WormBase Newsletter No. 2, February 2003

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WormBase User's Survey

In preparation for our annual Advisory Board Meeting, we are conducting an on-line survey. Please access it from the WormBase home page. Your opinion in setting priorities and feedback on our quality of service would be of great help in planning the next yearÕs activities. The survey is anonymous, but if you include your email, you will have a chance to win a WormBase mug with Thomas BoulinÕs award-winning WormBase Logo.

Release Schedule

The release schedule is now every two weeks. There have been occasional delays because of problems in the complex process of building the database caused by changes to its structure.


As many of you know, since the summer, access to Incyte/Proteome's useful wormPD database is now by subscription only. Over the past few years, we had purposely avoided focusing on information already being provided by wormPD. We have reset our priorities to provide users with the information most desired, based upon feedback at regional meetings this past summer. We have obtained additional resources from the NHGRI for this year to provide more information as soon as possible. Providing a brief description of each gene which is seen at the top of the newly reorganized Gene page is currently a high priority task we have undertaken. Curating RNAi data from individual papers as well as large-scale screens, and adding microarray data are other top priorities.

Expression patterns: Request for data and corrections

We are up-to-date with extracting gene expression patterns from published papers. We will do our best to keep up with this information as new papers come out.

Now that WormBase has a very useful collection of expression patterns, we ask for help in three ways (in order of priority):

First, please check WormBase for your expression data. We apologize for any omissions or mistakes that we have made, but please tell us if you notice any!

Second, please submit expression pattern data. If you have old data that is in danger of being forgotten, submit it to WormBase via the homepage, click on Submit data; click on GeneExpression/Regulation or go directly to http://minerva.caltech.edu/~azurebrd/cgi-bin/expr_pattern.cgi. If you are willing to share data before publication, please submit it and it will be attributed to you.

Third, if you have a paper about to come out, feel free to send us a pre-print and we can get a head start on extracting the information; text files are useful since we can scan them for information about transgenes, etc.

A complete C. elegans Genome Sequence!

The WS90 release of WormBase made available today has a complete C. elegans genome sequence. The 100,258,171 base pairs are present in six contiguous segments corresponding to the six C. elegans nuclear chromosomes. On behalf of the C. elegans community we thank the C. elegans Genome Sequencing Consortium at the Wellcome Trust Sanger Institute and Washington University's Genome Sequencing Center for this impressive accomplishment. In spite of the high quality of the sequence, there are undoubtedly remaining errors in the genome sequence, and thus the Sequencing Consortium will remain active in responding to and resolving any potential errors that arise. The Sequencing Consortium wants to know of any potential problems in the now contiguous six C. elegans chromosomes, for example, any evidence of deleted YACs, etc. Please inform Alan Coulson (alan@sanger.ac.uk) or WormBase.

Genomic Clone Requests

After January 1, 2003, please send all requests for C. elegans genomic clones to Audrey Fraser (aef@sanger.ac.uk) with a cc to Ratna Shownkeen (rs2@sanger.ac.uk); please include a FedEx or DHL account number.

Genome browser improvements

The genome browser now puts the track labels in the main image rather than in a key at the bottom.

The Textpresso search engine

WormBase has developed a search engine for C. elegans literature that allows queries with one or more key words as well as categories such as allele, gene, nucleic acid, pathway, etc. The search engine can be reached from the home page or directly at www.textpresso.org. Individual sentences in almost 2000 full text papers are included; more will be added in the coming months.

Persons and Authors

As part of an effort to better organize and correct mistakes in the connections between people and their papers, WormBase distinguishes Persons from Authors: Persons are unique individuals with contact information. We will be asking your help in making accurate connections between you and your publications. An extremely useful practice would be to use full names whenever possible in papers and abstracts. To check or update your contact information, please go to: http://minerva.caltech.edu/~azurebrd/cgi-bin/forms/author.cgi.


Not surprisingly there is a remarkable increase in RNAi experiments in papers. We appreciate that these often have more thorough phenotypic analysis than the large scale screens. For technical reasons, the large-scale data gets into WormBase faster even if published later. We are working to catch up with the considerable backlog of the individual RNAi experiments from papers. If any omission bothers you, please let us know and we will get it in as fast as possible.

RNAi search improvements

The RNAi search now allows you to combine phenotypes with either AND or OR criteria.

Coming Soon

  • More microarray data
  • A pipeline of data entry for Kim lab/Stanford microarrays has been established, and we will add data from published papers over the next few months.

People Of WormBase

New Curators/Progammers at the Sanger Institute: Anthony Rogers and Chao-Kung Chen have joined the WormBase group. Chao-Kung is half-time with the CGC, and is the key liason between WormBase and the CGC.

New Curators at Caltech: Andrei Petcherski (Ph.D. at the University of Wisconsin, Madison with Judith Kimble), Carol Bastiani (postdoc with Melvin Simon and Paul Sternberg at Caltech) and Igor Anteshechkin (former postdoc with Min Han at the University of Colorado, Boulder) have joined WormBase as biological curators. Ranjana Kishore (former postdoc with Meera Sundaram at the University of Pennsylvania) has joined WormBase as a Gene Ontology (www.geneontology.org) curator.

WormBase Advisory Board

Our advisory board helps set priorities and goals (and generally acts like a thesis committee). They ensure that the user community is best served, and that WormBase cooperates with other Model Organism Databases.

  • Thomas Blumenthal, C. elegans molecular biologist
  • Martin Chalfie, C. elegans developmental and neuro geneticist
  • Jonathan Hodgkin, C. elegans geneticist; curator of the CGC genetic map
  • Leon Avery, C. elegans neurobiologist; CGC website
  • William Gelbart, PI FlyBase
  • Janan Eppig, PI Mouse Genome Database (MGD)
  • Michael Cherry, PI Saccharomyces Genome Database (SGD)
  • Stanley Letovsky, bioinformatician.

Funding Sources

WormBase is in its third year of funding from the National Human Genome Research Institute (# P41 HG02223), and receives additional support from the British Medical Research Council. Applications to these agencies are pending.