From

EHRs to Linked Data: represen5ng and mining encounter data for clinical exper5se evalua5on
Carlo Torniai Shahim Essaid, Chris Barnes, Mike Conlon, Stephen Williams, Janos Hajagos, Erich Bremer, Jon Corson-Rikert, Melissa Haendel

CTSAConnect Project
Goals:
Iden?fy poten?al collaborators, relevant resources, and exper?se across scien?c disciplines Assemble transla?onal teams of scien?sts to address specic research ques?ons

Approach:
Create a seman?c representa?on of clinician and basic science researcher exper?se to enable Broad and computable representa?on of transla?onal exper?se Publica?on of exper?se as Linked Data (LD) for use in other applica?ons
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Merging VIVO and eagle-i

Seman5c People VIVO Clinical ac5vi5es

eagle-i
Resources

eagle-i

VIVO Coordina?on

eagle-i is an ontology-driven applica?on . . . for collec?ng and searching research resources. VIVO is an ontology-driven applica?on . . . for collec?ng and displaying informa?on about people. Both publish Linked Data. Neither addresses clinical exper5se. CTSAconnect will produce a single Integrated Seman5c Framework, a modular collec?on of ontologies that also includes clinical exper?se 4/5/13 CTSAconnect 3 www.ctsaconnect.org

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ISF Clinical module

ARG: Agents, Resources, Grants ontology CM: Clinical module IAO: Informa?on Ar?fact Ontology OBI: Ontology for Biomedical Inves?ga?ons OGMS: Ontology for General Medical Science FOAF: Friend of a Friend vocabulary BFO: Basic Formal Ontology

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ISF Clinical module: encounter

ARG: Agents, Resources, Grants ontology CM: Clinical module OGMS: Ontology for General Medical Science FOAF: Friend of a Friend vocabulary

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ISF Clinical module: encounter output

CM: Clinical module OBI: Ontology for Biomedical Inves?ga?ons OGMS: Ontology for General Medical Science

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ISF: Clinical exper5se representa5on

Leveraging billing codes to represent clinical exper?se - exper?se as weights associated to billing codes

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Compu5ng and publishing clinical exper5se

Step 1 Aggregate Clinical Data

Step 2 Compute Exper5se

Step 3 Map Data to ISF

Step 4 Publish Linked Data

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Aggregate clinical data

Step 1 Aggregate Clinical Data Step 2 Compute Exper5se Step 3 Map Data to ISF Step 4 Publish Linked Data

Provider ID 1234567 1234567 1234567 1234568

ICD Code Value 552.00 553.02 555.1 745.12

Code Count 1 8 4 10

Unique Pa5ent Count 1 6 1 5

Code Label

Unilateral or unspecied femoral hernia with obstruc?on (ICD9CM 552.00) Bilateral femoral hernia without men?on of obstruc?on or gangrene (ICD9CM 553.02) Regional enteri?s of large intes?ne (ICD9CM 555.1) Corrected transposi?on of great vessels (ICD9CM 745.12)

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Compute exper5se: weigh5ng the codes

Step 1 Aggregate Clinical Data Step 2 Compute Exper5se Step 3 Map Data to ISF Step 4 Publish Linked Data

Code Weight = code frequency * percentage of pa5ents A provider with 500 pa?ents has used Syndactyly (ICD9: 755.12) for 30 unique pa?ents 75 ?mes Percentage of pa?ents with code: 6% Code frequency: 75/30 = 2.5 Code weight: 6 * 2.5 = 15

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Compute exper5se: footprint

Step 1 Aggregate Clinical Data Step 2 Compute Exper5se Step 3 Map Data to ISF Step 4 Publish Linked Data

We group the codes according to the top level ICD code and get the top 10 codes to generate the exper?se footprint for each prac??oner
ICD code 366.1 250 366.9 250.2 . Weight 24.42 24 18.4 19.2 . ICD code 250 366 . . . Weight 43.2 42.82 . . . CTSAconnect

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Mapping Exper5se to the ISF

Step 1 Aggregate Clinical Data Step 2 Map Data to ISF Step 3 Map Data to ISF Step 4 Publish Linked Data

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Publish Linked Data

Step 1 Aggregate Clinical Data Step 2 Map Data to ISF Step 3 Compute Exper5se Step 4 Publish Linked Data

Linked Data cloud

Triple Stores

Several means to access and query data CTSAconnect

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SPARQL Endpoints Other APIs

What can be done with the published dataset

SELECT ?expertise ?label ?weight! WHERE! {! <http://ohsu.dev.eagle-i.net/i/1235281379> obo:BFO_0000086 ?expertise.! ! ! ! ! ?expertise_measurement obo:IAO_0000221 ? expertise.! ! ! ! ?expertise_measurement obo:ARG_2000012 ?label.! ?expertise_measurement obo:IAO_0000004 ?weight. ! ! }!

Select the exper?se for provider hkp://ohsu.dev.eagle-i.net/i/1235281379 Select the weight and the label for measurements rela?ve to the exper?se Select the weight and the label for measurements

The informa?on is enough to represent clinical exper?se as a tag cloud

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Sample encounter data published as LOD

Annota5ons and Proper5es

Health Care Encounter Instance URI Inferred Types

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Querying the sample encounter data

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Next steps: enhance exper5se representa5on by mapping ICD9 to MeSH

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Next steps: enhance exper5se calcula5on

More sophis?cated algorithm leveraging MeSH hierarchy

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Beyond exper5se

Exper5se linked to MeSH will enable meaningful connec5ons between clinicians, basic researchers, and biomedical knowledge
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Team
Stony Brook University: OHSU: Moises Eisenberg, Erich Melissa Haendel, Carlo Torniai, Bremer, Janos Hajagos Nicole Vasilevsky, Shahim Essaid, Eric Orwoll Harvard University: Daniela Bourges-Waldegg Cornell University: Sophia Cheng Jon Corson-Rikert, Dean Kraa, Brian Lowe Share Center: Chris Kelleher, Will University of Florida: Mike Conlon, Chris Barnes, Corbeb, Ranjit Das, Ben Sharma Nicholas Rejack University at Bualo: Barry Smith, Dagobert Soergel

CTSAconnect project ctsaconnect.org The clinical module source: hkp://bit.ly/clinical-isf

Resources

CTSAconnect ontology source hkp://code.google.com/p/connect-isf/ Dataset and queries documenta5on hkps://code.google.com/p/ctsaconnect/w/list

Support : NCATS through Booz Allen Hamilton CTSA 10-001: 100928SB23

CTSA 10-001: 100928SB23 www.ctsaconnect.org PROJECT #: 00921-0001

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