GUIDE TO SUBMITTING AN ANNOTATION FOR PROTEINS IN COMBREX

We realize that there may be cases where the annotation we have listed for a protein is incomplete or inaccurate. For example, we may list a protein's function as something generic, such as “protein-binding” when experimental evidence suggests a specific enzymatic function. In other cases, we may list a protein's current annotation as unverified, meaning that we do not have a reference, when an appropriate reference exists. If you notice any annotation on our site which could be improved, please submit an annotation update via the gene page.

We encourage you to use the annotation submission tool to:
  1. Update an existing annotation by making it more specific or correcting it
  2. Nominate a gene as a candidate for the set of gold standard annotated proteins. Please refer to the Gold Standard description document.
  3. Make a comment on the existing annotation.

Basic Steps to Update an Existing Protein Function Annotation in COMBREX

Finding Your Gene of Interest

Accessing the annotation submission form

Filling out the annotation submission form


Finding Your Gene of Interest

To find a gene of interest in the COMBREX gene database, enter information about the gene into the search field within the COMBREX homepage.

home_page_isomerase_example

In COMBREX, information about a gene is stored within its gene detail page. In order to locate the appropriate gene page, search for it using the search tools on the main page.

COMBREX supports searching for a gene using any of the following: keywords (e.g., "aspartate kinase", "methyl", "tRNA"), Entrez gene identifier (e.g., "899833"), protein GI, RefSeq protein accession number (e.g., "YP_780411", "NP_208251"), UniProt identifier (e.g., "Q02PQ5" "P24554"), gene symbol or Locus Tag (e.g., "radA", "HP1229"), and NCBI Protein Cluster accession number (e.g., "PRK09601" for curated clusters, "CLSK912335" for uncurated clusters).

In general, the more specific the information used in your search, the easier it is to locate a specific gene of interest. Therefore, whenever possible, we advise that you search for a specific gene using its Entrez gene ID or protein GI.

The advanced search functionality can be used to specify your query and consequently limit your search results, allowing you to more easily find your gene of interest. Advanced search can be used to specify the organism, the experimental validation status of the gene, and/or the experimental validation status of the cluster.

advanced_search

Currently, COMBREX organizes proteins within the context of NCBI protein clusters. Therefore, once you have submitted your search terms, COMBREX will return one or more appropriate NCBI protein clusters. If you search using an Entrez gene id or protein GI, you should see only one cluster. Below this cluster, your gene of interest will be listed. Clicking on this gene link will bring you directly to the appropriate gene page.

isomerase_search_results

If you search using keywords, COMBREX will in most cases return multiple protein clusters. You must then go through each protein cluster page until you find the appropriate gene link. Once you have located this link, clicking on it will bring you to the appropriate gene page.

If for some reason, your search does not return any results or the results do not contain your gene of interest, please review the search help documentation located in the COMBREX help center. If you still have questions, contact us at: mailto:help-desk@combrex.bu.edu.

Accessing the annotation submission form

Once you are on the appropriate gene page, scroll down to the section labeled “Predicted Function”, click on the “Submit” button. This section will show you the currently predicted functions for the current gene. Unless we have references which experimentally verify a given protein function annotation, we consider it to be a prediction. This can easily be determined by checking the "Experimental Validation" field of the "Status" section on the gene page.

1. Within the section named “Predicted Function”, click on the button labeled “Submit”.

submit_button

2. If you are not already logged in, you will be prompted to log into your COMBREX account.

In order to submit an annotation or make an update to an existing annotation, you will need to be registered with COMREX and currently logged into the system. More information on creating a free account within COMBREX can be found in the REGISTERING AND LOGGING IN section within the 'Guidelines For Navigating COMBREX' documentation.

login


Filling out the annotation submission form

3. Once logged in, you will be redirected to a submission form.

4. Locate the “Type” field at the bottom of the submission form and select “ANNOTATION”.

It is important that you change this from the preset of “PREDICTION” in order to have your annotation processed correctly.

prediction_annotation_submission_form

1. Fill in your updated annotation information using the text box labeled “Annotation or Comment:”.

a. If adding to or correcting the original functional annotation, please include the GO codes for the molecular function you are ascribing to the protein. If you are adding a reference to the annotation, please briefly state what the reference demonstrates and give the pubmed id if possible.

b. If you are nominating a gene for membership in the gold standard set of proteins, you will need to complete a gold standard nomination form and enter it into the annotation field box. The template for this is located here (link to blank gold standard template). More information on completing a gold nomination form can be found here (link to document on completing gold standard template).

As mentioned before, there are three main uses for the annotation submission tool: updating an annotation, nominating it for gold, or making a comment. You may combine updating an annotation and making a comment within the same submission. However, if you are nominating a gene for membership in the gold standard set of annotated proteins, please do not combine this nomination with any other tasks. If you do wish to make comments or updates to a protein in addition to nominating it as a gold standard member, please do so in a separate submission.

If you are updating a current annotation by adding more specific or additional functions, please use gene ontology, GO, terms. For more information, on the gene ontology project, please see: http://www.geneontology.org. If you are adding relevant references, please state what the reference demonstrates and include either the pubmed id, if available, or the full citation. If you have references which demonstrate the biochemical function of this protein, please consider nominating this protein for gold status.

If you are nominating a gene for gold status, please copy and paste the template located here (link to gold standard template) into the annotation/ comments text box. Please fill in as many of the fields as possible. Instructions for filling out each field are located here: Gold Standard Genes. An example of a completed nomination is here (link to example_gold_nomination.txt)

6. Once you have finished editing your submission, click the “Submit” at the bottom of the form.

After submitting your annotation, you will receive an email confirming that your submission has been received. Your annotation will be reviewed before integration into the COMBREX database.

You can access all of your submitted bids, annotations, and predictions through your user portal. If logged in, you can access your user portal by clicking on your user name, displayed as your email address, in the top right corner of any page in COMBREX.

my_predictions

In your user portal, click on “My Predictions” to access a list of predictions and annotations that you have submitted.