Transcript Cynthia Smith

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 precomposed 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 review
•
Comparisions to other ontologies
Sections of the MP are subject to organization
and content review, in conjunction with experts
in the field.
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/Users
Rat 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
• accommodate bio-specific terms
• computationally useful
• human friendly
DAGs
• 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 work
5. 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