Category Archives: fungidb

An open letter to the fungal research community regarding genome database resources

An open letter to the fungal research community regarding genome database resources (from the Broad Institute & FungiDB/EuPathDB):

As many of you are already aware, fungal genome websites at the Broad Institute are undergoing a major transition. These resources were originally developed in support of sequencing projects, many of which have long-since been completed. While we have tried to keep such sites operational for as long as possible without funding, infrastructure changes now underway will make these websites nonfunctional over the coming weeks. We are therefore replacing formerly interactive websites with a static page providing information on fungal projects, along with links to the Broad FTP site where datasets can still be downloaded, and links to NCBI – the primary repository for all genomic data, where all genomes and annotation have been deposited and can be accessed, queried, and downloaded. We are also working to incorporate genomic data into other sites that support comparative analysis of fungal genomes, including FungiDB and MycoCosm.

The EuPathDB family of databases (funded by NIAID/NIH and the Wellcome Trust) supports a wide range of microbial eukaryotes; FungiDB includes many fungal (and oomycete) species, including non-pathogens. This resource has been designed to provide sustainable, cost-effective automated analysis of multiple genomes, integrating curated information (when available), with comments and supporting evidence from the user community (PubMed IDs, phenotypic information, images, datasets, etc). In addition to gene records, browser views, and data downloads, FungiDB offers sophisticated tools for integrating and mining diverse Omics datasets that fungal biologists will find quite useful. See the sidebar on the FungiDB web site for access to tutorials, videos, and exercises.

MycoCosm (supported by JGI/DOE) offers the largest available collection of fungal genomes, for comparative genomics across phylo- and eco-groups, along with interactive web-based tools for genome downloading, searching and browsing, and a form for nominating new species for sequencing to fill gaps in the Fungal Tree of Life.

For many years the Broad has been pleased to work closely with various fungal research communities, and we will continue to work with EuPathDB and MycoCosm to transition data valued by the community. Please direct any inquires or requests for help to help@FungiDB.org

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