BIBFRAME Readiness: A Canadian Perspective

In 2018 the University of Alberta Library (UAL) joined the LD4P2 Cohort as a part of a wider strategy for linked data and BIBFRAME implementation. During the same year the Canadian BIBFRAME Readiness Task Force (CBRTF) was formed to produce documentation that outlines the impact of migrating from MARC to BIBFRAME on libraries in Canada; to assess the understanding of and readiness for BIBFRAME transition in libraries in Canada; and to make recommendations for how the Canadian Federation of Library Associations / Fédération canadienne des associations de bibliothèques (CFLA-FCAB), Fédération des milieux documentaires (FMD), and Library and Archives Canada can support Canadian libraries’ transition to BIBFRAME. In this session, UAL’s experience and successes working towards BIBFRAME implementation will be juxtaposed to the findings of the CBRTF survey that few libraries in Canada are fully prepared to transition from MARC to BIBFRAME in the near future. Through this juxtaposition we will examine the current state of BIBFRAME readiness in Canada and outline CBRTF recommendations for a shared path forward

Human and mouse essentiality screens as a resource for disease gene discovery

The identification of causal variants in sequencing studies remains a considerable challenge that can be partially addressed by new gene-specific knowledge. Here, we integrate measures of how essential a gene is to supporting life, as inferred from viability and phenotyping screens performed on knockout mice by the International Mouse Phenotyping Consortium and essentiality screens carried out on human cell lines. We propose a cross-species gene classification across the Full Spectrum of Intolerance to Loss-of-function (FUSIL) and demonstrate that genes in five mutually exclusive FUSIL categories have differing biological properties. Most notably, Mendelian disease genes, particularly those associated with developmental disorders, are highly overrepresented among genes non-essential for cell survival but required for organism development. After screening developmental disorder cases from three independent disease sequencing consortia, we identify potentially pathogenic variants in genes not previously associated with rare diseases. We therefore propose FUSIL as an efficient approach for disease gene discovery. Discovery of causal variants for monogenic disorders has been facilitated by whole exome and genome sequencing, but does not provide a diagnosis for all patients. Here, the authors propose a Full Spectrum of Intolerance to Loss-of-Function (FUSIL) categorization that integrates gene essentiality information to aid disease gene discovery

GWAS meta-analysis of intrahepatic cholestasis of pregnancy implicates multiple hepatic genes and regulatory elements

Intrahepatic cholestasis of pregnancy (ICP) is a pregnancy-specific liver disorder affecting 0.5–2% of pregnancies. The majority of cases present in the third trimester with pruritus, elevated serum bile acids and abnormal serum liver tests. ICP is associated with an increased risk of adverse outcomes, including spontaneous preterm birth and stillbirth. Whilst rare mutations affecting hepatobiliary transporters contribute to the aetiology of ICP, the role of common genetic variation in ICP has not been systematically characterised to date. Here, we perform genome-wide association studies (GWAS) and meta-analyses for ICP across three studies including 1138 cases and 153,642 controls. Eleven loci achieve genome-wide significance and have been further investigated and fine-mapped using functional genomics approaches. Our results pinpoint common sequence variation in liver-enriched genes and liver-specific cis-regulatory elements as contributing mechanisms to ICP susceptibility

Evolution of a summer research/writing workshop for first-year university students

Purpose To describe a framework for a summer research/writing workshop for new university students, and its evolution over time and across institutions. Design/Methodology/Approach The University of Toronto at Scarborough (UTSC) has successfully offered its award-winning two-day Summer Learning Institute on Research, Writing and Presentation Skills for four years (2004-2007), to increasing enrollments. Memorial University of Newfoundland (Memorial) adapted the UTSC model and successfully piloted its four-day workshop, SPARC (Summer Program in Academic Research and Communication), in August 2006. Both programs were low-cost, non-credit summer workshops for new students to help them prepare for university-level research and writing. Memorial offered its program a second time in August 2007. This paper focuses on the Memorial experience. Findings The success of these programs is attributed to a common framework used in each case: program planning, marketing, and delivery and assessment. Practical implications The framework described in this paper could be adapted by other institutions wishing to implement such a program. In addition, the SPARC team will continually improve the program by reflecting on each part of the framework. Originality/value Much research has been done to identify and address the specific needs of first-year university students. For example, some institutions offer “first year experience” courses for credit, while others place first year students into Interest Groups. Most academic libraries offer information literacy sessions to groups of undergraduate students during the regular semester. This paper presents a model for reaching first year students before they take their first class at university. Keywords: information literacy, collaboration, marketing, writing skill

From the Cloud to the Ground: Cataloguing, Linked Data and RDA Search Strategies

In the decision to move from AACR (Anglo-American Cataloging Rules) to RDA (Resource Description and Access), the international cataloguing community has recognized that the cataloguing formats and standards of the past have constrained how we as cataloguers – and thus our patrons – have come to think about how we access library materials. RDA, based on the Functional Requirements for Bibliographic Records (FRBR), is a fundamental change in how we think about the metadata connecting the increasingly wide variety of material we catalogue. After briefly reflecting on where we’ve come from, Heather Pretty will summarize the library world’s path to Linked Data thus far, and some of the ideas for our next steps. In the second portion of the session, Catelynne Sahadath will address some of the practical changes to the library catalogue. She will introduce practical examples of search strategies that public services librarians can employ to optimize results in RDA and AACR2/RDA hybrid environments

Are Canadian Libraries Ready To Transition From MARC To BIBFRAME?

This project seeks to assess the Canadian library community’s understanding of and readiness for the transition from the MARC format to the BIBFRAME model. Results indicate that knowledge of BIBFRAME is low among respondents and that most of the libraries surveyed do not know enough about BIBFRAME to consider planning a transitio

Identifying priorities for nutrient mitigation using river concentration-flow relationships: the Thames basin, UK

The introduction of tertiary treatment to many of the sewage treatment works (STW) across the Thames basin in southern England has resulted in major reductions in river phosphorus (P) concentrations. Despite this, excessive phytoplankton growth is still a problem in the River Thames and many of its tributaries. There is an urgent need to determine if future resources should focus on P removal from the remaining STW, or on reducing agricultural inputs, to improve ecological status. Nutrient concentration-flow relationships for monitoring sites along the River Thames and 15 of its major tributaries were used to estimate the relative inputs of phosphorus and nitrogen from continuous (sewage point sources) and rain-related (diffuse and within-channel) sources, using the Load Apportionment Model (LAM). The model showed that diffuse sources and remobilisation of within-channel phosphorus contributed the majority of the annual P load at all monitoring sites. However, the majority of rivers in the Thames basin are still dominated by STW P inputs during the ecologically-sensitive spring-autumn growing season. Therefore, further STW improvements would be the most effective way of improving water quality and ecological status along the length of the River Thames, and 12 of the 15 tributaries. The LAM outputs were in agreement with other indicators of sewage input, such as sewered population density, phosphorus speciation and boron concentration. The majority of N inputs were from diffuse sources, and LAM suggests that introducing mitigation measures to reduce inputs from agriculture and groundwater would be most appropriate for all but one monitoring site in this study. The utilisation of nutrient concentration-flow data and LAM provide a simple, rapid and effective screening tool for determining nutrient sources and most effective mitigation options

Extensive identification of genes involved in congenital and structural heart disorders and cardiomyopathy

Clinical presentation of congenital heart disease is heterogeneous, making identification of the disease-causing genes and their genetic pathways and mechanisms of action challenging. By using in vivo electrocardiography, transthoracic echocardiography and microcomputed tomography imaging to screen 3,894 single-gene-null mouse lines for structural and functional cardiac abnormalities, here we identify 705 lines with cardiac arrhythmia, myocardial hypertrophy and/or ventricular dilation. Among these 705 genes, 486 have not been previously associated with cardiac dysfunction in humans, and some of them represent variants of unknown relevance (VUR). Mice with mutations in Casz1, Dnajc18, Pde4dip, Rnf38 or Tmem161b genes show developmental cardiac structural abnormalities, with their human orthologs being categorized as VUR. Using UK Biobank data, we validate the importance of the DNAJC18 gene for cardiac homeostasis by showing that its loss of function is associated with altered left ventricular systolic function. Our results identify hundreds of previously unappreciated genes with potential function in congenital heart disease and suggest causal function of five VUR in congenital heart disease