1. Mouse Genome Informatics November 2008 Paul Szauter MGI User Support

2. Schedule Introduction and a few examples ~ 20 minutes Self-guided tutorial ~ 1 hour 30 minutes

3. The Jackson Laboratory Bar Harbor, Maine

4. The Jackson Laboratory Research Areas Computational Biology/Bioinformatics Immunology/Hematology Metabolic Disease Research Neurobiology Reproductive & Developmental Biology

5. Research & Education at TJL www.jax.org Research Areas and Investigators Courses & Conferences Mouse Genome Informatics

6. Introduction to MGI What is MGI? How does data get into MGI? Controlled vocabulary (e.g. phenotypes) Mouse models of human disease Options for power users There is always help - please ask!

7. Introduction to MGI What is MGI? How does data get into MGI? Controlled vocabulary (e.g. phenotypes) Mouse models of human disease Options for power users There is always help - please ask!

8. What is MGI? MGI is a free, publicly-funded database MGI contains data from the published literature and from other databases MGI contains data on mouse genes, mutant alleles and phenotypes, gene expression, homology

9. MGI is people powered 6 PIs > 30 curators ~ 25 software engineers, database administrators and support staff

10. Introduction to MGI What is MGI? How does data get into MGI? Controlled vocabulary (e.g. phenotypes) Mouse models of human disease Options for power users There is always help - please ask!

11. How does data get into MGI? Curators enter data from the published literature Bulk loads from other databases Collaborative development of tools for bioinformatics (vocabularies for Gene Ontology, Mammalian Phenotypes, Anatomy)

12. The process of curation

13. Introduction to MGI What is MGI? How does data get into MGI? Controlled vocabulary (e.g. phenotypes) Mouse models of human disease Options for power users There is always help - please ask!

14. Controlled Vocabularies Controlled vocabularies at MGI are hierarchical arrangements of terms “Controlled” means that only one term is used for something: no synonyms Terms from controlled vocabularies are associated with other database objects

18. Introduction to MGI What is MGI? How does data get into MGI? Controlled vocabulary (e.g. phenotypes) Mouse models of human disease Options for power users There is always help - please ask!

19. Models of Human Disease OMIM diseases mapped to Mammalian Phenotype Vocabulary 865 human diseases with mouse models Additional human disease/mouse phenotype associations with no mouse allele (yet)

21. Introduction to MGI What is MGI? How does data get into MGI? Controlled vocabulary (e.g. phenotypes) Mouse models of human disease Options for power users There is always help - please ask!

22. Options for Power Users Batch Query Form Flat files Public SQL account/Schema Browser Custom SQL through User Support Coming soon: BioMart

24. Flat Files

25. MGI Schema Browser

26. Introduction to MGI What is MGI? How does data get into MGI? Controlled vocabulary (e.g. phenotypes) Mouse models of human disease Options for power users There is always help - please ask!

27. For help, click the Help link

28. Contact MGI User Support Public SQL accounts

29. Live Demonstration