2 3 where in the body ? where in the cell ?

http://ontologist.com 1



where in the body ? where in the cell ?



what kind of organism ?



what kind of organism ?

what kind of disease process ?


to yield:

distributed accessibility of the data to humans

reasoning with the data

cumulation for purposes of research

incrementality and evolvability

integration with clinical data

Creating broad-coverage semantic annotation systems for biomedicine

7

8

9

Gene Ontology

a controlled structuredvocabularyfor annotation ofgene product data


The OBO Foundry Idea

MouseEcotope GlyProt

DiabetInGene

GluChem

sphingolipid transporter

activity


The OBO Foundry Idea

MouseEcotope GlyProt

DiabetInGene

GluChem

Holliday junction helicase complex

Sjöblöm et al.

analyzed 13,023 genes in 11 breast and 11 colorectal cancers

identified189 as being mutated at significant frequency and thus as providing targets for diagnostic and therapeutic intervention.

correlations between functional information captured by GO for given gene product types and the expression patterns detected experimentally in selected instances of these types can help to elucidate underlying pathologies

Sjöblöm T, et al. Science. 2006 Oct 13;314(5797):268-74.


13

Five bangs for your GO buck

1. based in biological science

2. incremental approach (low hanging fruit)

3. cross-species data comparability (human, mouse, yeast, fly ...)

4. cross-granularity data integration (molecule, cell, organ, organism)

5. cumulation of scientific knowledge in algorithmically tractable form which links people to software

14

what cellular component?

what molecular function?

what biological process?


a family of interoperable biomedical reference ontologies built around the Gene Ontology at its core and using the same principles

a modular annotation catalogue of English phrases

each module created by experts from the corresponding scientific community

http://obofoundry.org

The OBO Foundry


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 Componen

t(FMA, GO)

Cellular Function

(GO)

MOLECULEMolecule

(ChEBI, SO,RnaO, PrO)

Molecular Function(GO)

Molecular Process

(GO)

The OBO Foundry building out from the original GO

http://ontologist.com 17Karen Eilbecksong.sf.netproperties and features of

nucleic sequencesSequence Ontology

(SO)

RNA Ontology Consortium(under development)three-dimensional RNA

structuresRNA Ontology

(RnaO)

Barry Smith, Chris Mungallobo.sf.net/relationshiprelationsRelation Ontology (RO)

Protein Ontology Consortium(under development)protein types and

modificationsProtein Ontology

(PrO)

Michael Ashburner, Suzanna Lewis, Georgios Gkoutos

obo.sourceforge.net/cgi-bin/ detail.cgi?

attribute_and_valuequalities of biomedical entities

Phenotypic Quality Ontology

(PaTO)

Gene Ontology Consortiumwww.geneontology.orgcellular components, molecular functions, biological processes

Gene Ontology (GO)

FuGO Working Groupfugo.sf.netdesign, protocol, data

instrumentation, and analysis

Functional Genomics Investigation Ontology

(FuGO)

JLV Mejino Jr.,Cornelius Rosse

fma.biostr.washington.edu

structure of the human bodyFoundational Model of

Anatomy (FMA)

Melissa Haendel, Terry Hayamizu, Cornelius Rosse,

David Sutherland, (under development)

anatomical structures in human and model organisms

Common Anatomy Refer-

ence Ontology (CARO)

Paula Dematos,Rafael Alcantara

ebi.ac.uk/chebimolecular entitiesChemical Entities of Bio-logical Interest (ChEBI)

Jonathan Bard, Michael Ashburner, Oliver Hofman

obo.sourceforge.net/cgi-bin/detail.cgi?cell

cell types from prokaryotes to mammals

Cell Ontology (CL)

CustodiansURLScopeOntology


Ontologies being built to satisfy Foundry principles ab initio

Clinical Trial Ontology (CIO)Common Anatomy Reference Ontology (CARO, DB1

& DB2)Mosquito Anatomy Ontology (MAO)Ontology for Biomedical Investigations (OBI)Phenotypic Quality Ontology (PATO, DB1 & DB2)Protein Ontology (PRO)Relation Ontology (RO)RNA Ontology (RnaO)

19

Draft Ontology for Multiple Sclerosis


Entry point for creation of web-accessible biomedical data

GO initially low-tech to encourage users

Simple (web-service-based) tools created to support the work of biologists in creating annotations (data entry)

OBO OWL DL converters now making OBO Foundry annotated data immediately accessible to Semantic Web data integration projects

GO allows distributed web-based collaboration

the methodology gradually being evolved as service -based architecture by US National Center for Biomedical Ontology (http://ncbo.us)

companies vs. cross-border collaboration


22

what cellular component?

what molecular function?

what biological process?


compare: legends for mapscompare: legends for maps


compare: legends for mapscommon legends allow (cross-border) integration

25

legends for chemistry diagrams

26

MIAKT system

legends for images

27


ontologies as legends for data

Documents

2 3 where in the body ? where in the cell ?