Getting the most out of FlyBase

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

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

QuickSearch

Autocomplete QuickSearch

Autocomplete QuickSearch

Autocomplete QuickSearch

Autocomplete QuickSearch

Gene associations QuickSearch

Gene associations QuickSearch

Gene associations HitList QuickSearch

Gene associations HitList QuickSearch

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

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

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

Examples of CV usage twins (tws, FBgn ):  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

Examples of CV usage twins (tws, FBgn ):  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

Term Report Controlled Vocabularies and Term Reports

Class relationships Controlled Vocabularies and Term Reports

Part of relationships Controlled Vocabularies and Term Reports

How to search CVs QuickSearch TermLink Controlled Vocabularies and Term Reports

Searching with QuickSearch Controlled Vocabularies and Term Reports

Searching with QuickSearch Controlled Vocabularies and Term Reports

TermLink

TermLink - searching TermLink

TermLink - browsing TermLink

Searching using Term Report Controlled Vocabularies and Term Reports

Search using TermReport Controlled Vocabularies and Term Reports

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

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

Where is QueryBuilder? QueryBuilder / Where is 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 QueryBuilder / What is QueryBuilder?

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

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

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).

QueryBuilder Templates QueryBuilder / Templates

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

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

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

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

Selecting the output type QueryBuilder / Build your own Queries

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

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

Fast-track your Paper!

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!

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