Ontology Report – Annotations Help

What data is available in the ontolgy report

The “ONTOLOGY REPORT – ANNOTATIONS” page contains information about the term and links to objects annotated with the term.  The topmost section summarizes information about the term itself. This is followed by a rat chromosome ideograms from Genome Viewer  showing the positions of genetic objects annotated with the term.  After the diagram, is a gene table listing genes annotated with the term.  Lastly, the paths to the terms are listed together with an ontology tree at the bottom of the page.


Go to embedded Genome Viewer


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 t ontology term.  Synonyms includes names commonly used before standardization or other IDs used by different communities.   The underlined terms or phrases in this section are links  to further information of the term or phrase.

is a search box   allowing users to perform another  ontology search without leaving the report page. Search is initiated after enter or clicking the magnified lens within orange circle.   Users may go back to the  main ontology general search page by clicking the underlined phrase "go back to main search page."

2 " browse the term”   is clickable on either the branch  or the phrase underlined.  This link will bring users to a center column where the ontology term is presented with parent terms and child terms on either side.

3  Genome Viewer Diagram is the fully functional copy of the Genome Viewer (GViewer) embedded in the Ontology Report Page. This GViewer chromosome ideogram diagram displaying the genomic positions of  all rat  genetic objects annotated with the ontology term.  These genetic objects –genes in dark red , qtls in blue- are shown to the right of each chromosome. The congenic chromosomal section of a rat strain is shown in green.

Click on a chromosome to open a zoom pane which gives a closer look at objects mapped to the selected area. One more clicking locks the slider in a fixed location.  Links to the object report page are accessible by clicking on object symbols in the zoom pane. 

To the right of zoom pane, there are four tabs allowing users to zoom in to have a closer look of chromosome region or zoom out to get a bird's eye view of a bigger region. The “Send to GBrowse” tab will send the position information of selected chromosome region  to the RGD Genome Browser (GBrowse). The full set of genes and /QTLs in the region of interest is displayed in GBrowse to give a more complete view of data in that area.

At the bottom of the GViewer diagram, there are four tabs on each side. To the left of diagram, the four tabs allowing users to view all objects, download objects, and add  additional genomic objects to the diagram. 

List All Objects

One mouse click on this tab will show a list of all the objects in the diagrams grouped by chromosomes. Clicking on the object will put the object and flanking chromosome regions in the zoom pane.


CSV export

One mouse click allows exporting the data objects as a CSV file. Users have the options of downloading all objects, objects shared by multiple searches or unique objects.

Add objects

This function allows overlaying  additional objects to current GViewer diagram. One mouse click on this tab will bring up the window “Add objects to the Viewer.”  Users have options to  search for genes, QTLs, Markers or Ontology Terms and to display them in customized colors different from the existing objects in the current diagram. Click on one of the options will bring up the “Enter Keyword”  window.  Users can enter a search term for gene symbol, QTL symbol, marker symbol or an ontology term annotated to the bject of interest. .The example here is a QTL search with keyword "bp215" and brown color is picked for display. The search only returns with one QTL, Bp215.

Click on the symbol will  show the object' location along with other existing objects. Bp215 is colored yellow because it came up with both hypertension search and QTL keyword search.

All the objects annotated with the term are listed in the table below the Genome Viewer Diagram.  The options of viewing one species (Rat, Mouse or Human) or All three species are on the top left corner. Unchecking the box next to “show annotations for the term’s descendants” will refresh the table and show only objects annotated to the exact term.  The list can be sorted by any of the columns of  data in the table. The object symbols are links to gene, QTL or strain report pages. The user can click on GBrowse symbol to go to the Genome Browser View of the object. In the Evidence column, evidence codes indicate the type of source used for the annotation. These are also links to more detailed information about the annotations. Evidence code definitions are given below. Under the Reference column are links to references from which the annotations were made. Each reference used in our curation process is assigned a RGD ID.

On the far right is a link to the ontology report  page where users can view all annotations to the object.

Experimental Evidence Codes:

EXP: Inferred by EXPeriment
IAGP: Inferred by Association of Genotype with Phenotype
IDA: Inferred from Direct Assay
IED: Inferred from Experimental Data
IEP: Inferred from Expression Pattern
IGI: Inferred from Genetic Interaction
IMP: Inferred from Mutant Phenotype
IPI: Inferred from Physical Interaction
IPM: Inferred from Phenotype Manipulation

Author Statement Evidence Codes:

NAS: Non-traceable Author Statement
TAS: Traceable Author Statement

Computational Analysis Evidence Codes:

IBA: Inferred from Biological aspect of Ancestor
IBD: Inferred from Biological aspect of Descendant
IGC: Inferred from Genomic Context
IKR: Inferred from Key Residues
IRD: Inferred from Rapid Divergence
ISO: Inferred from Sequence Orthology
ISS: Inferred from Sequence or Structural Similarity
RCA: Inferred from Reviewed Computational Analysis

Curator Statement Evidence Codes:

IC: Inferred by Curator
ND: No biological Data available

Automatically-assigned Evidence Codes:

IEA: Inferred from Electronic Annotation
“Term paths to the root” at the bottom of the Ontology Report page allows options to display ontology path(s).  The selected term is in boldface with parent terms above and child terms below in the paths. A graph view showing all the paths and  ancestors terms between the term and top level term, Diseases, is shown on the right.  Both the paths and graph are interactive diagrams allowing users to browse any of the terms by clicking them.