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.
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
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.
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: