CoE Ontology Research Group (ORG) Barry Smith Center of Excellence in Bioinformatics and Life Sciences Ontology Research Group Department of Philosophy

CoE Ontology Research Group (ORG)

Barry SmithCenter of Excellence in Bioinformatics and Life Sciences

Ontology Research GroupDepartment of Philosophy

www.org.buffalo.edu

http://org.buffalo.edu

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Faculty and Staff

Directors– Werner Ceusters Medical School – Louis Goldberg Dental School– Barry Smith Philosophy Dept.

Other researchers: – 3 philosophers, 1 computer scientist, 1 business

process analyst


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Projects, funding & collaborationNational Center for Biomedical Ontology

(http://NCBO.us)

Collaborating Center for Terminology under the auspices of the World Health Organisation (WHO)

Advisory for the German national Electronic Health Record initiative

Cleveland Clinic, Duke University


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we need to know where in the body,

where in the cell

we need to know what kind of

disease process

= we need ontologies

we need semantic annotation of data


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Ontologies are systems of annotations


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• cellular locations

• molecular functions

• biological processes

used to annotate the entities represented in the major biochemical databases

thereby creating integration across these databases

A set of standardized textual descriptions of


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what cellular component?

what molecular function?

what biological process?


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This processyields a slowly growing computer-interpretable map of biological reality within which major databases are automatically integrated in semantically searchable form


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But alsoneed to extend the methodology to other domains, including clinical medicine

need disease, symptom (phenotype) ontologies


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the problem

need for prospective standards to ensure mutual consistency and high quality of clinical counterparts of GO

need to ensure consistency of the new clinical ontologies with the basic biomedical sciences

if we do not start now, the problem will only get worse


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the solution

establish common rules governing best practices for creating ontologies and for using these in annotations

apply these rules to create a complete suite of orthogonal interoperable biomedical reference ontologies


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a shared portal for (so far) 58 ontologies (low regimentation)

http://obo.sourceforge.net NCBO BioPortal

First step (2003)

http://obo.sourceforge.net/


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Second step (2004):reform efforts initiated, e.g. linking GO to other

OBO ontologies to ensure interoperability

id: CL:0000062name: osteoblastdef: "A bone-forming cell which secretes an extracellular matrix. Hydroxyapatite crystals are then deposited into the matrix to form bone." is_a: CL:0000055relationship: develops_from CL:0000008relationship: develops_from CL:0000375

GO

Cell type

New Definition

+

=Osteoblast differentiation: Processes whereby an osteoprogenitor cell or a cranial neural crest cell acquires the specialized features of an osteoblast, a bone-forming cell which secretes extracellular matrix.


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The OBO FoundryThe OBO Foundryhttp://obofoundry.org/http://obofoundry.org/

Third step (2006)Third step (2006)


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a family of interoperable gold standard biomedical reference ontologies to serve the annotation of

scientific literature model organism databases clinical data experimental results

The OBO FoundryThe OBO Foundry


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A prospective standarddesigned to guarantee interoperability of ontologies from the very start (contrast to: post hoc mapping)

established March 2006

12 initial candidate OBO ontologies – focused primarily on basic science domains

several being constructed ab initio

now 16 ontologies


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Ontology Scope URL Custodians

Cell Ontology (CL)

cell types from prokaryotes to mammals

obo.sourceforge.net/cgi-

bin/detail.cgi?cell

Jonathan Bard, Michael Ashburner, Oliver Hofman

Chemical Entities of Bio-

logical Interest (ChEBI)

molecular entities ebi.ac.uk/chebiPaula Dematos,Rafael Alcantara

Common Anatomy Refer-

ence Ontology (CARO)

anatomical structures in human and model

organisms(under development)

Melissa Haendel, Terry Hayamizu, Cornelius

Rosse, David Sutherland,

Foundational Model of Anatomy (FMA)

structure of the human body

fma.biostr.washington.

edu

JLV Mejino Jr.,Cornelius Rosse

Functional Genomics Investigation

Ontology (FuGO)

design, protocol, data instrumentation, and

analysisfugo.sf.net FuGO Working Group

Gene Ontology (GO)

cellular components, molecular functions, biological processes

www.geneontology.org

Gene Ontology Consortium

Phenotypic Quality Ontology

(PaTO)

qualities of anatomical structures

obo.sourceforge.net/cgi

-bin/ detail.cgi?attribute_and_value

Michael Ashburner, Suzanna

Lewis, Georgios Gkoutos

Protein Ontology (PrO)

protein types and modifications

(under development)Protein Ontology

Consortium

Relation Ontology (RO)

relationsobo.sf.net/

relationshipBarry Smith, Chris

Mungall

RNA Ontology(RnaO)

three-dimensional RNA structures

(under development) RNA Ontology Consortium

Sequence Ontology(SO)

properties and features of nucleic sequences

song.sf.net Karen Eilbeck

http://www.geneontology.org/

http://www.geneontology.org/


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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)

Building out from the original GO


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Disease Ontology (DO) [SNOMED CT]

Biomedical Image Ontology (BIO)

Environment Ontology (EnvO)

Biobank Ontology (BrO)

Clinical Trial Ontology (CTO) [with WHO Global Trial Bank, Immune Tolerance Network, ACGT Advancing Genomics Clinical Trials in Cancer EU IP]

Under construction


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OBO low-regimentation ontology portal

OBO Foundry high-regimentation collaborative initiative to create a gold standard suite of interoperable ontologies

The vision


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MICheck: ‘a common resource for minimum information checklists’ analogous to OBO / NCBO BioPortal

MICheck Foundry: will create ‘a suite of self-consistent, clearly bounded, orthogonal, integrable checklist modules’ *

* Taylor CF, et al. Nature Biotech, in press

The vision is spreading


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Transcriptomics (MIAME Working Group)

Proteomics (Proteomics Standards Initiative)

Metabolomics (Metabolomics Standards Initiative)

Genomics and Metagenomics (Genomic Standards Consortium)

In Situ Hybridization and Immunohistochemistry (MISFISHIE) Phylogenetics (Phylogenetics Community)

RNA Interference (RNAi Community)

Toxicogenomics (Toxicogenomics WG)

Environmental Genomics (Environmental Genomics WG)

Nutrigenomics (Nutrigenomics WG)

Flow Cytometry (Flow Cytometry Community)

MICheck/Foundry communities


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Current service offeringsAnalysis of data dictionairies, database

schema’s and database models for ontological adequacy

Curation of biomedical terminologies, ontologies and controlled vocabularies;

Ontology creation, support in database merging and mapping

Ontology support for clinical trialsOntology support for cross-disciplinary

research collaborations

Documents

CoE Ontology Research Group (ORG) Barry Smith Center of Excellence in Bioinformatics and Life Sciences Ontology Research Group Department of Philosophy