WormBase curates four different types of gene-to-gene interaction data: genetic, regulatory, physical, and predicted. These data are found in the interactions widget in each gene page. Aside from the predicted interactions, the other three types are curated with direct experimental evidence from the literature. Check out the micropublication which describes the Vennter tool. This tool is integrated into the interactions widget on WormBase gene pages and allows the visualization and analyses of interaction data.
Announcing the special edition of Textpresso covering coronavirus literature– it contains 31,000 articles from the PMC open access archive.
SimpleMine can now be used to obtain protein domains for a list of genes. You can select one or several attributes from a list, such as Gene ID, expression pattern, RNAi phenotype, allele phenotype, etc. Note that all attributes remain selected by default.
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.
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!