User Contributed Annotation System - Tutorial
This tutorial describes the User Contributed Annotation (UCA) system and how to use it.
Description of the UCA system
The UCA system facilitates annotation creation and submission by individual users for incorporation into AtGDB. Thus, the UCA system allows the community to contribute to the annotation integrity and accuracy of AtGDB - making AtGDB a true community database. Users will find that they can easily and swiftly create and submit annotations via the UCA system. After a submitted annotation is approved by the AtGDB administrator, it is incorporated into AtGDB and publicly viewable on the UCA track. Submitions are reviewed weekly. Additionally, accepted annotations are added to our BLAST databases.
Quick Steps for Submitting an Annotation
2. Click on the Provide Annotation link. This brings you to the User Annotation Submission page, which consists of a genomic plot, a gene evidence table, and text fields for entering annotation details. These combine for an interactive form to assist your annotation submission.
The provide annotation link is available on every Genomic Context Page.
3. Enter Gene Structure
The UCA system at AtGDB provides flexible and dynamic mechanisms for swiftly and confidently entering a gene structure. Exons can be entered through several means: selecting exons in the evidence table, clicking on exons in the genomic plot, clicking on a structure in the genomic plot, typing in custom User Defined exons, and pasting a complete structure. (Introns are automatically defined by flanking exons. As you enter your structure, it is displayed for your convenience. After a description of these mechanisms, there is a description of the priority of these methods.
The Evidence Table
The evidence table contains all exons of EST and cDNA spliced alignments, the 'evidence', in the current genomic region, which meet AtGDB quality thresholds. Exons are sorted by their left genomic coordinate and grouped into color coded rows, which are mutually exclusive and represent the variants of an exon. (1) Each row presents the coordinates, average GeneSeqer score, and EST and cDNA splice aligned sequences of the exon. Each evidence sequence id is hyperlinked to the GeneSeqer result files. (2) The scores and Geneseqer result file allow a user to view the spliced alignment on the sequence level and to provide a confident annotation. Complementary to this function, the transcript view displays evidence sequences and annotations textually and graphically, which is accesible by a link at the top of the page.
To select an exon, click on a button of a row.(1) To remove an exon, click the button a second time.
Only exons in the current genomic region are permitted to be entered through any of these mechanisms. To edit the range, enter new start and end values, select a chromosome, and click the Get Evidence Button. (3)
User Defined Exons
To enter an exon not represented in the sequence evidence, enter 5' and 3' coordinates for your exon and click add.(4) User defined exons are displayed in the larger box. To remove User Defined Exons, click on the 'clear user defined exons' button. individual User Defined Exon removal is available.
The Genomic Plot and Annotation Structure Preview
The Genomic Plot offers a quick way to select exons from evidence sequence splice alignments. The symbols of the Genomic Plot are identical to the Genomic Context View. Clicking on an exon (5), selects the exon. Coordinated to this selection, the button of the exon is selected in the Evidence Table (1), and the Annotation Structure Preview displays the current annotation gene structure with that exon.(7) Clicking on that exon, or on a similar exon in a different evidence sequence, a second time will remove that exon. Clicking on unique exons of Genbank annotations are inserted into the User Defined Exons box, since they are not sequence evidence.
Additionally, clicking on the id of a structure (6), resets current annotation structure, and selects all of the exons of that structure.
mRNA structure text entry
A structure can be directly into the mRNA structure box in Genbank or GeneSeqer format. Clicking outside the structure box will update the selected buttons in the Evidence Table, the User Defined Exons, and the Annotation Structure Preview. This method is recommended only for those using alternative programs.
To reset the mRNA structure for your annotation, click the 'reset annotation' button which will reset everything.
ab initio Portals
At the bottom of the page, there are several portals to ab initio gene prediction programs. These buttons open a new window with results of the program for the current range of genomic sequence, with a button beside each predicted exon. When a button is clicked, the exon is added to your annotation. If the coordinates are shared with an evidence supported exon, the exon in the Evidence Table is selected. If it is not supported by evidence, it is added to User Defined Exons. When you are done with the portal, close the window. Note: It is recommended that annotations have evidence supported exons to ensure inclusion in AtGDB.
4. Enter a protein coding region using the ATGDB Open Reading Frame Finder Portal.
- After entering a gene structure, click on ORF Finder.(8) A new window, containing the AtGDB Portal to NCBI ORF Finder, will open.
- Toggle between different open reading frames by clicking the rectangles. ORF Size, translated sequence, and location in the transcript are displayed.
- After selecting your open reading frame, (the selection is the magenta ORF) click on the button 'Select ORF for Annotation'. This will translate the transcript coordinates to genomic coordinates, paste them in the appropriate fields, display the arrows on the Annotation Structure Preview, update the mRNA and Protein preview fields, and close the ORF Finder Portal window.
5. Enter Annotation Description fields
- Enter a Annotation / LOCUS ID. Suggested format, UCA_At#g..., where # = chromosome number, . = chosen identifier. Example: UCA_At5g09920
- Enter Gene Aliases. (optional) Example: AL982373 AC008372
- Enter a description. Descriptions typically consist of a functional assignment, source of genomic material, or source of annotation. (optional)Example:contains zinc finger domain;supported by cDNA 21404796
- Enter a putative protein product. After, selecting Click on the blastn or blastp links. This pastes the appropriate sequence into NCBI's blast form. If satisfied with high scoring results, use this annotation information for your putative protein product field. Example: similar to exonuclease AY497556
7. Save or Submit Annotation. If satisfied with the current annotation, click on the submit button at the top of the page. To save save the annotation for future editing, click on the save button. This annotation is now accessible from the User Home page and will be available until you submit it or delete it.
Priority of Exon Entry Mechanisms
The following order of exon entry/removal mechanisms reflects their general priority in descending order:
- Reset mRNA structure button
- mRNA structure text entry = Graphic Plot Structure Selection
- Evidence Table button selection = Graphic Plot Exon Selection = User Defined Exon Entry
- Clear user defined exons button
- Changing the strand will update the mRNA structure and Annotation Struture Preview
- Use a range relatively close to the termini of your structure, so the resolution of the Graphic Plot and Annotation Preview Structure displays all of the exons accurately, and the size of the Evidence Table is reasonable. Ranges larger than >20kb are not recommended.
- The mRNA and Protein Fields are updated anytime the structure is updated. Blast links can be used to blast the current structure.
- Recommended Browsers: Linux Mozilla 1.4+, Windows Internet Explorer 6+, Macintosh Safari 1.1+, Macintosh Internet Explorer 5.2+
Example 1: Gene Model Split
Example 2: Gene Model Merge
User Annotation History
Upon logging in, user annotation history and status is presented, for the version of the Arabidopsis genome selected.
saved = saved by user, but not submitted to AtGDB
in review = submitted by user
accepted = incorporated into AtGDB
* Only the annotations for the selected version are displayed *