Download CTSA Ontology Key Function

Limning the CTS Ontology Landscape
Barry Smith
http://ontology.buffalo.edu/smith
1
What exists
HIPAA
Non-public
Hospital
#1 data
Hospital
#2 data
Clinic #1
data
Lab#1
data
Basic science (e.g.
pharma data)
translation
Data Warehouse
Basic science data
Public
2
Components
patient
PAYER
Secondary
users
portal
Allied
health
other
provider
HILS
Imaging lab
PAS
DSS
UPDATE
QUERY
Enterprise
Comprehensive
Path lab
notifications
Msg gateway
Basic
Patient
Record
identity
EHR
Clinical
ref data
Clinical
models
Interactions DS
Local
modelling
Online drug,
Interactions DB
With thanks to Tom Beale, Ocean Informatics
Multimedia
genetics
LAB
workflow
realtime
gateway
demographics
Online
Demographic
registries
ECG etc
billing
terms
guidelines
protocols
Online
terminology
Online
archetypes
telemedicine
What every CTS institution would like to
have
HIPAA
Non-public
Hospital
#1 data
Hospital
#2 data
Clinic #1
data
Lab#1
data
Basic science (e.g.
pharma data)
translation
translation
Data Warehouse
Basic science data
Public
4
More (and better?) EHR data
HIPAA
Non-public
Hospital
#1 data
Hospital
#2 data
Clinic #1
data
Lab#1
data
“Meaningful Use”
Coding Systems
Basic science (e.g.
pharma data)
translation
translation
Data Warehouse
Basic science data
Public
5
Strategies to overcome the complexity and
incompatibility of coding schemes of EHRs
HIPAA
Non-public
Hospital
#1 data
Hospital
#2 data
Clinic #1
data
Lab#1
data
“Meaningful Use”
Coding Systems
Basic science (e.g.
pharma data)
translation
translation
Data Warehouse
i2b2 (with
ontology
cells)
HOM
(Health
Ontology
Mapper
Basic science data
Public
6
Coding schemes and terminologies
ICD, SNOMED, …
– are slow to change
– do not interoperate well with structured basic
biology data
– are not fully open source
– are tied to multiple competing EHR systems
– are not optimized for research
And therefore
– do not support translation
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It is generally recognized that ontologies must play
some part in the solution to these problems
Non-public
HIPAA
Hospital
#1 data
Hospital
#2 data
Clinic #1
data
Roswell
data
Data Warehouse
i2b2 (with
ontology
cells)
HOM
(Health
Ontology
Mapper
Basic science (e.g.
pharma data)
Gene
Ontology
Basic science data
Public
8
Proposed solution: extend the Gene Ontology with
a consistent set of small, agile, open ontology
modules for clinical domains
Non-public
HIPAA
Hospital
#1 data
Hospital
#2 data
Clinic #1
data
Roswell
data
Basic science (e.g.
pharma data)
Data Warehouse
Open Biomedical
Ontologies Foundry
Basic science data
Public
9
RELATION
TO TIME
CONTINUANT
INDEPENDENT
OCCURRENT
DEPENDENT
GRANULARITY
ORGAN AND
ORGANISM
Organism
(NCBI
Taxonomy)
CELL AND
CELLULAR
COMPONENT
Cell
(CL)
MOLECULE
Anatomical
Organ
Entity
Function
(FMA,
(FMP, CPRO) Phenotypic
CARO)
Quality
(PaTO)
Cellular
Cellular
Component Function
(FMA, GO)
(GO)
Molecule
(ChEBI, SO,
RnaO, PrO)
Molecular Function
(GO)
Biological
Process
(GO)
Molecular Process
(GO)
Open Biomedical Ontologies (OBO) Foundry
(First Draft)
10
OBO Foundry approach extended
into other domains
NIF Standard
Neuroscience
Information Framework
ISF Ontologies
Integrated Semantic
Framework
OGMS and Extensions Ontology for General
Medical Science
IDO Consortium
Infectious Disease
Ontology
cROP
Common Reference
Ontologies for Plants
11
OGMS and Its Extensions
Ontology of Medically Relevant Social Entities (OMRSE)
Vital Sign Ontology (VSO)
Mental Diseases
Examples of OGMS applied to specific diseases.
Oral Health and Disease ontology
Infectious Disease Ontology (IDO)
http://code.google.com/p/ogms/
12
IDO and Its Extensions
IDO – Brucellosis
IDO – Dengue Fever
IDO – Influenza
IDO – Malaria
IDO – Staphylococcus Aureus Bacteremia
IDO - Vector Surveillance and Management
VO – Vaccine Ontology
13
HIPAA
Hospital
#1 data
Hospital
#2 data
Clinic #1
data
Roswell
data
Non-public
Basic science (e.g.
pharma data)
Data Warehouse
Alzheimer’s
Disease
Staph
Aureus
Bacteremia
Sleep
Disorders
Using OGMS as basis, create
small ontologies for specific
clinical domains
Open Biomedical
Ontologies Foundry
Basic science data
Public
14
HIPAA
Non-public
Hospital
#1 data
Hospital
#2 data
Clinic #1
data
Roswell
data
Basic science (e.g.
pharma data)
Data Warehouse
Clinical
Neurology
Cancer
Pathology
Semi-public
etc.
Extend this approach
to the workings of the
CTS institution itself
Resource data
Publications, patents, equipment,
samples, expertise, grants, lab
activities, clinical research
activities, clinical trials
Basic science data
15
HIPAA
Non-public
Hospital
#1 data
Hospital
#2 data
Clinic #1
data
Roswell
data
Basic science (e.g.
pharma data)
Data Warehouse
Clinical Trial
Ontology
Consent
Ontology
etc.
Extend this approach
to the workings of the
CTS institution itself
OBI : Ontology for
Biomedical
Investigations
Semi-public
OGMS
Resource data
Publications, patents, equipment,
samples, expertise, grants, lab
activities, clinical research
activities, clinical trials
Open Biomedical
Ontologies Foundry
16