BioGPS Spotlight on WormBase and WormMine

If worms are your model organism of choice, you’re probably already familiar with WormBase. WormBase was founded in 2000 and is a multi-institutional consortium led by Paul Sternberg of the California Institute of Technology (CalTech), Paul Kersey of the European Bioinformatics Institute (EBI), Matt Berriman of the Wellcome Trust Sanger Institute, and Lincoln Stein of the Ontario Institute for Cancer Research (OICR). WormBase hosts a number of valuable tools for researchers, and is responsible for the development of WormMine, an Intermine-based tool that replaced WormMart. One of WormBase’s database curators, Ranjana Kishore, was kind enough to answer our questions for this series.

  1. In one tweet or less, introduce us to WormBase:
    WormBase is the central repository for data related to the genetics, genomics and biology of C. elegans and related nematodes.
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  3. How did WormBase get its start? What was WormMart? At what point in WormBase’s history was InterMine integrated for the creation of WormMine?
    In the beginning was AceDB (A C. elegans database) a database developed by Richard Durbin and Jean Thierry-Mieg in 1989, for hosting genomic data, which included a graphical user interface with specific displays and tools for querying data. In early 2000, Paul Sternberg and colleagues at Caltech who worked with C. elegans as a model system realized that there was no online repository of information for this model organism that was increasingly being used, as a result of a fast-growing community of researchers. Fly researchers had FlyBase, but there was no online database for C. elegans. The C. elegans model system was drawing more and more researchers because of the several advantages it has–rapid generation time, simple nervous system, invariant cell lineage, transparent body, etc. Data was rapidly accumulating but there was no place to collect, organize or disseminate it for the good of the community. Thus began WormBase!

    WormMart was the WormBase implementation of BioMart for querying data in batch mode. WormBase switched to WormMine in 2013 which is based on InterMine, an open source data warehouse built specifically for the integration and analysis of complex biological data.
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  5. Who is WormBase’s target audience?
    The C. elegans research community, the wider nematode research community, biomedical researchers and anyone interested in nematode model systems including college and high school teachers and students!
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  7. WormBase seems to serve a thriving community of researchers. What is your greatest success story so far?
    WormBase serves a thriving and dynamic community of nematode researchers who use the C. elegans and other nematode systems to study diverse topics such as systems biology, signaling pathways, cell death, human diseases, drug efficacy and potential new drug screening. Research in C. elegans has won two Nobel prizes, in 2002 and 2006. WormBase itself has expanded to include diverse types of data including a portal, WormBase Parasite, which is dedicated to supporting helminth research. WormBase supports at least nine ‘core’ nematode species, hosting their genomes and providing tools such as genome browsers, including parasitic species that impact human health such as Onchocerca volvulus (causative agent of river blindness) and Strongyloides ratti (the rat laboratory analog of the causative agent of threadworm infection).

    Our user community not only includes Nobel prize winning researchers but also college and high school teachers who use C. elegans in their labs to teach basic biology and who use WormBase as an example of how to use a biological database. Our help-desk routinely fields questions from teachers and students who would like to obtain some worms and use WormBase to design simple experiments!
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  9. WormBase actually encouraged users to sign a petition in support of the Model Organism Databases. What role does WormBase play in the Alliance of Genome Resources?
    WormBase is a member of the Alliance of Genome Resources (AGR) and is playing an active role in the Alliance’s plan to build an integrated data resource comprising of data from several model organisms, including yeast, worm, fly, zebrafish, mouse and rat. WormBase will help in the integration of data from these model organism databases in order to increase accessibility for the biomedical researcher to model organism data, from a single integrated resource. AGR will also serve as a portal to the individual model organism databases.
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  11. What improvements are coming in the future for WormBase? For WormMine?
    WormBase is increasing focus on curating and improving displays for data relevant to human health which includes curating human gene orthologs in the worm that serve as genetic models for disease, and associating mutant alleles in C. elegans with orthologous genomic variants in human. In addition, WormBase Parasite will focus on features for the identification of putative targets for anti-helminthic drugs.

    WormBase is currently in the process of moving to a more flexible and dynamic database architecture. In the future we plan to do more frequent data updates (currently WormBase has a two month release cycle) and eventually updates in real time, so that Users can access new data as soon as they are curated. We plan on even greater involvement of the community through contributions of data–not just large-scale data, but small scale data from authors of individual papers, and edits to existing data in WormBase. We plan to make these community curated data available on the website.

    For WormMine: In the future we plan to include several more data sets in WormMine, that are currently in WormBase.
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  13. Who is the team behind WormBase and WormMine?
    WormBase is an international consortium led by Paul Sternberg, Lincoln Stein, Paul Kersey and Matthew Berriman. It consists of three groups, each located in–the European Bioinformatics Institute (EBI) at Hinxton, UK, the Ontario Institute for Cancer Research (OICR) in Toronto, Canada, and the California Institute of Technology (Caltech) in Pasadena, USA. (See the WormBase 2016 reference below for the current list of people).

    The development of WormMine takes place at the Ontario Institute for Cancer Research under Lincoln Stein and Todd Harris. Currently, Paulo Nuin is the primary developer of WormMine.

Thanks to Ranjana, for guiding us through this extremely useful and FREE tool. Be sure to check out their plugin in the plugin library. If you use WormBase in your research, be sure to cite their recent publication:

WormBase 2016: expanding to enable helminth genomic research.
Kevin L. Howe, Bruce J. Bolt, Scott Cain, Juancarlos Chan, Wen J. Chen, Paul Davis, James Done, Thomas Down, Sibyl Gao, Christian Grove, Todd W. Harris, Ranjana Kishore, Raymond Lee, Jane Lomax, Yuling Li, Hans-Michael Muller, Cecilia Nakamura, Paulo Nuin, Michael Paulini, Daniela Raciti, Gary Schindelman, Eleanor Stanley, Mary Ann Tuli, Kimberly Van Auken, Daniel Wang, Xiaodong Wang, Gary Williams, Adam Wright, Karen Yook, Matthew Berriman, Paul Kersey, Tim Schedl, Lincoln Stein, Paul W. Sternberg (2016). Nucleic Acids Res, 44, D774-80. PMID: 26578572. PMCID: PMC4702863. DOI: 10.1093/nar/gkv1217


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