REMINDER!! – Gene Ontology (GO) Survey – Closes Sunday, November 15th

Attention GO users!!  The Gene Ontology Consortium would love to hear your feedback about GO.  Please assist the GO project by completing a short survey. The results will help us learn more about how you use GO, how GO can serve your research needs better, and will aid in preparation for the upcoming GO grant renewal. Surveys completed by November 15th 2015 will be eligible for a prize drawing for a $400 Apple Store voucher.  Thanks in advance for your time!

WormMart Sunset Period: to be retired 01 Jan 2016

Today we are announcing the “sunset” period for WormMart at WormBase. WormMart will be formally retired from WormBase at the end of 2015.

For many years, WormMart was the primary data mining facility at WormBase. Later, we replaced it with WormMine based on the Intermine platform. In that time, we have maintained the two in parallel, although WormMart updates were frozen at the WS220 release of WormBase.

With the new release of WormMine for WS250, WormMine is now in a position to replace much of the existing functionality of WormMart but with a raft of more powerful and useful features. Over coming releases starting with WS251 (due for release at the end of 2015), we will be rapidly expanding the content of WormMine, starting with orthology, RNAi, and sequence features such as binding sites.

Questions or concerns? Please do not hesitate to contact us. We’re here to help.

WormBook in Genetics: access and choices

Dear All,

I would like to address some questions that have come up regarding the partnership with the GSA and access to WormBook in the journal GENETICS.

As I said in a quote to the GSA blog, “WormBook in GENETICS will continue a great community tradition and will strengthen our longstanding association with GENETICS, which began with the publication in 1974 of Sydney Brenner’s landmark paper.   That association has grown, which is apparent in the many papers that appear every year in GENETICS and G3, as well as in the GSA’s sponsorship of the C. elegans meetings.”

GSA provides a sustainable platform for publishing WormBook, as well as the editorial and production resources of GENETICS.  However, because the GSA will be fully funding publication of new WormBook content, WormBook chapters will adhere to the journal’s current access policies, unless authors or institutions choose to subsidize immediate open access, including a Creative Commons license.

In practice, the journal’s access policy will not make much difference for most members of the community, who will continue to have immediate access to GENETICS content through their libraries and GSA memberships–which includes very low cost membership categories.  Furthermore, anyone who cannot pay may request individual article PDFs from the GENETICS Editorial Office.

The access issue was the subject of much discussion before we finalized the relationship.  But it is important to understand that there are costs to publishing, even on the web, and full open-access of WormBook at Caltech was possible only while they had sufficient funds to support it.  However, available funding, including some from WormBase, has been reduced to the point that WormBook was no longer sustainable.  Thus, the choice was to freeze WormBook in its current form altogether or find another way forward.

Several options were considered, and this association with the GSA emerged as the best option to finance and produce WormBook going forward.  Whether this arrangement should continue can be evaluated in 4-5 years.  For now, we have a fantastic opportunity, and the Section Editors are already commissioning great chapters.

It is too complicated to respond to questions about the economics of open access versus subscription publishing here–and I’m not an expert, though I know from having served as an editor of Development during the rise of the web and now, as an editor of PNAS and member of the PNAS Publications Committee, that it is very expensive to publish papers.*  Different journals have different business models, but the current access model used by GENETICS (and PNAS) is one way to keep costs down for authors, readers, and libraries.

So, thank you for your interest in, and continued support for, WormBook.

Best regards,


* It may interest some of you to see this report about the true cost of publishing a paper, where they calculate the cost in eLife as $14,000, and Nature itself estimates the cost of publishing in its own journal of $10,000!  (See

Announcement of WormBook in GENETICS

WormBook is excited to announce that we have partnered with The Genetics Society of America to publish new WormBook content in GENETICS. GENETICS will publish about 50 new chapters over the course of four years. Existing chapters will remain available at, and several new and updated chapters will appear there over the next six months. Letters describing these changes from Marty Chalfie and Iva Greenwald, who succeeds Marty as WormBook Editor-in-Chief, can be found in the blog posts below.

–Jane Mendel

Announcement of WormBook in GENETICS

From Martin Chalfie:

Dear Members of the C. elegans Community,

A little over twelve years ago several of us starting talking about the possibility of having an online review of C. elegans that would replace the outdated Cold Spring Harbor monographs (The Nematode Caenorhabditis elegans and C.elegans II).  These discussions led to the establishment of WormBook, and I became its Editor-in-Chief.  Now after shepherding over 150 articles into WormBook and reestablishing The Worm Breeders Gazette I feel that we have created a wonderful resource.  But I have found that my time has been taken up by so many other commitments recently that I no longer feel able to put the effort into WormBook that I believe it deserves (also 12 years is more than enough time for one person to be in charge).

For these reasons I have decided to step down as Editor-in-Chief.  Fortunately, Iva Greenwald, who has served as a spectacular section editor, has agreed to become the next Editor-in-Chief and oversee the changes that are necessary to keep WormBook a strong and essential resource for our community.  I know she will do a terrific job.

Before ending this letter, I want to thank the people that really made WormBook possible.  These people include Paul Sternberg as the publisher of WormBook through WormBase, whose support and enthusiasm have been essential; our two hard working editors Lisa Gerard and Jane Mendel, who made WormBook a reality; Oliver Hobert, who officially is the editor of WormMethods, but has really served as an assistant Editor-in-Chief; Lincoln Stein, Tristan Fiedler, Todd Harris, and Qinghua (Daniel) Wang, who brought WormBook to life on the web; and you the members of the Editorial Board [for the Gazette: and the past and present members of the Editorial Board], whose involvement and support made WormBook the model for all the other organism “Books.”  We have made something wonderful, and I thank all of you for showing once again the strength and dedication of the C. elegans community.

All the best,