Room for Lunch: Arlington Room Room for Evening Reception: Grand Prairie Room.

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Presentation transcript:

Room for Lunch: Arlington Room Room for Evening Reception: Grand Prairie Room

NCBO National Center for Biomedical Ontology

Open Biomedical Ontologies (OBO) Foundry

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 computer- aided selection from ever larger populations of candidates for clinical trials

6 RELATION TO TIME GRANULARITY CONTINUANTOCCURRENT INDEPENDENTDEPENDENT ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality (PaTO) Biological Process (GO) CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Process (GO) Clinical phenotype (SNAPSHOT)

7 RELATION TO TIME GRANULARITY CONTINUANTOCCURRENT INDEPENDENTDEPENDENT ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality (PaTO) Biological Process (GO) CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Process (GO) Clinical phenotype (SNAPSHOT)

time pre-clinical clinical

9 RELATION TO TIME GRANULARITY CONTINUANTOCCURRENT INDEPENDENTDEPENDENT ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality (PaTO) Biological Process (GO) CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Molecular Process (GO) To address the problem of too many standards: impose orthogonality

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

Sivaram Arabandi: Reasoning with clinical exam and laboratory findings 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