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.
C. elegans sORFs
sORFs.org is a public repository of small open reading frames (sORFs) identified by ribosome profiling (RIBO-seq).
It contains predicted sORF regions for several species, including C. elegans.
We have annotated 118 predicted sORF regions as coding (CDS) isoforms of the existing genes. It is likely that in the next release, where these isoforms do not overlap with existing isoforms, these sORF regions will be changed to be individual genes and not isoforms.
52 of these annotated sORF regions do not start with the canonical Methionine AUG initiation codon. It is possible that they use a non-canonical initiation codon. Some of these non-canonical initiation codons are not the expected non-canonical initiation codon Isoleucine, but code for residues like Valine.
This release we see the integrated of the Edinburgh strain of Trichuris muris version TMUE3.1. This species has been fully integrated as a core species meaning there are stable IDs and tracking with inclusion in all additional pipelines and analysis.
The genome assembly and gene annotation has been taken directly from the Pathogen Genomics group at the WTSI. Additional mapping of gene mergers, splits and transfer of IDs from the TMUE2.2 has been done to allow users to identify their genes of interest.
This release includes the Caenorhabditis nigoni genome assembly and gene set described in “Rapid genome shrinkage in a self-fertile nematode reveals sperm competition proteins” by Da Yin, et. al (Science 359,55-61 2018) as non-core species set.
This species should be of special interest, due to its phylogenetic closeness to C.briggsae and its differences in sexual reproduction.
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.
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.
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.