During the process of curation of RNA interference (RNAi) data, WormBase routinely maps the targets of any given RNAi experiment to the genome based on information present in the paper that describes the experiment. Recently WormBase has refined this process and addressed inconsistencies in target determination.  Previously, we were not filtering out the highly fragmented hits that occurred. That is, when many very short alignments occurred close together on the genome our mapping script was concatenating these splits, much like it would do when it skips over introns. These hits caused errant primary and secondary targets to be displayed. Most targets for RNAi experiments remain unchanged, but errant hits have been removed from WormBase.
The criteria for primary and secondary target determination (these descriptions are also on the individual RNAi report pages) are as follows:
Primary targets: These are targets that have sequence identity to the RNAi probe of at least 95%, over a stretch of at least 100 nucleotides, identified using a
combination of BLAST and BLAT algorithms.  These are usually the intended target genes of an RNAi experiment.
Secondary targets: These are targets that have between 80 and 94.99% sequence identity over a stretch of at least 200 nucleotides to the RNAi probe. Targets (and overlapping genes) that satisfy these criteria may or may not be susceptible to a RNAi effect with the given probe and represent secondary (unintended) genomic targets of an RNAi experiment.

WormBase has been collaborating with the journal ‘Genetics’ and Textpresso (www.textpresso.org) to markup online text and pdf versions of papers accepted for publication.  The goal of this collaboration is to link entities/database objects, e.g. gene names, alleles, anatomy terms, etc., within a paper to pages in WormBase. Entities from a total of nine data classes are currently being marked up, these classes include genes, proteins, variations, clones, anatomy terms, authors. We will soon begin the markup of phenotypes. In particular, we will be linking phenotype short names, eg., dpy, which are commonly used by the worm community and may be confusing for readers not familiar with the C. elegans nomenclature for phenotypes.  This project has pioneered the development of a markup pipeline that is starting to be used for marking up papers curated by other model organism databases, and has been in production since October of 2009.  We have marked up 23 papers so far.

We request authors to participate in this effort by alerting us about objects in your paper that don’t exist in WormBase.