 | How to to do a manual annotation in AFAWE? |
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Everybody is able to assign a manual annotation to a specific protein, but he or she has to login first.
This login is necessary, because so we are able to exclude junk and we can inform you about downtimes and updates.
If you register with your true email address and name, your manual annotation will be displayed and will used for updating functional annotations in genome projects.
Prerequisites:
Please open first a specific protein, for which you like to add a manual functional annotation by using the "Keyword Search", the "AFAWE ID Search" or the "Automatic Annotation".Login:
To login please click on "Login & Registration" in the main menu bar at the down left side
Here you have the possibility to login or if you don't have a login yet, register yourself.
Press afterwards the "send" button.
After login you will see a new link "add manual annotation" in the "query protein information pane" at the top left of the window and below the menu bar a text appears, that tells you, that you are now logged in.
After login you can add manual annotations to as much proteins as you like without logging in again.Open the Manual Annotation
Click on the "add manual annotation" tab at the left side.Insert values
At the manual annotation page you can add your manual annotation.Add description line
Insert into the Description text area your function description line.Add Gene Ontology terms
Click on "add" to get the full GO graph and search the GO term, which you like to add.
By clicking on the "+" nodes inside the tree you can extend nodes, the "-" will collapse the nodes again.
If you don't know where the GO term is in the tree, use the search field on the right side. If you insert a keyword or a GO term inside this field and click on "search" the tree is searched for this keyword or GO term respectively, and a new expanded tree with the paths to your query will appear (matches to your query are highlighted in red).
By clicking on one GO term, the GO term will be automatically added as "Selected GO terms" in the same window.
Before you add this GO term to your manual annotation, please insert also an evidence code to the GO term, which gives the information how you found out, that this GO term is true and if it is experimentally verified or reviewed.
Additionally it is important, that you tell AFAWE, if the GO term is true or wrong (like: this GO term with evidence code X is false). Afterwards click on "add" to add this GO term inside the GO term text area in the Manual Annotation window.
You can add as much GO terms as you like.Add KEGG Ontology terms
Click on "add" to get the full KO tree and search the KO term, which you like to add.
By clicking on the "+" nodes inside the tree you can extend nodes, the "-" will collapse the nodes again.
If you don't know where the KO term is in the tree, use the search field on the right side. If you insert a keyword or a KO term inside this field and click on "search" the tree is searched for this keyword or KO term respectively, and a new expanded tree with the paths to your query will appear (matches to your query are highlighted in red)
By clicking on one KO term, the KO term will be automatically added as "Selected KO term" in the same window.
Before you add this KO term to your manual annotation, please insert also an "true" or "false" to it, which tells AFAWE, that this KO term is true or wrong (like: this KO term is wrong). You can add as much KO terms as you like. If a KO term is added, the corresponding EC number belonging to this KO term is also added.
Add EC numbers
Click on "add" to get the full EC number tree and search the EC number, which you like to add.
By clicking on the "+" nodes inside the tree you can extend nodes, the "-" will collapse the nodes again.
If you don't know where the EC number is in the tree, use the search field on the right side. If you insert a keyword or an EC term inside this field and click on "search" the tree is searched for this keyword or EC term respectively, and a new expanded tree with the paths to your query will appear (matches to your query are highlighted in red)
By clicking on one EC number, the EC number will be automatically added as "Selected EC Number" in the same window.
Before you add this EC Number to your manual annotation, please insert also an "true" or "false" to it, which tells AFAWE, that this EC Number is true or wrong (like: this EC Number is wrong). You can add as much EC numbers as you like.Add Funcats
Click on "add" to get the full Funcat tree and search the Funcat, which you like to add.
By clicking on the "+" nodes inside the tree you can extend nodes, the "-" will collapse the nodes again.
If you don't know where the Funcat is in the tree, use the search field on the right side. If you insert a keyword or a Funcat term inside this field and click on "search" the tree is searched for this keyword or Funcat term respectively, and a new expanded tree with the paths to your query will appear (matches to your query are highlighted in red)
By clicking on one Funcat, the Funcat will be automatically added as "Selected Funcat" in the same window.
Before you add this Funcat to your manual annotation, please insert also an "true" or "false" to it, which tells AFAWE, that this Funcat is true or wrong (like: this Funcat is wrong). You can add as much Funcats as you like.Add database accessions or protein names
Insert the database accession or the protein name in the first text area and in the second drop down box choose the namespace.
Namespace is a word, which semantically describes the name.
For example: "AT1G12300" (name) "agi_locus_code" (namespace) or "CYB5B_HUMAN" (name) "uniprot_id" (namespace)
Please choose namespace, which is stored in the database (entries in drop down list).
If your namespace is not displayed in the drop down list, you can also create a new one by just writing the new namespace in the drop down box.
If you like to add more than one name or database accession to a protein, please press the "More Names" button and a second name text area with the corresponding namespace drop down list will appear below the first one.Add Pathways, PDB IDs and Pubmed IDs
Add pathways, PDB IDs and Pubmed IDs in the corresponding text areas.
Please enter more than one entry as a comma separated list.
Please note, that you are also able to add false annotations, like: This protein has not function X.
At the end press "Send" to add the manual annotation to the current protein.