Research data management education for future curators

Science has progressed by “standing on the shoulders of giants” and for centuries research and knowledge have been shared through the publication and dissemination of books, papers and scholarly communications. Moving forward, much of our understanding builds on (large scale) datasets, which have been collected or generated as part of the scientific process of discovery. How will this be made available for future generations? How will we ensure that, once collected or generated, others can stand on the shoulders of the data we produce?Educating students about the challenges and opportunities of data management is a key part of the solution and helps the researchers of the future to start to think about the problems early on in their careers. We have compiled a set of case studies to show the similarities and differences in data between disciplines, and produced a booklet for students containing the case studies and an introduction to the data lifecycle and other data management practices. This has already been used at the University of Southampton within the Faculty of Engineering and is now being adopted centrally for use in other faculties. In this paper, we will provide an overview of the case studies and the guide, and reflect on the reception the guide has had to date

Wormbase Curation Interfaces and Tools

Curating biological information from the published literature can be time- and labor-intensive especially without automated tools. WormBase1 has adopted several curation interfaces and tools, most of which were built in-house, to help curators recognize and extract data more efficiently from the literature. These tools range from simple computer interfaces for data entry to employing scripts that take advantage of complex text extraction algorithms, which automatically identify specific objects in a paper and presents them to the curator for curation. By using these in-house tools, we are also able to tailor the tool to the individual needs and preferences of the curator. For example, Gene Ontology Cellular Component and gene-gene interaction curators employ the text mining software Textpresso2 to indentify, retrieve, and extract relevant sentences from the full text of an article. The curators then use a web-based curation form to enter the data into our local database. For transgene and antibody curation, curators use the publicly available Phenote ontology annotation curation interface (developed by the Berkeley Bioinformatics Open-Source Projects (BBOP)), which we have adapted with datatype specific configurations. This tool has been used as a basis for developing our own Ontology Annotator tool, which is being used by our phenotype and gene ontology curators. For RNAi curation, we created web-based submission forms that allow the curator to efficiently capture all relevant information. In all cases, the data undergoes a final scripted data dump step to make sure all the information conforms into a readable file by our object oriented database

WormBase - Nematode Biology and Genomes

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 other closely related nematode species including _C. briggsae_, _C. remanei_, _C. brenneri_, _C. japonica_ and _Pristionchus pacificus_. WormBase has developed tools to mine the data held within the database and compare the hosted species. Over the years we have developed a variety of curation pipelines which often begin in a "first-pass" literature curation step. This involves a brief overview of the literature before directing it to specialised data curators who extract all relevant information. Curators focus on particular data types or experimental techniques such as gene structure changes (see the Sequence curation poster), variations, phenotypes or RNAi and their expertise in these fields make curation efficient. WormBase works with many other groups and consortiums to validate, process and integrate both large and small scale data resources. WormBase also provides data that will be of interest to the wider biomedical and bioinformatics communities allowing researchers to utilise the information and techniques offered by nematodes to study wider aspects including medicine and disease.
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IUPHAR-DB: An Expert-Curated, Peer-Reviewed Database of Receptors and Ion Channels

The International Union of Basic and Clinical Pharmacology database (IUPHAR-DB) integrates peer-reviewed pharmacological, chemical, genetic, functional and anatomical information on the 354 non-sensory G protein-coupled receptors (GPCRs), 71 ligand-gated ion channel subunits and 141 voltage-gated ion channel subunits encoded by the human, rat and mouse genomes. These genes represent the targets of about a third of currently approved drugs and are a major focus of drug discovery and development programs in the pharmaceutical industry. Individual gene pages provide a comprehensive description of the genes and their functions, with information on protein structure, ligands, expression patterns, signaling mechanisms, functional assays and biologically important receptor variants (e.g. single nucleotide polymorphisms and splice variants). The phenotypes resulting from altered gene expression (e.g. in genetically altered animals) and genetic mutations are described. Links are provided to bioinformatics resources such as NCBI RefSeq, OMIM, PubChem, human, rat and mouse genome databases. Recent developments include the addition of ligand-centered pages summarising information about unique ligand molecules in IUPHAR-DB. IUPHAR-DB represents a novel approach to biocuration because most data are provided through manual curation of published literature by a network of over 60 expert subcommittees coordinated by NC-IUPHAR. Data are referenced to the primary literature and linked to PubMed. The data are checked to ensure accuracy and consistency by the curators, added to the production server using custom-built submission tools and peer-reviewed by NC-IUPHAR, before being transferred to the public database. Data are reviewed and updated regularly (at least biennially). Other website features include comprehensive database search tools, online and downloadable gene lists and links to recent publications of interest to the field, such as reports on receptor-ligand pairings. The database is freely available at "http://www.iuphar-db.org":http://www.iuphar-db.org. Curators can be reached at curators [at] iuphar-db.org. We thank British Pharmacological Society, UNESCO (through the ICSU Grants Programme), Incyte, GlaxoSmithKline, Novartis, Servier and Wyeth for their support

Becoming Sustainable Together: How Data Curators Support Large-scale Digitalisation Initiatives

The paper is driven by an interest to study the work practices of data curators who clean and preserve scientific data and support large-scale digitalisation and data accumulation initiatives. We posit that a neglect of this work could lead to the potential impact of such initiatives being over- or under- estimated. In this paper, we draw on a qualitative case study that examined the work practices of data curators who share scientific data openly and over extended time periods. Drawing from the practice lens perspective, we identify three data curation practices – characterising, augmenting, and liaising – as important work practices that explains how data curators support distributed and long-term digitalisation initiatives. Implications for theory and practice are discussed

Data curators at work: Focus on projects and experiences

Editor's Summary Three postdoctoral fellows in a program sponsored by the Council on Library and Information Resources/Digital Library Foundation are exploring and contributing to the field of digital curation through very different perspectives. With a neuroscience background, Katherine Akers is encouraging scientists to preserve and share research datasets and analyzing the use of library resources. For Inna Kouper, building cyberstructure and facilitating and promoting user engagement are primary. Matthew Lavin is working to make digital tools and approaches serve the needs of humanists, focusing on digitally conveying the physical features and histories of books. With different definitions of data and a variety of research goals, the scholars apply hybrid professional approaches to digital curation, stimulating expanded information, intellectual cross fertilization and a broader view of data, research and knowledge.Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/102231/1/1720400113_ftp.pd