A new test version of WormMart WS220 is now available. We caution users to verify results before further downstream analyses. Please send problems or bug reports to [email protected].
New publication describes creation of a worm Phenotype Ontology
WormBase curators have published a new paper describing a controlled vocabulary for worm phenotypes. The paper is now available at BMC Bioinformatics in provisional form.
Use Textpresso for all your literature searching needs.
Are you writing a paper, review or research proposal? Or just need to search the ever-growing literature for information about a gene, allele or a cell? Searching the literature manually for information can be a daunting task. Textpresso (see links below) is an extremely useful tool to use for both information retrieval and extraction. Using Textpresso, you can perform searches using either keywords or categories (one or more) or both.  Searches using gene names are powerful because Textpresso has the capability to search for synonyms of a given gene, as some gene names have changed with time, in publications as well as in the WormBase database. Advanced search options allow you to choose the section of a paper that you would like Textpresso to search in, for example, you can select ‘results’ and/or  ‘discussion’. You can set the search scope to be a sentence or the entire document. You can sort the results using specified filters like ‘journal’, ‘year’, etc. The ‘Article Exclusions’ section allows you to exclude meeting abstracts and paper supplementals. Textpresso has also been implemented on the literature of other model organisms like the fly, yeast, rat, mouse, zebrafish and the literature of other biological domains. Textpresso also powers the literature search function in WormBase.
Textpresso Home page: http://www.textpresso.org/
Textpresso for C. elegans: http://www.textpresso.org/celegans/
Announcing webinars for exploring modENCODE data
The modENCODE Data Coordination Center is starting a series of monthly webinars conducted via WebEx teleconference services starting Feb 3rd 2011. The webinars are designed to provide a better understanding of the data generated by the modENCODE project and facilitate further analyses. More information can be obtained on the modENCODE wiki (accessible via anonymous login).
Help us by acknowledging WormBase in your publications.
We would like to enlist your help in ensuring that WormBase continues to exist and is successful. You can do this by explicitly acknowledging WormBase in each of your papers when you have used it in the planning, design, execution, analysis, or reporting of the research described.
This simple task will help us make the case to administrators at NIH and others for the utility of WormBase. You can do this in two ways:
1. Include in your acknowledgments, a statement thanking WormBase, ‘We thank WormBase’. To save characters, it can be included in a list:  ‘We thank XYZ for reagents, ABC for comments and WormBase’. If this is a problem, just mention the particular WormBase release (WSnnn) in the text. When you use these methods, the acknowledgements of WormBase are amenable to searching and reporting.
2. As a reviewer or editor, you could check that WormBase is acknowledged, if appropriate.
Thanks for your help!