1. FlyBase 2018: New look, new features Steven Marygold London Fly Meeting, April 2018

2. Typical use case: SEARCH FILTER/REFINE BROWSE REPORT(S)
ANALYSE
DOWNLOAD/EXPORT

3. Outline Basic Searches HitLists Reports New tools Feedback/Help
Jump to Gene, QuickSearch
HitLists
Filters, List/Table view, Export/Download
Reports
Navigation, summaries, GO ribbons, protein domains...
New tools
GAL4, Orthologs, Human Disease, Sequence Downloader
Feedback/Help

4. Outline Basic Searches HitLists Reports New tools Feedback/Help
Jump to Gene, QuickSearch
HitLists
Filters, List/Table view, Export/Download
Reports
Navigation, summaries, GO ribbons, protein domains...
New tools
GAL4, Orthologs, Human Disease, Sequence Downloader
Feedback/Help

5. Jump to Gene/Search J2G for quick navigation to gene pages
Search for general searching of website

6. QuickSearch
Default ‘Search FlyBase’ tab is a simplified, Google-like search box – same functionality as J2G ’Search’ box
Other QS tabs search specific subsets of FB data with specialized options/links – return to some of these later

7. Outline Basic Searches HitLists Reports New tools Feedback/Help
Jump to Gene, QuickSearch
HitLists
Filters, List/Table view, Export/Download
Reports
Navigation, summaries, GO ribbons, protein domains...
New tools
GAL4, Orthologs, Human Disease, Sequence Downloader
Feedback/Help

8. HitLists – List view
Now searches and returns ontology terms in addition to standard DB data classes
In-page filtering - categories with hits shown on left; species filter (in progress)
‘List view’ shows more info and links - e.g. gene snapshots & reference abstracts, data associated with an object

9. HitLists – Table view
(Available when showing results from a single data category)
Table view has more compact view and WILL allow sorting by column
Convert/export/analyze available

10. HitLists – Convert/Export/Analyze
Options will change depending on the content of your list.

11. HitLists – Analyze

12. Outline Basic Searches HitLists Reports New tools Feedback/Help
Jump to Gene, QuickSearch
HitLists
Filters, List/Table view, Export/Download
Reports
Navigation, summaries, GO ribbons, protein domains...
New tools
GAL4, Orthologs, Human Disease, Sequence Downloader
Feedback/Help

13. Gene Report
Floating navigation panel on right – all reports

14. General Information Snapshots Other summaries
Link to the equivalent page at the ‘Alliance of Genome Resources’

15. Genomic data Link to Sequence Downloader tool – mention later
- Links to Genome browsers

16. GO Summary Ribbons

17. Gene Groups
‘Ready-to-use’ lists of functionally related genes, manually curated from the literature or expert databases

18. Protein domain graphics

19. JBrowse - Protein domains
Domains mapped to genomic scaffold
Can see how domain is affected by different isoforms.

20. Human Disease Model data
‘Human Disease Model’ section of Gene Reports (here = tefu) illustrates 3-pronged approach:
Diseases associated with human ortholog(s) (via OMIM)
Experimental models (and genetic modifiers) annotated with terms from the Disease Ontology (similar to GO annotation)
HDM reports, which integrate these 2 approaches and display additional relevant data -> next slide

21. Functional Complementation Data

22. Datasets
- Links to our redesigned dataset reports, which summarize key aspects of a project and provide details on the biosamples, raw data and results generated. (Only a small fraction of datasets have been curated so far, but we're aiming for a comprehensive catalog in a few years.)
- Example gene here = twi

23. Reference filtering
On all reports
Example gene here = Egfr

24. Outline Basic Searches HitLists Reports New tools Feedback/Help
Jump to Gene, QuickSearch
HitLists
Filters, List/Table view, Export/Download
Reports
Navigation, summaries, GO ribbons, protein domains...
New tools
GAL4, Orthologs, Human Disease, Sequence Downloader
Feedback/Help

25. QuickSearch

26. ‘GAL4 etc.’ search

27. Frequently Used GAL4 Drivers

28. Orthology search 1. DIOPT ortholog dataset (DRSC)
humans, flies, + 7 other model organisms
integrates 14 orthology algorithms

29. Orthology search 2. OrthoDB: 50 species (in FlyBase set)
other Drosophila species
non-Drosophila dipterans (e.g. mosquitos)
non-dipteran insects (e.g. bees, ants, beetle)
non-insect arthropods (e.g. water flea, deer tick)

30. Orthology search results
Includes several links (e.g. alignments) & TSV download
Note: Orthology data from DIOPT and OrthoDB presented on Gene Reports in similar fashion

31. Human Disease search
Searches across DO terms, Disease Models, Alleles, and Genes.

32. Human Disease search
Search term = ‘Troyer”

33. Sequence Downloader

34. Sequence Downloader Three modes, by ID, Batch, and by location.
Genes and all subtypes of genes.

35. Sequence Downloader

36. Sequence Downloader

37. Outline Basic Searches HitLists Reports New tools Feedback/Help
Jump to Gene, QuickSearch
HitLists
Filters, List/Table view, Export/Download
Reports
Navigation, summaries, GO ribbons, protein domains...
New tools
GAL4, Orthologs, Human Disease, Sequence Downloader
Feedback/Help

38. Keeping in touch
Links to several outreach & feedback activities are organized on the Community link on the menu bar

39. Further information
Explore the the ‘About’ and ‘Help’ menus to get help and find out more
Note the FB release number in header - please use!

40. Acknowledgements & funding
FB-Harvard (USA):
Norbert Perrimon (PI)
Julie Agapite
Kris Broll
Lynn Crosby
Gil dos Santos
David Emmert
Sian Gramates
Kathleen Falls
Beverley Matthews
Susan Russo Gelbart
Christopher Tabone
Pinglei Zhou
Mark Zytkovicz
FB-Cambridge (UK):
Nick Brown (PI)
Giulia Antonazzo
Helen Attrill
Silvie Fexova
Phani Garapati
Alex Holmes
Aoife Larkin
Steven Marygold
Gillian Millburn
Clare Pilgrim
Vitor Trovisco
Pepe Urbano
FB-Indiana (USA):
Thomas Kaufman (PI)
Brian Calvi (PI)
Bryon Czoch
Josh Goodman
Victor Strelets
Jim Thurmond
FB-New Mexico (USA):
Richard Cripps (PI)
Maggie Werner- Washburne (PI)
Phillip Baker
Funding:
NHGRI at the U.S. National Institutes of Health (U41HG000739)
UK Medical Research Council (G )

41. Website Access Fee