Transcript ADRC2010_GetTheMostOutofFlyBase

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