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The Mammalian Phenotype Ontology. Development and Use in Phenotypic Data Annotation at Mouse Genome Informatics. Cynthia L. Smith, Ph.D. Mammalian Phenotype Ontology. Over 7955 pre-composed terms OBO-Edit OBO format RGD, OMIA, Europhenome - PowerPoint PPT Presentation
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The Mammalian Phenotype Ontology
Development and Use in Phenotypic Data
Annotation at Mouse Genome Informatics
Cynthia L. Smith, Ph.D
Mammalian Phenotype Ontology
• Over 7955 pre-composed terms
• OBO-Edit• OBO format• RGD, OMIA, Europhenome
• On-line tools PhenoGO, PhenomicDB, PhenoHM, MamPhEA etc
Total No. of Annotations 202263
Genotypes with MP 42574
Alleles Annotated 25938
Genes/Markers Annotated 8997
Mammalian Phenotype Ontology Development
• Curation-driven approach Terms are added as required by
curators (MGI, RGD and others) when annotations are made.
• Systematic reviewSections of the MP are subject to organization and content review, in conjunction with experts in the field.
• Comparisions to other ontologies
Building a mouse phenotyping data resource• Large scale ENU mutagenesis programs worldwide -
continuing
• Large scale gene trap programs (International Gene Trap Consortium) www.genetrap.org - gene trap cell lines loaded, with Lexicon
• International Mouse Knockout Consortium• KOMP – Knockout Mouse Project (USA) www.knockoutmouse.org• EUCOMM – European Conditional Mouse Mutagenesis www.eucomm.org • NorCOMM – North American Conditional Mouse Mutagenesis http://norcomm.phenogenomics.ca • Texas Institute for Genomic Medicine Knockouts www.tigm.org
• Collaborative Cross www.complextrait.org and the Diversity Outcross
• Literature and lab submissions
• New recombinase (cre, flp, etc) and reporter database is online and data is being populated www.creportal.org
Mammalian Phenotype-Current Status
9/08/2008
MP terms: 6185
MP Annotations in MGI:
Total No. of Annotations 128262
Genotypes with MP 25178
Alleles Annotated 18866/21693
Genes/Markers Annotated 8412
Collaborators/UsersRat Genome Database
Mouse Mutagenesis Centers Human (NCBI/dbSNP)
OMIA (Online Mendelian Inheritance in Animals)Proprietary Databases
International Mouse Knockout Projects
Making Mammalian Phenotype Ontology Work
DAGs
• accommodate bio-specific terms• computationally useful
• human friendly
• practical for curation
• cross-reference to other ontologies
Lightning talks (no more than 5 slides, 5 minutes):1. Who you are (ontology developer/contributor, ontology
consumer)?2. Why are you making or using ontologies or why do you want to
use ontologies? What are you doing with them?3. What tools are you using? A little nitty gritty here... obo-edit,
protege, excel,...4. Biggest roadblock in your work5. Vision: where you’d like to go...
6. Collaborators? Type of person or resource who could help?
I did initially mention some other groups such as RGD, OMIA and Europhenome, but the last sentence was running on too long. I was planning to put that in the 5 minute talk, though, along with
other on-line tools such as PhenoGO, PhenomicDB, PhenoHM, MamPhEA etc