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.