From Human Salivary Proteome Wiki
Protein Annotation
Annotating a protein on the wiki is one of the many ways you can contribute to the effort of enriching the salivary proteome catalog. Annotation is a knowledge-intensive effort that involves interpretation and verification of experimental data and mining of information from the literature or knowledge bases. As the state of science changes constantly, contents in this wiki need to be updated continuously to reflect our best and latest understanding of the saliva proteome.
There are two types of annotations on the protein pages: comments (general annotations) and features (sequence annotations). The major difference between the two is that features are position-specific while comments are not. This guide will go through some examples to demonstrate how you can add or modify these annotations.
See also: Help:Salivary Proteins
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Adding an Annotation
Registered users have the ability to annotate proteins on the wiki. Each new annotation has to go through the curation process and be approved by a curator before it can be officially incorporated. To add an annotation, go to the protein page that you want to annotate. Check the page to see if an identical or equivalent annotation already exists. You may want to modify an existing annotation rather than adding a new one. Otherwise, click on the Annotate tab on top of the page, and the form in which you can create an annotation will appear.
See also: Help:Curation Process
Components of an Annotation
Figure 1 shows the annotation form for the protein Alpha-amylase 1 (HSPW:PD0564E). Each annotation is composed of several properties. Some of these properties are required while others are not. However, we courage you to include as much details as available to help ensure high quality of the proteome catalog.
Annotation type
The annotation type is a required field. The list of available selections is divided into two sections, for comments and features, respectively. Please use your expert judgment to make the most appropriate selection. The annotation type list is derived from the UniProt knowledgebase, and you can refer to http://www.uniprot.org/manual/general_annotation and http://www.uniprot.org/manual/sequence_annotation for the definition of each item.
Description
The description field is a free text area that allows you to describe the protein. Some of the annotation types gives you the option to use terms from designated controlled vocabularies, e.g. the Gene Ontology (GO), as values for the field. If that's the case, as shown in Figure 1, a link will be available underneath the description text box to launch the ontology selector. You can look for the appropriate term either by browsing or by searching.
Browsing - Figure 2 shows the Browse interface. In the case of a hierarchical ontology, use the "+" icon to expand the list in the Available Terms box. To make a selection, check the box in front of the term. The term(s) that you have selected will be placed in the Current Selections box. It is not recommended that you enter more than one term in a single annotation.
Searching - If you already have a term in mind, manually looking for it among all the available terms may not be very effective. Instead you can enter the term in the text box under than Search panel (Figure 3). Terms that match your search string either in the official term name or as a synonym will be listed. To select a term, highlight it in the search result and use the "right arrow" button to move it to the right side. Terms that have already been selected will be grayed out.
See also: Help:Ontology Lookup
Evidence
The supporting evidence for an annotation is composed of two parts. First is the evidence code, which is a required field. The wiki uses evidence codes derived from the Gene Ontology (GO) project. The codes indicate how the annotation is supported and provide a sense of the degree of trustworthiness one can put on the annotation. The following guide will help you select the correct evidence code for an annotation: http://www.geneontology.org/GO.evidence.shtml.
The second part is one or more literature references that describe the work supporting the association between the protein and the annotation. Currently, only citations indexed by the PubMed database can be submitted. Enter each PMID of the citations separated by a comma in the Evidence references box. For example, "PubMed:18361515,PubMed:7228490".
See also: Help:PubMed Citations
Scope
If your annotation applies to a particular form of the protein only, you can limit the scope of the annotation by choosing one of the sequences in the Scope drop-down box. The selected sequence will be shown at the bottom of the form. By default, it is assumed that your annotation is applicable to all variants of the protein.
Positions
If you want to create a feature or sequence annotation, you should specify the region of the sequence to where the annotation is applied. You can do that by first selecting the desired sequence in the Scope box, then entering the residual positions in the "Starts at" and "Ends at" text boxes. If you don't specify a sequence, your annotation will be applied to the canonical sequence or the first isoform on the list.
Credit
When you load the annotation form, the Reported by field is automatically filled with your username. Other users will be able to see clearly that you are the submitter of the annotation on the protein page. We hope that this will encourage everyone to contribute to the annotation effort.
Not all the annotations in the wiki are created by the user community. Some of the annotations are generated by sequence analysis programs, and some are imported from other knowledge bases. In these cases, credit will be given to the software or knowledge base that produced the annotation.
Annotation Listing
Once the annotation has been approved by a curator, the annotation will appear on the protein page in either the Comments or Features section. From the example above, the annotation (encircled in red) is added to the table in the Comments section as shown in Figure 4. In addition, the citation associated with this annotation is automatically added to the References section.
