Help:GONUTS gene page maker

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The GONUTS gene page maker creates a gene page where you can add GO annotations for any gene that has a UniProt Identifier (ID/Entry or Accession) or a NCBI Identifier (GI Number, RefSeq Accession, GenPept Accession). The information generated by the GONUTS gene page maker is UniProt centric. If NCBI identifiers are used to create a gene page, they are mapped to the corresponding UniProt Accession using in-house tools adapted from the documentation listed here.

To create a gene page, use the pull-down menu and enter the appropriate protein identifier from the database of your choice. If the gene is from an organism which we recognize to be an existing model organism database (MOD), a link will be provided which would allow the user to access the community annotation or other input system implemented by the respective MOD. Once the GONUTS gene page maker creates a gene page, it would have a table containing GO Annotations (if any) as it exists for the UniProt Record. Annotators can also edit the table and add GO annotations for the gene.


Contents

GONUTS gene pages

The newly created gene page is given a name that is a permutation of the UniProt identifier, so that the organism code obtained from the UniProt Entry/ID goes first. The top of the page has information taken from the UniProt record, such as:

Under this standard information, each gene page has two key editable sections:

  • The annotations table - clicking on "Edit table" launches a forms-based editor that allows you to add or edit rows containing annotations
  • The notes section - click the edit link on the right of the Notes section to bring up a wiki editing box where you can add free text commentary about the annotations.

Useful search strategies on the UniProt page to obtain your favorite gene/protein

You could search using the pull-down menu on the UniProt search page - make sure you choose Protein Knowledgebase (UniProtKB) and input your search parameters in the appropriate fields (Gene Name, Protein, Organism, Taxonomy).

If you want to save yourself the trouble of multiple clicks to "Fields" to enter the different parameters in the different "Fields" and doing "Add & Search" mutliple times, you could use the different search tags with the appropriate search parameters and build a query. Here are some examples:

  1. search for "dim-5" gene in Neurospora crassa organism
  2. search for "Calmodulin Kinase" protein in Gallus gallus organism
  3. search for All UniProt proteins in a particular organism say Bacillus subtilis
  4. search for only reviewed UniProt entries for an organism Mycobacterium tuberculosis
  5. if you happen to know the taxon ID (NCBI, UniProt taxon ID Listing of all organisms) for your favorite organism and want to retrieve all UniProt records for that ID (say 7460 - the taxon ID for Apis mellifera)

Marking gene pages for special interest groups

You can create a list of the genes you are particularly interested in by adding them to a wiki Category. For example, to add a gene to a list of genes being annotated by a class on Chromosome biology at Texas A&M you might use [[Category:TAMU Seminar in Chromosome Biology]]. You can add as many categories as you want to any page.

Known limitations and future plans

We are planning to address each of the following limitations in the future versions:

  • Pages are not updated when information in the UniProt record changes.

Bulk loading gene pages from your favorite organism

Contact us! ecoliwiki@gmail.com

References

See Help:References for how to manage references in GONUTS.

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