Difference between revisions of "FlyBase:CV Term Report"

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).

@@ Line 1: / Line 1: @@
-The Term Report provides information regarding a term from one of the [FlyBase:Controlled vocabularies used by FlyBase | vocabularies] used in FlyBase.
+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.
-Where available, a definition and references are provided, along with a hierarchy tree, detailing the relationship of the term to other terms within the vocabularies hierarchy (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'''.
-This is a field-by-field guide to the information provided in the Term Report.
+See also the related '''video tutorial''' [https://www.youtube.com/watch?v=jgCON15SiRo Finding related genes/alleles in FlyBase: Vocabularies].
 == General Information ==
 === Term ===
 The current valid name for the term.
@@ Line 11: / Line 12: @@
 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 vocabularies currently used in FlyBase have the following prefixes:
+The ontologies currently used by FlyBase and their usage is described [[FlyBase:Controlled vocabularies used by FlyBase|here]]
-* GO - [http://www.geneontology.org/ Gene Ontology]
-* FBbt - [http://sourceforge.net/p/fbbtdv/wiki/Home/ Fly Anatomy]
-* FBdv - [http://sourceforge.net/p/fbbtdv/wiki/Home/ Fly Development]
-* SO - [http://www.sequenceontology.org/ Sequence Ontology]
-* FBcv - [http://sourceforge.net/p/fbcv/wiki/Home/ FlyBase CV including phenotypic class]
-* DOID - [http://disease-ontology.org/ Disease Ontology]
-* FBsv - [http://{{SERVERNAME}}/static_pages/downloads/bulkdata7.html FlyBase stock ontology]
-* FBbi - [http://bioportal.bioontology.org/ontologies/FBbi Biological Imaging Methods Ontology]
-* MI - [http://www.psidev.info/groups/controlled-vocabularies Molecular Interactions Ontology]
 === Definition ===
@@ Line 32: / Line 24: @@
 A comment might be added to a term as an explanatory note on something stated in the definition or regarding nomenclature.
-=== Records annotated with this exact term ===
+=== Links to External Ontologies ===
-This section lists the object types (data class column) and number of records annotated with the exact 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.
+Links to Ontology Reports from External sources.
-The 'Field' column identifies which section on the object type report (eg. [http://{{SERVERNAME}}/reports/FBgn0004956.html gene report page] or [http://{{SERVERNAME}}/reports/FBal0003003.html allele report page]) the information can be found.  For example, for anatomy, the data is in the subsection 'Phenotype Manifest in' and in the 'Phenotypic Data' section.
-Clicking on a button will show a hit list for that specific object type. Please note that the hitlist will include not only ''Drosophila melanogaster'' records, but also other species.
+== Annotations ==
-=== Records annotated with this term or any of its children terms ===
+=== 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.
@@ Line 46: / Line 36: @@
 Please note that, as in the previous section, the hitlist will include not only ''Drosophila melanogaster'' records, but also other species.
-===Compound statements including this term, and relevant reports===
+Note that GO annotations with the qualifier NOT are excluded from this search.
-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 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 columns on the table lists the object type and the number or records that exist. Clicking on the number, will show a hitlist for that particular compound statement and object type.
+===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 compound statements table does not list records annotated with children of the CV term, only the exact term.
+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 [http://www.geneontology.org/GO.ontology.relations.shtml here] and [https://code.google.com/p/obo-relations/ here].
+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 vocabularies.
@@ Line 65: / Line 58: @@
 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://code.google.com/p/obo-relations/ here].
+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.