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.

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. (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.

Paul Davis et al. (2007) International Worm Meeting "Caenorhabditae Genome Curation - WormBase."

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

[International Worm Meeting, 2007]

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 (http://www.wormbase.org) is a freely available information resource primarily for the nematode Caenorhabditis elegans but is continually expanding to include data from other related nematodes such as C. briggsae and C. remanei. Although the genome sequence and associated gene set of C. elegans has been annotated and curated for over a decade, corrections are still regularly made with each tri-weekly release. WormBase sequence curators rely on many sources of evidence for identifying gene refinements and additions, an important one being our users. We would like to point out that we appreciate feedback from the Worm Community and suggested modifications are always given top priority. Here we illustrate some of the sources of gene modifications/additions, tools that have been developed to aid curators in their work as well as highlight some issues (positive and negative) that our users should be aware of. As other Caenorhabitae sequencing projects progress to yield reliable assemblies and gene sets (utilising the knowledge gained from the nGASP project), WormBase aims to start limited curation and maintenance of these genomes. This has already begun for C. briggsae where the new genetic map based Ultra/Super contig assembly has been adopted and the backlog of community suggested corrections are being processed.

Paul Davis et al. (2008) European Worm Meeting "WormBase - The future of nematode annotation."

Paul Davis, The WormBase Consortium

[European Worm Meeting, 2008]

WormBase, The repository for C. elegans biology is set to continue. supporting the C. elegans scientific community and wider nematode. researchers by increasing the complement of nematodes for which we provide. data. A three tier system will be adopted where C. elegans remains the. main focus (tier 1), but we will strive to offer similar tools to those. provided for elegans for all tier 2 species (C. briggsae, C. remanei, C.. brenneri, C, japonica, Pristionchus pacificus, and Heterorhabditis. bacteriophora). The final tier will contain distantly related nematode. species of medical and agricultural significance. This poster highlights. how we will identify and flag potentially incorrect gene structures or the. location of un-annotated genes in all species. A new infrastructure will be. needed to allow annotation of these genomes as it will have both in-house. and community based elements. It also describes some of the future ideas. and infrastructure initiatives we hope to develop to allow the respective. communities to drive the improvement of the gene sets.

Williams, Gareth et al. (2010) C. elegans: Development and Gene Expression, EMBL, Heidelberg, Germany "WormBase Gene Curation"

Williams, Gareth, Davis, Paul

[C. elegans: Development and Gene Expression, EMBL, Heidelberg, Germany, 2010]

WormBase is a central data repository for nematode biology. Initially created as a service to the Caenorhabditis elegans research field, WormBase has evolved into a powerful research tool in its own right. In the past 2 years, we expanded WormBase to include the complete genomic sequence, gene predictions and orthology assignments from a range of related nematodes. WormBase continues to utilise other database resources such as miRBase, RFam and modENCODE to aid in the curation of worm gene structures and sequence based data types. As part of a collaboration with modENCODE submitters we have conducted a genome wide review of the WormBase C. elegans Pseudogene set which has resulted in the conversion of some pseudogene loci back to coding loci. One of our newest challenges has come with with the advent of next generation sequencing technologies. The scale of data production has increased enormously, and this has provided challenges for data incorporation but has greatly increased our ability to detect erroneous gene models and new alternate Isoforms. This RNASeq data and other modENCODE data will shortly be available from the WormBase website.

Starr, D. et al. (2015) International Worm Meeting "UC Davis-University of Maryland Eastern Shore Graduate Admissions Pathway: Collaborating to broaden participation in molecular and cellular biology."

Starr, D., Hom, C.

[International Worm Meeting, 2015]

STEM professionals in the 21st century remain predominantly Caucasian/white, in spite of decades of work by professional societies, colleges and universities, and individual scientists to broaden participation. This multifaceted problem includes concerns among students and faculty at minority-serving institutions about the economics of career choice, family pressure to pursue a career in a biomedical field, and limited exposure to natural history. Further, institutional efforts in recruitment by research universities remain rooted in graduate fairs that target senior undergraduates from groups underrepresented in science, whereas connections made via shared research networks provide a more sure means to admission in molecular and cell biology. The UC Davis-University of Maryland Eastern Shore (UMES) Molecular and Cellular Biology Graduate Admissions Pathways (MCBGAP) program addresses this challenge via collaborations between faculty at the two institutions and a research co-mentoring program that brings UMES undergraduates to UC Davis for summer research. The program is funded by a grant from the University of California Office of the President and the UC Davis College of Biological Sciences.MCBGAP supported two cohorts of five UMES students in the summers of 2014 and 2015. The MCBGAP program consists of reciprocal student-faculty visits, close interactions between key UC Davis and UMES faculty, monthly Skype meetings that involve mentors and students, and research, professional development, and field trips in the summer. MCBGAP has catalyzed change both at UMES, where students are given the opportunity to self-identify as researchers at a tier 1 research university, and at UC Davis, where increased numbers of faculty recognize the need to be proactive in graduate recruiting and admissions, and multiple deans have committed time to mentor students and funds to support additional undergraduates from Historically Black Colleges and Universities for summer research and mentoring. The experience has also inspired us to apply for a Postbaccalaureate Research Education Program (PREP) from the NIH.

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. (2013) International Worm Meeting "another can of worms - more genomes & sequences at WormBase."

Williams, Gareth, Tuli, Mary Ann, Davis, Paul, Howe, Kevin, Paulini, Michael

[International Worm Meeting, 2013]

Since 2011, the number of nematode species represented in WormBase increased by half from 12 to 19. These species can be divided into close relatives of Caenorhabditis elegans and parasitic nematodes. In addition the in-depth curation of a limited set of core species has been extended, with the support of the wider research community, to include Brugia malayi, a nematode of clade III and one of the causative agents of lymphatic filariasis in human. Support for multiple alternative reference genomes for a single species (like Ascaris suum somatic/germline assemblies) has been added. To support the extension of WormBase to non-Caenorhabditis species and provide a standardised nomenclature across nematodes, we have also extended our gene-naming service to include B.malayi and helped to provide a first pass gene nomenclature based on a combination of publications and predictions through orthologs. Another development focus was the mapping procedure for RNAi and expression probes, which now allows for more accurate mappings in a species-agnostic way. Also the use of RNASeq by WormBase increased and mappings of RNASeq libraries deposited in the Short Read Archive are not only provided as BAM files, but are also post processed and used in the curation process providing information on TSL sites, splicing, expression asymmetry, polycistronic transcripts and tissue and life-stage specific expression levels (available through SPELL). This is supplemented by the integration sequence features from modENCODE data, like transcription factor, RNA polymerase II and histone binding sites as well as genelets and transcripts.

Konop C et al. (2010) Neuronal Development, Synaptic Function and Behavior, Madison, WI "Cellular Localization of AF19 and Related Peptides in the Cephalic Region of the Nematode Ascaris suum."

Reinitz C, Konop C, Jarecki J, Knickelbine J, Stretton A OW

[Neuronal Development, Synaptic Function and Behavior, Madison, WI, 2010]

Over fortyAscaris FMRFamide-like (AF) peptides have been sequenced in the parasiticnematode Ascaris suum by the Strettonlab. Many of these peptides have beenshown to have potent effects on the A.suum locomotory nervous system (Davis & Stretton, 1996). Locomotion isvital to the survival of the parasite in its host so an in-depth knowledge ofpeptide localization and behavioral effects is essential to develop neweffective anthelmintics. The FMRFamide-like peptide AF19 (AEGLSSPLIRFamide)has been shown to have inhibitory effects on locomotion (Davis & Stretton,2001). Injection of the peptide in the head-restricted behavioral assayabolished all locomotory waveforms and their propagations (Reinitz &Stretton, 2000). Ananti-peptide antibody specific to AF19 reproducibly stains a subset of neuronsin the cephalic region of A. suum. ALA , one of the two cells in the dorsal ganglion , shows AF19-immunoreactivity. This isdata is corroborated by single cell mass spectrometric (MS) and MS/MS data. Cloning, based on th sequence ofa novel peptide in ALA, yieldedthe transcript that encodes AF19 (afp-13)and two other amidated peptides. In situ hybridizationexperiments are planned to further corroborate the cellular localization ofAF19. Supported by NIH grant AI15429.