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Animal and Bio-Materials Resources The problem with resources Limitations of current informatics support Examples of sol

Linking Translational Research to Animal and Bio-Materials Resources. Animal and Bio-Materials Resources The problem with resources Limitations of current informatics support Examples of solutions Ontologies to describe resources Using ontologies to link resources with human disease.

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Animal and Bio-Materials Resources The problem with resources Limitations of current informatics support Examples of sol

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  1. Linking Translational Research to Animal and Bio-Materials Resources Animal and Bio-Materials Resources • The problem with resources • Limitations of current informatics support • Examples of solutions • Ontologies to describe resources • Using ontologies to link resources with human disease

  2. 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 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

  3. How can researchers find appropriate models for human disease research? Human diseases ? Biological models

  4. Search: Retinal degeneration

  5. Problems that impede finding animals & biological materials as models for human disease • Lack of centralized “one stop shopping” • Heterogeneous information • Multiple sites • Inconsistent search mechanisms • Inconsistent use of descriptive terms • Lack of support for synonyms

  6. Linking Translational Research to Animal and Bio-Materials Resources Animal and Bio-Materials Resources • The problem with resources • Limitations of current informatics support • Examples of solutions • Ontologies to describe resources • Using ontologies to link resources with human disease

  7. ZFIN: Melissa Haendel Doug Howe Erik Segerdell Sierra Taylor FlyBase: Michael Ashburner Rachel Drysdale George Gkoutos

  8. Animal disease models: Animal models Mutant Gene Mutant or missing ProteinMutant Phenotype (disease model)

  9. Animal disease models: Humans Animal models Mutant Gene Mutant or missing ProteinMutant Phenotype (disease) Mutant Gene Mutant or missing ProteinMutant Phenotype (disease model)

  10. Animal disease models: Humans Animal models Mutant Gene Mutant or missing ProteinMutant Phenotype (disease) Mutant Gene Mutant or missing ProteinMutant Phenotype (disease model)

  11. Animal disease models: Humans Animal models Mutant Gene Mutant or missing ProteinMutant Phenotype (disease) Mutant Gene Mutant or missing ProteinMutant Phenotype (disease model)

  12. Vocabulary Animal Central nervous system Diencephalon Nervous system Photoreceptor Retina

  13. Ontology Animal Nervous system Central nervous system Diencephalon Retina Photoreceptor

  14. D Ontology P Nervous system Ectoderm CNS Neural plate Diencephalon P D

  15. D Ontology P Nervous system Ectoderm CNS Neural plate Diencephalon P D

  16. Linking Translational Research to Animal and Bio-Materials Resources Animal and Bio-Materials Resources • The problem with resources • Limitations of current informatics support • Examples of solutions • Ontologies to describe resources • Using ontologies to link resources with human disease

  17. SHH-/+ SHH-/- shh-/+ shh-/-

  18. Phenotype (clinical sign) = entity + attribute + value shh-/-

  19. Phenotype (clinical sign) = entity + attribute + value P1 = eye + placement + hypoteloric shh-/-

  20. Phenotype (clinical sign) = entity + attribute + value P1 = eye + placement + hypoteloric + P2 = midface + development hypoplastic shh-/-

  21. Phenotype (clinical sign) = entity + attribute + value P1 = eye + placement + hypoteloric + P2 = midface + development hypoplastic + P3 = kidney + size hypertrophied shh-/-

  22. Phenotype (clinical sign) = entity + attribute + value P1 = eye + placement + hypoteloric + P2 = midface + development hypoplastic + P3 = kidney + size hypertrophied ZFIN: eye midface kidney PATO: placement hypoteloric development hypoplastic size hypertrophied

  23. 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)

  24. Phenotype (clinical sign) = entity + attribute + value P1 = eye + placement + hypoteloric + P2 = midface + development hypoplastic + P3 = kidney + size hypertrophied Syndrome = P1 + P2 + P3 (disease) = holoprosencephaly

  25. Zebrafish shh Human holo- prosencephaly Zebrafish oep

  26. Zebrafish shh Human holo- prosencephaly Zebrafish oep

  27. Linking Translational Research to Animal and Bio-Materials Resources Animal and Bio-Materials Resources • The problem with resources • Limitations of current informatics support • Examples of solutions • Ontologies to describe resources • Using ontologies to link resources with human disease

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