Tag Archives: HOWTO

Annotating genes in FungiDB

As part of our newly launched FungiDB I wanted to demonstrate the capabilities of attaching additional annotation to gene records.  This is an important feature that allows the community to contribute to the knowledge base about an organism’s genes and gene functions.  This can be done by anyone in the community who has registered an account. Once the information is entered is also searchable so that added gene names are immediately part of the searchable text across the entire database.

We encourage you to register for an account (which allows you to also save your strategies and queries) and also to provide feedback about the look and feel (interface), the datasets that are provided, the need for additional species, and the capabilities and tools in the system.

Linking to a gene page
Here is a record for the C. neoformans var. grubii gene SXI1.  If you look at that URL you can see I am using one of the built-in shortcut URLs for EuPathDB/FungiDB which is http://fungidb.org/gene/GENENAME. Since we need names to be unique across the whole database we have chosen to prefix names with the species and strain prefix separated by two underscores.  So the link is  http://fungidb.org/gene/CneoH99__CNAG_06814 which gets expanded into a full accessible record which is much longer as you’ll see when you click on it.  This redirection gives us some flexibility to indicates that we’re talking to the beta release version of the database at this time.  This full (and long URL) has some flexibility so that in the future we can still have a beta and production server or even frozen release servers.

SXI1 top
Screen shot of SXI1 page on FungiDB

Comment pages
Comment pages provide a way to add additional information from the community to a page. This can be as simple as the gene name assigned, a link to a publication, GenBank Accession of the sequence, or descriptive text about a mutant phenotype. The comments can also describe corrections or additions to the gene model which can be noted. Currently the EuPathDB system does not allow direct manipulation of the gene model from the page as these types of updates need vetting and technical work to re-analyze the updated protein sequence in the downstream analyses (e.g. Pfam, InterPro, homology assignments, etc). For SXI1 there is a comment which links the gene to several publications and submitted accession numbers.  Since multiple strains have been studied for this gene, but not all are part of FungiDB, it may be useful to have direct links to the sequence variants for someone wanting to do followup work on the gene and the key residues.

SXI1 comment
How a comment looks on a gene page when it is entered
SXI1 comment
A comment page showing the linked pubmed records and genbank accessions