Building Ontologies with Basic Formal Ontology Barry Smith May 27, 2015.

Slides:



Advertisements
Similar presentations
Species-Neutral vs. Multi-Species Ontologies Barry Smith.
Advertisements

PRIME Program for Research on Immune Modeling and Experimentation PI: Stuart Sealfon, Mount Sinai School of Medicine.
On the Future of the NeuroBehavior Ontology and Its Relation to the Mental Functioning Ontology Barry Smith
IAO-Core Towards a General-Purpose, Top-Level Information Artifact Ontology Barry Smith University at Buffalo USA Tatiana Malyuta New York City College.
Goal and Status of the OBO Foundry Barry Smith. 2 Semantic Web, Moby, wikis, crowd sourcing, NLP, etc.  let a million flowers (and weeds) bloom  to.
Development of the Field of Biomedical Ontology Barry Smith New York State Center of Excellence in Bioinformatics and Life Sciences University at Buffalo.
1 Introduction to Biomedical Ontology Barry Smith University at Buffalo
1 The OBO Foundry Towards Gold Standard Terminology Resources in the Biomedical Domain Thomas Bittner (based on a presentation by Barry Smith)
1 Intelligence Ontology: A Strategy for the Future Barry Smith University at Buffalo
1 How Ontologies Create Research Communities Barry Smith
What is an ontology and Why should you care? Barry Smith with thanks to Jane Lomax, Gene Ontology Consortium 1.
1 The OBO Foundry 2 A prospective standard designed to guarantee interoperability of ontologies from the very start (contrast.
The Problem of Reusability of Biomedical Data OBO Foundry & HL7 RIM Barry Smith.
What is an ontology and Why should you care? Barry Smith with thanks to Jane Lomax, Gene Ontology Consortium 1.
Underlying Ontologies for Biomedical work - The Relation Ontology (RO) and Basic Formal Ontology (BFO) Thomas Bittner SUNY Buffalo
Using Ontologies to Represent Immunological Networks Lindsay G. Cowell, Anne Lieberman, Anna Maria Masci Duke University Center for Computational Immunology.
1 Logical Tools and Theories in Contemporary Bioinformatics Barry Smith
The Future of Ontology in Buffalo Barry Smith 1.
Room for Lunch: Arlington Room Room for Evening Reception: Grand Prairie Room.
New York State Center of Excellence in Bioinformatics & Life Sciences Biomedical Ontology in Buffalo Part I: The Gene Ontology Barry Smith and Werner Ceusters.
Why a Credit Card Number is Not a Number Barry Smith 1.
The RNA Ontology RNAO Colin Batchelor Neocles Leontis May 2009 Eckart, Colin and Jane In Cambridge.
1 BIOLOGICAL DOMAIN ONTOLOGIES & BASIC FORMAL ONTOLOGY Barry Smith.
CoE Ontology Research Group (ORG) Barry Smith Center of Excellence in Bioinformatics and Life Sciences Ontology Research Group Department of Philosophy.
How to Organize the World of Ontologies Barry Smith 1.
New York State Center of Excellence in Bioinformatics & Life Sciences Biomedical Ontology in Buffalo Part I: The Gene Ontology Barry Smith and Werner Ceusters.
The Core Infectious Disease Ontology. Purpose: To make infectious disease-relevant data deriving from different sources comparable and computable Across.
1 How Ontologies Create Research Communities Barry Smith
BFO and Disease Barry Smith Milan, September 4,
The OBO Foundry approach to ontologies and standards with special reference to cytokines Barry Smith ImmPort Science Talk / Discussion June 17, 2014.
Building the Ontology Landscape for Cancer Big Data Research Barry Smith May 12, 2015.
Ontology in Buffalo September 29, 2014 Barry Smith.
Formal Empirical Applied Mathematical and technical methods and theories Cognitive, behavioral, and organizational techniques and theories ImagingBioInformaticsClinical.
Limning the CTS Ontology Landscape Barry Smith 1.
Computational Biology and Informatics Laboratory Development of an Application Ontology for Beta Cell Genomics Based On the Ontology for Biomedical Investigations.
2007 CDISC International Interchange Ontologies in Clinical Research: Representation of clinical research data in the framework of formal biomedical ontologies.
The CROP (Common Reference Ontologies for Plants) Initiative Barry Smith September 13,
Ontology of Sensors: Some Examples from Biology
Ontological realism as a strategy for integrating ontologies Ontology Summit February 7, 2013 Barry Smith 1.
Intelligence Ontology A Strategy for the Future Barry Smith University at Buffalo
Ontology for General Medical Science Overview and OBO Foundry Criteria Albert Goldfain Blue Highway / University at Buffalo ICBO.
Resurrecting SOWG BS, Baltimore, CTS Ontology Workshop April
Ontological Engineering Barry Smith Computers and Information in Engineering Conference, Buffalo August 19,
IDO-Staph: An Ontology of Staphylococcus aureus Infectious Disease Albert Goldfain, Ph.D. Researcher, Blue Highway, Inc. Problems.
Brian Donohue, J. Neil Otte, and Barry Smith University at Buffalo November 2014.
What is an ontology? Barry Smith 1.
Ontologies for Neuroscience and Neurology The Neuroscience Information Framework Fahim Imam, Stephen Larson, Georgio Ascoli, Gordon Shepherd, Anita Bandrowski,
Introduction to Biomedical Ontology for Imaging Informatics Barry Smith, PhD, FACMI University at Buffalo May 11, 2015.
Towards an Ontology of Military Plans and Planning Barry Smith National Center for Ontological Research, Buffalo.
How to integrate data Barry Smith. The problem: many, many silos DoD spends more than $6B annually developing a portfolio of more than 2,000 business.
2 3 where in the body ? where in the cell ?
Ontology and the Semantic Web Barry Smith August 26,
Need for common standard upper ontology
What developers need to know about ontologies? Barry Smith 1.
Introduction to Biomedical Ontology for Imaging Informatics Barry Smith, PhD, FACMI University at Buffalo May 11, 2015.
Influenza Ontology Infectious Disease Ontology Workshop 2008 Burke Squires.
FHIR and ontology Barry Smith Charleston, September 24,
1 An Introduction to Ontology for Scientists Barry Smith University at Buffalo
Immunology Ontology Rho Meeting October 10, 2013.
OBO Foundry Principles BFO RO Barry Smith 1. OBO Foundry Principles  open  common formal language (OBO Format, OWL DL, CL)  commitment to collaboration.
Basic Formal Ontology Barry Smith August 26, 2013.
Immunology Ontology Workshop Buffalo, NY June 11-13, 2012.
Building Ontologies with Basic Formal Ontology Barry Smith May 27, 2015.
New York State Center of Excellence in Bioinformatics & Life Sciences R T U Buffalo Blue Cloud Health Information Center: the vision Werner Ceusters, MD.
An Ontology Ecosystem Approach to Electronic Health Record Interoperability Barry Smith Ontology Summit April 7,
Distributed Common Ground System – Army (DCGS-A)
Why do we need upper ontologies? What are their purported benefits?
How BFO Deals with Data from Multiple Contexts
OBO Foundry Update: April 2010
Presentation transcript:

Building Ontologies with Basic Formal Ontology Barry Smith May 27, 2015

2

3

John Fox (Director, OpenClinical) As a user and teacher of ontological methods in medicine and engineering I have for years warned my students that the design of domain ontologies is a black art with no theoretical foundations and few practical principles. 4

Ontology success stories, and some reasons for failure Linked Open Data, from Musicbrainz to Mouse Genome Informatics 5

John Fox, OpenClinical As a user and teacher of ontological methods in medicine and engineering I have for years warned my students that the design of domain ontologies is a black art with no theoretical foundations and few practical principles. … I now have a much more positive story for my students. … 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) Original OBO Foundry ontologies (Gene Ontology in yellow) 7

CONTINUANTOCCURRENT INDEPENDENTDEPENDENT ORGAN AND ORGANISM Organism (NCBI Taxonomy) Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Phenotypic Quality (PaTO) Organism-Level Process (GO) CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) Cellular Process (GO) MOLECULE Molecule (ChEBI, SO, RNAO, PRO) Molecular Function (GO) Molecular Process (GO) rationale of OBO Foundry coverage GRANULARITY RELATION TO TIME 8

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) Environment Ontology (EnvO) Environments 9

RELATION TO TIME CONTINUANT OCCURRENT GRANULARITY INDEPENDENT CONTINUANT DEPENDENT CONTINUANT ORGAN AND ORGANISM Organism NCBI Taxonomy Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Biological Process (GO) Ontology for Biomedical Investigations (OBI) 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) Environment Ontology (ENVO) 10 Phenotypic Quality (PATO) Recognizing a new family of protocol-driven processes (investigation, assay, clinical trial …)

RELATION TO TIME CONTINUANT OCCURRENT GRANULARITY INDEPENDENT CONTINUANT DEPENDENT CONTINUANT INFORMATION ARTIFACT ORGAN AND ORGANISM Organism NCBI Taxonomy Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) IAO Software, Algorithms, … Sequence Data, EHR Data … Biological Process (GO) OBI CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Images, Image Data, Flow Cytometry Data, … Molecular Process (GO) OBI: Imaging Environment Ontology (ENVO) 11 Phenotypic Quality (PATO) Recognizing a new family of information entities: data, publications, images, algorithms …

examples of BFO/OBO Foundry approach extended into other domains 12 NIF StandardNeuroscience Information Framework UNEP Ontology Framework United Nations Environment Program Ontologies IDO ConsortiumInfectious Disease Ontology Suite MilPortalIntelligence and Information Warfare Directorate, US Army cROPCommon Reference Ontologies for Plants

Common Reference Ontologies for Plants (cROP)

Introduction to Biomedical Ontology for Imaging Informatics Barry Smith, PhD, FACMI University at Buffalo May 11, 2015

RELATION TO TIME CONTINUANT OCCURRENT GRANULARITY INDEPENDENT CONTINUANT DEPENDENT CONTINUANT ORGAN AND ORGANISM Organism NCBI Taxonomy Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Biological Process (GO) Ontology for Biomedical Investigations (OBI) 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) OBI: Imaging Ontology Branch Environment Ontology (ENVO) 15 Phenotypic Quality (PATO) Recognizing a new family of processes (investigation, assay, protocol-driven process)

Anatomy Ontology (FMA*, CARO) Disease Ontology (OGMS, IDO, HDO, HPO) Biological Processes Assays (Protocol- driven processes) Cell Ontology (CL) Subcellular Anatomy Ontology (SAO) Phenotypic Quality Ontology (PATO) Sequence Ontology (SO) Molecular Function Ontology (GO) Protein Ontology (PRO) Extension Strategy + Modular Organization I NDEPENDENT C ONTINUANT (~T HING )) D EPENDENT C ONTINUANT (~A TTRIBUTE ) O CCURRENT (~P ROCESS ) Basic Formal Ontology (BFO) 16

Structure of a typical investigation as viewed by OBI (from The Ontology for Biomedical Investigations

RELATION TO TIME CONTINUANT OCCURRENT GRANULARITY INDEPENDENT CONTINUANT DEPENDENT CONTINUANT INFORMATION ARTIFACT ORGAN AND ORGANISM Organism NCBI Taxonomy Anatomical Entity (FMA, CARO) Organ Function (FMP, CPRO) Software, Algorithms … Patient Demographic Data, EHR Data, Public Health Data, … Biological Process (GO) OBI CELL AND CELLULAR COMPONENT Cell (CL) Cellular Component (FMA, GO) Cellular Function (GO) MOLECULE Molecule (ChEBI, SO, RnaO, PrO) Molecular Function (GO) Images, Image Data, Flow Cytometry Data, … Molecular Process (GO) OBI: Imaging Environment Ontology (ENVO) 18 Phenotypic Quality (PATO) Recognizing a new family of attributes (data, information artifacts, including images)

Anatomy Ontology (FMA*, CARO) Disease Ontology (OGMS, IDO, HDO, HPO) Images, Image Data, Image Metadata … Biological Process Ontology (GO) Assays Cell Ontology (CL) Subcellular Anatomy Ontology (SAO) Phenotypic Quality Ontology (PATO) Sequence Ontology (SO) Molecular Function Ontology (GO) Protein Ontology (PRO) Extension Strategy + Modular Organization I NDEPENDENT C ONTINUANT (~T HING )) D EPENDENT C ONTINUANT (~A TTRIBUTE ) INFORMATION A RTIFACT (~D ATA ) O CCURRENT (~P ROCESS ) Basic Formal Ontology (BFO) 19

Structure of a typical investigation as viewed by OBI (from The Ontology for Biomedical Investigations

specimen extraction purification imaging data collection assay transformation OBI Pipeline applied to Imaging Assays

22 need to extend this pipeline also to clinical diagnosis and treatment (from OGMS*) *Ontology for General Medical Science

specimen extraction purification imaging data collection assay transformation need to extend this pipeline also to clinical diagnosis and treatment

24 Even here, things are not as bad as they seem

25

26

27

28 obo/IAO_ http://purl.obolibrary.org/ obo/IAO_ : algorithm

IAO = Information Artifact Ontology: on-artifact-ontology/ 29

30

A list of ontologies using IAO Adverse Event Reporting Ontology (AERO) Bioinformatics Web Service Ontology Biological Collections Ontology (BCO) Chemical Methods Ontology (CHMO) Cognitive Paradigm Ontology (COGPO) Comparative Data Analysis Ontology Computational Neuroscience Ontology Core Clinical Protocol Ontology (C2PO) Document Act Ontology Eagle-I Research Resource Ontology (ERO) The Ontology Emotion Ontology (MFOEM) Experimental Factor Ontology (EFO) Exposé Ontology IAO-Intel Infectious Disease Ontology (IDO) Influenza Research Database (IRD) Information Entity Ontology Mental Functioning Ontology (MF) Ontology for Biomedical Investigations Ontology for Drug Discovery Investigations Ontology for General Medical Science (OGMS) Ontology for Newborn Screening Follow- up and Translational Research (ONSTR) Ontology of Clinical Research (OCRE) Ontology of Data Mining (OntoDM) Ontology of Medically Related Social Entities (OMRSE) Ontology of Vaccine Adverse Events Oral Health and Disease Ontology (OHDO) Population and Community Ontology Proper Name Ontology Semanticscience Integrated Ontology Software Ontology (SWO) Translational Medicine Ontology (TMO) Twitter Ontology Vaccine Ontology (VO)

The Ontology for Biomedical Investigations 32

The Ontology for Biomedical Investigations 33

OBI and IAO 34

Patient Demograp hics Phenotype (Disease, …) Disease processes Data about all of these things including image data … Algorithms, software, protocols, … Instruments, Biomaterials, Functions Parameters, Assay types, Statistics … Anatomy Histology Genotype (GO) Biological processes (GO) Chemistry I NDEPENDENT C ONTINUANT (~T HING )) D EPENDENT C ONTINUANT (~A TTRIBUTE ) O CCURRENT (~P ROCESS ) IAOOBI Basic Formal Ontology (BFO) 35

Patient Demograp hics Phenotype (Disease, …) Disease processes Data about all of these things including image data … Algorithms, software, protocols, … Instruments, Biomaterials, Functions Parameters, Assay types, Statistics … Anatomy Histology Genotype (GO) Biological processes (GO) Chemistry I NDEPENDENT C ONTINUANT (~T HING )) D EPENDENT C ONTINUANT (~A TTRIBUTE ) O CCURRENT (~P ROCESS ) IAOOBI Basic Formal Ontology (BFO) 36 CMPO OBI- Imaging

BFO 37 Ontology for General Medical Science Cardiovascular Disease Ontology Genetic Disease Ontology Cancer Disease Ontology Genetic Disease Ontology Immune Disease Ontology Environmental Disease Ontology Oral Disease Ontology Infectious Disease Ontology IDO Staph Aureus IDO MRSA IDO Australian MRSA IDO Australian Hospital MRSA …

patient OBI: pathology specimen PIO: pathology slide PIO: pathology image PIO: pathologist PIO: software pipeline OBI: histology assay OBI: annotations various automated histology assay PIO: annotations various RDF database slide preparation part of output input agent slide imaging specimen collection Pathology Image Workflow