The recording of the WormBase webinar “Data mining strategies and workflows” is now available. Please write to us at help@wormbase.org if you would like access to view this. For past and upcoming webinars and to register, see this form.
Register for upcoming WormBase webinars
The next two webinars “Data mining strategies and workflows” and “Author First Pass and Textpresso” will be held on Feb 22nd and Feb 26th, 2021. Registration is required if you want to attend. Please go to our form to see the complete list of past and upcoming webinars.
Textpresso for coronovirus
Announcing the special edition of Textpresso covering coronavirus literature– it contains 31,000 articles from the PMC open access archive.
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!