Textpresso searches now available on WormBase pages

Textpresso is a powerful full text search engine for several biomedical literatures. Textpresso searches are now available on many types of pages in WormBase such as gene pages, variation/allele pages, molecule/chemical pages, etc., in the References widget. Note that you should have the ‘References’ widget open (by clicking on it) from the side bar on a gene, allele, or molecule page. Click on the ‘Textpresso’ link in ‘Find references identified by Textpresso’ at the bottom of the references to trigger a search for that entity by the Textpresso search engine. For example, clicking this link in the ‘References’ widget on the lin-10 page will trigger a full text search by the Textpresso search engine for lin-10 in the C. elegans literature and return a page displaying the search results.

New and Improved Author First Pass Pipeline!

Community curation is a valuable part of WormBase. For the past ten years, C. elegans researchers have participated in our ‘Author First Pass’ pipeline using a web-based form to alert WormBase curators to entities and data types in their newly published papers.

We are very excited to announce a new and improved ‘Author First Pass’ pipeline that uses the Textpresso Central text mining system to automatically extract entities and identify data types in new C. elegans papers.

As before, corresponding authors will receive an email (Help WormBase curate your paper!) shortly after publication of their paper with a link to the new form.

But now, instead of having to enter all information de novo, authors simply need to verify the results and, if need be, modify them using simple check boxes and autocomplete menus of WormBase entities.

Links from the ‘Author First Pass’ form to select data entry forms allow for more detailed community curation, if desired.

We look forward to your participation and welcome any feedback you might have on your user experience!

Many thanks to Hannes Buelow, Simon Harvey, Hang Lu, Judith Kimble, Dayong M Wang, and Kunitoshi Yamanaka for helping to test our new 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/