The Mammalian Phenotype Ontology

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