Overview of WormBase, Sept 2020

If you’d like to get an overview of WormBase datatypes, tools, the Author first pass form and learn about Micropublication Biology, please take a look at the slides from a talk given by Chris Grove, a WormBase curator. This was presented at the Boston area worm meeting on Sept 23rd, 2020.

WormBase workshop talks at the 2019 IWM available on Youtube

Talks delivered at the WormBase workshop as part of the International C. elegans meeting at UCLA in June 2019 are now available on Youtube. Please note that these are recordings done at the workshop with external cameras and microphones, so apologies if they are not of the highest quality.  They are linked from their titles below–

  1. Introduction to the WormBase webpages and widgets
  2. WormBase data mining tools: SimpleMine, WormMine, BioMart
  3. WormBase ontologies and gene set enrichment analysis
  4. WormBase JBrowse: tutorial and demo
  5. Community curation
  6. Introduction to the Alliance of Genome Resources


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.

Creating Hi-Res Screenshots in JBrowse

higher-res screenshot of JBrowse

While the new genome browser (JBrowse) implemented at WormBase has several advantages, like faster browsing and a faceted track selector, it does lack a few features from the venerable GBrowse instance that has been at WormBase for many years.  While we and the JBrowse developers are working on addressing those minor shortcomings, this article is about how to circumvent one of those issues now.  

JBrowse lacks the ability to make a high resolution image like GBrowse.  While taking a screenshot can sometimes result in an acceptable image (for example, Macs with a retina display work pretty well), the result is not always suitable for publication or putting on a poster.  The method described here still does not allow for making an SVG image, but it does allow for higher quality PNG images than just taking a screenshot and also allows for the creation of a PDF document with the image in it.  Unfortunately, this method requires downloading a tool where we must edit one of the source files and then execute it on the command line.  While this is a little bit of a hassle, once it is set up, creating screenshots is quite easy.

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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 “http://www.ebi.ac.uk/~mh6/tspiralis.phylop.wib” 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.