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Landscape Analysis for the Specimen Data Refinery

This report reviews the current state-of-the-art applied approaches on automated tools, services and workflows for extracting information from images of natural history specimens and their labels. We consider the potential for repurposing existing tools, including workflow management systems; and areas where more development is required. This paper was written as part of the SYNTHESYS+ project for software development teams and informatics teams working on new software-based approaches to improve mass digitisation of natural history specimens

Mouse Phenome Database: towards a more FAIR-compliant and TRUST-worthy data repository and tool suite for phenotypes and genotypes.

The Mouse Phenome Database (MPD; https://phenome.jax.org; RRID:SCR_003212), supported by the US National Institutes of Health, is a Biomedical Data Repository listed in the Trans-NIH Biomedical Informatics Coordinating Committee registry. As an increasingly FAIR-compliant and TRUST-worthy data repository, MPD accepts phenotype and genotype data from mouse experiments and curates, organizes, integrates, archives, and distributes those data using community standards. Data are accompanied by rich metadata, including widely used ontologies and detailed protocols. Data are from all over the world and represent genetic, behavioral, morphological, and physiological disease-related characteristics in mice at baseline or those exposed to drugs or other treatments. MPD houses data from over 6000 strains and populations, representing many reproducible strain types and heterogenous populations such as the Diversity Outbred where each mouse is unique but can be genotyped throughout the genome. A suite of analysis tools is available to aggregate, visualize, and analyze these data within and across studies and populations in an increasingly traceable and reproducible manner. We have refined existing resources and developed new tools to continue to provide users with access to consistent, high-quality data that has translational relevance in a modernized infrastructure that enables interaction with a suite of bioinformatics analytic and data services

Mouse phenome database: curated data repository with interactive multi-population and multi-trait analyses.

The Mouse Phenome Database continues to serve as a curated repository and analysis suite for measured attributes of members of diverse mouse populations. The repository includes annotation to community standard ontologies and guidelines, a database of allelic states for 657 mouse strains, a collection of protocols, and analysis tools for flexible, interactive, user directed analyses that increasingly integrates data across traits and populations. The database has grown from its initial focus on a standard set of inbred strains to include heterogeneous mouse populations such as the Diversity Outbred and mapping crosses and well as Collaborative Cross, Hybrid Mouse Diversity Panel, and recombinant inbred strains. Most recently the system has expanded to include data from the International Mouse Phenotyping Consortium. Collectively these data are accessible by API and provided with an interactive tool suite that enables users\u27 persistent selection, storage, and operation on collections of measures. The tool suite allows basic analyses, advanced functions with dynamic visualization including multi-population meta-analysis, multivariate outlier detection, trait pattern matching, correlation analyses and other functions. The data resources and analysis suite provide users a flexible environment in which to explore the basis of phenotypic variation in health and disease across the lifespan

The Ontology of Biological Attributes (OBA)-computational traits for the life sciences.

Existing phenotype ontologies were originally developed to represent phenotypes that manifest as a character state in relation to a wild-type or other reference. However, these do not include the phenotypic trait or attribute categories required for the annotation of genome-wide association studies (GWAS), Quantitative Trait Loci (QTL) mappings or any population-focussed measurable trait data. The integration of trait and biological attribute information with an ever increasing body of chemical, environmental and biological data greatly facilitates computational analyses and it is also highly relevant to biomedical and clinical applications. The Ontology of Biological Attributes (OBA) is a formalised, species-independent collection of interoperable phenotypic trait categories that is intended to fulfil a data integration role. OBA is a standardised representational framework for observable attributes that are characteristics of biological entities, organisms, or parts of organisms. OBA has a modular design which provides several benefits for users and data integrators, including an automated and meaningful classification of trait terms computed on the basis of logical inferences drawn from domain-specific ontologies for cells, anatomical and other relevant entities. The logical axioms in OBA also provide a previously missing bridge that can computationally link Mendelian phenotypes with GWAS and quantitative traits. The term components in OBA provide semantic links and enable knowledge and data integration across specialised research community boundaries, thereby breaking silos

Reconstructing Metaphorical Meaning

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Crop Updates 2003 - Geraldton

This session covers twenty eight papers from different authors Seasonal Outlook: What is in store for 2003, David Stephens, Department of Agriculture Examining The Management Options For Wheat Crops In The Coming Season, James Fisher, Department of Agriculture GMO’s – what do they offer? Ian Edwards, Grain Bio Tech Australia Pty Ltd The Big Gamble – Wheat prices for 2003, Dennis Wise, Profarmer Market outlook for other grains, Andrew Young, General Manager Agricorp Stripe rust – where to now for the WA wheat industry? Robert Loughman, Ciara Beard and Greg Shea, Department of Agriculture Baudin and Hamlin – new generation of malting barley developed in Western Australia, Blakely Paynter, Roslyn Jettner and Kevin Young, Department of Agriculture DBM in Canola, Kevin Walden, Department of Agriculture The latest on Lupin diseases, Geoff Thomas, Department of Agriculture Wheat variety performance in 2002 compared to the long term, Robin Wilson, Iain Barclay, Robyn McLean, Robert Loughman, Jenny Garlinge, Bill Lambe, Neil Venn and Peter Clarke, Department of Agriculture Do wide rows drought proof lupins on red loam? Martin Harries, Bob French, Wayne Parker and Murray Blyth, Department of Agriculture Do wide rows drought proof lupins on a sandy loam? Martin Harries, Bob French, Wayne Parker and Murray Blyth, Department of Agriculture Profit Proving Precision Agriculture, Peter Norris, Agronomy For Profit, Greg Lyle, CSIRO Land and Water, Yuna Farm Improvement Group Annual ryegrass seedbanks: the good, the bad, and the ugly, Kathryn Steadman, University of Western Australia, Amander Ellery, CSIRO Plant Industry, Sally C Peltzer, Department of Agriculture Wheat management packages for low rainfall areas, Kari-Lee Falconer, Department of Agriculture Ground water 1. Atrazine, Russell Speed, Department of Agriculture Groundwater 2. Current Trends, Russell Speed, Department of Agriculture Herbicide tolerance of wheat, lupins and pastures, Terry Piper and Harmohinder Dhammu, Department of Agriculture Farming with Tramlines, Bindi Webb, Paul Blackwell, Department of Agriculture, Phil Logue, Binnu, Nigel Moffat, Geraldton, Rohan Ford, Binnu, Miles Obst, Mingenew, The role of green manure crops in renovating poor performing paddocks: What’s it worth? Frances Hoyle, Leanne Schulz and Judith Devenish Department of Agriculture The looming threat of wild radish, Peter Newman, Department of Agriculture Does one ‘size’ fit all? Grant Morrow, Syngenta Crop Protection Climate Forecasts on the Internet, Ian Foster and David Stephens, Department of Agriculture Moisture delving = more reliable lupin establishment, Paul Blackwell, and Wayne Parker, Department of Agriculture Tramline Designs for better Weed control and Wheat value from non-spraying tramlines in a dry season, Paul Blackwell, Bindi Webb and Darshan Sharma, Department of Agriculture Biserrula Grazing Trial, Marnie Thomas, Department of Agriculture Performance of IT and TT canola varieties in the medium and high rainfall agzones of W.A., 2001-02, Graham Walton, Hasan Zaheer and Paul Carmody, Department of Agriculture Rapid Catchment Appraisal in Northern Agricultural Region, Mike Clarke, Paul Raper, Department of Agricultur

Crop Updates 2002 - Geraldton

This session covers twenty seven papers from different authors: 1. Taking the Why out of Wyalkatchem – the new widely adapted wheat variety, Steve Penny Jr, Department of Agriculture 2. Future wheat varieties, Robin Wilson, Iain Barclay,Robyn McLean, Robert Loughman, Jenny Garlinge, Bill Lambe, Neil Venn and Peter Clarke Department of Agriculture 3. Maximising wheat variety performance through agronomic management, Wal Anderson, Raffaele Del Cima, James Bee, Darshan Sharma, Sheena Lyon, Melaine Kupsch, Mohammad Amjad, Pam Burgess, Veronika Reck, Brenda Shackley, Ray Tugwell, Bindi Webb and Steve Penny Jr Department of Agriculture 4. Cereal rust update 2002 – a new stem rust on Camm wheat, Robert Loughman1and Robert Park2 1Department of Agriculture, 2University of Sydney 5. Influence of nutrition and environmental factors on seed vigour in wheat, Darshan Sharma, Wal Anderson and Daya Patabendige, Department of Agriculture 6. Cereal aphids and direct feeding damage to cereals, Phil Michael, Department of Agriculture 7. A decision support system for control of aphids and BYDV in cereal crops, Debbie Thackray, Jenny Hawkes and Roger Jones, Department of Agriculture and Centre for Legumes in Mediterranean Agriculture 8. Summary of 2001 weather and seasonal prospects for 2002, David Stephens, Department of Agriculture 9. Towards a management package for grain protein in lupins, Bob French, Senior Research Officer, Department of Agriculture 10. Lupin genotypes respond differently to potash, Bob French and Laurie Wahlsten, Senior Research Officer and Technical Officer, Department of Agriculture 11. Time of harvest for improved seed yield of pulses, G. Riethmuller and B. French, Department of Agriculture 12. Comparing the phosphorus requirement of field pea and wheat, M. Bolland and P. White, Department of Agriculture Western Australia 13. Field pea variety evaluation, T. Khan, Department of Agriculture Western Australia 14. Diamondback moth (DBM) in canola, Kevin Walden, Department of Agriculture 15. WA blackleg resistance ratings on canola varieties for 2002, Ravjit Khangura, Martin J. Barbetti and Graham Walton, Department of Agriculture 16. The effect of single or multiple spray treatments on the control of Diamondback moth (Plutella xylostella) and yield of canola at Wongan Hills, Françoise Berlandier, Paul Carmody and Christiaan Valentine, Department of Agriculture 17. Perennial pastures in annual cropping systems: Lucerne and beyond, Roy Latta and Keith Devenish, Department of Agriculture 18. Nutrition in 2002: Decisions to be made as a result of last season, Bill Bowden,Department of Agriculture 19. Profitability of deep banding lime, Michael O\u27Connell, Chris Gazey and David Gartner, Department of Agriculture 20. Economic comparisons of farming systems for the medium rainfall northern sandplain, Caroline Peek and David Rogers, Department of Agriculture 21. The use of Twist Fungus as a biosecurity measure against Annual Ryegrass Toxicity (ARGT), Greg Shea, GrainGuard Coordinator and George Yan, Biological and Resource Technology 22. Major outcomes from IWM demonstration sites, Alexandra Douglas, Department of Agriculture 23. Understanding the weed seed bank life of important agricultural weeds, Sally Peltzer and Paul Matson, Department of Agriculture 24. Seeding rate, row spacing and herbicides for weed control, David Minkey, Department of Agriculture 25. Improving weed control in grazed pastures using legumes with low palatability, Clinton Revell and Giles Glasson, Department of Agriculture, Dean Thomas, Faculty of Agriculture, University of Western Australia 26. Group F resistant wild radish: What’s new? Aik Cheam1, Siew Lee1and Mike Clarke2, 1Department of Agriculture WA, 2Aventis Crop Science 27. Knockdown herbicides do not reliably kill small grass weeds, Peter Newman and Glenn Adam, Department of Agricultur

Seven features of safety in maternity units: a framework based on multisite ethnography and stakeholder consultation

Background: Reducing avoidable harm in maternity services is a priority globally. As well as learning from mistakes, it is important to produce rigorous descriptions of ‘what good looks like’. Objective: We aimed to characterise features of safety in maternity units and to generate a plain language framework that could be used to guide learning and improvement. Methods: We conducted a multisite ethnography involving 401 hours of non-participant observations 33 semistructured interviews with staff across six maternity units, and a stakeholder consultation involving 65 semistructured telephone interviews and one focus group. Results: We identified seven features of safety in maternity units and summarised them into a framework, named For Us (For Unit Safety). The features include: (1) commitment to safety and improvement at all levels, with everyone involved; (2) technical competence, supported by formal training and informal learning; (3) teamwork, cooperation and positive working relationships; (4) constant reinforcing of safe, ethical and respectful behaviours; (5) multiple problem-sensing systems, used as basis of action; (6) systems and processes designed for safety, and regularly reviewed and optimised; (7) effective coordination and ability to mobilise quickly. These features appear to have a synergistic character, such that each feature is necessary but not sufficient on its own: the features operate in concert through multiple forms of feedback and amplification. Conclusions: This large qualitative study has enabled the generation of a new plain language framework—For Us—that identifies the behaviours and practices that appear to be features of safe care in hospital-based maternity units