Throw the Semantic Web at Today's Health-care


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Health-care needs functioning IT - and there is finance available. Yet still, it lumbers along, mired in the same talking points: we need Portable Health Records; we need to exchange clinical care information; we need fuller descriptions. Is the Semantic Web the answer? Can it get to work right now?

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  • Beyond the paper piles, our health data is in data silo’s
  • Many practitioners - more perfect union Not covering Security or Ownership (both contentious and often take over) Primary and Secondary uses Patient-accessible, Doctor-complete Trial Recruitment, Drug Safety, Outcomes research ... right now, more Iraq, than US
  • HL7 carries much of our health data HL7 everywhere means v2. Don’t Blink or you’ll miss V3. Another story ... Only one enabler. Going to ignore the filing cabinets for now
  • Of course, more structured than your average tweet Pick out message type, patient name, contact relationship, body weight observation
  • Step back and inside the soup again and ... Most of all you see codes! Messages are just the trucks. “What do you drive?” fixation. LN=LOINC for labs, CVX == , HL7’s 162 table says?, MVX [???]
  • Back in the real world Work in progress with codes. Restructuring. Mapping. Entering the Semantic Web. Patient data still off in bunkers
  • Ala web of documents, all documents get a URI. Everything gets a URI. Payoff soon.
  • Automatic
  • Links are labeled Nodes and Literals
  • One standard code is 30949-2.
  • - Some warehouse now - even their HL7. Modeled their own way. - People are sick of moving to “the next best” format, this year’s “solution to every problem” - but not just another reformat/syntax work: yes semi-structured data in graphs but real payoff is linkage
  • URI == open address
  • CDC Example. Query only standard if
  • Middleware or Active Data.
  • Linked Data! From: HCLS == the w3c Health Care and Life Sciences Interest Group A same-as into RxNorm and the greater ontologies can be leveraged Stanford Drug Ontology gives compounds that treat conditions. RxNorm relates compounds to branded drugs. Hoot72 Clinical Data has branded drugs. RxNorm not yet an ontology but has web api so can represent it as a SPARQL end point Simplied to fit. Ingredient = consists of to ingredient to brand name etc.
  • Growing in number ... Billions of triples, ready to be leveraged Obvious PubMed, Drug Bank, GeneID But also take demographics - geo names, census data
  • Graph enhancers ... in context. Skill levels. They will vary, depending on the extent of modeling done. And so will the quality of your Clinical Care data. Better links. Yields more.
  • Dangerous part. The bit people are concerned about. Real “meaningful use”?
  • Throw the Semantic Web at Today's Health-care

    1. 1. Hoot72 <ul><li>Throw the Semantic Web at Today’s Health-Care </li></ul>
    2. 2. Land of Silo’s <ul><li>Health Data in “islands”, “silo’s” </li></ul><ul><ul><li>Admissions/Pharmacy/Lab ... Systems </li></ul></ul><ul><ul><li>Billing data does leave the premises! </li></ul></ul><ul><li>Clinical data scattered </li></ul><ul><li>Research, portable records, management? </li></ul>
    3. 3. Possible? A View for Everyone Linked Health Data Patient Doctor Manager Researcher Insurance IT
    4. 4. One Enabler: Silo’s chat Source: Neotool, V3 vs V2 “ HL7 version 2 is a major breakthrough and market success. More than 93% hospitals in US are using this standard” - Health Level Horizon (HLH) Project
    5. 5. A “tweet” ... <ul><li>MSH|^~&|REGADT|MCM|IFENG||199112311501|| ADT ^A04^ADT_A01|000001|P|2.4||| </li></ul><ul><li>EVN|A04|199901101500|199901101400|01||199901101410 </li></ul><ul><li>PID|||191919^^GENHOS^MR~371-66-9256^^^USSSA^SS|253763| MASSIE^JAMES^A ||19560129|M|||171 ZOBERLEIN^^ISHPEMING^MI^49849^&quot;&quot;^||(900)485-5344|(900)485-5344||S^^HL70002|C^^HL70006|10199925^^^GENHOS^AN|371-66-9256|| </li></ul><ul><li>NK1|1|MASSIE^ELLEN| SPOUSE^^HL70063 |171 ZOBERLEIN^^ISHPEMING^MI^49849^&quot;&quot;^ </li></ul><ul><li>|(900)485-5344|(900)545-1234~(900)545-1200|EC1^FIRST EMERGENCY CONTACT^HL70131 </li></ul><ul><li>NK1|2|MASSIE^MARYLOU|MOTHER^^HL70063|300 ZOBERLEIN^^ISHPEMING^MI^49849^&quot;&quot;^ </li></ul><ul><li>|(900)485-5344|(900)545-1234~(900)545-1200|EC2^SECOND EMERGENCY CONTACT^HL70131 </li></ul><ul><li>NK1|3 </li></ul><ul><li>NK1|4|||123 INDUSTRY WAY^^ISHPEMING^MI^49849^&quot;&quot;^||(900)545-1200|EM^EMPLOYER^HL70131|19940605||PROGRAMMER|||ACME SOFTWARE COMPANY </li></ul><ul><li>PV1||O|O/R||||0148^ADDISON,JAMES|0148^ADDISON,JAMES||AMB|||||||0148^ADDISON,JAMES|S|1400|A|||||||||||||||||||GENHOS|||||199501101410| </li></ul><ul><li>PV2||||||||199901101400|||||||||||||||||||||||||199901101400 </li></ul><ul><li>ROL||AD|CP^^HL70443|0148^ADDISON,JAMES </li></ul><ul><li>OBX||NM| 3141-9^BODY WEIGHT^LN || 62 |kg|||||F </li></ul>James was admitted ... his wife is his emergency contact ... here’s his weight ...
    6. 6. Focus on Information MSH|^~&||GA0000||VAERS PROCESSOR| 20010331605 ||ORU^R01|20010422GA03|T|2.3.1|||AL|PID|||1234^^^^SR~1234-12^^^^LR~00725^^^^MR|| Doe^John^Fitzgerald ^JR^^^L||20001007|M||2106-3^ White^HL70005 |123 Peachtree St^APT 3B^Atlanta^GA^30210^^M^^GA067||(678) 555-1212^^PRN|ORC|CN|||||||||||1234567^Welby^Marcus^J^Jr^Dr.^MD^L|||||||||Peachtree Clinic|101 Main Street^^Atlanta^GA^38765^^O^^GA121|(404) 554-9097^^WPN|101 Main Street^^Atlanta^GA^38765^^O^^GA121|OBR|1|||^CDC VAERS-1 (FDA) Report|||20010316|OBX|1|CE| 30955-9&30956-7^Vaccine type^LN |1| 08^HepB-Adolescent/pediatric^CVX |OBX|2|CE|30955-9&30957-5^Manufacturer^LN|1|MSD^Merck^MVX|OBX|3|ST|30955-9&30959-1^Lot number^LN|1|MRK12345|OBX|4|CE|30955-9&30958-3^Route^LN|1| IM^Intramuscular^HL70162 |OBX|5|CE|30955-9&31034-2^Site^LN|1|LA^Left arm^ HL70163|OBX|6|NM|30955-9&30960-9^Number of previous doses^LN|1|01I <ul><li>Messages just “trucks” </li></ul><ul><li>People and Codes and Relationships </li></ul><ul><li>Leave “what do you drive” behind </li></ul>
    7. 7. What if? From obscure Soup to query-ready Graph OR|20010331605||ORU^R01|20010422GA03|T|2.3.1|||AL|725^^^^MR||Doe^John^Fitzgerald^JR^^^L||20001007|M||2106-3^White^HL70005|123 Peachtree St^APT 3B^Atlanta^GA^30210^^M^^GA067||(678) 555-1212^^PRN||||||||||Peachtree Clinic|101 Main Street^^Atlanta^GA^38765^^O^^GA121|(404) 554-9097^^WPN|101 Main Street^^Atlanta^GA^38765^^O^^GA121|
    8. 8. Graph? <ul><li>Format for Web of Data, not Documents </li></ul><ul><ul><li>RDF (Things) vs HTML (Documents) </li></ul></ul><ul><li>Web: link anywhere by URI (http://...) </li></ul><ul><ul><li>every Thing gets an address </li></ul></ul><ul><li>Semi -Structured: query through links </li></ul><ul><ul><li>SPARQL: SQL-like </li></ul></ul>
    9. 9. Enter Hoot72 <ul><li>Hoot (w3c’s OWL), 72 (HL7 v2) </li></ul><ul><li>A Mapping: message to graph assertions </li></ul><ul><li>Open Source Reference Implementation </li></ul><ul><li>Painless Deployment </li></ul><ul><ul><li>Sssh - listens quietly </li></ul></ul><ul><ul><li>doesn’t disturb the existing </li></ul></ul>
    10. 10. Two plus Two Hoot72 Mapper HL7 Messages HL7 Message Definitions Hoot72 Ontology Clinical Data Graph
    11. 11. Observation (OBX) PID||| 1234^^^^SR~1234-12^^^^LR~00725^^^^MR || Doe^John^Fitzgerald^JR^^^L | ... OBX|4|CE| 30949-2 ^Vaccination adverse event outcome^ LN |1| H ^required hospitalization^ NIP005 | LN 30949-2 CodingSystem Code H NIP005 CodingSystem Code observation observationValue Doe John Fitzgerald personName familyName givenName middleName context Patient type Identifiers and Time not shown
    12. 12. Now Just Ask ... <ul><li>All Patients with adverse outcome from vaccine ... </li></ul>SELECT DISTINCT ?givenName ?familyName WHERE { ?patient hoot72:personName [ hoot72:givenName ?givenName ; hoot72:familyName ?familyName ] . [ hoot72:tcontext ?patient ; ?codePredicate [ hoot72:nameOfCodingSystem &quot;LN&quot; ; hoot72:simpleIdentifier &quot;30949-2&quot; ] ] }
    13. 13. So? <ul><li>A Clinical Care Warehouse </li></ul><ul><ul><li>I warehouse already! Just another silo </li></ul></ul><ul><li>Quick, easy way to Integrated View </li></ul><ul><ul><li>I have my own ways </li></ul></ul><ul><li>Standard format (RDF), query (SPARQL) </li></ul><ul><ul><li>Another? I like SQL/XML etc </li></ul></ul><ul><li>Difference: born to link, semantically ! </li></ul>
    14. 14. Link Out, Anywhere <ul><li>First HTML browser disappointed some </li></ul><ul><ul><li>“ Nicer” links in CD-ROM encyclopedias </li></ul></ul><ul><li>Power: link any Document = “world-wide” </li></ul><ul><ul><li>No site, an island; every document, a URI </li></ul></ul><ul><li>Web of Data: link any Thing </li></ul><ul><ul><li>No store, an island; every thing, a URI </li></ul></ul>
    15. 15. Link Local Codes CodingSystem Code Text Hoot72 Graph LOINC Code SameAs <ul><li>Local Lab “same-as” Lab Standard (LOINC) </li></ul><ul><li>Run standard, off-the-shelf queries </li></ul>LN 13317-3 CodingSystem Code Local 182253 MRSA Culture
    16. 16. Link Categories <ul><li>Question: Patients taking “Weight Loss Drugs” </li></ul><ul><li>Hoot72 Graph: very particular </li></ul><ul><ul><li>Patient drugs as NDC codes: DESOXYN TABLETS (00074337701) ... </li></ul></ul><ul><li>Too big a gap? </li></ul><ul><li>Not for “the Ontologies” ... </li></ul>
    17. 17. The Ontologies? <ul><li>Ontology: “an implementable model of the entities that need to be understood in common in order for some group of software systems and their users to function and communicate at the level required for a set of tasks” -- Alan Rector </li></ul><ul><li>Define Concepts: hierarchies, equivalence ... </li></ul><ul><li>The “middleware” of the Semantic Web </li></ul><ul><li>Growing every day: in Colleges, Corporations, ... </li></ul><ul><li>OWL (WOL) - Web Ontology Language </li></ul>
    18. 18. RxNorm picks Joe Name NDC: 00074337701 Desoxyn 5MG Tablet Name SameAs Ingredient Medication SameAs RxNorm Stanford Drug Ontology Hoot72 Graph * Dotted: composite of links to save space ** w3c HCLS Example RxNorm:6816 Methamphetamine Methamphetamine StanDrug: C0025611 Name Obese May Treat Patient Joe NDC: 00074337701
    19. 19. Ontologies are Standing by
    20. 20. Only As good as your Links <ul><li>Link out: to Ontologies (drugs, conditions) </li></ul><ul><ul><li>avoid re-invention </li></ul></ul><ul><li>Run powerful queries </li></ul><ul><ul><li>leverage the definitions of others </li></ul></ul><ul><li>Run off-the-shelf queries </li></ul><ul><ul><li>avoid re-invention </li></ul></ul><ul><li>Who’s your “link man”? </li></ul>
    21. 21. Link an Individual <ul><li>“ The ultimate aim in public health infrastructure is to allow two organizations to exchange patient and other health information seamlessly.” -- Kun, Ray Merrell, Kwankam </li></ul><ul><li>URIs: </li></ul><ul><li>Portable health records </li></ul><ul><li>sameas : “Alex Ben” in X, “Alex J. Ben” in Y </li></ul><ul><li>Security concerns - de-identify sometimes </li></ul><ul><li>Clearing houses ala Google Health? True “meaningful use”? </li></ul>
    22. 22. The Urgency of Now <ul><li>Health-care needs functioning IT </li></ul><ul><ul><li>the now-financed EHR push </li></ul></ul><ul><li>Semantic Web ready and waiting </li></ul><ul><ul><li>standards, ontologies, tools </li></ul></ul><ul><ul><li>ideal for health-care </li></ul></ul><ul><li>The slow pace of alternatives </li></ul><ul><ul><li>no traction (HL7 v3 etc.) </li></ul></ul>
    23. 23. Interested? <ul><li>Hear more? </li></ul><ul><li>Your messages graphed? </li></ul><ul><li>Participate? </li></ul>Go to: and Contact!