Post on 31-Dec-2015
description
The Future of Health Information
Barry Smith
Ontology Research Group
Center of Excellence in Bioinformatics and Life Sciences
University at Buffalo
ontology.buffalo.edu/smith
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Collaborations
• National Center for Biomedical Ontology (http://NCBO.us)
• WHO Collaborating Center for Terminology
• Cleveland Clinic Semantic Database
• SNOMED CT – Disease Ontology
• German national Electronic Health Record initiative [Health Version 11]
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Overview of this talk
• The role of ontology
• The role of HL7
• The future of health information
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• The role of ontology
• The role of HL7
• The future of health information
Overview of this talk
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we need to know where in the body,
where in the cell
we need to know what kind of
disease process
= we need ontologies
we need semantic annotation of data
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Ontologies are systems of terms for annotating data
They are controlled vocabularies designating the types of entities in reality
Data designate the instances of these types
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• cellular locations
• molecular functions
• biological processes
• used to annotate the entities represented in the major biochemical databases
• thereby creating integration across these databases
The Gene Ontology: A set of standardized textual descriptions of
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what cellular component?
what molecular function?
what biological process?
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The process of data annotation
• yields a slowly growing computer-interpretable map of biological reality within which major databases are automatically integrated in semantically searchable form
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But now
need to extend the methodology to other domains, including clinical medicine
need disease, symptom (phenotype) ontologies
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The Problem
need for prospective standards to ensure mutual consistency and high quality of clinical counterparts of GO
need to ensure consistency of the new clinical ontologies with the basic biomedical sciences
if we do not start now, the problem will only get worse
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The Solution
• establish common rules governing best practices for creating ontologies and for using these in annotations
• apply these rules to create a complete suite of orthogonal interoperable biomedical reference ontologies
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• a shared portal for (so far) 58 ontologies • (low regimentation)
• http://obo.sourceforge.net NCBO BioPortal
First step (2003)
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Second step (2004):reform efforts initiated, e.g. linking GO to other OBO ontologies to ensure
interoperability
id: CL:0000062name: osteoblastdef: "A bone-forming cell which secretes an extracellular matrix. Hydroxyapatite crystals are then deposited into the matrix to form bone." is_a: CL:0000055relationship: develops_from CL:0000008relationship: develops_from CL:0000375
GO
Cell type
New Definition
+
=Osteoblast differentiation: Processes whereby an osteoprogenitor cell or a cranial neural crest cell acquires the specialized features of an osteoblast, a bone-forming cell which secretes extracellular matrix.
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The OBO FoundryThe OBO Foundryhttp://obofoundry.org/http://obofoundry.org/
Third step (2006)Third step (2006)
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• a family of interoperable gold standard biomedical reference ontologies to serve the annotation of
scientific literature model organism databases clinical data experimental results
The OBO FoundryThe OBO Foundry
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Compare the UMLS Metathesaurus
a system of post hoc mappings between independent source vocabularies
built by trained experts
massively useful for information retrieval and information integration
creates out of literature a semantically searchable space
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for UMLS
local usage respected
regimentation frowned upon
cross-framework consistency not important
no concern to establish consistency with basic science
different grades of formal rigor, different degrees of completeness, different update policies
no path towards improvement
no path towards support for logical reasoning
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The OBO Foundry is a prospective standard
designed to guarantee interoperability of ontologies from the very start (contrast to: post hoc mapping)
established March 2006
12 initial candidate OBO ontologies – focused primarily on basic science domains
several being constructed ab initio
now 16 ontologies
Ontology Scope URL Custodians
Cell Ontology (CL)
cell types from prokaryotes to mammals
obo.sourceforge.net/cgi-
bin/detail.cgi?cell
Jonathan Bard, Michael Ashburner, Oliver Hofman
Chemical Entities of Bio-
logical Interest (ChEBI)
molecular entities ebi.ac.uk/chebiPaula Dematos,Rafael Alcantara
Common Anatomy Refer-
ence Ontology (CARO)
anatomical structures in human and model
organisms(under development)
Melissa Haendel, Terry Hayamizu, Cornelius
Rosse, David Sutherland,
Foundational Model of Anatomy (FMA)
structure of the human body
fma.biostr.washington.
edu
JLV Mejino Jr.,Cornelius Rosse
Functional Genomics Investigation
Ontology (FuGO)
design, protocol, data instrumentation, and
analysisfugo.sf.net FuGO Working Group
Gene Ontology (GO)
cellular components, molecular functions, biological processes
www.geneontology.orgGene Ontology
Consortium
Phenotypic Quality Ontology
(PaTO)
qualities of anatomical structures
obo.sourceforge.net/cgi
-bin/ detail.cgi?attribute_and_value
Michael Ashburner, Suzanna
Lewis, Georgios Gkoutos
Protein Ontology (PrO)
protein types and modifications
(under development)Protein Ontology
Consortium
Relation Ontology (RO)
relationsobo.sf.net/
relationshipBarry Smith, Chris
Mungall
RNA Ontology(RnaO)
three-dimensional RNA structures
(under development) RNA Ontology Consortium
Sequence Ontology(SO)
properties and features of nucleic sequences
song.sf.net Karen Eilbeck
RELATION TO TIME
GRANULARITY
CONTINUANT OCCURRENT
INDEPENDENT DEPENDENT
ORGAN ANDORGANISM
Organism(NCBI
Taxonomy)
Anatomical Entity(FMA, CARO)
OrganFunction
(FMP, CPRO) Phenotypic
Quality(PaTO)
Biological Process
(GO)CELL AND CELLULAR
COMPONENT
Cell(CL)
Cellular Compone
nt(FMA, GO)
Cellular Function
(GO)
MOLECULEMolecule
(ChEBI, SO,RnaO, PrO)
Molecular Function(GO)
Molecular Process
(GO)
Building out from the original GO
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OBO low-regimentation ontology portal
OBO Foundry high-regimentation collaborative initiative to create a gold standard suite of interoperable ontologies
The vision
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Common Anatomy Reference Ontology
Disease Ontology (DO) [SNOMED CT]
Biomedical Image Ontology (BIO)
Environment Ontology (EnvO)
Biobank Ontology (BrO)
Clinical Trial Ontology (CTO) [with WHO Global Trial Bank, Immune Tolerance Network, ACGT Advancing Genomics Clinical Trials in Cancer EU IP]
Ontologies under construction
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Clinical Trial Ontology
• part of a larger project called the Ontology for Biomedical Investigations (OBI)
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controlled vocabulary for biomedical investigations including
protocols instrumentationmaterialdata types of analysis and statistical tools
applied to the data
OBI
http://obofoundry.org/http://obofoundry.org/
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Clinical Trial Ontology
• To serve merger of data schemas• To serve flexibility of collaborative clinical trial
research• To serve design and management of clinical trials• To serve data access and reuse – send me all trials
which ...
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Ontology vs. Database Schema
• Separate development of data schemas and ‘information models’ (HL7) and terminologies such as SNOMED CT
• the two do not work together
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Ontology vs. Database Schema
• diabetes => disease
• diabetes => string
• temperature => quality
• temperature => integer
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CTO
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CTO Continuant
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CTO Occurrent
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Clinical Trial Ontology Working Group
• http://www.bioontology.org/wiki/
• Workshop on May 16-17, 2007
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• The role of ontology
• The role of HL7
• The future of health information
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HL7 V3
“the data standard for
biomedical informatics”
• http://aurora.regenstrief.org/~schadow/ HL7TheDataStandardForBiomedicalInformatics.ppt
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HL7 V2
a workable messaging standard faced the problem of local dialects
seeks to solve this problem by having all HL7 artifacts conform to a single ‘Reference
Information Model’ (the RIM)
HL7 V3
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After 10 years?And many attempts?
And gigantic investments of energy and funding?
is there a single, successful RIM-implementation?
There are clear examples of failure of billion-dollar implementations resting on the RIM
and of programmers involved in such failures who are tearing out their hair, and blaming HL7
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Is it justified, in these circumstances, to promote HL7 V3 as an ISO Standard
in the domain of patient care?
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One indispensable foundation for a successful standard
a correct and uniform interpretation of its basic terms
• Act• Participation• Entity• Role• ActRelationship• RoleLink
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• Sometimes ‘Act’ means information about an act
• Sometimes ‘Act’ means real-world action
• Sometimes ‘Act’ means a mixture of the above
• Sometimes in the very same sentence
Demonstrably, the HL7 community does not understand its own basic terms
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Consequences of unclarity here
• Different user groups have interpreted the same classes in different ways
• Different message specifications used different interpretations
• This recreates interoperability problems
• Can we be sure that these problems will not lead to incidents relevant to patient safety?
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Even with clarity – and clear documentation – the RIM would still be in bad shape
http://hl7-watch.blogspot.com/
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Where are diseases
• Acts ?• Things, Persons, Organizations ?• Participations ?• Roles ?• ActRelationships ?• RoleLinks ?
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The HL7 Clinical Genomic Standard
• defines an allele as the observation of an allele
• defines a phenotype as the observation of an observation
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The $ 35 bn. NHS Program “Connecting for Health”
• has applied the RIM rigorously, using all the normative elements, and it discovered that it needed to create dialects of its own to make the V3-based system work for its purposes (it still does not work)
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The RIM has no coherent answer
• Basic categories cannot be agreed upon even for common phenomena like snakebites.
• HL7 V3 dialects are formed – and the RIM does not do its job.
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The moral of this story
• Don’t claim to be
• “the data standard for biomedical informatics”
• until you have a system that works
• http://aurora.regenstrief.org/~schadow/
HL7TheDataStandardForBiomedicalInformatics.ppt
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• The role of ontology
• The role of HL7
• The future of health information
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A New Paradigm for Health Information
• How achieve semantic interoperability amongst healthcare applications?
• Through referent tracking
www.org.buffalo.edu/RTU
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The myth of ‘unambiguous’ understanding through biomedical terminologies
5572 04/07/1990 26442006 closed fracture of shaft of femur
5572 04/07/1990 81134009 Fracture, closed, spiral
5572 12/07/1990 26442006 closed fracture of shaft of femur
5572 12/07/1990 9001224 Accident in public building (supermarket)
5572 04/07/1990 79001 Essential hypertension
0939 24/12/1991 255174002 benign polyp of biliary tract
2309 21/03/1992 26442006 closed fracture of shaft of femur
2309 21/03/1992 9001224 Accident in public building (supermarket)
47804 03/04/1993 58298795 Other lesion on other specified region
5572 17/05/1993 79001 Essential hypertension
298 22/08/1993 2909872 Closed fracture of radial head
298 22/08/1993 9001224 Accident in public building (supermarket)
5572 01/04/1997 26442006 closed fracture of shaft of femur
5572 01/04/1997 79001 Essential hypertension
PtID Date ObsCode Narrative
0939 20/12/1998 255087006 malignant polyp of biliary tract
*
*
*
* cause, not disorder
How many disorders have patients 5572, 2309 and 298 each had thus far in their lifetime ?
How many numerically different disorders are listed here ?
How many different types of disorders are listed here ?
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Does seeing the labels help ?
5572 04/07/1990 26442006 closed fracture of shaft of femur
5572 04/07/1990 81134009 Fracture, closed, spiral
5572 12/07/1990 26442006 closed fracture of shaft of femur
5572 12/07/1990 9001224 Accident in public building (supermarket)
5572 04/07/1990 79001 Essential hypertension
0939 24/12/1991 255174002 benign polyp of biliary tract
2309 21/03/1992 26442006 closed fracture of shaft of femur
2309 21/03/1992 9001224 Accident in public building (supermarket)
47804 03/04/1993 58298795 Other lesion on other specified region
5572 17/05/1993 79001 Essential hypertension
298 22/08/1993 2909872 Closed fracture of radial head
298 22/08/1993 9001224 Accident in public building (supermarket)
5572 01/04/1997 26442006 closed fracture of shaft of femur
5572 01/04/1997 79001 Essential hypertension
PtID Date ObsCode Narrative
0939 20/12/1998 255087006 malignant polyp of biliary tract
Same patient, same hypertension code:Same (numerically identical) hypertension ?
Different patients, same fracture codes:Same (numerically identical) fracture ?
Same patient, different dates, same fracture
codes: same (numerically identical)
fracture ?
Same patient, same date,2 different fracture codes:
same (numerically identical) fracture ?
Same patient, different dates, Different codes. Same (numericallyidentical) polyp ?
Different patients. Same supermarket? Maybe the same freezer section ?Or different supermarkets, but always in the freezer sections ?
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We have unique IDs
• for patients
• for healthcare deliverers
• for images
• for invoices
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Let’s introduce unique IDs
• for everything that is mentioned in the record:– lesions– fractures– presentings– surgical procedures
http://sourceforge.net/projects/rtsystem
• IUI = instance unique identifier
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Better public health statistics
5572 04/07/1990 26442006 closed fracture of shaft of femur
5572 04/07/1990 81134009 Fracture, closed, spiral
5572 12/07/1990 26442006 closed fracture of shaft of femur
5572 12/07/1990 9001224 Accident in public building (supermarket)
5572 04/07/1990 79001 Essential hypertension
0939 24/12/1991 255174002 benign polyp of biliary tract
2309 21/03/1992 26442006 closed fracture of shaft of femur
2309 21/03/1992 9001224 Accident in public building (supermarket)
47804 03/04/1993 58298795 Other lesion on other specified region
5572 17/05/1993 79001 Essential hypertension
298 22/08/1993 2909872 Closed fracture of radial head
298 22/08/1993 9001224 Accident in public building (supermarket)
5572 01/04/1997 26442006 closed fracture of shaft of femur
5572 01/04/1997 79001 Essential hypertension
PtID Date ObsCode Narrative
0939 20/12/1998 255087006 malignant polyp of biliary tract
IUI-001
IUI-001
IUI-001
IUI-003
IUI-004
IUI-004
IUI-005
IUI-005
IUI-005
IUI-007
IUI-007
IUI-007
IUI-002
IUI-012
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‘John Doe’s ‘John Smith’s
liver liver
tumor tumor
was treated was treated
with with
RPCI’s RPCI’s
irradiation device’ irradiation device’
‘John Doe’s
liver
tumor
was treated
with
RPCI’s
irradiation device’
Better reasoning over health information
#1
#3
#2
#4
#5
#6
treating
person
liver
tumor
clinic
device
instance-of at t1
instance-of at t1
instance-of at t1
instance-of at t1
instance-of at t1
#10
#30
#20
#40
#5
#6
inst-of at t2
inst-of at t2
inst-of at t2
inst-of at t2
inst-of at t2
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Application principles
#IUI-1 ‘affects’ #IUI-2#IUI-3 ‘affects’ #IUI-2#IUI-1 ‘causes’ #IUI-3
Referent TrackingDatabase
EHR
CAG repeat
Juvenile HD
persondisorder
continuantOntology
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Goal: A New Form of Evidence Based Medicine
• Now:– Decisions based on the outcomes of (reproducible)
results of well-designed studies• Guidelines and protocols
– Evidence is hard to get, takes time to accumulate.
• Future:– Each discovered fact or expressed belief should
instantly become available as contributing to the total body evidence, wherever its description is generated.
– Data ‘eternally’ reusable independent of the purpose for which they have been generated.