Transcript ISO 15926 – Integration of Lifecycle data

http://ontologist.com
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where in the body ?
where in the cell ?
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where in the body ?
where in the cell ?
what kind of
organism ?
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where in the body ?
where in the cell ?
what kind of
organism ?
what kind of
disease process ?
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Creating broad-coverage semantic
annotation systems for biomedicine
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
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Gene
Ontology
a controlled
structured
vocabulary
for annotation of
gene product data
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The OBO Foundry Idea
GlyProt
MouseEcotope
sphingolipid
transporter
activity
DiabetInGene
GluChem
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The OBO Foundry Idea
GlyProt
MouseEcotope
Holliday junction
helicase complex
DiabetInGene
GluChem
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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.
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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
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what cellular component?
what molecular function?
what biological process?
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The OBO Foundry
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
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RELATION
TO TIME
CONTINUANT
INDEPENDENT
OCCURRENT
DEPENDENT
GRANULARITY
ORGAN AND
ORGANISM
CELL AND CELLULAR
COMPONENT
MOLECULE
Organism
Anatomical
Organ
(NCBI
Entity
Function
Taxonomy) (FMA, CARO) (FMP, CPRO)
Cell
(CL)
Cellular
Component
(FMA, GO)
Molecule
(ChEBI, SO,
RnaO, PrO)
Phenotypic
Quality
(PaTO)
Biological Process
(GO)
Cellular
Function
(GO)
Molecular Function
(GO)
Molecular Process
(GO)
The OBO Foundry building out from the original GO
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Ontology
Scope
URL
Custodians
Cell Ontology
(CL)
cell types from prokaryotes
to mammals
obo.sourceforge.net/cgibin/detail.cgi?cell
Jonathan Bard, Michael
Ashburner, Oliver Hofman
Chemical Entities of Biological Interest (ChEBI)
molecular entities
ebi.ac.uk/chebi
Paula Dematos,
Rafael Alcantara
Common Anatomy Reference 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 analysis
fugo.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 biomedical entities
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)
relations
obo.sf.net/relationship
Barry Smith, Chris Mungall
RNA Ontology
(RnaO)
three-dimensional RNA
structures
(under development)
RNA Ontology Consortium
Sequence Ontology
properties and features of
nucleic sequences
song.sf.net
Karen Eilbeck
http://ontologist.com
(SO)
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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)
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Draft Ontology
for Multiple
Sclerosis
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Entry point for creation of webaccessible 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
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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
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what cellular component?
what molecular function?
what biological process?
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compare: legends for maps
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common legends
allow
(cross-border)
compare:
legends
for mapsintegration
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legends for chemistry diagrams
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legends for images
MIAKT system
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ontologies as legends for data
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