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.
We mourn the passing of one of the founders of our field. John Sulston was personally responsible for establishing the use of C. elegans to study development – with his stunning determination of the entire embryonic cell lineage by direct observation – as well as obtaining a complete genome sequence. He was a mentor and role model for many of us in the field who had the opportunity to work with him or know him personally, and an inspiration for many others who only knew him through papers and oral history. He demonstrated that comprehensive and careful description can lead to fundamental, mechanistic insights into biology and genomes. John also exemplified being collegial, community-minded, intellectually rigorous, scientifically intense and personally friendly.
We would like to announce the availability of the WormBase WS263 release on the WormBase website and FTP.
Some of the highlights of this release are:
New Pristionchus Assembly and Gene Set
The new data made available through WormBase is described in “Single-Molecule Sequencing Reveals the Chromosome-Scale Genomic Architecture of the Nematode Model Organism Pristionchus pacificus“ by Christian Roedelsperger, et al. in Cell.
ID mapping was carried out to try and preserve the existing IDs. The published IDs were also incorporated into the database so that they are searchable on wormbase.org.
New PantherDB data
DNAseI hypersensitive Sites
We have created 42,728 Features with a Method=DNAseI_hypersensitive_site to mark DNase hypersensitivity sites found in C. elegans ’embryo’ and ‘L1 arrest’ life-stages in non-coding regions from the paper WBPaper00053259. These sites, together with Transcription Factor footprints, will be added to the tracks available in the genome browsers.
Genome Res. 2017 Dec;27(12):2108-2119. “Genome-wide discovery of active regulatory elements and transcription factor footprints in Caenorhabditis elegans using DNase-seq.” Ho MCW, Quintero-Cadena P, Sternberg PW.
Check out the new chapter in WormBook, GENETICS: Sexual Dimorphism and Sex Differences in Caenorhabditis elegans Neuronal Development and Behavior by Maureen M. Barr, L. Rene García and Douglas S. Portman.
If you noticed, version WS262 has been out for several days. The version number present at the top of the WormBase home page is now a link to the Release Notes which is a concise summary listing the various data types and their numbers. Check it out if you want to get a quick view of the breadth and depth of the data in WormBase and to see what has changed since the last release. Also find the list of data files available for this release, on our FTP site.