FlyBase:Vocabularies Tool

Vocabularies Search and Browser Help The Vocabularies tool allows you to search the controlled vocabularies (CVs) used by FlyBase and takes you to the associated controlled vocabulary (CV) term reports. Term reports display a definition, synonyms, references, show how a particular term relates to other terms within the same controlled vocabulary hierarchy and provide links to objects in FlyBase that have been annotated with the term. For more help on how to use this tool see Vocabularies Help.

See the related video tutorials “Finding related genes/alleles in FlyBase: Vocabularies” and “Finding related genes in FlyBase: The Gene Ontology” on YouTube.

How to Search or Browse 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. The autocomplete feature, guided by the text that you type, provides help with finding valid CV terms. The default is to search all of the FlyBase CVs. You can choose to search in a specific CV hierarchy such as “FlyBase anatomy (FBbt)” or “Gene Ontology (GO)” by selecting the CV ontology of choice in 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 beginning 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 doing a direct search, you may choose to browse different CV hierarchies using the interface below the horizontal line. Select the radio-button for the Vocabulary type of choice on the left and then click on a term in the top level CV hierarchy tree in the grey box on the right. This will take you to a term report from which you can explore the tree (See hints on exploring the CV hierarchy In the Vocabularies Report Help Page). 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 go to the term report page for that term. Other Features Each term report allows you to retrieve any gene, allele, insertion, construct, Human disease, or image reports annotated with this term or with any of its children, using the buttons in the section ”'Records annotated with this term OR any of its CHILD terms”. Some of the types of information that you can access from term reports 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.