Difference between revisions of "FlyBase:CV Term Report"

Revision as of 19:24, 12 June 2014

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 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 of objects annotated with the CV term or any of its children and the number of records for each object type. Objects can be, for example, genes, alleles, images or 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.

Relationships

A list of the different types of relationship between the term of interest and other terms in the hierarchy, subdivided into fields by the type of relationship.

For more information on the type of relationships available click here and here.

The Is a and Part of relationships are always displayed on an individual Term Report (see below for a description), but for other types of relationship (e.g. Develops from), only those containing data are shown.

Clicking on a term listed in this section will take you to the corresponding CV Term Report.

Is a

An 'Is a' relationship means that the term is a subclass of its parent. For example, 'mitotic cell cycle' is a subclass of 'cell cycle'.

Part of

A 'Part of' relationship refers to when the term is part of another term or process, for example 'wing disc development' is a subprocess of 'imaginal disc morphogenesis'.

Synonyms & Secondary IDs

Synonyms

A list of other names for the term, subdivided into fields by the type of synonym: exact, related, narrow or broad. References for each synonym are given when available.

For a detailed description of the synonym types, which are common to all OBO language ontologies, click here.

Secondary IDs

A list of secondary identifier numbers for the term.

If a term has a secondary identifier number, it indicates that at some point the term has been merged with or split from other terms.

External Crossreferences & Linkouts

Linkouts

Linkouts to external databases are provided where possible, for CV terms from GO or anatomy.

Links currently displayed in this section are to:

@@ Line 1: / Line 1: @@
 The term report page provides information regarding a [http://flybase.org/static_pages/docs/refman/refman-G.html#G.2. 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.
+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 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.
@@ Line 24: / Line 24: @@
 === 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.
+The buttons show the type of objects annotated with the CV term or any of its children and the number of records for each object type. Objects can be, for example, genes, alleles, images or 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.