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.
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.
1 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.
3Genome 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
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.
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.
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,
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
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.