1 / 10

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

louis
Download Presentation

The Mammalian Phenotype Ontology

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. The Mammalian Phenotype Ontology Development and Use in Phenotypic Data Annotation at Mouse Genome Informatics Cynthia L. Smith, Ph.D

  2. Mammalian Phenotype Ontology • Over 7955 pre-composed terms • OBO-Edit • OBO format • RGD, OMIA, Europhenome • On-line tools PhenoGO, PhenomicDB, PhenoHM, MamPhEA etc

  3. Mammalian phenotype term Total No. of Annotations 202263 Genotypes with MP 42574 Alleles Annotated 25938 Genes/Markers Annotated 8997

  4. Mammalian Phenotype Ontology Development Curation-driven approach Terms are added as required by curators (MGI, RGD and others) when annotations are made. Systematic review Sections of the MP are subject to organization and content review, in conjunction with experts in the field. Comparisions to other ontologies

  5. 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

  6. 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

  7. Collaborators/Users Rat Genome Database Mouse Mutagenesis Centers Human (NCBI/dbSNP) OMIA (Online Mendelian Inheritance in Animals) Proprietary Databases International Mouse Knockout Projects

  8. Making Mammalian Phenotype Ontology Work DAGs • accommodate bio-specific terms • computationally useful • human friendly • practical for curation • cross-reference to other ontologies

  9. 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

More Related