www.flybase.org getting the most out of flybase. tools –quicksearch – controlled vocabularies,...
TRANSCRIPT
www.flybase.org
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
QuickSearchQuickSearch
www.flybase.org
AutocompleteQuickSearch
www.flybase.org
AutocompleteQuickSearch
www.flybase.org
AutocompleteQuickSearch
www.flybase.org
AutocompleteQuickSearch
www.flybase.org
Gene associationsQuickSearch
www.flybase.org
Gene associationsQuickSearch
www.flybase.org
Gene associations HitListQuickSearch
www.flybase.org
Gene associations HitListQuickSearch
www.flybase.org
• Tools– QuickSearch
– Controlled Vocabularies, Term Reports and TermLink
– QueryBuilder and Templates
• Fast-Track Your Paper
www.flybase.org
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
www.flybase.org
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
www.flybase.org
Examples of CV usage
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
Controlled Vocabularies and Term Reports
www.flybase.org
Examples of CV usage
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
Controlled Vocabularies and Term Reports
www.flybase.org
Term ReportControlled Vocabularies and Term Reports
www.flybase.org
Class relationshipsControlled Vocabularies and Term Reports
www.flybase.org
Part of relationshipsControlled Vocabularies and Term Reports
www.flybase.org
How to search CVs
QuickSearch
TermLink
Controlled Vocabularies and Term Reports
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
TermLinkTermLink
www.flybase.org
TermLink - searchingTermLink
www.flybase.org
TermLink - browsingTermLink
www.flybase.org
Searching using Term Report
Controlled Vocabularies and Term Reports
www.flybase.org
Search using TermReportControlled Vocabularies and Term Reports
www.flybase.org
Allele HitListControlled 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?
• 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?
www.flybase.org
QueryBuilder Start Page
3 options:
• Select from one of our Pre-constructed templates • Import a saved query
• Build your own queries
QueryBuilder / Start Page
www.flybase.org
QueryBuilder Templates
• Templates are divided by output class
• Clicking on a template takes you to the finished query
QueryBuilder / Templates
www.flybase.org
QueryBuilder Templates8. 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 TemplatesQueryBuilder / Templates
www.flybase.org
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 operatorsAND, 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
www.flybase.org
QueryBuilder Start Page
3 options:
• Select from one of our Pre-constructed templates • Import a saved query
• Build your own queries
QueryBuilder / Start Page
www.flybase.org
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
www.flybase.org
Uncoordinated alleles in the Bloomington Stock Center
QueryBuilder / Build your own Queries
www.flybase.org
Selecting the output typeQueryBuilder / Build your own Queries
www.flybase.org
QueryBuilder / Build your own Queries
Uncoordinated alleles in the Bloomington Stock Center
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!