We would like to announce the availability of the WormBase WS261 release on the WormBase website and FTP.
Some of the highlights of this release are:
Manual curation of C. briggsae has continued, concentrating on genes with low levels of curation.
The WormBook chapter “Operon and non-operon gene clusters in the C. elegans genome” describes SL1-type operons and dicistronic mRNA loci. These look like a single gene containing two isoforms with little or no overlap. During the examination of the C. briggsae gene structures about 30 novel, conserved examples of these loci were found.
As result of a cooperation on the GeMoMa tool with the Julius Kuehn-Institute, Quedlinburg (Germany), loci with missing annotation have been identified and curation of these has started.
Cross references and orthology data from PantherDB has been updated to the PantherDB release 12.0 .
In an effort to improve our annotation practice and provide more direct associations between C. elegans genes and GO Biological Process terms, we have removed annotations made via our Phenotype2GO pipeline. These annotations, supported by an Inferred from Electronic Annotation (IEA) evidence code, were derived automatically from mappings between terms in the Worm Phenotype Ontology (WPO) and GO BP terms. However, since observed phenotypes can sometimes be far downstream from the direct action of a gene product, these annotations are no longer as precise as we would like. Going forward, we hope to replace any missing information with more direct manual annotations as well as GO-CAM models, a new approach to GO annotation that uses well defined semantics to model biological systems and describe, more clearly, how a gene product functions within that system. If you have any questions about GO annotations, please contact us at email@example.com
The Oscheius tipulae genome will be imported as non-core species in one of the next WormBase releases.