Micropublication: incentivizing community curation and placing unpublished data into the public domain

Large volumes of data generated by research laboratories coupled with the required effort and cost of curation present a significant barrier to inclusion of these data in authoritative community databases. Further, many publicly funded experimental observations remain invisible to curation simply because they are never published: results often do not fit within the scope of a standard publication; trainee-generated data are forgotten when the experimenter (e.g. student, post-doc) leaves the lab; results are omitted from science narratives due to publication bias where certain results are considered irrelevant for the publication. While authors are in the best position to curate their own data, they face a steep learning curve to ensure that appropriate referential tags, metadata, and ontologies are applied correctly to their observations, a task sometimes considered beyond the scope of their research and other numerous responsibilities. Getting researchers to adopt a new system of data reporting and curation requires a fundamental change in behavior among all members of the research community. To solve these challenges, we have created a novel scholarly communication platform that captures data from researchers and directly delivers them to information resources via Micropublication. This platform incentivizes authors to publish their unpublished observations along with associated metadata by providing a deliberately fast and lightweight but still peer-reviewed process that results in a citable publication. Our long-term goal is to develop a data ecosystem that improves reproducibility and accountability of publicly funded research and in turn accelerates both basic and translational discovery

Micropublication: Incentivizing community curation and placing unpublished data into the public domain

UNLABELLED: Large volumes of data generated by research laboratories coupled with the required effort and cost of curation present a significant barrier to inclusion of these data in authoritative community databases. Further, many publicly funded experimental observations remain invisible to curation simply because they are never published: results often do not fit within the scope of a standard publication; trainee-generated data are forgotten when the experimenter (e.g. student, post-doc) leaves the lab; results are omitted from science narratives due to publication bias where certain results are considered irrelevant for the publication. While authors are in the best position to curate their own data, they face a steep learning curve to ensure that appropriate referential tags, metadata, and ontologies are applied correctly to their observations, a task sometimes considered beyond the scope of their research and other numerous responsibilities. Getting researchers to adopt a new system of data reporting and curation requires a fundamental change in behavior among all members of the research community. To solve these challenges, we have created a novel scholarly communication platform that captures data from researchers and directly delivers them to information resources via Micropublication. This platform incentivizes authors to publish their unpublished observations along with associated metadata by providing a deliberately fast and lightweight but still peer-reviewed process that results in a citable publication. Our long-term goal is to develop a data ecosystem that improves reproducibility and accountability of publicly funded research and in turn accelerates both basic and translational discovery. DATABASE URL: www.micropublication.org

Worm Phenotype Ontology: Integrating phenotype data within and beyond the C. elegans community

Background: Caenorhabditis elegans gene-based phenotype information dates back to the 1970’s, beginning with Sydney Brenner and the characterization of behavioral and morphological mutant alleles via classical genetics in order to understand nervous system function. Since then C. elegans has become an important genetic model system for the study of basic biological and biomedical principles, largely through the use of phenotype analysis. Because of the growth of C. elegans as a genetically tractable model organism and the development of large-scale analyses, there has been a significant increase of phenotype data that needs to be managed and made accessible to the research community. To do so, a standardized vocabulary is necessary to integrate phenotype data from diverse sources, permit integration with other data types and render the data in a computable form. Results: We describe a hierarchically structured, controlled vocabulary of terms that can be used to standardize phenotype descriptions in C. elegans, namely the Worm Phenotype Ontology (WPO). The WPO is currently comprised of 1,880 phenotype terms, 74% of which have been used in the annotation of phenotypes associated with greater than 18,000 C. elegans genes. The scope of the WPO is not exclusively limited to C. elegans biology, rather it is devised to also incorporate phenotypes observed in related nematode species. We have enriched the value of the WPO by integrating it with other ontologies, thereby increasing the accessibility of worm phenotypes to non-nematode biologists. 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. Conclusions: We provide a phenotype ontology (WPO) that will help to facilitate data retrieval, and cross-species comparisons within the nematode community. In the larger scientific community, the WPO will permit data integration, and interoperability across the different Model Organism Databases (MODs) and other biological databases. This standardized phenotype ontology will therefore allow for more complex data queries and enhance bioinformatic analyses

Publishing Interactive Articles: Integrating Journals And Biological Databases

In collaboration with the journal GENETICS, we've developed and launched a pipeline by which interactive full-text HTML/PDF journal articles are published with named entities linked to corresponding resource pages in "WormBase":http://www.wormbase.org/ (WB). Our interactive articles allow a reader to click on over ten different data type objects (gene, protein, transgene, etc.) and be directed to the relevant webpage. This seamless connection from the article to summaries of data types promotes a deeper level of understanding for the naïve reader, and incisive evaluation for the sophisticated reader. Further, this collaboration allows us to identify and collect information before the publication of the article. The pipeline uses automated recognition scripts to identify entities that already exist in the database and a self-reporting form we created at WB that is sent to the author by GENETICS for submitting entities that do not already exist in our database. We include a manual quality control step to make sure ambiguous links are corrected, and that all new entities have been reported and linked properly. The automated entity recognition scripts allows us to potentially link any object found in a database as well as to expand this pipeline to other databases. We have already adapted this pipeline for linking _Saccharomyces cerevisiae_ GENETICS articles to the "Saccharomyces Genome Database":http://www.yeastgenome.org/ (SGD) and are currently expanding this pipeline for linking genes in _Drosophila_ articles to "FlyBase":http://flybase.org/. By integrating journals and databases, we are integrating the major modes of communication in the biological sciences, which will undoubtedly increase the pace of discovery.
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WormBase - Annotating many nematode genomes

WormBase (www.wormbase.org) has been serving the scientific community for over 11 years as the central repository for genomic and genetic information for the soil nematode Caenorhabditis elegans. The resource has evolved from its beginnings as a database housing the genomic sequence and genetic and physical maps of a single species, and now represents the breadth and diversity of nematode research, currently serving genome sequence and annotation for around 20 nematodes. In this article, we focus on WormBase’s role of genome sequence annotation, describing how we annotate and integrate data from a growing collection of nematode species and strains. We also review our approaches to sequence curation, and discuss the impact on annotation quality of large functional genomics projects such as modENCODE

Using Textpresso for Information Retrieval, Fact Extraction

Ten years ago WormBase^1^ started as a repository for sequence data for the model
organism Caenorhabditis elegans and has since striven to include the curation of all
genetic and molecular data published for this nematode. With a publication rate in the C.
elegans field of approximately 800 papers per year, WormBase (WB) has the opportunity to include information from every paper published. Currently there are ~11,000 full text research papers (mid-1970's to the present) downloaded into the WB curation database, from which over 27 data types (i.e. genetic interactions, transgene objects, gene expression patterns, mutant phenotypes etc.) are extracted by curators. Textpresso^2^ is an open source text-mining tool capable of rapid searches for keywords, as well as concepts, from the full text of research papers. Curators at WB use Textpresso on a daily basis for many aspects of literature curation, from simple keyword searches to semi- or fully automated entity and fact extraction, which feed into curation pipelines or directly into the curation database itself. In addition, Textpresso greatly aids prioritization of literature curation by retrieving papers based on their full contents rather than solely on their abstracts. Such retrievable contents can range from the very particular (such as a gene simply being mentioned in the Materials and Methods section of a paper) to the complex (such as molecular functions that involve cellular components). As WB expands to incorporate the genomes of other nematodes, we will be working with Textpresso developers to set up a library of literature for related nematodes. We expect Textpresso to be crucial for most efficiently directing our efforts in literature curation, and for most quickly providing data to users searching the literature. In this workshop we will show how we use Textpresso in our curation pipeline to help with literature queries, to prioritize our workflow, and to automate data and fact extraction.
1 "WormBase":http://www.wormbase.org
2 "Textpresso":http://www.textpresso.or

WormBase 2012: more genomes, more data, new website

Since its release in 2000, WormBase (http://www.wormbase.org) has grown from a small resource focusing on a single species and serving a dedicated research community, to one now spanning 15 species essential to the broader biomedical and agricultural research fields. To enhance the rate of curation, we have automated the identification of key data in the scientific literature and use similar methodology for data extraction. To ease access to the data, we are collaborating with journals to link entities in research publications to their report pages at WormBase. To facilitate discovery, we have added new views of the data, integrated large-scale datasets and expanded descriptions of models for human disease. Finally, we have introduced a dramatic overhaul of the WormBase website for public beta testing. Designed to balance complexity and usability, the new site is species-agnostic, highly customizable, and interactive. Casual users and developers alike will be able to leverage the public RESTful application programming interface (API) to generate custom data mining solutions and extensions to the site. We report on the growth of our database and on our work in keeping pace with the growing demand for data, efforts to anticipate the requirements of users and new collaborations with the larger science community

WormBase: a comprehensive resource for nematode research

WormBase (http://www.wormbase.org) 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. This comparative data enrich the C. elegans data with improved gene predictions and a better understanding of gene function. In turn, they bring the wealth of experimental knowledge of C. elegans to other systems of medical and agricultural importance. Here, we describe new species and data types now available at WormBase. In addition, we detail enhancements to our curatorial pipeline and website infrastructure to accommodate new genomes and an extensive user base