Check out the Eukaryotic Genomic Databases book!

The Eukaryotic Genomic Databases book has just been released by Springer (Editors: Kollmar, Martin) and contains detailed chapters related to the eukaryotic databases such as WormBase, FlyBase, the yeast databases, SGD and PomBase, etc. The chapters describe database contents and classic use-cases, which assist in accessing eukaryotic genomic data and encouraging comparative genomic research.

Registering Lab, Strain and Allele designations

If you would like to register a new lab and/or receive strain and allele designations please consult the WormBase documentation page here.  This page also describes the nomenclature that WormBase requires and uses to describe genes, alleles, strains, gene knockouts, modifiers (suppressors, revertants and enhancers), and chromosomal aberrations (duplications, deficiencies, inversions and translocations) .

WormBase Workshop presentation slides at IWM 2017 available

WormBase hosted a workshop at the recently concluded International Worm Meeting at UCLA, which included presentations on community curation, Micropublications and the demonstration of tools for simple queries, data mining and data visualization. The slides for these presentations are available here.  The slides are also available from the WormBase FTP site.

WormBase HUBs

As shown during the WormBase Workshops of the International Worm Meeting 2015 at UCLA:

(Slides/Notes of the WormBase ParaSite / HUBs section)

To enable use of up to date data on external sites, WormBase is providing with each release (starting with WS248), selected annotations and comparative tracks as assembly hubs.

there are currently two types of hubs,

the UCSC version:

and a version compatible with Ensembl Genomes (future WormBase ParaSite , Ensembl and BioDalliance releases)

(production HUBs are in synch with the current live WormBase release)

Parasite Focus – BigWig External Annotations

This is an example of attaching an external annotation file to the ParaSite browser.

As annotation, we will use a BigWig file containing a PhyloP profile of the Trichinella spiralis genome, which is available here. In addition we need to put it onto a public accessible HTTP server.

We will use BigWig as format, as the size of WIG files is limited to 5MB, which would only cover parts of the Trichinella spiralis genome (as the format contains a score for each base pair).

Disclaimer: this data is just an example and should not be used for a in depth study of conservation

We will start at the ParaSite main page and choose Trichinella spirlalis
ParaSite main page

From there we should end up on a species specific page, where we can search for, as example, EFV62134 (which is a INSDC identifier of an T.spiralis gene)
T.spiralis main page

This will return a gene page, which includes a genome track to which we can attach our annotation.
example gene page for T.spiralis

We can also switch to the genome location view and attach it there (but note: if you want to see it on both, you need to attach it to both)
example genome location view

both should contain a “Manage Your Data”, which we will use to attach the bigwig file using the “add custom track” link at the bottom of the view
data management view

from there we will pick “Trichinella spiralis” as genome, “BigWig” as file format and put “” into the URL (which you potentially need to change to wherever you host it from).
data details view

You can also pick the colour scheme (the examples below use the cyan one) and then you should get on the gene view something like that
PhyloP track for EFV62134

and for the location view, respectively that
location view PhyloP

It is also possible to change the display of the track by clicking on the gear shaped icon next to it.