FlyBase:CV Term Report
The term report page provides information regarding a controlled vocabulary term used in FlyBase.
Where available a definition and references are provided, along with a spanning tree, detailing the relationship of the term to other terms in the structured controlled vocabulary (ontology) (eg. term A is a subclass of term B, or is part of term C). The spanning tree can be expanded or collapsed both up and down the tree from the term of interest. Synonyms and external linkouts are also provided where possible.
This is a field-by-field guide to the information provided in the CV Term Report.
General Information
Term
The current valid name for the term.
ID (Ontology)
The unique identifier for the term, used to uniquely identify the term in the controlled vocabulary term. It contains prefix of two or more letters which identify the ontology where it originates, followed by a colon, followed by a series of numbers (eg. FBbt:00000017).
The controlled vocabularies currently used in FlyBase have the following prefixes:
- GO - The Gene Ontology
- FBbt - Anatomy
- FBdv - Development
- SO - Sequence Ontology
- FBcv - Other FlyBase controlled vocabulary
- DOID - Disease Ontology
Definition
A definition of the term together with references, where available.
Records annotated with this term or any of its children terms
The buttons show the type and of objects annotated with the CV term or any of its children and the number for each object type. Objects can be, for example, genes, alleles, images and transposons. Clicking on a button will show a hit list for that specific object type. In the term report page for neurodegenerative disease, the 'Genes' button will list, not only, all cases of a gene annotated with 'neurodegenerative disease' but also any of its children, such as Huntington's disease or Parkinson's disease.
Spanning Tree (Parents/Children)
A tree shows the parent and child terms of the selected term. By default, the tree shows 'is_a' relationships (eg. subclasses), but this can be changed by using the drop-down menu 'Only view relationship(s)' which lists all relationships available for that term. The tree is automatically redrawn when this menu is changed. For more information on the type of relationships available click here and here.
A search box on the right allows a new search in all ontologies.
Spanning Tree View Settings
In this section the number of hierarchy levels of the 'Spanning Tree' can be altered. 'Parents' refers to those terms above the term of interest (i.e. less-specific), while 'children' refers to those terms below the term of interest (i.e. more-specific). The number of hierarchy levels can be altered using the drop-down menus for parents and/or children, then clicking on the 'Redraw' button.
Compound statements
Compound statements including this term and relevant reports
CV terms can be used on their own or in combination with other CV terms, to improve the detail of the annotation (compound statement). For example, combining an anatomy term with a developmental stage term (pole cell | embryonic stage 11) or adding a qualifier to disease terms (model of | neurodegenerative disease). This section lists all unique instances of compound statements. For each of these, you can retrieve all object types (alleles, insertions or constructs) that have been annotated with that specific compound statement. The right column on the table lists the object type and the number or records that exist. Clicking on the number, will show a hit list for that particular compound statement and object type.
The compound statements table does not list records annotated with children of the CV term, only the exact term.
Records annotated with this exact term
This section lists the object types (data class column) and number of records annotated with the exact CV term (Records). For a disease term for example, it show the number of alleles that interact with a disease (annotated with ameliorates or exacerbates or its negative form, DOES NOT ameliorate or exacerbate), or that model a disease (annotated with model of or its negative form DOES NOT model). For GO terms, it will list genes, and for anatomy terms, alleles, insertions and transposons.
The 'Field' column identifies which section on the object type report (eg. gene report page or allele report page) the information can be found. For example, for anatomy, the data is in the subsection 'Phenotype Manifest in' in the 'Phenotypic Data' section.