How are the Phenotype Annotation Tables Used?
Phenotype Annotation tables are located on every Literature page and are used to link Phenotype Ontology terms to genes, mutant strains, or other data in a specific paper. If you would like to add a phenotype-related annotation to the table, or deem an existing annotation incorrect, please edit the table. The directions on how to do so are described in detail below. Remember: YOU MUST BE SIGNED INTO YOUR ACCOUNT TO EDIT ANYTHING!!!
How to Edit the Table
This link is located in the lower left hand corner of the Phenotype Annotation table. These tables are located on every literature page.
2.Add or Edit Content
From here, you have two options. You may either:
- Edit, copy or delete an existing row
- Add new content to the table
Edit Button If you want to modify an existing row in any way, click the "Edit" button for the row you wish to modify. You will then be able to modify the existing content of that row.
Delete Button If you find that a row is incorrect, you may delete that row. Click the "Delete" button to the left of the row you wish to delete. After clicking this button, the row will disappear from the table. If you accidentally deleted a row, click "cancel" or your browser's Back button.
Copy Button If you want to edit an existing row, select the appropriate action button for the row you wish to modify. Copying a row is used as a way to "auto-complete" identical sections of different rows. After clicking this button, a duplicate row will appear in the table. You must then click the "Edit" button to modify the content as described above.
Add row If there is no content in the table or you would prefer a clean slate on which to write, click the "Add row" button underneath the table to add a single row. "Add multiple" will allow you to add multiple rows at once if you prefer to do so.
When working large amounts of data, such as high throughput papers, it is convenient to work with a loader that can add several annotation rows at any one time. EcoliWiki solves this with the multiloader table. Please see this help page.
3.What Information Goes in the Table
Below you will find a quick description of what information goes in each column in order to fully complete a row. If you don't know some of the information requested or it is not provided in the paper, please persevere and fill in what is known. You will not encounter error messages hindering your submission's progress due to incomplete sections. Some information is better than no information at all.
Species You must specify the organism from which the phenotype is characterized.
Taxon ID The taxon ID number corresponds to the specific number identifying the species. Right now, we use the NCBI taxon ID, but may add others. Select NCBI from the drop-down menu and fill in the corresponding ID. Click here to look up the ID number for your organism of interest.
Strain The name the specific strain the authors are describing goes here. The genotype, however, should not be described here; you may enter that information in the "Materials and Methods Used" section above.
Gene (if known) If the authors attribute a phenotype to a certain gene, the name of the gene goes here.
OMP This column is reserved for the specific ontology-specific phenotype term/number from the ontology database.
Phenotype In this column you will pick which term best describes the general type of phenotype from a drop down menu. If the phenotype depicts an altered expression or regulation, staining pattern, resistance or sensitivity to a compound, etc.
Details Details you deem important about this phenotype that are not inferred by the term itself.
Evidence In this column you will pick which term best describes the type of experiment used to characterize the phenotype from a drop down menu. Options here may include a biochemical or binding assay, microscopy, etc.
Notes Any additional information worth mentioning goes here. Entering the location of the data (i.e. Figure X, Table X, pg. X) within the paper has been quite helpful to other users.
4.Preview your Contribution
After you have taken the time to enter data into the table, the next step is to save your work to the literature page table. Actually, this is a two-step process. First, you will click the "Save" button at the bottom of the text boxes. This will preview the table, providing you the opportunity to see what your row looks like integrated into the table.
5.Save the Table to the Literature page
If you are satisfied with the submission and are ready to save the table to the literature page, click the "Save Table to wiki page" link underneath the previewed table as shown in the figure below. You MUST click this button to permanently integrate your changes into the main literature page. Your contribution will be available to view immediately.
Thank you for curating!
- If everyone can view my contribution, can they edit my work as well?
- That depends. Each row can have a "public" or "private" designation. The default option when you edit the table is public, which means that anyone can view the information you've added, and registered users can edit your work. You may select the private option from the drop down menu depicted in the figure below if you prefer, which restricts the editing privileges of registered users only. Everyone can still view your work. Under the "private" restriction, you are the only user (aside from OMP system administrators) allowed to edit or delete your contributions. However, in keeping with the wiki-spirit, we do recommend that all settings be left public.
- Why should I use the "edit table" link inside the table instead of the "edit" link to the right of the section?
- There are certain formatting constraints that must be followed in order to view the information in table form. Using the "edit table" link in the lower left corner of the table allows the formatting of the table to be preserved. As a result, any information you contribute is therefore automatically integrated into the table properly.