Difference between revisions of "FlyBase:CV Term Report"
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| − | The | + | The CV (Controlled Vocabulary) Term Report provides information regarding a term from one of the [[FlyBase:Controlled vocabularies used by FlyBase | ontologies]] used in FlyBase. |
| − | This is a field-by-field guide to the information provided in the CV Term Report. | + | This is a field-by-field guide to the information provided in the '''CV Term Report'''. |
| + | |||
| + | See also the related '''video tutorial''' [https://www.youtube.com/watch?v=jgCON15SiRo Finding related genes/alleles in FlyBase: Vocabularies]. | ||
== General Information == | == General Information == | ||
| + | |||
=== Term === | === Term === | ||
The current valid name for the term. | The current valid name for the term. | ||
| − | === ID ( | + | === ID (ontology) === |
| − | The unique identifier for the term, used to | + | The unique identifier for the term, used to identify it in the [[FlyBase:Controlled vocabularies used by FlyBase| ontology]]. It contains a 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 | + | The ontologies currently used by FlyBase and their usage is described [[FlyBase:Controlled vocabularies used by FlyBase|here]] |
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
| − | |||
=== Definition === | === Definition === | ||
A definition of the term together with references, where available. | A definition of the term together with references, where available. | ||
| − | === Records annotated with this term | + | === Also Known As=== |
| − | The buttons show the type | + | Three exact synonyms of this term are shown here. All synonyms, together with references, when available, are shown in the field 'Synonyms & Secondary IDs'. |
| − | + | ||
| + | === Comment === | ||
| + | A comment might be added to a term as an explanatory note on something stated in the definition or regarding nomenclature. | ||
| + | |||
| + | === Links to External Ontologies === | ||
| + | Links to Ontology Reports from External sources. | ||
| + | |||
| + | == Annotations == | ||
| + | |||
| + | === Records annotated with this term OR any of its CHILD TERMS === | ||
| + | The buttons show the type of objects annotated with the 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. | ||
| + | |||
| + | For example, 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. | ||
| + | |||
| + | Please note that, as in the previous section, the hitlist will include not only ''Drosophila melanogaster'' records, but also other species. | ||
| + | |||
| + | Note that GO annotations with the qualifier NOT are excluded from this search. | ||
| + | |||
| + | ===Full annotation statements including this term (annotations to child terms are NOT included), and relevant FlyBase records=== | ||
| + | |||
| + | Terms can be used on their own or in combination with other ones, 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 by adding a qualifier to a disease term (model of | neurodegenerative disease). This section lists all unique instances of this term in annotation statements. For each of these, you can retrieve all object types (e.g. alleles, genes, images, insertions, or constructs) that have been annotated with that specific term. The right columns of the table list the object type and the number of records that exist. Clicking on the number, will show a hitlist for that particular compound statement and object type. | ||
| + | |||
| + | The table does not list records annotated with children of the CV term, only the exact term. | ||
== Spanning Tree (Parents/Children) == | == 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. | 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 [ http://www.geneontology.org/GO.ontology.relations.shtml here] and [https:// | + | For more information on the type of relationships available click [http://www.geneontology.org/GO.ontology.relations.shtml here] and [https://github.com/oborel/obo-relations/wiki here]. |
| − | A search box on the right allows a new search in all | + | |
| + | A search box on the right allows a new search in all vocabularies. | ||
| + | |||
| + | The numbers in green to the right of the terms on the tree indicate the number of records annotated with that term and its children, including compound statements (see below). | ||
=== Spanning Tree View Settings === | === 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. | 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. | ||
| − | == | + | == 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 [http://www.geneontology.org/GO.ontology.relations.shtml here] and [https://github.com/oborel/obo-relations/wiki 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 to the right of the relationship will take you to the corresponding Term Report for that CV term. | ||
| + | |||
| + | === 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. A reference is provided when possible. | ||
| + | |||
| + | For a detailed description of the synonym types, which are common to all OBO language ontologies, click [http://www.geneontology.org/GO.ontology.structure.shtml#opt here]. | ||
| + | |||
| + | ==External Crossreferences & Linkouts== | ||
| + | This section lists any linkouts to external websites, most commonly AmiGO, QuickGO or Virtual FlyBrain (VFB). | ||
Latest revision as of 18:41, 12 October 2023
The CV (Controlled Vocabulary) Term Report provides information regarding a term from one of the ontologies used in FlyBase.
This is a field-by-field guide to the information provided in the CV Term Report.
See also the related video tutorial Finding related genes/alleles in FlyBase: Vocabularies.
General Information
Term
The current valid name for the term.
ID (ontology)
The unique identifier for the term, used to identify it in the ontology. It contains a 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 ontologies currently used by FlyBase and their usage is described here
Definition
A definition of the term together with references, where available.
Also Known As
Three exact synonyms of this term are shown here. All synonyms, together with references, when available, are shown in the field 'Synonyms & Secondary IDs'.
Comment
A comment might be added to a term as an explanatory note on something stated in the definition or regarding nomenclature.
Links to External Ontologies
Links to Ontology Reports from External sources.
Annotations
Records annotated with this term OR any of its CHILD TERMS
The buttons show the type of objects annotated with the 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.
For example, 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.
Please note that, as in the previous section, the hitlist will include not only Drosophila melanogaster records, but also other species.
Note that GO annotations with the qualifier NOT are excluded from this search.
Full annotation statements including this term (annotations to child terms are NOT included), and relevant FlyBase records
Terms can be used on their own or in combination with other ones, 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 by adding a qualifier to a disease term (model of | neurodegenerative disease). This section lists all unique instances of this term in annotation statements. For each of these, you can retrieve all object types (e.g. alleles, genes, images, insertions, or constructs) that have been annotated with that specific term. The right columns of the table list the object type and the number of records that exist. Clicking on the number, will show a hitlist for that particular compound statement and object type.
The table does not list records annotated with children of the CV term, only the exact term.
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 vocabularies.
The numbers in green to the right of the terms on the tree indicate the number of records annotated with that term and its children, including compound statements (see below).
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.
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 to the right of the relationship will take you to the corresponding Term Report for that CV term.
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. A reference is provided when possible.
For a detailed description of the synonym types, which are common to all OBO language ontologies, click here.
External Crossreferences & Linkouts
This section lists any linkouts to external websites, most commonly AmiGO, QuickGO or Virtual FlyBrain (VFB).