Gary Williams et al. (2006) European Worm Meeting "Curating Wormbase Gene Structures"

Tamberlyn Bieri, Darin Blasiar, John Spieth, Anthony Rogers, Gary Williams, Philip Ozersky, Paul Davis

[European Worm Meeting, 2006]

Gary Williams1, Paul Davis1, Anthony Rogers1, Philip Ozersky2, John Spieth2, Tamberlyn Bieri2, Darin Blasiar2. WormBase is an international consortium of biologists and computer scientists from Caltech (USA), Cold Spring Harbor Laboratory (USA), Wellcome Trust Sanger Institute (UK) and the Genome Sequencing Center at Washington University (USA).. WormBase is dedicated to providing the research community with accurate, current, accessible information concerning the genetics, genomics and biology of C. elegans, and some related nematodes. WormBase can be freely accessed at www.wormbase.org, and is also available for download at ftp://ftp.wormbase.org/pub/wormbase A new data release is produced every three weeks. Recently some new datasets have been added to the database to aid curation.The protein products from automated gene prediction in C. remanei have been mapped to the C. elegans genome; InterPro motifs are no longer taken from SwissProt annotations, but are directly predicted from the C. elegans proteins; contigs of ESTs from other nematode species produced by the NEMBASE and Nematode.net projects have been mapped to the genome and a new set of TEC-REDs have been mapped to the genome resulting in 3,325 new trans-spliced sites which mark the 5'' ends of genes or isoforms. Work is underway to classify and curate transposons and we intend to add Mass-Spec data from several sources to improve coding sequence validation.. Over the last year the curated coding sequences have increased from 19,854 to 20,060 and alternately spliced isoforms have increased from 2,772 to 2,883. The number of genes where every base of every exon is confirmed by EST evidence has increased from 6,427 to 6,584. In the C. elegans proteins there have been 630 modified entries, 440 deleted entries, 709 new entries and 64 reappeared entries.. WormBase is supported by a grant from the National Human Genome Research Institute at the US National Institute of Health #P41 HG02223 and the British Medical Research Council.

Tuli, Mary-Ann et al. (2013) International Worm Meeting "Genomic variation data in WormBase."

Davis, Paul, Williams, Gary, Tuli, Mary-Ann, Howe, Kevin, Paulini, Michael

[International Worm Meeting, 2013]

We continue to see growth in volume and diversity of nematode genomic variation data, in large part due to increasing research effort in whole-genome sequencing (WGS) of numerous C.elegans mutant and wild-isolate strains. WormBase have responded to the challenges presented by this growth by making changes to the way in which we curate, store and display variation data. One significant change has been to more-clearly distinguish between naturally-occurring polymorphisms and laboratory-induced mutations at the display level. These are now show in two separate tables on Gene Summary pages, with laboratory-induced alleles identified by the allele designation of the laboratory of origin, and naturally-occurring polymorphisms identified by WormBase variation accessions. We have also begun to consolidate redundant data from independent wild-isolate sequencing projects. Previously, if a specific molecular variation had been identified by multiple independent projects, and/or in multiple strains, a separate variation object would have been created for each. Now, a single reference variation is created which cross-references all studies that have characterised that variation and all strains that carry it. A new version of the WormBase website was launched in early 2012, and we continue to refine and improve the display of variation data. Coloured fields in the Strain widget on the Variation Summary Page clearly show which strains carry a variation and whether the strain is available from the CGC. The Gene Summary Page now allows customisation in the the way Variations are viewed; both variation tables can be sorted by various properties, including type of molecular change, effect on the protein, and the number of associated phenotypes. We have also increased the complement of variation tracks on the genome browser, clearly separating classical alleles from those generated by large-scale sequencing projects, and creating additional tracks for single-nucleotide variants that confer a putative change-of-function on a protein. We we continue to refine the presentation of this data, and welcome feedback from the C.elegans research community.

Paulini, Michael et al. (2019) International Worm Meeting "Supporting nematode research outside of Caenorhabditis."

Russel, Matthew, Williams, Gary, Paulini, Michael, Davis, Paul, Rodgers, Faye, Howe, Kevin

[International Worm Meeting, 2019]

WormBase (http://www.wormbase.org) is a central data repository for genetic and genomic data relating to C. elegans and other well studied nematodes. WormBase is also a founding member of the Alliance of Genome Resources (https://www.alliancegenome.org), an effort to align data representation and curation workflows between the major model organism databases (MODs). We will present an update on the curation of nematode genomes outside the Caenorhabditis genus, demonstrate how we use data-mining to add information from current and historical publications, and show examples of the use and benefit to the nematode community. The genome of Trichuris muris has been added by WormBase to act as a representative reference genome for Blaxter clade I group. WormBase have performed first-pass annotation of the genome and manual curation of selected gene structures, with the aim of helping with annotation efforts of closely related Trichuris species. We have also added an updated version of the Pristionchus pacificus genome. This represents the start of a formal collaboration between WormBase and pristionchus.org on the joint maintenance and curation of the reference annotation. Finally, the curation of the Brugia malayi genome is ongoing, and reference annotation provided by WormBase is being used by research groups to analyse the evolution of filarial nematodes and the diseases they cause.

Davis, Paul et al. (2019) International Worm Meeting "C. elegans Strains and Variations in WormBase and the Alliance of Genome Resources."

Williams, Gary, Howe, Kevin, Russell, Matthew, Davis, Paul, Schedl, Tim, Paulini, Michael

[International Worm Meeting, 2019]

WormBase (http://www.wormbase.org) is a central data repository for nematode biologists and scientists enabling experimental research in C. elegans. WormBase is also a founding member of the Alliance of Genome Resources (https://www.alliancegenome.org), an effort to align data representation and curation workflows between the major model organism databases (MODs). We will describe how WormBase acquires Strain and Variant data from a variety of sources, keeps up to date and feeds improvements back to third parties. One particular change has been to preserve all strain data in perpetuity, so as to not lose information about historical Strains. A project that we will be undertaking in the near future is to formally accession Strains to allow for inter-resource stability and reliability. This is particularly important for the representation of cross-species strain and population data in the Alliance of Genome Resources. Two of the primary sources of data are the CGC (Caenorhabditis Genetics Center) and CeNDR (Caenorhabditis elegans Natural Diversity Resource). WormBase uses a variety of techniques to distribute the data from these centers and advertise the availability of Strains from these resources. We will describe the status of C. elegans variation data, summarising the different types and the completeness of information from these data types. Common representation of variation data between the MODs is an important project for the Alliance of Genome Resources, and we will provide an update of progress and plans in that area. Finally, nomenclature is a key area within WormBase and the C. elegans community as a whole. For decades the Worm Community has been a leading the way, having formal nomenclature for genes, variations and strains for all labs actively working long term in the field. We will summarise some of the aspects of this activity and how the various processes work.

Bolt, Bruce et al. (2015) International Worm Meeting "Parasitic WormBase."

Lomax, Jane, Howe, Kevin, Paulini, Michael, Bolt, Bruce, Down, Thomas, Williams, Gary, Davis, Paul

[International Worm Meeting, 2015]

Debilitating disease in humans caused by parasitic worms (helminths) is estimated to be equivalent to the loss of at least fifty million productive years of life, whilst agricultural losses can be measured in hundreds of millions of dollars. As international efforts to sequence helminth genomes and transcriptomes gather pace, a systematic approach to the curation, integration and presentation of this data is needed to provide maximum utility for biomedical and agricultural research.WormBase (http://www.wormbase.org) has approached this problem from two directions. Firstly, we have expanded our sequence curation activities to include selected parasitic nematodes with defined research communities, namely: Brugia malayi (causative agent of lymphatic filariasis), Onchocerca volvulus (river blindness), and Strongyloides ratti (rat model for strongyloidiasis). We now administer the reference genomes for these species, and actively curate the gene models and other annotations. Secondly, we have created a sub-portal, WormBase ParaSite (http://parasite.wormbase.org), aimed at researchers engaged in parasitic worm genomics. WormBase ParaSite encompases flatworms as well as nematodes, and provides genome sequence, genome browsers, semi-automatic annotation and comparative genomics data for approximately one hundred species. Additional tools include a cross-species data-mining platform, protein and nucleotide sequence search, and a variant effect predictor to enable the analysis of different strain/isolate genomes in the context of the reference.

Ozersky, Philip et al. (2009) International Worm Meeting "Sequence Curation in WormBase."

Davis, Paul, Spieth, John, Bieri, Tamberlyn, Williams, Gary, Ozersky, Philip, Rogers, Anthony, Blasiar, Darin

[International Worm Meeting, 2009]

While C. elegans remains WormBase sequence curators'' top priority to maintain gene structures and other genomic features, WormBase (http://www.wormbase.org) has expanded its scope of curation to include C. brenneri, C. briggsae, C. japonica and C. remanei. Initial gene predictions were created for each species through nGASP (the nematode genome annotation assessment project), resulting in a set of high-quality and consistent gene predictions, which has increased the amount of comparative data available for gene curation. Manual curation on each new species has further improved the initial predictions. Over the last year we''ve made 1166 changes to C. elegans coding gene structures and added 10000 more non-coding RNA genes. Additionally, the modENCODE project and other individual labs are now producing data such as tiling array transcriptome expression levels and short-read high-throughput transcriptome data, which are being used to refine gene models. We have continued to develop tools to automatically detect genomic regions that require curation and to quickly and accurately make the required changes. WormBase encourages researchers to submit their data and provide feedback at wormbase-help@wormbase.org.

Sternberg, Paul et al. (2015) International Worm Meeting "WormBase 2015."

Berriman, Matt, Howe, Kevin, Kersey, Paul, Stein, Lincoln, Harris, Todd, Sternberg, Paul, Schedl, Tim

[International Worm Meeting, 2015]

WormBase has existed for 15 years and has evolved in many ways. The new website is fully operational and has made the process of adding new data types, displays, and tools easier. Behind the scenes we are piloting an overhaul of the underlying database infrastructure to allow us to handle the ever increasing data, have the website perform faster, and allow more frequent updates of information. This is a critical time for the project, as we face considerable pressure from two directions. The first is that our funders really want us to do more with less. We are responding to this by leading the way in making curation (the process of extracting information from papers and data sets into computable form) more efficient using a new version of Textpresso (to be released later this calendar year); by discussing with other model organism information resources ways to work together to be more efficient and inter-connected; and by seeking additional sources of funding. The second, delightful, pressure is an increase in data and results generated by the C. elegans and nematode communities. While we are handling this increase by changes in our software for curation, the database infrastructure, and the website, we do need your help. Many of you have helped us over the last few years to identify data in your papers or by sending us data directly. We now need you to help with a few types of information by submitting the data via specially designed, user-friendly forms that ensure good quality and the use of standard terminology. In particular, we have a large backlog of uncurated information associating alleles with phenotypes. We pledge to make this process as painless as possible, and to improve WormBase's description of phenotypes with your feedback, starting at this meeting at the WormBase booth, workshops and posters. With your help, continual improvement of our efficiency, and additional sources of funding, we are optimistic that we can do much more with even somewhat less effort.Consortium: Paul Davis, Michael Paulini, Gary Williams, Bruce Bolt, Thomas Down, Jane Lomax, Todd Harris, Sibyl Gao, Scott Cain, Xiaodong Wang, Karen Yook, Juancarlos Chan, Wen Chen, Chris Grove, Mary Ann Tuli, Kimberly Van Auken, D. Wang, Ranjana Kishore, Raymond Lee, John DeModena, James Done, Yuling Li, H.-M. Mueller, Cecilia Nakamura, Daniela Raciti, Gary Schindelman.

Davis, Paul et al. (2011) International Worm Meeting "WormBase Gene Sets & Sequence Curation -."

Nash, William, Davis, Paul, Bieri, Tamberlyn, Spieth, John, Ozersky, Philip, Williams, Gary, Howe, Kevin

[International Worm Meeting, 2011]

WormBase (www.wormbase.org) is an online resource of biological data that has been collated and curated from the literature and other scientific sources. The primary goal of the resource is to facilitate the use of C. elegans as a model biological system and to achieve this WormBase continues to add new types of data. Over the past decade the curation of C. elegans genes and its associated sequence data has served as a primary focus for the WormBase consortium but this is changing. During the current funding cycle, the scope of curational effort has broadened to include that of other Caenorhabditids and selected other worm species. The basis of our biological knowledge about any of these species is underpinned by the genomic sequences and associated gene sets. WormBase remains the reference point for the most up to date genome and gene set for C. elegans and we are constantly working to achieve this status for the growing number of closely related and significant roundworm species provided by the resource. In this poster we outline what is being done for C. elegans and the other worm species in WormBase. We give examples of curational activities being undertaken with an emphasis on gene curation. WormBase encourages the research community to submit data, feedback and corrections so that we can make this resource as accurate and complete as possible. WormBase curators can be contacted via the help@wormbase.org email address or by filling in the web form (http://www.wormbase.org/db/misc/feedback).

Davis, Paul et al. (2015) International Worm Meeting "WormBase - Challenges in gene curation."

Howe, Kevin, Bolt, Bruce, Williams, Gary, Davis, Paul, Down, Thomas, Paulini, Michael, Lomax, Jane

[International Worm Meeting, 2015]

WormBase is the major public online database resource for the Caenorhabditis research community. The database was developed primarily for the nematode C. elegans but expanded to host genomes and biological data from closely related nematodes and nematodes of agricultural or medical significance. WormBase has a team of curators who are responsible for gathering, incorporating and curating a large collection of scientific data types from a variety of sources. One area of curation targets sequence based data types which are used to confirm or allow curators to improve the quality of gene structures and their products. Within this area there has been significant manual curation of the genes of Caenorhabditis elegans, with "Topic" based or bursts of curation on other core species and user driven response curation of the species not currently in primary focus. This curatorial activity draws on the large amount of data that has been incorporated to give as complete representation of the gene as possible. Often a curator will have to deal with conflicting or problematic data to resolve the correct structure. This poster illustrates some of the data that has been incorporated, interesting observations made by curators as well as some of the challenges faced by curators and MODs in general.

X Lin et al. (1999) International C. elegans Meeting "Isolation of the pat-6and pat-12genes"

BD Williams, X Lin

[International C. elegans Meeting, 1999]

Caenorhabditis elegans body-wall muscle cell development is an advantageous system for the study of integrin signal transduction in vivo. Mutations in the pat-2 and pat-3 genes, which code for integrin alpha and beta subunits, respectively, severely disrupt early cytoskeletal assembly events that occur at the muscle cell membrane. The mutant embryos arrest development with the Pat phenotype ( P aralyzed, A rrested-elongation at T wo-fold), characterized by non-functional body wall muscle cells. The pat-2 and pat-3 genes were identified in a previously reported genome-wide screen for mutants with the Pat phenotype (Williams and Waterston, 1994). We have recently shown that a third gene identified in this screen, pat-4, codes for the C. elegans homologue of Integrin-Linked Kinase, a serine-threonine kinase implicated in integrin-mediated signal transduction (see abstract by Mackinnon and Williams). With the goal of identifying other proteins involved in the integrin-mediated events of muscle cell development, we are pursuing the positional cloning of the pat-6 and pat-12 genes, which were also defined in our original screen for Pat mutants. pat-6 maps genetically to the right end of chromosome IV. We are attempting to molecularly isolate pat-6 by transformation rescue and are currently injecting pools of cosmid DNA from the corresponding region of the physical map. We are taking a similar approach with pat-12. We will present our progress at the meeting. We will also present additional characterization of the muscle assembly defects in pat-6 and pat-12 mutants as revealed by immunostaining experiments with an existing panel of antibodies to many different muscle cell proteins.