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Ontology Report – Annotations Help

Summary of data available in the ontology report

The “ONTOLOGY REPORT – ANNOTATIONS” page contains information about the term and links to objects annotated with the term. The page contains 5 primary sections:

(A) The topmost section summarizes information about the term itself.

(B) The next section presents rat chromosome ideograms from Genome Viewer showing the genomic positions of genetic objects annotated with the term.

(C) Below the Genome Viewer is a gene table listing genes, QTLs, and rat strains annotated with the term.

(D) The following section displays the selected term’s ontology lineage presented as a tree and a directed acyclic graph.

(E) The final Help section provides a summary of evidence codes.

 

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Ontology Report-Annotations Page

The term is shown on top of the page followed by Accession, Definition and Synonyms. The Accession given here can be used for ontology general search to get the exact ontology term. Synonyms include names commonly used before standardization or other IDs used by different communities.
 
 
 

(1) A search field allows for a general ontology search from within the page and
 
 
 
(2) A link is also provided to navigate back to the main ontology search page.
 
 
 
(3) The green branch icon and underlined “browse the term” are links to the ontology browser. These links will bring users to a center column where the ontology term is presented with sibling terms and flanked by parent terms on the left and child terms on the right.
 
 
 
(4) An additional link is provided to navigate to more term-specific information at the Alliance of Genome Resources website.

 

 

Genome Viewer (GViewer)-Embedded

 

Genome Viewer Diagram is the fully functional copy of the Genome Viewer (GViewer) embedded in the Ontology Report Page.

(5) The GViewer chromosome ideogram displaying the genomic positions of all rat genetic objects annotated with the ontology term.
 
 
 

(6) Genes are displayed in dark red , (7) QTLs in blue, (8) and congenic chromosomal sections of rat strains shown in green are presented to the right of each chromosome. (9) Clicking on a chromosome will open a zoom pane which gives a closer look at objects mapped to the selected area. One more click locks the slider in a fixed location. Links to the object report pages are accessible by clicking on object symbols in the zoom pane.

 
 
 
 

 

 

(10) Additional features can be accessed from links in the horizontal gray bar between the two panes.
 
 
 
 

(11) The first link from the left, “List All Objects”, opens a popup window which lists all objects from the diagram, ordered by chromosome. Each object in the list can be selected to locate the object on the zoom pane and on the chromosome.  
 
 
 

(12) The adjacent link to the right, “CSV Export”, presents the user with options for downloading all objects, objects shared by multiple searches or unique objects from the diagram to a CSV file.  
 
 
 

(13) The “Add Objects” link, opens a separate popup window and allows the user to select gene, QTL, strain, or ontology term annotations to overlay on the current diagram. After selecting the object type, new options are offered to search by keyword and choose the color of the displayed objects. The next link to the right, “Clear”, removes all annotated objects from the diagram.
The right side of the gray panel contains four additional features with links. The “Zoom In” and “Zoom Out” links allow the user to change the chromosomal distance covered in the zoom pane. The link, “Close Zoom Pane”, furthest to the right allows the user to toggle the zoom pane off. Again, toggling the pane back on simply requires clicking on a chromosome.  
 
 
 

(14) By selecting the “Send to JBrowse” link, the user will navigate to a new window or tab containing the more comprehensive and interactive genome browser, JBrowse. The initial view shown depicts all genes and transcripts that have been annotated to the current rat reference genome in the user’s selected region. The JBrowse tool also presents the user with options to add additional object tracks to their selected region such as: Disease related tracks, Gene Models, Gene-Chemical Interaction, QTLs, Reference Data, RNA-Seq, Strains, and Variant tracks.

 

Annotation Term Browser Page

Below the Genome Viewer diagram is a table of all objects (genes, QTLs, strains) annotated to the selected ontology term and all descendent terms.

(15) At the top left of the table, a check box is selected by default to display information for all descendent terms in addition to the selected term. The user can deselect this option by clicking the checkbox if they desire to view genes associated with only their selected term.  
 
 
Options for sorting are available in dropdown boxes to the right of the check box. Selecting the first dropdown menu to the right of “Sort by:” provides the user with options to sort by symbol, object name, position, or reference of objects within each annotated term. Clicking the next dropdown menu to the right of that allows the user to select a sort option of either ascending (asc) or descending (desc). 
 
 

(16) Selecting the “download” button exports the terms, associated objects, and annotation information from the table to a text file.  
 
 

(17) The user has the option of selecting from two rows of tabs for species used in the annotations and the objects annotated. The user simply clicks the tab with the name of the species of interest (i.e., Rat, Mouse, Human, Chinchilla, Bonobo, Dog, Squirrel, Pig, or All). The numbers in parentheses represent the number of selected objects annotated to the term for each species. The user may also select from the second row of tabs for their desired object used in the annotation, i.e., Genes, QTLs, or Strains. Again, these options are presented with the number of annotations in parentheses from the selected species. 
 
 
(18) The light blue pane contains the ontology term name, with the selected term at the top of the table. Selecting the term name will bring the user to a new ontology report for the term. Selecting the green branch icon brings the user to the ontology browser for the term to the left of the branch. Selecting the tool icon at the right of the pane (gene table view only) opens a popup window with options to export the term-specific annotated genes to other analysis tools at RGD.

 

 

(19) The symbols within the table can be selected to bring the user to the gene, QTL, or strain report page. The colored box with a letter to the left of the symbol designates gene (dark red, “G”), QTL (blue, “Q”), or Strain (green, “S”).

(20) Selecting the evidence code will bring the user to the gene – term annotation report which can be viewed as a list (default) or a table. For more information describing evidence code abbreviations, please see part E below.

(21) External source data (e.g., ClinVar, OMIM, CTD) can be selected from the source column to view additional information about the import and annotation pipeline.

(22) PubMed references can be selected to bring the user to the PubMed website to view the publication that the annotation was made from. Selecting an RGD reference brings the user to a publication reference page containing information about the publication and all associated annotations.

(23) Selecting the JB icon to the right of the object position information opens the JBrowse webpage with the selected object in focus.

 

Ontology Term Browser Lineage

 

The final section of the ontology report displays the selected term’s ontology lineage presented as a tree and a directed acyclic graph.

(24) The tree format presents the lineage of the selected term beginning with the highest level root term (“disease” in this example) down to the selected term’s direct child terms. The purple box with a letter to the left of the term name represents the relationship from the lower level term to the next higher level term. When the user hovers over the box, a text box with a description of the relationship will appear (e.g., “is-a”). The user can select each term name to reach an ontology report for the selected term. Hovering over the plus sign next to a child term of the selected term will produce a text box with the number of descendent terms associated with the term next to the plus sign. The “Annotations” column presents the number of annotations to the term on the same row to the left and all descendent terms. The green branch icon can be selected to bring the user to the ontology browser for the associated term.
 
 
 

(25) The directed acyclic graph presents the lineage of the selected term and the pathways with relationship from each child term to parent term to reach the root term. Each term within a yellow box may be selected to reach the associated ontology report page. A dropdown menu above the tree graph next to “Terms path to the root” allow the user to select the how the graph is displayed.

Summary of Evidence Codes

 

Evidence codes are attached to an annotation to describe what type of evidence supports the association between the gene, QTL, strain or other data object and the ontology/vocabulary term. Many evidence codes used at RGD come from the GO Consortium. The evidence code help page lists the evidence codes that can be found in annotations at RGD. Examples of evidence code locations in the ontology report with several linked evidence pages are shown below.

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RGD is funded by grant HL64541 from the National Heart, Lung, and Blood Institute on behalf of the NIH.