CTSAconnect aims to (1) identify potential collaborators and relevant resources across scientific disciplines and (2) assemble translational teams by creating a semantic representation of clinician and researcher expertise. It will integrate VIVO and eagle-i, which publish Linked Data on people and research resources, by extending them to also represent clinical expertise. Clinical data will be aggregated, mapped to an Integrated Semantic Framework, and expertise will be computed by mapping codes like ICD9 to controlled vocabularies like MeSH. This will enable publishing expertise as Linked Data for other applications to use.

1. From billing codes to expertise:
mining, representing and sharing
clinical research profiles in the
Linked Data Cloud
Carlo Torniai
Shahim Essaid, Chris Barnes, Stephen Williams, Janos Hajagos
Nicole Vasilevsky, Melissa Haendel

2. CTSAConnect Project
Needs:
– Identify potential collaborators, relevant resources, and
expertise across scientific disciplines
– Assemble translational teams of scientists to address specific
research questions
Approach:
Create a semantic representation of clinician and basic science
researcher expertise to enable
– more effective linking of information about clinicians and basic
science researchers
– publication of expertise data as Linked Data (LD) for use in
other applications
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3. Integrating VIVO and eagle-i
VIVO
eagle-i
 VIVO is an ontology-driven application . . . for collecting and
displaying information about people
 eagle-i is an ontology-driven application . . . for collecting and
searching research resources
 Both publish Linked Data. Neither addresses clinical expertise
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4. Extending eagle-i and VIVO to represent
clinical expertise
Semantic
VIVO
Clinical
eagle-i activities
Researcher Characterization Clinician Characterization
• Organizational affiliations • Research resources • Training and credentials
• Grant and project participation – Reagents • Clinical research topic
• Activities – Biospecimens • Specialization inferred from EHR
– Teaching courses – Animal models – Procedures
– Mentoring students – Instruments – Diagnosis
– (Co)-authoring publications – Techinque – Prescriptions
CTSAconnect will produce a single Integrated Semantic Framework that includes
clinical expertise
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5. ISF Clinical module
ARG: Agents, Resources, Grants ontology
CM: Clinical module
IAO: Information Artifact Ontology
OBI: Ontology for Biomedical
Investigations
OGMS: Ontology for General Medical
Science
FOAF: Friend of a Friend vocabulary
BFO: Basic Formal Ontology
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6. 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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7. ISF Clinical module: encounter output
CM: Clinical module
OBI: Ontology for Biomedical
Investigations
OGMS: Ontology for General
Medical Science
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8. Collecting and publishing clinical expertise
as represented by encounter
Step 1 Step 2 Step 3 Step 4
Aggregate Map Data to Compute Publish Linked
Clinical Data ISF Expertise Data
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9. Aggregate clinical data
Step 1 Step 2 Step 3 Step 4
Aggregate Map Data to Compute Publish Linked
Clinical Data ISF Expertise Data
Provider ICD Code Unique Patient
ID Code Value Count Count Code Label
Unilateral or unspecified femoral hernia
1234567 552.00 1 1 with obstruction (ICD9CM 552.00)
Bilateral femoral hernia without mention
1234567 553.02 8 6 of obstruction or gangrene (ICD9CM
553.02)
Regional enteritis of large intestine
1234567 555.1 4 1 (ICD9CM 555.1)
Corrected transposition of great vessels
1234568 745.12 10 5 (ICD9CM 745.12)
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10. Map data to ISF
Step 1 Step 2 Step 3 Step 4
Aggregate Map Data to Compute Publish Linked
Clinical Data ISF Expertise Data
Java scripts RDF
Unique
Provider ID ICD Code Value Code Count
Patient
Count Code Label OWL API triples
Unilateral or unspecified
femoral hernia with
1234567 552.00 1 1
obstruction (ICD9CM
552.00)
Bilateral femoral hernia
without mention of
1234567 553.02 8 6
obstruction or gangrene
(ICD9CM 553.02)
Regional enteritis of large
1234567 555.1 4 1
intestine (ICD9CM 555.1)
Corrected transposition of
1234568 745.12 10 5 great vessels (ICD9CM
745.12)
Aggregated
Clinical Data
ISF
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11. Compute Expertise
Step 1 Step 2 Step 3 Step 4
Aggregate Map Data to Compute Publish Linked
Clinical Data ISF Expertise Data
• Unified Medical Language System (UMLS) aggregates Medical
Subjects Heading (MeSH) and other terminologies by linking them
to UMLS concept unique identifiers (CUI)
• UMLS CUIs will be used to map ICD9 and CPT codes to MeSH
• Expertise indexed by MeSH will enable meaningful connections
between clinicians, basic researchers, and biomedical knowledge
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12. Compute Expertise: Mapping ICD9 to MeSH
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13. Compute Expertise: weighting
Step 1 Step 2 Step 3 Step 4
Aggregate Map Data to Compute Publish Linked
Clinical Data ISF Expertise Data
• Provider X has 500 patients
• S/he has used Syndactyly
(ICD9: 755.12) for 30 unique
patients 75 times
Percentage of patients with
code: 30/500*100 = 6%
Code frequency: 75/30 = 2.5
Code weight: 6 * 2.5 = 15
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14. Publish Linked Data
Step 1 Step 2 Step 3 Step 4
Aggregate Map Data to Compute Publish Linked
Clinical Data ISF Expertise Data
Other APIs
Endpoints
SPARQL
…
Linked Data Several means
Triple Stores to access and
cloud
query data
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15. Sample encounter data published as LOD
Health care encounter
Annotations and Instance URI
Properties
Inferred Types
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16. Querying the data
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17. Beyond expertise
• Encounter data represented using ISF and published as Linked
Data, in addition to enhance linkage between clinical and basic
expertise, will enable integration with multiple datasets which
could be used in a variety of ways to discover useful clinical
associations and patterns
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18. Information
 CTSAconnect project  Carlo Torniai
torniai@ohsu.edu
ctsaconnect.org
 CTSAconnect ontology source  Shahim Essaid
http://code.google.com/p/connect-isf/ essaids@ohsu.edu
 The clinical module can be directed  Chris Barnes
accessed at http://bit.ly/clinical-isf cpb@ufl.edu
 Linked Data generation code
http://bit.ly/isf-lod-code  Janos Hajagos
janos.hajagos@stonybrook.edu
 eagle-i federated search
eagle-i.net  Stephen V Williams
 VIVO integrated search swilliams@ctrip.ufl.edu
vivosearch.org  Nicole Vasilevski
 CTSA ShareCenter vasilevs@ohsu.edu
ctsasharecenter.org
 Melissa Haendel
haendel@ohsu.edu
CTSA 10-001: 100928SB23
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PROJECT #: 00921-0001 Reveal Connections. Realize Potential.