You can submit various types of data via our data specific forms found here. The ‘Submit Data’ button is also prominently displayed on our menu bar on the home page on the left hand side. Click on this to be taken to the various data submission forms.
Extra time on your hands? Help WormBase curate phenotypes
WormBase is doing a big push to address the backlog of phenotype curation. Please use our phenotype data submission form to submit phenotype data. Note that you can still submit phenotype data from published papers even if you are not an author on these papers.
C. elegans and related meeting changes
Meetings related to C. elegans and other topics have been postponed, moved to virtual spaces or cancelled due to the ongoing COVID-19 outbreak. Look in our Meetings widgets on the home page to find information about plans for these meetings.
Under stay at home? Consider submitting a microPublication.
Lab or university closed? Under at stay at home directive, doing your part to help slow the rate and spread of Covid-19? Need a diversion and a break from the news? Consider drafting and submitting a microPublication.
microPublications are brief, single experiment peer-reviewed publications. You can also sign up to become a microPublication reviewer.
The difference between expression pattern and expression cluster data in WormBase
Chris Grove explains how expression pattern data differs from expression cluster data in WormBase:
It’s important to understand that we have two avenues of gene expression curation at WormBase: one for individual gene expression pattern evaluation (e.g. using expression reporters like GFP or by performing an in situ hybridization of mRNA) which get captured in our “Expression Pattern” database objects (the “Expr_pattern” class) and a second avenue for larger scale (e.g. genome-wide) analyses of gene expression (e.g. RNA-Seq or microarray analyses) under certain conditions or in certain cells (or in certain life stages) which get captured in our “Expression Cluster” database objects (the “Expression_cluster” class).
In “Expression Pattern” annotations, genes may be associated with an anatomy term via a qualifier which can be one of three terms: Certain, Uncertain, or Partial. If authors declare that a gene is clearly and specifically expressed in a particular anatomical object, we flag it as “Certain”. If authors state that a gene might be expressed in a particular anatomical object, we flag it as “Uncertain”. If authors state that a gene is expressed in part of (or in a subset of) a particular anatomical object, we flag it as “Partial”.
In “Expression Cluster” annotations, genes may be associated with an anatomy term via a qualifier which can be one of three terms: Expressed, Depleted, Enriched. When large scale studies like RNA-Seq are performed in a particular neuron, for example, gene expression can be detected for even very lowly expressed genes and can sometimes include 10,000-15,000 genes (almost the entire set of protein coding genes) and these are considered “Expressed”, albeit possibly very lowly expressed, or expressed at a moderate level but not really more so than in any other tissue (e.g. housekeeping genes). Therefore, genes in these Expression cluster sets are typically evaluated as to whether they are “Enriched” in a particular anatomical object (i.e. statistically much more likely to be expressed there than in other tissues) of “Depleted” in a particular anatomical object (i.e. statistically much less likely to be expressed there than in other tissues). For our expression summary files, such as the “anatomy_association” file on the WormBase FTP site, we only include gene-anatomy associations from the “Expression Cluster” data class when the association is considered “Enriched” (hence why you don’t see the qualifiers “Expressed” or “Depleted” in the file).