Transcript NCRR Animal Model Resources

Linking Translational Research to
Animal and Bio-Materials Resources
Animal and Bio-Materials Resources
1. The problem with resources
2. Limitations of current informatics support
3. Examples of solutions
•
•
Ontologies to describe resources
Using ontologies to link resources with human
disease
NCRR Comparative Medicine Biological Resources
Invertebrate Resources
• Bloomington Drosophila Stock Center
• Caenorhabditis Genetics Center
• National Resource for Aplysia
• National Resource for Cephalopods
Non-human Primate Resources
• National Primate Research Centers (8)
• Baboon and Monkey Research Resources (3)
• Chimpanzee Biomedical Research Resources (6)
• Specific-Pathogen-Free Macaque Resources (4)
Zebrafish International Resource Center
Rodent Resources
• Mutant Mouse Regional Resource Centers (4)
• Induced Mutant Resource
• Special Mouse Strains Resource
• Peromyscus Genetic Stock Center
• Rat Resource and Research Center
• Transgenic Mice With Altered Calcium Handling
Resource
Biological Materials Resources
• Adult Mesenchymal Stem Cell Resource
• National Cell Culture Center
• National Stem Cell Resource
• Viper Resource Center
• Yeast Genetic Stock Center
How can researchers find appropriate
models for human disease research?
Human
diseases
?
Biological
models
Search: Retinal degeneration
Problems that impede finding animals & biological
materials as models for human disease
1. Lack of centralized “one stop shopping”
•
Heterogeneous information
•
Multiple sites
2. Inconsistent search mechanisms
3. Inconsistent use of descriptive terms
4. Lack of support for synonyms
Linking Translational Research to
Animal and Bio-Materials Resources
Animal and Bio-Materials Resources
1. The problem with resources
2. Limitations of current informatics support
3. Examples of solutions
•
•
Ontologies to describe resources
Using ontologies to link resources with human
disease
QuickT ime™ and a
T IFF (LZW) decompressor
are needed to see t his picture.
ZFIN:
FlyBase:
Melissa Haendel
Michael Ashburner
Doug Howe
Rachel Drysdale
Erik Segerdell
George Gkoutos
Sierra Taylor
Animal disease models:
Animal models
Mutant Gene
Mutant or missing
Protein
Mutant Phenotype
(disease model)
Animal disease models:
Humans
Animal models
Mutant Gene
Mutant Gene
Mutant or missing
Protein
Mutant or missing
Protein
Mutant Phenotype
(disease)
Mutant Phenotype
(disease model)
Animal disease models:
Humans
Animal models
Mutant Gene
Mutant Gene
Mutant or missing
Protein
Mutant or missing
Protein
Mutant Phenotype
(disease)
Mutant Phenotype
(disease model)
Animal disease models:
Humans
Animal models
Mutant Gene
Mutant Gene
Mutant or missing
Protein
Mutant or missing
Protein
Mutant Phenotype
(disease)
Mutant Phenotype
(disease model)
Vocabulary
Animal
Central nervous system
Diencephalon
Nervous system
Photoreceptor
Retina
Ontology
Animal
Nervous system
Central nervous system
Diencephalon
Retina
Photoreceptor
Ontology
Nervous system
Ectoderm
D
P
CNS
Neural plate
P
D
Diencephalon
Ontology
Nervous system
Ectoderm
D
P
CNS
Neural plate
P
D
Diencephalon
Linking Translational Research to
Animal and Bio-Materials Resources
Animal and Bio-Materials Resources
1. The problem with resources
2. Limitations of current informatics support
3. Examples of solutions
•
•
Ontologies to describe resources
Using ontologies to link resources with human
disease
SHH-/+
SHH-/-
shh-/+
shh-/-
Phenotype
(clinical sign) =
entity
+ attribute
shh-/-
+ value
Phenotype
(clinical sign) =
P1
entity
= eye
+ attribute
+ value
+ placement
+ hypoteloric
shh-/-
Phenotype
(clinical sign) =
entity
+ attribute
+ value
+ placement
+ hypoteloric
P1
= eye
P2
= midface + development + hypoplastic
shh-/-
Phenotype
(clinical sign) =
entity
+ attribute
+ value
+ placement
+ hypoteloric
P1
= eye
P2
P3
= midface + development + hypoplastic
+ hypertrophied
= kidney + size
shh-/-
Phenotype
(clinical sign) =
entity
+ attribute
+ value
+ placement
+ hypoteloric
P1
= eye
P2
P3
= midface + development + hypoplastic
+ hypertrophied
= kidney + size
ZFIN:
eye
PATO:
placement hypoteloric
midface
development hypoplastic
kidney
size hypertrophied
Phenotype
(clinical sign) =
entity
+ attribute
+ value
Anatomical ontology
Cell & tissue ontology
Developmental ontology
Gene ontology
biological process
molecular function
cellular component
+
PATO
(phenotype and trait ontology)
Phenotype
(clinical sign) =
entity
+ attribute
+ value
+ placement
+ hypoteloric
P1
= eye
P2
P3
= midface + development + hypoplastic
+ hypertrophied
= kidney + size
Syndrome = P1 + P2 + P3
(disease)
= holoprosencephaly
Human holoprosencephaly
Zebrafish
shh
Zebrafish
oep
Human holoprosencephaly
Zebrafish
shh
Zebrafish
oep
Linking Translational Research to
Animal and Bio-Materials Resources
Animal and Bio-Materials Resources
1. The problem with resources
2. Limitations of current informatics support
3. Examples of solutions
•
•
Ontologies to describe resources
Using ontologies to link resources with human
disease
QuickTime™ and a
TIFF (Uncompressed) decompressor
are needed to see this picture.