1. www.flybase.org Getting the most out of FlyBase

2. www.flybase.org Tools –QuickSearch – Controlled Vocabularies, Term Reports and TermLink –QueryBuilder and Templates Fast-Track Your Paper

3. www.flybase.org Tools –QuickSearch – Controlled Vocabularies, Term Reports and TermLink –QueryBuilder and Templates Fast-Track Your Paper

4. www.flybase.org QuickSearch

5. www.flybase.org Autocomplete QuickSearch

6. www.flybase.org Autocomplete QuickSearch

7. www.flybase.org Autocomplete QuickSearch

8. www.flybase.org Autocomplete QuickSearch

9. www.flybase.org Gene associations QuickSearch

10. www.flybase.org Gene associations QuickSearch

11. www.flybase.org Gene associations HitList QuickSearch

12. www.flybase.org Gene associations HitList QuickSearch

13. www.flybase.org Tools –QuickSearch – Controlled Vocabularies, Term Reports and TermLink –QueryBuilder and Templates Fast-Track Your Paper

14. www.flybase.org What are CVs? Collections of unique, defined terms belonging to a particular subject/class, organized into a hierarchical tree Tree structure indicates how each specific CV term relates to others within that particular vocabulary aka ‘ontologies’ Controlled Vocabularies and Term Reports

15. www.flybase.org Why use CVs? Use of unique terms essential for accurate annotation, database structure and generation of cross-links Organization into hierarchical tree allows powerful searches of the database Controlled Vocabularies and Term Reports

16. www.flybase.org Examples of CV usage twins (tws, FBgn0004889):  is a protein coding gene  is expressed in the oocyte and nurse cell  at least one mutant allele is classed as a hypomorph  mutant animals show a recessive, lethal phenotype, exhibited at the larval stage  the encoded protein has protein phosphatase type 2A regulator activity, is involved in the regulation of mitosis, and is located in the cell cytoplasm Controlled Vocabularies and Term Reports

17. www.flybase.org Examples of CV usage twins (tws, FBgn0004889):  is a protein coding gene  is expressed in the oocyte and nurse cell  at least one mutant allele is classed as a hypomorph  mutant animals show a recessive, lethal phenotype, exhibited at the larval stage  the encoded protein has protein phosphatase type 2A regulator activity, is involved in the regulation of mitosis, and is located in the cell cytoplasm Controlled Vocabularies and Term Reports

18. www.flybase.org Term Report Controlled Vocabularies and Term Reports

19. www.flybase.org Class relationships Controlled Vocabularies and Term Reports

20. www.flybase.org Part of relationships Controlled Vocabularies and Term Reports

21. www.flybase.org How to search CVs QuickSearch TermLink Controlled Vocabularies and Term Reports

22. www.flybase.org Searching with QuickSearch Controlled Vocabularies and Term Reports

23. www.flybase.org Searching with QuickSearch Controlled Vocabularies and Term Reports

24. www.flybase.org TermLink

25. www.flybase.org TermLink - searching TermLink

26. www.flybase.org TermLink - browsing TermLink

27. www.flybase.org Searching using Term Report Controlled Vocabularies and Term Reports

28. www.flybase.org Search using TermReport Controlled Vocabularies and Term Reports

29. www.flybase.org Allele HitList Controlled Vocabularies and Term Reports Alleles with a phenotype in the nurse cell

30. www.flybase.org Tools –QuickSearch – Controlled Vocabularies, Term Reports and TermLink –QueryBuilder and Templates Fast-Track Your Paper

31. www.flybase.org Where is QueryBuilder? QueryBuilder / Where is QueryBuilder?

32. www.flybase.org What is QueryBuilder? Powerful Search Tool Searches every field on every report page Fields are organized in the same way as report pages Can combine between fields, between reports Searches can be as simple or as complex as you like QueryBuilder / What is QueryBuilder?

33. www.flybase.org QueryBuilder Start Page 3 options: Select from one of our Pre-constructed templates Import a saved query Build your own queries QueryBuilder / Start Page

34. www.flybase.org QueryBuilder Templates Templates are divided by output class Clicking on a template takes you to the finished query QueryBuilder / Templates

35. www.flybase.org QueryBuilder Templates 8. QueryBuilder / Templates List the Drosophila melanogaster genes associated with a gene ontology term (e.g. mushroom body development) that have at least one allele of a specified functional class (e.g. loss of function).

36. www.flybase.org QueryBuilder Templates QueryBuilder / Templates

37. www.flybase.org How QueryBuilder works Searches are broken down into segments, with each segment corresponding to a particular field search Each segment can be combined using the Boolean operators AND, OR, BUT NOT Templates can be altered to search specifically what you want, or to give ideas for what types of searches can be performed Can take results from other searches and import them into QueryBuilder to refine the search QueryBuilder / How to use QueryBuilder

38. www.flybase.org QueryBuilder Start Page 3 options: Select from one of our Pre-constructed templates Import a saved query Build your own queries QueryBuilder / Start Page

39. www.flybase.org Building your own Queries Field selection mirrors the report pages Select your field of interest and type text in the QueryBox at the top All report page fields can be searched QueryBuilder / Build your own Queries

40. www.flybase.org Uncoordinated alleles in the Bloomington Stock Center QueryBuilder / Build your own Queries

41. www.flybase.org Selecting the output type QueryBuilder / Build your own Queries

42. www.flybase.org QueryBuilder / Build your own Queries Uncoordinated alleles in the Bloomington Stock Center

43. www.flybase.org Tools –QuickSearch – Controlled Vocabularies, Term Reports and TermLink –QueryBuilder and Templates Fast-Track Your Paper

44. www.flybase.org Fast-track your Paper!

45. www.flybase.org Fast-track your Paper! Tell us which genes feature in your paper, and we'll link your paper to those genes for the next release cycle. Provide additional information during the submission process about your publication and help our Curators to speed up your curation. The whole process takes about 5mins!

46. www.flybase.org Thank you very much!