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Getting the most out of FlyBase www.flybase.org • Tools – QuickSearch – Controlled Vocabularies, Term Reports and TermLink – QueryBuilder and Templates • Fast-Track Your Paper www.flybase.org • Tools – QuickSearch – Controlled Vocabularies, Term Reports and TermLink – QueryBuilder and Templates • Fast-Track Your Paper www.flybase.org QuickSearch QuickSearch www.flybase.org Autocomplete QuickSearch www.flybase.org Autocomplete QuickSearch www.flybase.org Autocomplete QuickSearch www.flybase.org Autocomplete QuickSearch www.flybase.org Gene associations QuickSearch www.flybase.org Gene associations QuickSearch www.flybase.org Gene associations HitList QuickSearch www.flybase.org Gene associations HitList QuickSearch www.flybase.org • Tools – QuickSearch – Controlled Vocabularies, Term Reports and TermLink – QueryBuilder and Templates • Fast-Track Your Paper www.flybase.org 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’ www.flybase.org 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 www.flybase.org 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 www.flybase.org 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 www.flybase.org Term Report Controlled Vocabularies and Term Reports www.flybase.org Class relationships Controlled Vocabularies and Term Reports www.flybase.org Part of relationships Controlled Vocabularies and Term Reports www.flybase.org How to search CVs Controlled Vocabularies and Term Reports QuickSearch TermLink www.flybase.org Searching with QuickSearch Controlled Vocabularies and Term Reports www.flybase.org Searching with QuickSearch Controlled Vocabularies and Term Reports www.flybase.org TermLink TermLink www.flybase.org TermLink - searching TermLink www.flybase.org TermLink - browsing TermLink www.flybase.org Searching using Term Report Controlled Vocabularies and Term Reports www.flybase.org Search using TermReport Controlled Vocabularies and Term Reports www.flybase.org Allele HitList Controlled Vocabularies and Term Reports Alleles with a phenotype in the nurse cell www.flybase.org • Tools – QuickSearch – Controlled Vocabularies, Term Reports and TermLink – QueryBuilder and Templates • Fast-Track Your Paper www.flybase.org Where is QueryBuilder? QueryBuilder / Where is QueryBuilder? www.flybase.org 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 www.flybase.org QueryBuilder Start Page QueryBuilder / Start Page 3 options: • Select from one of our Pre-constructed templates • Import a saved query • Build your own queries www.flybase.org QueryBuilder Templates QueryBuilder / Templates • Templates are divided by output class • Clicking on a template takes you to the finished query 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). www.flybase.org QueryBuilder Templates QueryBuilder / Templates www.flybase.org 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 www.flybase.org QueryBuilder Start Page QueryBuilder / Start Page 3 options: • Select from one of our Pre-constructed templates • Import a saved query • Build your own queries www.flybase.org 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 www.flybase.org Uncoordinated alleles in the Bloomington Stock Center QueryBuilder / Build your own Queries www.flybase.org Selecting the output type QueryBuilder / Build your own Queries www.flybase.org Uncoordinated alleles in the Bloomington Stock Center QueryBuilder / Build your own Queries www.flybase.org • Tools – QuickSearch – Controlled Vocabularies, Term Reports and TermLink – QueryBuilder and Templates • Fast-Track Your Paper www.flybase.org Fast-track your Paper! 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! www.flybase.org Thank you very much! www.flybase.org