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

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

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

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

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

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

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

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

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

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

HitLists – Analyze

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

Gene Report Floating navigation panel on right – all reports

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

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

GO Summary Ribbons

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

Protein domain graphics

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

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

Functional Complementation Data

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

Reference filtering On all reports Example gene here = Egfr

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

QuickSearch

‘GAL4 etc.’ search

Frequently Used GAL4 Drivers

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

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)

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

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

Human Disease search Search term = ‘Troyer”

Sequence Downloader

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

Sequence Downloader

Sequence Downloader

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

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

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!

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 (G1000968)

Website Access Fee