There appears to be a problem of contamination with the genome assemblies of species 7 and 9. The Caenorhabditis Sequencing Consortium and the Washington University Genome Institute are working together to resolve this problem as quickly as possible.
A report on Japanese worm labs
WormBase is relieved to know that members of the Japanese worm community are safe. We hope that they can resume normal lab operations as soon as possible. This report has been compiled by Dr. Ikue Mori and kindly passed on to WormBase by Dr. Martin Chalfie.
Ikue Mori:
Several labs that suffered from the horrible earthquake explained their situations in the Japanese worm community mailing list. As you see, they are safe in the lab. However, shut down of electricity in particular, and tapped water and gas for up to several days seemed to increase the damage. Safe labs are now trying to help them. However, entering to the damaged area is prohibited. Also we cannot send any supplies. At least we could visit Tsukuba area just north of Tokyo by “Tsukuba express train”. In case they emailed us to help, we will be ready to go there and come back in one-day trip.
From Hidehiko Kuroyanagi at Tokyo Medical and Dental University,
http://www.tmd.ac.jp/english/index.html
Chiyoda-ku, KandaSurugadai, Tokyo.
His lab is on the fifth floor in the nine-story building. Lab members were fine in seminar room at the earthquake. Some apparatus such as incubator (for bacteria), computer, a microwave fell down on the floor, but heavier items like lab benches, other incubators (for cultured cells and worms), freezer, refrigerator, centrifuge, and microscopes and reagent bottles on top of them were okay, although they all moved 10 cm on the floor, by keeping their positions. Precious machines and glassware were not damaged. The problem was in going back home. The commuter trains stopped until midnight and some people failed to go home on the day of earthquake. Another problem he found was the lack of food and drinks in grocery store and drug stores on the next day after the earthquake. Starting on 14th, the electricity will be shut down in a certain period of time in different regions in the Tokyo area due to the nuclear plant problem in Fukushima prefecture. Accordingly, many lines of commuter trains stopped, which made some people living in a bit distant fail to come to the labs. Also, his lab purposely shut off most of the machines in the lab except for incubators, refrigerators and freezers. There is no emergency self-supplied electricity in his building. He doubts if his lab will start working in a month.
From Asako Sugimoto at Tohoku University,
http://www.tohoku.ac.jp/english/
Sendai, Miyagi Prefecture.
At the time of the earthquake, her lab members were in the lab (actually, Asako became a full professor of Tohoku University, and just moved to the University on the day of this horrible earthquake!), although she never experienced such a tremendously big shake. Fortunately, all the members in her lab and the members in the lab next door were safe. Although many items were all over the place on the floor, the building itself and experimental machines seemed fine. However, electricity was off for at least almost two days after the earthquake, thus being unable to receive and send emails and to watch television at home. Unfortunately, the frozen worm stocks in the freezer may be severely affected. She was told that electricity will be on on 15th and tapped water will be available on 14th in the University, but she said that there are some places in Sendai city, where there are no water and electricity as of 14th. Gas supply will recover at least three weeks later (as of 14th) in the whole city (I think). All the public transportations, commuter trains, Shinkansen (the fastest train) and metros all stopped. People from other areas who happened to come to Sendai due to business or to take entrance examination for the Universities were trapped in Sendai City. The shortage of gas limits using cars. Usual mailing and express mailing services are being stopped, and any items cannot be sent and not be received. Food is so far fine but in the long term, it is uncertain to be be supplied.
Asako said that after electricity was on, she was surprised to know through watching television that the earthquake was one of the largest ones in history and Sendai City was really near to the epicenter. She also said that knowing where she was, she feels miracle that the damage was less than expected. The immediate problem she thinks is that a liquid nitrogen tank with frozen worm stocks will get liquid nitrogen supply to keep the worm stocks, since the worms in the freezer are perhaps all dead due to no electricity. We all know now that Tohoku University postponed to start a new academic year (usually April 1st in Japan) until the end of April. This will be applicable to all the students including new students who just graduated high school in this month.
From Yuichi Iino at University of Tokyo,
http://www.u-tokyo.ac.jp/index_e.html
Bunkyo-ku, Tokyo.
Like Kuronayagi at Tokyo Medical and Dental University, Yuichi said that electricity is unstable in the University and some commuter trains stopped.
From Tokumitsu Wakabayashi at Iwate University,
http://www.iwate-u.ac.jp/english/index.html
Morioka City, Iwate Prefecture.
Dr. Wakabayashi is working with Professor Shingai. There was no big damage in buildings including the University and all the people he knows are safe. The similar problem happened though due to a long-time no electricity supply. Some worm strains were perhaps dead in the freezer. He however thawed the very important strains when the electricity was off. In Morioka City, also the shortage of food and gas will make a complication in the City. He worries what will happen in mid-long term in lab life.
From Ryosuke Niwa at Tsukuba University,
http://www.tsukuba.ac.jp/english/
Tsukuba City, Ibaraki Prefecture.
There are different degrees of damages in different floors or in different buildings by the earthquake. The worst lab he knows was filled with water due to the damage in a water pipe in the ceiling of several story-up that lab, resulting in the complete crash of the whole lab items. Fortunately, his lab was better in terms of damage. Immediately after the earthquake, all the life-related supplies were off. It took three days to have the electricity on in the University. Like other labs, samples like proteins, antibodies, RNAs and enzymes in the freezer would be probably all dead. He worried if liquid nitrogen would not be supplied sooner, all the frozen samples would be dead also. The difficulty he found is that there is still no tapped water in the lab, although water supply is available though a supply car coming near people’s houses. As of 14th, gasoline and food have been gone in the city. In his case, he struggled to get his family’s food for a week in the grocery store. Because of the lack of gasoline, he will have to give up to drive to the lab. Rather he is thinking to buy a bicycle. As of 14th, he suffers from an aftershock at least once every hour. He proposed that important worm stocks in every lab should be distributed in other labs.
From Ayako Ohashi at Iwate Medical University,
http://www.iwate-med.ac.jp/eng/index.html
Morioka, Iwate Prefecture.
As of 13th, electricity was supplied again, and tapped water and gas supplies became normal as of 14th. Although some buildings in the University have cracks, but no complete crashes are found. Internet became usable at last (as of 14th), although unstable. Any items cannot be sent or be received. Citizens are prohibited to by gasoline.
Motomichi Doi at AIST,
http://www.aist.go.jp/index_en.html
Tsukuba, Ibaraki Prefecture.
Electricity was off for four days and finally was on as of 15th, thus enabling to read emails. As other labs, all the frozen stocks were dead. Like Tsukuba University, there is no water and gas (as of 15th). Microscope moved 50cm on the lab bench and fell on the floor. Also, Inverted microscope placed next to the microscope was heavily damaged probably when the microscope was dropped on the floor. Fortunately, all dissecting microscopes are safe.
Paper that describes the Worm Phenotype Ontology
You might have come across the term ‘ontology’ in the biomedical literature or in a database. You might have knowingly or unknowingly used it to query data. An ontology consists of well-defined terms that describe entities (for example, the entity might be a gene) and the relationships between them. The goal of building an ontology is to reflect the current knowledge in a particular domain using a controlled vocabulary, to provide a guide for organizing new data, and to allow users to conduct queries. The Worm Phenotype Ontology (WPO) is a hierarchically structured, controlled vocabulary of terms that can be used to standardize phenotype descriptions in C. elegans. Although the WPO was created in order to help manage and disseminate C. elegans phenotypic data, it is not exclusively limited to C. elegans biology, but rather devised to also incorporate phenotypes observed in related nematode species. The WPO will help facilitate data retrieval, and cross-species comparisons within the nematode community and in the larger scientific community, will permit data integration, and interoperability across different biological databases. We are actively developing the WPO to continue to fulfill the evolving needs of the scientific community and hope to engage researchers in this crucial endeavor. To know more, please visit this recent publication that describes the WPO: http://www.biomedcentral.com/1471-2105/12/32
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/
Help us by acknowledging WormBase in your publications.
We would like to enlist your help in ensuring that WormBase continues to exist and is successful. You can do this by explicitly acknowledging WormBase in each of your papers when you have used it in the planning, design, execution, analysis, or reporting of the research described.
This simple task will help us make the case to administrators at NIH and others for the utility of WormBase. You can do this in two ways:
1. Include in your acknowledgments, a statement thanking WormBase, ‘We thank WormBase’. To save characters, it can be included in a list:  ‘We thank XYZ for reagents, ABC for comments and WormBase’. If this is a problem, just mention the particular WormBase release (WSnnn) in the text. When you use these methods, the acknowledgements of WormBase are amenable to searching and reporting.
2. As a reviewer or editor, you could check that WormBase is acknowledged, if appropriate.
Thanks for your help!