SimpleMine Update: Biotype, GO term, RNAi clone and more

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We have added new data fields to SimpleMine, a batch download tool for essential gene information. Users can now access biotype, GO term, and RNAi clones through this simple web interface.

We also added more information to previously existing data fields. All references, including books, reviews, meeting abstracts, and primary research articles, are now listed in the Reference field. For genetic map position, we display error rates of the genetic mapping data. In addition to all “live” gene objects, users can now search for pseudogene or “suppressed” gene objects. 

Changes to the web interface include: improved performance, species-specific or mixed-species searches and a search button for all genes in one species. There are 32 data fields in SimpleMine, organized into five categories so that users can quickly select them. 

Note that WormBase SimpleMine provides essential information for genes in nine nematode species. There is a prototype of the SimpleMine tool for the Alliance of Genome Resources with data related to human, mouse, rat, zebrafish, fly, yeast, and worm (C. elegans only):  https://www.alliancegenome.org/prototypes

Introducing the Alliance Community Forum

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Dear WormBase and Worm Community Forum Users —

As previously discussed, the Worm Community Forum is moving.

Today, along with the Alliance of Genome Resources, we are pleased to introduce a new online discussion forum, the Alliance Community Forum.

Alliance Community Forum

In keeping with the spirit of the Alliance of Genome Resources, we’ve chosen to organize topics by organism and not by Model Organism Database. Rest assured that it’s easy to only follow specific areas that you may be interested in. Worm related discussions, for example, can be found here, subdivided in a variety of topics. You can choose a variety of notifications for topics of interest.

The Alliance Community Forum represents the first place for discussions across six model organism communities — flies, mice, yeast, rats, worms, and zebrafish (from the participating MODs of FlyBase, MGI, SGD, RGD, WormBase, ZFIN, respectively).

We hope that this Forum provides an opportunity for stimulating discussions, finding new collaborations, raising awareness about techniques from other fields, as well as providing a convenient place for posting notes of interest to the broader community of biomedical researchers (meeting details, job postings, funding announcements, etc).

If you are an existing member of the Worm Community Forum

We have migrated most existing accounts. Please reclaim your account on the Alliance Community Forum by requesting a password reset on the new forum. You will be sent a link to reset your password. If you have trouble logging in, please contact todd@wormbase.org.

Note that due to a technical issue, if you created an account in the last several months, you will need to create a new account in the Alliance Community Forum.

If you are not an existing member of the Worm Community Forum

You can log in with a new account on the forum, or a Google or Github account if you so choose.

Preserving the Worm Community Forum history

We have migrated [b]most[/b] posts from the nearly 20 year history of the forum. Some posts could not be migrated, nor have posts created in the last few months. Feel free to recreate these topics in the new forum.

Interested in working as a moderator on the Alliance Community Forum?

Please contact todd@wormbase.org.

Migration Timeline

July 6, 2021: New registrations disabled on the Worm Community Forum.
July 9, 2021: The “Discussion” panel of the WormBase home page will start displaying entries from the Alliance Community Forum; posting on the Worm Community Forum will be disabled.
August 30, 2021: The Worm Community Forum will be retired.

Questions?
Please either post here, on the new forum, or email either the WormBase (help@wormbase.org) or the Alliance (help@alliancegenome.org) Help Desks.

Technical Details

The Alliance Community Forum is using Discourse, a widely used and full-featured online discussion platform.
User guide and FAQ on using Discourse

Announcing version 2 of the Author First Pass form

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WormBase is happy to announce that we’ve released a new version of the Author First Pass (AFP) form.  We’ve improved our methods for identifying relevant genes and alleles and added an FAQs section to help guide you through the process.  Full details are available in the V2 Release Notes.  Thank you for your participation and feedback; we look forward to seeing your future submissions!

The URL for the V2 Release Notes link is:  https://github.com/WormBase/author-first-pass#release-notes

WormBase updates in WS277 – new protein schematic images!

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We have released the 277th version of WormBase! As always, for a detailed report please look at the WS277 release notes.

New features: We’ve updated the protein schematic image in the homology widget on protein pages (see, for example, the UNC-2, isoform a page.) This image displays protein domains and exons mapped to amino acid coordinates, making it easy to see which regions of a transcript correspond to specific features. Driven by JBrowse — the genome browser at WormBase — users can click through the image to an interactive view in amino acid coordinates. From that familiar interface, one can scroll, export sequence (can they?), get additional information on specific features, and zoom in to single amino acid residue resolution, color-coded by chemical property.  The previous static protein schematic image remains available by clicking on the “Legacy Protein Schematics” link, but will be removed after the WS278 release.

New data sets:

C. elegans: Additional Nanopore transcript data has been added.

C. elegans VC20210: The VC2010 strain data includes gene annotation which has been manually curated to improve the coding gene structures lifted over from the N2 strain annotation. This process is substantially complete, with some work still to be done on chromosome X. The number of coding genes which do not map correctly has been reduced so far from around 400 down to 50 genes which cannot yet be located and 10 which appear to be pseudogenes in VC2010. There are 20 genes which appear to be duplicated in N2 and have disappeared in VC2010. There have been 39 novel coding genes created.



Check out Venn diagrams for interaction data in WormBase
 

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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.