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.

Include strain names in publications!

We urge you to explicitly state strains used in your experiments to foster reproducibility and to help WormBase biocurators get your results into WormBase.

 Historically, C. elegans researchers just stated the alleles used, based on the reasonable idea that all strains were close to Brenner’s N2.  As the years and hundreds of worm generations passed, strains diverged.  We usually don’t know the full genotype of our strains (and really won’t even with whole genome sequencing since copy number variation is often hard to detect). Including strain names will greatly help sort out any background effects that are realized later.

 We thus would like to see editors and reviewers (both anonymous and within the laboratory) help enforce the inclusion of strain names in C. elegans papers.

-Paul Sternberg

Wondering how to cite WormBase?

If you are looking to cite WormBase please take a look at: https://wormbase.org/about/citing_wormbase#012–10. This can also be accessed from the Menu at the bottom of the WormBase home page on the extreme left, under WormBase–>How to cite.  Please do explicitly acknowledge WormBase in your published work when you have used it in the planning, design, execution, analysis, or reporting of the research described.  We can then search for these acknowledgements and use these numbers in various reports, eg. for funding agencies, etc.

Please specify allele and strain names in publications

WormBase curates data from published papers and attaches different types of data such as phenotype, overview, expression, human disease model, etc., to genetic entities such as genes, alleles, strains or transgenes. These are also bonafide  ‘objects’ in our database which allow us to attach data to them.  If we cannot find these named genetic entities in your paper it becomes extremely difficult for us to curate the paper.  It is not enough to just specify the amino acid or nucleic acid change of a mutation, we need either the strain or allele name to curate the paper.