ontology in buffalo -- big data 2013

Ontology in Buffalo

June 6, 2013Barry Smith

Watson’s law of bioinformatics ontologies

“As the time spent discussing a particular bioinformatics topic grows longer, the probability that someone will suggest the group develops an ontology for that topic approaches 1”

http://biomickwatson.wordpress.com

http://biomickwatson.wordpress.com/

http://biomickwatson.wordpress.com/

Watson’s Ontology of Bioinformaticians

Top level is

bioinformatician

bioinformation bioinformationinterested in ontology not interested in ontology

Ontology in Buffalo

June 6, 2013Barry 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 4.11

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

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

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

25

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

28

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


• 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


• 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


• 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


• 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


• 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


• 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


• 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: Institute for Healthcare Informatics

Big (Biomedical) Data

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

Acknowledgement• 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)

Further reading

National Center for Ontological Researchhttp://ncor.buffalo.edu

[email protected]

http://ncor.buffalo.edu/

ontology in buffalo -- big data 2013

Documents