ontology in buffalo september 29, 2014 barry smith
TRANSCRIPT
Ontology in Buffalo
September 29, 2014Barry Smith
• Stanford University Biomedical Informatics Research • Mayo Clinic Department of Biomedical Informatics• University at Buffalo Department of Philosophy
Three US partner institutions:
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)Open Biomedical Ontologies (OBO) Foundry
(Gene Ontology marked in yellow)
© Ocean Informatics 2005 4.8
Enterprise
Comprehensive Basic
Components
EHR
Multimediagenetics
workflow
identity
Clinicalref data Clinical
models
terms
Security / access control
realtimegateway
telemedicine
HILS
otherprovider
UPDATEQUERY
demographics
guidelinesprotocolsInteractions
DSLocal
modelling
notifications
DSS
PAS
billing
portal
Alliedhealth
patientPAYER
Msg gateway
Imaging lab
ECG etc
Path lab
LAB
Secondaryusers
Online drug,Interactions DB Online
archetypes
Online terminology
Online Demographic
registries
PatientRecord
Grants• IDO: Immune System Biological Networks: A Case Study
in Improved Data Integration & Analysis (NIH / NIAID)• ImmPort: Bioinformatics Integration Support Contract
(NIH/NIAID)• Plant Ontology (NSF)• OPMQoL: Ontology for Pain and Related Disability,
Mental Health and Quality of Life (NIH/National Institute of Dental and Craniofacial Research)
• PRO: A Protein Ontology in Open Biomedical Ontologies (NIH/NIGMS)
• NCBO: National Center for Biomedical Ontology (NIH/NHGRI)
Military Ontology
11
Explosion of “biomedical ontology” since 1999
Biomedical Ontology in Buffalo
BS, Alan Ruttenberg, Alex Diehl
PhilosophyDental School,
IHI Neurology
Werner Ceusters, Dagobert Soergel, Peter Elkin
Psychiatry, IHIDental School,
Library and Information Studies
BiomedicalInformatics
IHI: Institute for Healthcare Informatics
Peter Winkelstein
IHI Ontology Machine
Biomedical Ontologies co-developed at UBBCO Biocollections OntologyBFO Basic Formal OntologyCL Cell OntologyENVO Environment Ontology FMA Foundational Model of AnatomyGO Gene OntologyIDO Infectious Disease OntologyND Neurological Disease OntologyMFO Mental Functioning OntologyNPT Neuropsychological Testing OntologyOBI Ontology for Biomedical InvestigationsOGMS Ontology for General Medical ScienceOHD Oral Health and Disease OntologyPCO Population and Community OntologyPO Plant OntologyPRO Protein Ontology
Biomedical Ontologies co-developed at UBBCO Biocollections OntologyBFO Basic Formal OntologyCL Cell OntologyENVO Environment Ontology FMA Foundational Model of AnatomyGO Gene OntologyIDO Infectious Disease OntologyND Neurological Disease OntologyMFO Mental Functioning OntologyNPT Neuropsychological Testing OntologyOBI Ontology for Biomedical InvestigationsOGMS Ontology for General Medical ScienceOHD Oral Health and Disease OntologyPCO Population and Community OntologyPO Plant OntologyPRO Protein Ontology
http://www.ifomis.org/bfo/users
Biomedical Ontologies co-developed at UBBCO Biocollections OntologyBFO Basic Formal OntologyCL Cell OntologyENVO Environment Ontology FMA Foundational Model of AnatomyGO Gene OntologyIAO Information Artifact OntologyIDO Infectious Disease OntologyND Neurological Disease OntologyMFO Mental Functioning OntologyNPT Neuropsychological Testing OntologyOBI Ontology for Biomedical InvestigationsOGMS Ontology for General Medical SciencePCO Population and Community OntologyPO Plant OntologyPRO Protein Ontology
OGMS Big Picture
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From BFO to OGMS
• Material Entity• Disposition• Process
• Disorder• Disease• Disease Course
BFO
Top-level terms in the OGMS ontology
• Disorder = part of an organism which deviates from the normal (a necrotic liver …)
• Disease = a disposition to bad things which exists in virtue of one or more disorders
• Disease course = the realization (manifestation) of such a disposition
OGMS Big Picture
27
Huntington’s Disease - genetic
• Etiological process - inheritance of >39 CAG repeats in the HTT gene– produces
• Disorder - chromosome 4 with abnormal mHTT– bears
• Disposition (disease) - Huntington’s disease– realized_in
• Pathological process - accumulation of mHTT protein fragments, abnormal transcription regulation, neuronal cell death in striatum– produces
• Abnormal bodily features– recognized_as
• Symptoms - anxiety, depression• Signs - difficulties in speaking and swallowing
HNPCC - genetic pre-disposition• Etiological process - inheritance of a mutant mismatch repair gene
– produces• Disorder - chromosome 3 with abnormal hMLH1
– bears• Disposition (disease) - Lynch syndrome
– realized_in• Pathological process - abnormal repair of DNA mismatches
– produces• Disorder - mutations in proto-oncogenes and tumor suppressor
genes with microsatellite repeats (e.g. TGF-beta R2)– bears
• Disposition (disease) - non-polyposis colon cancer
HNPCC - genetic pre-disposition• Etiological process - inheritance of a mutant mismatch repair gene
– produces• Disorder - chromosome 3 with abnormal hMLH1
– bears• Disposition (disease) - Lynch syndrome
– realized_in• Pathological process - abnormal repair of DNA mismatches
– produces• Disorder - mutations in proto-oncogenes and tumor suppressor
genes with microsatellite repeats (e.g. TGF-beta R2)– bears
• Disposition (disease) - non-polyposis colon cancer
Pre-disposition = A disposition to acquire a disposition
Influenza - infectious
• Etiological process - infection of airway epithelial cells with influenza virus– produces
• Disorder - viable cells with influenza virus– bears
• Disposition (disease) - flu– realized_in
• Pathological process - acute inflammation– produces
• Abnormal bodily features– recognized_as
• Symptoms - weakness, dizziness• Signs - fever
Cirrhosis - environmental exposure
• Etiological process - phenobarbitol-induced hepatic cell death– produces
• Disorder - necrotic liver– bears
• Disposition (disease) - cirrhosis– realized_in
• Pathological process - abnormal tissue repair with cell proliferation and fibrosis that exceed a certain threshold; hypoxia-induced cell death– produces
• Abnormal bodily features– recognized_as
• Symptoms - fatigue, anorexia• Signs - jaundice, splenomegaly
Systemic arterial hypertension
• Etiological process – abnormal reabsorption of NaCl by the kidney– produces
• Disorder – abnormally large scattered molecular aggregate of salt in the blood– bears
• Disposition (disease) - hypertension– realized_in
• Pathological process – exertion of abnormal pressure against arterial wall– produces
• Abnormal bodily features– recognized_as
• Signs – elevated blood pressure
Type 2 Diabetes Mellitus• Etiological process –
– produces• Disorder – abnormal pancreatic beta cells or abnormal muscle/fat
cells– bears
• Disposition (disease) – diabetes mellitus– realized_in
• Pathological processes – diminished insulin production, diminished muscle/fat uptake of glucose– produces
• Abnormal bodily features– recognized_as
• Symptoms – polydipsia, polyuria, polyphagia, blurred vision• Signs – elevated blood glucose and hemoglobin A1c
Type 1 hypersensitivity to penicillin
• Etiological process – sensitizing of mast cells and basophils during exposure to penicillin-class substance– produces
• Disorder – mast cells and basophils with epitope-specific IgE bound to Fc epsilon receptor I– bears
• Disposition (disease) – type I hypersensitivity– realized_in
• Pathological process – type I hypersensitivity reaction– produces
• Abnormal bodily features– recognized_as
• Symptoms – pruritis, shortness of breath• Signs – rash, urticaria, anaphylaxis
Huntington’s Disease - genetic
• Etiological process - inheritance of >39 CAG repeats in the HTT gene– produces
• Disorder - chromosome 4 with abnormal mHTT– bears
• Disposition (disease) - Huntington’s disease– realized_in
• Pathological process - accumulation of mHTT protein fragments, abnormal transcription regulation, neuronal cell death in striatum– produces
• Abnormal bodily features– recognized_as
• Symptoms - anxiety, depression• Signs - difficulties in speaking and
swallowing
Symptoms & Signs used_in
Interpretive process produces
Hypothesis - rule out Huntington’s suggests
Laboratory tests produces
Test results - molecular detection of the HTT gene with >39CAG repeats used_in
Interpretive process produces
Result - diagnosis that patient X has a disorder that bears the disease Huntington’s disease
Information Artifacts
Influenza - infectious
• Etiological process - infection of airway epithelial cells with influenza virus– produces
• Disorder - viable cells with influenza virus– bears
• Disposition (disease) - flu– realized_in
• Pathological process - acute inflammation– produces
• Abnormal bodily features– recognized_as
• Symptoms - weakness, dizziness• Signs - fever
Biomedical Ontologies co-developed at UBBCO Biocollections OntologyCL Cell OntologyENVO Environment Ontology FMA Foundational Model of AnatomyGO Gene OntologyIDO Infectious Disease OntologyND Neurological Disease OntologyMFO Mental Functioning OntologyNPT Neuropsychological Testing OntologyOBI Ontology for Biomedical InvestigationsOGMS Ontology for General Medical SciencePCO Population and Community OntologyPO Plant OntologyPRO Protein Ontology
From OGMS to IDO Core
• Disorder• Disease• Disease Course
• Infection• Infectious Disease• Infectious Disease Course
Core and Extensions
IDO Infectious Disease Ontology IDO-BRU Brucellosis Ontology IDO-HIV HIV Ontology IDO-FLU Influenza Ontology IDO-DENGUE Dengue Ontology IDO-STAPH Staph. Aureus Ontology IDO-PLANT Plant Infectious Disease Ontology IDO-MRSA Methicillin-Resistant Staph. Aureus Ontology IDO-Vector Vector-Borne Infectious Disease Ontology IDO-MAL Malaria Ontology
Core and Extensions
IDO Core Infectious Disease Ontology IDO-BRU Brucellosis Ontology IDO-HIV HIV Ontology IDO-DENGUE IDO-STAPH Staph. aureus Ontology IDO-MRSA Methicillin-Resistant Staph. aureus Ontology IDO-Vectorborne Vector-Borne Infectious Disease Ontology IDO-MAL Malaria Ontology
From IDO Core to IDO STAPH
• Sa Infection• Sa Bacteremia• Sa Bacteremia Disease Course
• Infection• Infectious Disease• Infectious Disease Course
From BFO to IDO Core to IDO STAPH
IDOCore
IDO STAPH
OGMS
IDOHIV
IDOFLU
BFO
IDO STAPH and its Extensions
IDOCore
IDO STAPH
IDOHumanSa
IDORatSa
IDOStrep
IDORatStrep
IDOHumanStrep
IDOMRSa
IDOHumanBacterial
IDOAntibioticResistant
IDOMAL IDOHIV
IDOFLU
How we ensure consistent data as new Staph. aureus strains evolve
IDOCore
IDO STAPH
IDOHumanSa
IDORatSa
IDOStrep
IDORatStrep
IDOHumanStrep
IDOMRSa
IDOHumanBacterial
IDOAntibioticResistant
IDOMAL IDOHIV
IDOFLU
IHI• using BFO, OGMS and their extension ontologies
to provide a consistent framework for the representation of the types of particulars
• developing systematic ways for the consistent tracking of particulars (patients, disorders, encounters …)
• putting these together to serve consistent representation of the assertional knowledge in the IHI repository