography” “the pyramidal height of land” Mammoths Volcano NEDS 2008

  19. RxSafe:Myths and Legends NDC and RxNorm talking about same things • NDC tradenames: 18913 • RxNorm brand names: 7600 • Strings in common: 418 All RxNorm relationships have explicit inverses NEDS 2008

  20. Lewis & Clark:Evaluating Maps Maps were incomplete Alexander MacKenzie. Source: U. Virginia Library NEDS 2008

  21. Aaron Arrowsmith. Source: www.monticello.org NEDS 2008

  22. RxSafe:Incomplete Maps NEDS 2008

  23. RxSafe:Incomplete Maps Source: National Library of Medicine Doesn’t mention atoms, attributes Doesn’t include SY, ET, OCD, OBD NEDS 2008

  24. Lewis & Clark:Mapping Conventions European maps: Distance, direction Indian maps might be • Measured in time • Diagrammatic • Non-constant direction • Routes vs. geographic features Can depend on primary means of travel: foot, horse, river, sea NEDS 2008

  25. Shehek-Shote Map (Mandan) NEDS 2008

  26. Clatsop Map NEDS 2008

  27. RxSafe:Understanding Diagrams RxNorm diagram is for instances Multi-ingredient drug case not covered NEDS 2008

  28. Independence of Sources Lewis & Clark: Maps not independent Arrowsmith Map  King Map MacKenzie Map  RxSafe RxNorm based in part on NDCD (including errors) NEDS 2008

  29. Lewis & Clark:Alternative World Models European view of North America Britain US Russia Spain NEDS 2008

  30. Indian Division of the Territory NEDS 2008 Souce: Library of Congress

  31. Structural Differences • European: Political hierarchy – central authority speaks for all • Indian: Individual relationships – different leaders camp, hunting, war Different meaning of relationships Parent-child • European: patriarchal • Indian: formal adoption w/ responsibilities NEDS 2008

  32. RxSafe:Different World Models Product/Package Drug/Class Drug/Component NDC NDF-RT RxNorm Clinical Drug Branded Drug consists_of Component Component* + BN Component NEDS 2008

  33. Lewis & Clark:Translating Between Languages English Lewis French François Labiche Hidatsu Toussaint Charbonneau Shoshone Sacagawea Cameahwait NEDS 2008

  34. RxSafe:Translating Between Languages Hydrocodone 5mg/Acetaminophen 500mg PO TID Physician Pharmacist Vicodin, by mouth, 3x day ALF White oblongpill w/ meals NDC: 6258402300 Patient Manufacturer NEDS 2008

  35. Surveying the Countryside Lewis & Clark • Dead reckoning, compass • Celestial observation, chronometer RxSafe: Data profiling NDC • 45,972 listings • 18,913 tradenames • 109,988 package rows • 2,952 labeler codes NEDS 2008

  36. Lewis & Clark:Generic Description Languages Chinook Wawa (Chinook Jargon) • Small number of concepts • Combine to get more complex descriptions and relationships • Not very domain specific NEDS 2008

  37. Chinook Wawa Examples hyas tyee high chief hyas pusspuss high cat salt chuck salt water skookum chuck powerful water mamook muckamuck make food hyas muckamuck hyas tyee high chief king hyas pusspuss high cat  cougar salt chuck salt water  ocean skookum chuck powerful water  rapids mamook muckamuck make food cook  someone who eats at the high table NEDS 2008

  38. You Try It olo moosum hungry for sleep  sleepy olo chuck hungry for water  thirsty mamook tusgh illahemake split the land  plow opitsaht yakka sikhsthe knife his friend  fork NEDS 2008

  39. RXNAT rxcui att_name att_value RXNCONSO RXNREL rxcui term_type string_val src_abbr rxcui1 rxcui2 rel src_abbr RxSafe: Generic Description Language RxNorm uses UMLS, not domain-specific More complex than this – can have several atoms in each concept NEDS 2008

  40. Changing Landscape Lewis & Clark • Range of tribes: nomadic, smallpox, war • Wouldn’t find some river features today RxSafe Representation convention for synonyms changes across versions in RxNorm NEDS 2008

  41. What I Want:Dataspace Charting Toolkit Familiarization, Profiling, Enhancement • Inspector for generic models • Dataspace profiler • Assumption tracker and checker • Structure discovery techniques • Customization to task based on discovered characteristics NEDS 2008

  42. “Green Field” Tools for Unfamiliar Dataspaces (Howe) • Goal: A working, extensible application with the least possible (human) effort • We need at least: • a Data Model • “Lowest Common Denominator” • minimal modeling decisions • an API • easy to use for domain experts • uniformly efficient NEDS 2008

  43. Quarry Data Model • resource, property, value • (subject, predicate, object) if you prefer • no intrinsic distinction between literal values and resource values • no explicit types or classes NEDS 2008

  44. Example: RxNorm Concept Relationship Atom userkey prop value 10001 NDC 1 10001 ORIG_CODE 123 10001 ingredient_of 10004 10001 type DC up to 23M triples describing 0.6M concepts and atoms NEDS 2008

  45. Depth = “7” Variable = “Salinity” Type = “Animation” Region = “Estuary” path prop value …/anim-sal_estuary_7.gif depth 7 …/anim-sal_estuary_7.gif variable salt 7.5M triples describing 1M files …/anim-sal_estuary_7.gif region estuary …/anim-sal_estuary_7.gif type anim Example: Metadata for Scientific Data Repository …/anim-sal_estuary_7.gif NEDS 2008

  46. SKIP NEDS 2008

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