throw the semantic web at today's health-care
Post on 17-Dec-2014
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Land of Silo’s
•Health Data in “islands”, “silo’s”
• Admissions/Pharmacy/Lab ... Systems
• Billing data does leave the premises!
•Clinical data scattered
•Research, portable records, management?
Possible?
A View for Everyone
Linked Health Data
Patient
Doctor
Manager
Researcher
Insurance
IT
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
A “tweet” ...MSH|^~\&|REGADT|MCM|IFENG||199112311501||ADT^A04^ADT_A01|000001|P|2.4|||EVN|A04|199901101500|199901101400|01||199901101410PID|||191919^^GENHOS^MR~371-66-9256^^^USSSA^SS|253763|MASSIE^JAMES^A||19560129|M|||171 ZOBERLEIN^^ISHPEMING^MI^49849^""^||(900)485-5344|(900)485-5344||S^^HL70002|C^^HL70006|10199925^^^GENHOS^AN|371-66-9256||NK1|1|MASSIE^ELLEN|SPOUSE^^HL70063|171 ZOBERLEIN^^ISHPEMING^MI^49849^""^|(900)485-5344|(900)545-1234~(900)545-1200|EC1^FIRST EMERGENCY CONTACT^HL70131NK1|2|MASSIE^MARYLOU|MOTHER^^HL70063|300 ZOBERLEIN^^ISHPEMING^MI^49849^""^|(900)485-5344|(900)545-1234~(900)545-1200|EC2^SECOND EMERGENCY CONTACT^HL70131NK1|3NK1|4|||123 INDUSTRY WAY^^ISHPEMING^MI^49849^""^||(900)545-1200|EM^EMPLOYER^HL70131|19940605||PROGRAMMER|||ACME SOFTWARE COMPANYPV1||O|O/R||||0148^ADDISON,JAMES|0148^ADDISON,JAMES||AMB|||||||0148^ADDISON,JAMES|S|1400|A|||||||||||||||||||GENHOS|||||199501101410|PV2||||||||199901101400|||||||||||||||||||||||||199901101400ROL||AD|CP^^HL70443|0148^ADDISON,JAMESOBX||NM|3141-9^BODY WEIGHT^LN||62|kg|||||F
James was admitted ... his wife is his emergency contact ... here’s his weight ...
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
•Messages just “trucks”
•People and Codes and Relationships
•Leave “what do you drive” behind
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|
Graph?
•Format for Web of Data, not Documents
•RDF (Things) vs HTML (Documents)
•Web: link anywhere by URI (http://...)
•every Thing gets an address
•Semi-Structured: query through links
•SPARQL: SQL-like
Enter Hoot72
• Hoot (w3c’s OWL), 72 (HL7 v2)
• A Mapping: message to graph assertions
• Open Source Reference Implementation
• Painless Deployment
• Sssh - listens quietly
• doesn’t disturb the existing
Two plus Two
Hoot72 Mapper
HL7 Message
s
HL7 Message Definitions
Hoot72 Ontology
Clinical Data Graph
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
CodingSystemCode
observation observationValue
Doe
John Fitzgerald
personName
familyName
givenName
middleName
contextPatient
type
Identifiers and Time not shown
Now Just Ask ...
All Patients with adverse outcome from vaccine ...
SELECT DISTINCT ?givenName ?familyName WHERE { ?patient hoot72:personName [ hoot72:givenName ?givenName ; hoot72:familyName ?familyName ] . [ hoot72:tcontext ?patient ; ?codePredicate [ hoot72:nameOfCodingSystem "LN" ; hoot72:simpleIdentifier "30949-2" ] ] }
So?
•A Clinical Care Warehouse
•I warehouse already! Just another silo
•Quick, easy way to Integrated View
•I have my own ways
•Standard format (RDF), query (SPARQL)
•Another? I like SQL/XML etc
•Difference: born to link, semantically!
Link Out, Anywhere
•First HTML browser disappointed some
•“Nicer” links in CD-ROM encyclopedias
•Power: link any Document = “world-wide”
•No site, an island; every document, a URI
•Web of Data: link any Thing
•No store, an island; every thing, a URI
Link Local Codes
LN 13317-3
CodingSystem Code
Local 182253
CodingSystem
Code
MRSA Culture
Text
Hoot72 Graph LOINC Code
SameAs
•Local Lab “same-as” Lab Standard (LOINC)
•Run standard, off-the-shelf queries
Link Categories
•Question: Patients taking “Weight Loss Drugs”
•Hoot72 Graph: very particular
• Patient drugs as NDC codes: DESOXYN TABLETS (00074337701) ...
•Too big a gap?
•Not for “the Ontologies” ...
The Ontologies?• 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
• Define Concepts: hierarchies, equivalence ...
• The “middleware” of the Semantic Web
• Growing every day: in Colleges, Corporations, ...
• OWL (WOL) - Web Ontology Language
RxNorm picks Joe
Name
RxNorm:6816
Methamphetamine
Methamphetamine
StanDrug: C0025611
Name
ObeseMay Treat
NDC: 00074337701
Desoxyn 5MG Tablet
Name
SameAs
Ingredient
Patient Joe
Medication
NDC: 00074337701
SameAs
RxNorm
Stanford Drug Ontology
Hoot72 Graph
* Dotted: composite of links to save space
** w3c HCLS Example
Ontologies are Standing by
Only As good as your Links
•Link out: to Ontologies (drugs, conditions)
•avoid re-invention
•Run powerful queries
•leverage the definitions of others
•Run off-the-shelf queries
•avoid re-invention
•Who’s your “link man”?
Link an Individual• “The ultimate aim in public health infrastructure
is to allow two organizations to exchange patient and other health information seamlessly.” -- Kun, Ray Merrell, Kwankam
•URIs: www.ucla.com/patient/36600
•Portable health records
•sameas: “Alex Ben” in X, “Alex J. Ben” in Y
•Security concerns - de-identify sometimes
•Clearing houses ala Google Health? True “meaningful use”?
The Urgency of Now
•Health-care needs functioning IT
•the now-financed EHR push
•Semantic Web ready and waiting
•standards, ontologies, tools
•ideal for health-care
•The slow pace of alternatives
•no traction (HL7 v3 etc.)
Interested?
•Hear more?
•Your messages graphed?
•Participate?
Go to: http://www.hoot72.org and Contact!
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