Data Management with Ontologies Bijan Parsia bparsia@cs.man.ac.uk 1 Friday, 7 December 2012 1
The Future is Coming...Soon Reducing Paperwork and Administrative Costs. Health care remains one of the few industries that relies on paper records. The new law will institute a series of changes to standardize billing and requires health plans to begin adopting and implementing rules for the secure, confidential, electronic exchange of health information . Using electronic health records will reduce paperwork and administrative burdens, cut costs, reduce medical errors and most importantly, improve the quality of care. First regulation effective October 1, 2012. —http://www.whitehouse.gov/healthreform/timeline http://uncyclopedia.wikia.com/wiki/File:Uncle_Sam_I_Want_You_1.jpg http://en.wikipedia.org/wiki/File:ColumbiaStahrArtwork.jpg Friday, 7 December 2012 2
50% of doctors use EHR • This is up from 25% in 2005 http://www.washingtonpost.com/blogs/ezra-klein/wp/2012/07/19/about-half-of-doctors-use-electronic-records/ Friday, 7 December 2012 3
50% of doctors use EHR • This is up from 25% in 2005 ...not as impressive as it seems! http://thehealthcareblog.com/blog/2011/12/02/2011-ehr-adoption-rates/ Friday, 7 December 2012 4
What’s Stopping Us? (1) “I wish the doctor had spent as much time with me as she did with her PC” Many years ago, an excited friend who worked for one of the electronic health record (EHR) vendors at that time — it was really more of a billing and patient tracking and management system than an EHR — was desperate to show me some of their latest applications. In particular, a new module they had developed to capture clinical data. My friend pulled out his laptop (see here for visual), fired up the application, selected a patient and proceeded to enter blood pressure (BP). Some 20-plus clicks later, he had entered a BP of 120/80. While he was excited, I was dumbfounded. When it comes to patient care, doctors didn’t have time for 20 clicks to record BP years ago and they definitely don’t have that luxury in today’s demanding medical environment. http://ehrintelligence.com/2012/07/12/clinical-documentation-in-the-ehr/ Friday, 7 December 2012 5
Clinical Data Capture Choose terms from a coding scheme cystitis Too Big enter search: Cystitis, NOS Cholecystitis, NOS Iatrogenic cystitis ...picking lists Chronic cholecystitis Acute cystitis Chemical cystitis too long Acute cholecystitis Postoperative cystitis Subacute cystitis, NOS Drug induced cystitis Bacterial Cholecystitis Follicular cystitis Too Small Radiation cystitis Bacterial cystitis Idiopathic cystitis etc next page ...not enough clinical detail http://www.cs.man.ac.uk/~rector/presentations/snomed-rector-history-and-future-of-terminology.ppt Friday, 7 December 2012 6
Shape and value sensitivity Friday, 7 December 2012 7
What (else) is Stopping Us? A separate and much more complex piece of technology — electronic health records — is proving difficult and expensive. Knitting together incompatible computer systems across the 35 medical sites so they can easily share detailed patient medical records could costs the city millions beyond what is included in the official price tag. An incomplete survey of technology costs borne by the clinics themselves this year reveals spending of at least $15 million in addition to what was budgeted for the whole program...But that sum is likely millions higher, since eight clinics could not or would not say how much they spent or were planning to spend integrating their patient records . The current patchwork of at least 11 different computer systems across the network do not easily talk with one another. ... This incompatibility of record keeping sometimes causes delays, repeated tests, unnecessary procedures and gaps in care as patients move from doctor to doctor. Ideally, say technology planners, there ought to be just one system citywide. But that is unlikely to happen soon. http://thehealthcareblog.com/blog/2012/01/27/medical-records-supporting-san-francisco%E2%80%99s- universal-care-add-millions-to-official/ Friday, 7 December 2012 8
Database Modelling and Integration 9 Friday, 7 December 2012 9
Simple ER Representation http://www.inf.unibz.it/~franconi/icom/tutorial-1.html Friday, 7 December 2012 10
INFERENCE! http://www.inf.unibz.it/~franconi/icom/tutorial-1.html Friday, 7 December 2012 11
Modify the Schema http://www.inf.unibz.it/~franconi/icom/tutorial-1.html Friday, 7 December 2012 12
Unwanted Consequences http://www.inf.unibz.it/~franconi/icom/tutorial-1.html Friday, 7 December 2012 13
Strengthen a Constraint http://www.inf.unibz.it/~franconi/icom/tutorial-1.html Friday, 7 December 2012 14
The Problem Spreads http://www.inf.unibz.it/~franconi/icom/tutorial-1.html Friday, 7 December 2012 15
Data Integration • The prior example was single schema – So Design Support – Developing, extending, evolving, exploring a schema – (We could treat it as two, of course.) • Often must combine schemata – Either different schemas for the “same” data – Disparate schemas for “overlapping” data – Different schemas for separate but related data • Development Time only?! Friday, 7 December 2012 16
Two Schemata; “Same” data http://www.inf.unibz.it/~franconi/icom/tutorial-2.html Friday, 7 December 2012 17
http://www.inf.unibz.it/~franconi/icom/tutorial-2.html Friday, 7 December 2012 18
INFERENCE!!! http://www.inf.unibz.it/~franconi/icom/tutorial-2.html Friday, 7 December 2012 19
Where’s the error!!! 1 4 3 5 2 http://www.inf.unibz.it/~franconi/icom/tutorial-2.html Friday, 7 December 2012 20
What should we change? 1 2 3 http://www.inf.unibz.it/~franconi/icom/tutorial-2.html Friday, 7 December 2012 21
Insert a Fix and Verify Friday, 7 December 2012 22
Ontology Use at Run Time • Ontology at run time? – More, ontology for the end user!??! • By end user, I mean, “someone writing queries” – Ontology Based Data Access (ODBA) • Familiar – Controlled vocabulary based – Query by example • New – “Better” queries – Integrated views of data Friday, 7 December 2012 23
Person “Better” queries Student Employee • Better how? hasAge hasSalary – Consider a simple schema – What does the logical schema look like? create table employee (id number(4) – Lots of variants hasAge number(3), hasSalary number(6); • Sane queries create table student (id number(4) – SELECT hasAge FROM employee hasAge number(3), hasSalary number(5); WHERE hasSalary >= 50000; – SELECT hasAge FROM student WHERE hasSalary >= 50000; – What about Persons? • Union query? • Rather write – SELECT hasAge FROM Person WHERE hasSalary >= 50000; – no matter what kind of persons there are Friday, 7 December 2012 24
Integrating with Legacy Query Clinical Model OBDA Aware Report Query Engine OBDA Model (Mappings) Data Entry Form Legacy Database Data Entry Query Report Form https://babbage.inf.unibz.it/trac/obdapublic/raw-attachment/wiki/ObdalibQuestIntro/virtual.png Friday, 7 December 2012 25
Data Integration Query Clinical Model OBDA Aware Report Query Engine Data Entry Form OBDA Model (Mappings) Data Entry Legacy Form Database Data Entry Legacy Form Report Database OBDA Model (Mappings) Report Query Query Friday, 7 December 2012 26
What do we need? • Richer query language! – Need at least conjunctive queries • I.e., patterns with explicit varibles • Tree queries don’t cut it! • SQLesque – Ontology sensitive! • The queries should respect the semantics • Data access! – ETL...populate an ABox from a Database – Distributed • Leave my database ALOOOOOONNNNNEE!!!!! – Need mappings • Good computation – Some fragments of OWL tuned for this • Cf OWL QL and OWL EL • Polynomial; OWL QL has pure query expansion implementations Friday, 7 December 2012 27
OWL and Data (Properties) Friday, 7 December 2012 28
OWL Has Two “Worlds” • The world of logic – Classes, individuals, (object) object properties – Java analogue: • Classes, instances, and object valued instance variables • The world of “data” – Datatypes, data values, data properties (well, these span worlds) – Java analogue: • Primitive types, primitive data values, primitively-valued instance vars Friday, 7 December 2012 29
The World of Logic • “Abstract” – Individuals are members of classes – We know nothing about them except what the ontology says • Individual: Bijan Types: Person. • Individual: Sean Types: Person. • Class: Instructor SubClassOf: Person • What do we know about Bijan, Sean, Instructor, and Person? – Individuals (etc.) are characterized entirely by the user axioms • Ok, mostly! – Tautologies hold: Bijan Types: owl:Thing. • What’s left unsaid may or may not hold – Open world assumption (and no unique name assumption) – Think of the various models • Remember: The Domain is Arbitrary Friday, 7 December 2012 30
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