1. WormBase Workshop: 2015 International C. elegans Meeting Tools & Resources InterMine / WormMine – Chris Grove JBrowse – Scott Cain The WormBase Ontology Browser – Raymond Lee ParaSite, Ensembl Genomes, and UCSC Assembly Hub for C. elegans – Kevin Howe/Michael Paulini Gene Ontology: annotations and enrichment tools – Kimberly Van Auken

2. Community Annotation Tools Introduction & Overview – Genetic variations annotation – Mary Ann Tuli Contributing & editing gene concise descriptions – Ranjana Kishore Micropublications – Daniela Raciti WormBase Workshop: 2015 International C. elegans Meeting

3. WormBase Data Mining Options WormMine Flat files (click “FTP site” under “Downloads” at bottom of WormBase homepage) Website API Perl interface Bioperl interface to sequence feature databases And more…

4. WormMine The WormBase instance of the InterMine biological data warehouse

5. WormMine: An Overview WormMine Biological EntitiesWormMine Entities GenesProteins ListsQueriesTables

6. WormMine: An Overview Genes Alleles Allele-phenotypes Genomic coordinates CDSs, transcripts GO annotations Expression patterns – Life stages, anatomy Expression clusters – Co-expressed genes Proteins – Amino acid sequences – Molecular weight – CDSs, transcripts – Motifs, domains Biological Entities:

7. WormMine: An Overview Lists – Lists of biological entities – Constrain queries on lists – Compare & contrast, intersection, union, etc. Queries – Template and custom queries – Constrain on biological entities or lists Tables – Lists and query results – Sortable, downloadable – Export as a WormMine list WormMine Entities:

8. Finding WormMine Click on “WormMine” under the WormBase homepage “Tools” menu

9. WormMine Homepage

14. WormMine Lists

15. WormMine Lists: Uploading a list

16. WormMine Lists: Browsing existing lists

18. Attributes Entities

19. WormMine Lists: Browsing existing lists

20. WormMine Queries

23. WormMine Query Templates

25. WormMine Query Template Options

26. WormMine Query Template Results

27. WormMine QueryBuilder

28. WormMine QueryBuilder: Genes

34. WormMine QueryBuilder: Import query from XML

37. Questions? E-mail help@wormbase.org anytime, for any questions!help@wormbase.org Thank you!! Acknowledgements WormBase Web Development Team: Todd Harris Sibyl Gao Paulo Nuin