Getting the most out of FlyBase

1. Getting the most out of FlyBase

2. Tools • QuickSearch • Controlled Vocabularies, Term Reports and TermLink • QueryBuilder and Templates • Fast-Track Your Paper

3. Tools • QuickSearch • Controlled Vocabularies, Term Reports and TermLink • QueryBuilder and Templates • Fast-Track Your Paper

4. QuickSearch QuickSearch

5. Autocomplete QuickSearch

6. Autocomplete QuickSearch

7. Autocomplete QuickSearch

8. Autocomplete QuickSearch

9. Gene associations QuickSearch

10. Gene associations QuickSearch

11. Gene associations HitList QuickSearch

12. Gene associations HitList QuickSearch

13. Tools • QuickSearch • Controlled Vocabularies, Term Reports and TermLink • QueryBuilder and Templates • Fast-Track Your Paper

14. What are CVs? Controlled Vocabularies and Term Reports • 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’

15. Why use CVs? Controlled Vocabularies and Term Reports • 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

16. Examples of CV usage Controlled Vocabularies and Term Reports 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

17. Examples of CV usage Controlled Vocabularies and Term Reports 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, lethalphenotype, 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

18. Term Report Controlled Vocabularies and Term Reports

19. Class relationships Controlled Vocabularies and Term Reports

20. Part of relationships Controlled Vocabularies and Term Reports

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

22. Searching with QuickSearch Controlled Vocabularies and Term Reports

23. Searching with QuickSearch Controlled Vocabularies and Term Reports

24. TermLink TermLink

25. TermLink - searching TermLink

26. TermLink - browsing TermLink

27. Searching using Term Report Controlled Vocabularies and Term Reports

28. Search using TermReport Controlled Vocabularies and Term Reports

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

30. Tools • QuickSearch • Controlled Vocabularies, Term Reports and TermLink • QueryBuilder and Templates • Fast-Track Your Paper

31. Where is QueryBuilder? QueryBuilder / Where is QueryBuilder?

32. What is QueryBuilder? QueryBuilder / 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

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

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

35. 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. QueryBuilder Templates QueryBuilder / Templates

37. How QueryBuilder works QueryBuilder / How to use QueryBuilder • 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

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

39. Building your own Queries QueryBuilder / Build 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

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

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

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

43. Tools • QuickSearch • Controlled Vocabularies, Term Reports and TermLink • QueryBuilder and Templates • Fast-Track Your Paper

44. Fast-track your Paper!

45. 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. Thank you very much!