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Vocabularies Search and Browser Help

The Vocabularies tool allows you to search the controlled vocabularies (CVs) used by FlyBase for a controlled vocabulary (CV) term report. A term report displays a definition, references, shows how that particular term relates to other terms within the same controlled vocabulary and provides links to objects in FlyBase that have been annotated with that term. For more help on how to use this tool see [here].

There is a video tutorial on YouTube.

How to Search using Vocabularies

You can search for a specific CV term using the search box at the top of the page by entering the official CV term name, the term identification number, or a synonym for the term. You can choose to search in a specific hierarchy or in all, by changing the ‘CV Hierarchy’ pull-down menu above the search box. Below are some search examples:

Example Search Term Controlled vocabulary Notes
Malpighian tubule Anatomy This is the official CV name
mushroom body heel Anatomy This is a synonym for mushroom body spur
GO:0005703 GO: Cellular Component This is the ID for polytene chromosome puff
tracheal liquid clearance GO: Biological Process This is the official CV term
third instar larval stage Development This is the official CV term
EMS Other FlyBase CV This is a synonym for ethyl methanesulfonate

Wild cards (*) can be added to the begining or the end of a search term. For example, searching for the term pup* finds any term whose name or synonyms contain a word that starts with 'pup' (e.g. pupa, pupal dorsal branch, protein pupylation, pharate adult stage P11, which has the synonym pupal stage P11), while searching with *pup* finds any term with 'pup' anywhere within any of the words of the name or synonyms (e.g. prepupa, and prepupal epidermis).

Instead of a direct search, you can also browse different sub-hierarchies by using the tree in the grey box on the right. For example, for the Gene Ontology, you can choose between Biological Process, Cellular Component and Molecular Function and browse the hierarchy by clicking on a term on the tree.

Search results For each search performed, the Vocabularies tool returns a hit list of CV term reports that match the search term. These are listed alphabetically in the following order: terms whose name starts with the search query, terms whose name contains the search query, terms whose synonyms contain the search query. Obsoleted terms (no longer used for annotation) are shown at the bottom.

Click on the CV term to see the term report page for that term.

You can also watch a tutorial video for using GO in FlyBase.

Other Features

Each term report allows you to retrieve gene, allele, transcript, polypeptide or image reports associated with the term or with any of its children, using the buttons on the sections 'Records annotated with this exact term' or 'Records annotated with this term or any of its children'.

Some of the information that you can access from each term report is listed below:

  • To find out how many genes have been curated with a particular GO term within FlyBase, search Vocabularies for the appropriate GO term and click on the 'Genes' box.
  • To find genes or constructs that are expressed within a particular part of the fly's anatomy, search with the desired anatomy term and click on the 'Genes' or 'Insertions' boxes. The same strategy can be used to find which genes are expressed at a certain stage of development.
  • If you are interested in a particular phenotype and want to search for all alleles that have been known to cause it, search for the phenotypic class term and click on the 'Alleles' box.
  • To find alleles that are a model of a human disease, ameliorate and exacerbate it, search for the disease name. Clicking on the top 'Alleles' box will return alleles in either of those categories. To search for alleles that are within a specific category, e.g. are a model of a human disease, use the 'Compound Statements' section.