Transcript Diehl - Buffalo Ontology Site

Comprehensive Annotation System
for Infectious Disease Data
Alexander Diehl
University at Buffalo/The Jackson Laboratory
IDO Workshop 2010
12/9/2010
Comprehensive Annotation System
of Infectious Disease Data
for
in a Model Organism
Alexander Diehl
University at Buffalo/The Jackson Laboratory
IDO Workshop 2010
12/9/2010
The Gene Ontology
• Three linked ontologies:
– Biological Process
• operations or sets of molecular events with a defined
beginning and end, pertinent to the functioning of
integrated living units: cells, tissues, organs, and
organisms
– Molecular Function
• the elemental activities of a gene product at the
molecular level, such as binding or catalysis
– Cellular Component
• the parts of a cell or its extracellular environment
www.geneontology.org
The Gene Ontology
• Many Terms:
– 33103 terms (as of 12/7/10)
• 19950 biological_process
• 2781 cellular_component
• 8910 molecular_function
• Many Annotations:
– 461487 genes annotated (as of 12/4/10)
• 354119 biological_process
• 379529 cellular_component
• 320525 molecular_function
amigo.geneontology.org
The Gene Ontology and
Infectious Disease
• GO Immunology revision of 2006 resulted in 700+
new terms for describing immunological aspects
of gene products. Over 1000 terms in current GO
describe immunologically related properties of
genes.
• The PAMGO group (Plant-Associated Microbe Gene
Ontology) prepared over 900 terms for GO between
2005-2009 to cover aspects of interactions
between organisms, including processes related
to infectious diseases.
The Gene Ontology and
Infectious Disease
• adhesion to host
– Type IV pili-dependent localized adherence to
host
• response to bacteria
• adaptive immune response
– immunoglobulin mediated immune response
• evasion or tolerance of host immune
response
GO Annotation
• The association of a gene product (protein)
with a GO term based on experimental data
constitutes a GO annotation.
• The data itself is an instance. The annotation
relates that instance to a type, a GO term.
• GO annotations are publicly available via the
GO Consortium’s Amigo browser,
http://amigo.geneontology.org
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GO Annotation
• Structure of a GO annotation:
– Gene product identifier
– GO term
– Evidence Code
• IDA, IMP, IPI, ISS, IEA
– Reference
– Extended Annotation Data
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Anatomy
Cell type
Target of process
Isoform used
Dual-taxon ID
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GO Annotation of Genes Involved
in Host Responses to S. aureus
• Selected papers for annotation that used S.
aureus as a model pathogen for study of host
responses in the mouse.
• Annotated 25 papers of an initial selection of
over 60 identified papers.
• GO annotations entered using Mouse Genome
Informatic’s editorial interface.
• The annotations are available at MGI, and have
been propagated to AmiGO, NCBI, and QuickGO.
Annotation Effort
• 295 annotations generated for a variety of gene
products involved in response to S aureus and
other pathogens, including NOD2, TLR2, TLR4, IL10, CD36, Scd1, and others.
• Anatomical details, cell type ID, taxon IDs, and
specific strain information collected where
appropriate.
• Some annotations are made to human genes and
appear for orthologous mouse genes as ISS
annotations.
Value of this Annotation Set
• Provide representation of key GO processes
for genes involved in responses to pathogens.
• Strengthen the utility of GO in term
enrichment analysis of gene sets, e.g.
microarray experiments.
• Drives development of new terms for the GO,
“annotation-driven ontology development.”
– 44 new GO terms were created.
A More Comprehensive Approach
• Collect additional information from paper or
study in the form of ontology terms describing
details of experiment method, organisms and
reagents used, and relations between
experimental components.
• Provide a convenient “annotation ID” that
enables easy reference to a particular annotation.
• Link individual annotations to draw more
complex conclusions.
Enhanced GO Annotation for Infectious Disease Ontology
Enhanced GO Annotation for Infectious Disease Ontology
Enhanced GO Annotation for Infectious Disease Ontology
Enhanced GO Annotation for Infectious Disease Ontology
Enhanced GO Annotation for Infectious Disease Ontology
Conclusions
• Comprehensive manual annotation can rely on all
OBO-Foundry ontologies and other taxonomies.
• A variety of material entities and qualities can be
annotated.
• A system of annotation dependencies can be built to
allow for more complicated chains of inference.
• Such a system can leverage existing GO and MP
annotation where appropriate.
• Collections of annotations can be modeled into a BFObased application ontology for a particular domain.
A proto-MS application ontology
Acknowledgments
MGI
Judith Blake
Jason Bubier
Duke University/UT Southwestern
Lindsay Cowell
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