Transcript SMITH - Buffalo Ontology Site

Room for Lunch: Arlington Room
Room for Evening Reception: Grand
Prairie Room
NCBO
National Center for Biomedical Ontology
Open Biomedical Ontologies (OBO)
Foundry
http://obofoundry.org
Session 2: Ontological approaches to
describing the clinical phenotype
Background
1. No common standards of representation for
molecular biology for diseases
2. Biomedical ontologies don’t interoperate
3. Most health data focused on billing needs
4. EHR systems don’t interoperate
5. Personalized medicine requires computeraided selection from ever larger populations
of candidates for clinical trials
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)
Biological
Process
(GO)
Molecular Function
(GO)
Molecular Process
(GO)
Clinical phenotype (SNAPSHOT)
6
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)
Biological
Process
(GO)
Molecular Function
(GO)
Molecular Process
(GO)
Clinical phenotype (SNAPSHOT)
7
time
pre-clinical
clinical
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)
Biological
Process
(GO)
Molecular Function
(GO)
Molecular Process
(GO)
To address the problem of too many standards:
impose orthogonality
9
Strategy for adoption
1. Build on success of Gene Ontology
2. Create and test guidelines on the basis of
what works
3. Find champions of good practice in use of
terminology in clinical domains
4. who demonstrate research success and
clinical success (“quality measures”)
Cleveland Clinic Semantic DB
40 years of legacy data of Cleveland Clinic
Thoracic and Cardiovascular Surgery
Gene Blackstone
Examples
Measure outcomes of different types of surgical
procedures in a standard way
Provide resource to personalized medicine to
identify ever larger populations of candidates
for clinical trials
Sivaram Arabandi:
Reasoning with clinical exam and
laboratory findings