A teaching and training framework to promote findable, accessible, interoperable, and reusable data generation in agriculture

Database · 2025-01-01 · 4 citations

Abstract Advances in agricultural genetic, genomic, and breeding (GGB) technologies generate increasingly large and complex datasets that need to be adequately managed and shared. While several agricultural biological databases maintain and curate GGB data, not all scientists are aware of them and how they can be used to access and share data. In addition, there is the need to increase scientists’ awareness that appropriate data archiving and curation increases data longevity and value and bolsters scientific discoveries’ reproducibility and transparency. The AgBioData Education working group aims to address these unmet needs and developed a modular curriculum for educators teaching the basics of biological databases and the findable, accessible, interoperable, and reusable (FAIR) principles to undergraduate and graduate students (https://www.agbiodata.org/). The present paper provides an overview of the topics covered within the curriculum, called ‘AgBioData Curriculum for Ag FAIR Data,’ its audience and modalities, and how it will positively impact all the different stakeholders of the agricultural database ecosystem. We hope the modular curriculum presented here can help scientists and students understand and support database use in all aspects of improving our global food system. Database URL: https://zenodo.org/records/14278084

The need for robust, FAIR phenomic databases supporting agricultural efficiency and resiliency

Science and Public Policy · 2025-07-17 · 2 citations

Abstract The US agriculture and food systems research and education system remains the envy of the world, and the US Department of Agriculture and the Land-Grant University system lead the public and private partnerships that have improved agricultural productivity and human health phenomenally for over 160 years. The continuation of these improvements relies on equitable access to trustworthy data—particularly in genetics and phenomics—and the ability to leverage such data to address future scientific challenges. In this article, we discuss the growing need in agriculture for phenomic databases that follow findable, accessible, interoperable, and reproducible data (FAIR) guidelines, as well as the need for public policy supporting a sustainable funding model for these databases.

Incorporating Clinical Examination Skills Into a Preclinical Anatomy Course: A Method for Facilitating Engagement and Interest

Clinical Anatomy · 2025-04-04

Anatomy instruction is enhanced when students are engaged and interested in course material, and the relevance of the subject matter to their academic success and professional careers is emphasized. We developed a learning activity for a pre-clinical anatomy course using the clinical skills of inspection and palpation of a cadaver donor to demonstrate the value of those skills in learning anatomy and to facilitate anatomical understanding in a format similar to that used in clinical practice. Students were instructed to inspect and palpate various anatomical structures and relationships on their donor cadavers to identify features that could help in recognizing potential abnormalities, understanding disease mechanisms, and learning the anatomical bases of certain medical interventions and surgical procedures. Using these techniques, a tumor mass involving the medial end of the clavicle was identified. Student interest was increased, which led to further study and subsequent pathological identification of the tumor as a rare osteochondroma. We found that the addition of inspection and palpation as methods for learning human anatomy in the dissection laboratory, methods not commonly used, facilitated both engagement and interest in a particular area of the subject. Students also developed a respect for their donors, viewing them as their first patients. In light of the diversity in lifestyles, medical conditions, and causes of death within donor populations, we believe the approach described here can contribute greatly to the value of human anatomy courses that use cadaver donors.

What If Universities Started Collaborating More and Competing Less? An Approach for Statewide Shared Responsibility for STEM Teacher Education

Change The Magazine of Higher Learning · 2024-05-03

Collaborative Preclinical/Clinical Efforts Aimed at Strengthening a Neurology Residency Program: Challenges, Activities and Outcomes

Medical Science Educator · 2024-10-15 · 1 citations

Recent trends in medical education have included efforts to better integrate traditionally preclinical content with subject matter included in the clinical years of the curriculum. The participation of clinical faculty in preclinical courses is well established; however, involvement of biomedical science faculty in resident education is less common. We describe here a project in which a basic science faculty member participated in a neurology residency program to address specific basic science knowledge weaknesses identified by the neurology department chair. We address issues and challenges associated with planning and implementation. Benefits to both the residents and the biomedical scientist are described.

A method for assessing student ability to apply anatomical knowledge within a traditional anatomy laboratory examination

Anatomical Sciences Education · 2024-04-24

Fidelity between teaching activities and assessment methods is an important goal of knowledge and performance evaluations in medical education. Ideally, assessment methods provide evidence of learning that reflects the types of knowledge described in the learning objectives of the course. The most reliable assessments involve the same or similar tasks as those used during the instructional components of the course. Our preclinical human anatomy course includes, in addition to traditional lecture and cadaver-based laboratory learning activities, a series of applied human anatomy learning activities intended to emphasize human anatomy as it is encountered in living human individuals. The learning activities involve psychomotor behaviors including inspection, palpation, and auscultation, techniques used in the physical examination, as well as other activities designed to emphasize anatomical structures and tissues as they may be found in patient populations. We describe here our method for measuring student success in learning human anatomy in this manner, highlighting the direct linkage between the learning activities and the assessment tasks. We describe our performance scoring method and how we include this data in the calculation of an anatomy examination grade. As an indicator of our success with this approach, we include performance scores for the applied anatomy questions included on the laboratory component of our unit examinations for two successive academic years. We conclude with summary comments from students regarding the applied anatomy learning activities and assessment approach and offer suggestions for addressing specific challenges associated with the use of these types of assessment methods.

Horseshoe kidney: Morphologic features, embryologic and genetic etiologies, and surgical implications

Clinical Anatomy · 2023 · 16 citations

• Medicine
• Pathology
• Surgery

The horseshoe kidney (HSK) is the most common congenital abnormality of the upper urinary tract with an incidence of approximately 1 in 500 in the general population. Although individuals with HSK are often asymptomatic, they are at increased risk for neoplasms, infections, ureteropelvic obstruction secondary to lithiasis or vascular compression. Direct injury from trauma is increased in these individuals as is the risk of intraoperative complications secondary to damage involving the typically complex renal or adrenal vascular supply. We briefly review etiological factors including renal and urinary system embryology, genetic mutations, abnormalities related to faulty cell signaling, aberrant cell migration, and other possible causes including environmental exposures and trauma. In addition, we call attention to factors that might influence the success of surgical procedures in patients with HSK. We argue that an understanding of possible etiologies of the HSK and its different subtypes may be useful when planning surgical procedures or considering risk-benefit ratios associated with different surgical options. We briefly present the organization of a HSK in a 100-year-old male demonstrating an unusual vascular supply discovered during a dissection laboratory session in a medical school anatomy course. We describe the structure of the HSK, the position and relationships of the HSK to other structures within the abdomen, and the associated vascular relationships.

A method for rewarding collaborative efforts in preclinical assessments

Clinical Anatomy · 2023-05-22

Student success in basic medical science courses is typically determined by their individual performance on examinations of various types. Previous research both within and outside medical education has shown that the use of educational assessment activities can increase learning as demonstrated by performance on subsequent examinations, a phenomenon known as the testing effect. Activities primarily designed and used for assessment and evaluation purposes can also be used as teaching opportunities. We developed a method for measuring and evaluating student accomplishment in a preclinical basic science course that incorporates both individual and collaborative efforts, encourages and rewards active participation, does not compromise the reliability of the assessment outcome and is perceived by the students as helpful and valuable. The approach involved a two-part assessment activity composed of an individual examination and a small group examination with each component differentially weighted in determining an overall examination score. We found that the method was successful in encouraging collaborative efforts during the group component and provided valid measures of student grasp of the subject matter. We describe the development and implementation of the method, provide data derived from its use in a preclinical basic science course and discuss factors to be addressed when utilizing this approach to ensure fairness and reliability of the outcome. We include brief summary comments from students regarding their impressions of the value of this method.

NAPPN Annual Conference Abstract: Can we make phenomic, genetic, and genomic data FAIR? The AgBioData road trip towards best practices of data sharing and management in agricultural research and education

2023-01-30

69 The Bigger Picture of Phenomics: Whole-System Support for Systems Research, Models and Databases

Journal of Animal Science · 2023-11-06

Abstract Phenomics started with Mendel’s elegantly simple empirical studies. Soon after, Fisher discovered purines were rich in nuclei of all cells. A century later, we have the technology to compare the actual base pair sequence of DNA and RNA with the outward expressions of phenotypes. We have sire evaluation based on genomic and phenomic measure. But, being human, it is quite common to get immersed in exciting technology and tend to forget why we developed the technology in the first place. We only refer to ensuring a stable efficient food supply of plants and animals in the reports that we expect decision makers to read and give us more money. It is, however, truly wonderful that we now have the techniques to study the questions of the ages. But the future of phenomics is built on the foundations of the past. In 1974, A. E. Freeman and others convened a meeting under the mechanism of the newly formed Regional Research Project 2 on Defining the Inefficiency of Animal Production. From that workshop came the first modern multistate genetic study in dairy cattle with the objective to compare the phenotypes (milk component production, energy and nitrogen metabolism, hormones) of dairy animals that were born from bulls of High (+795 kg PTAM) and Low (167 kg PTAM) bulls. Please remember this study was designed in the mid 1970s and the first data collected in the early 1980s, decades before efficient methods of DNA and RNA composition were available. Studies conducted at Washington State University demonstrated marked genetic and environmental differences in adipose tissues of dairy animals. Enzymes involved with catabolic reactions were highly associated with High PTAM bulls while enzymes associated with anabolic reactions in adipose tissue were more closely related to increased energy intake regardless of genetic background. With mRNA chips, we were able, after almost 40 years, to directly relate variation in mRNA expression in the adipose tissue with the genetic background of the animals. This was the first such discovery in the field, and has led to more defined and expansive phenomics studies. In the year 2023, the use of genomics, phenomics, databases, large scale, cooperative studies and team science are specific recommendations, strategies and goals of the USDA, NIFA, The National Academies, and Land-Grant Universities. The AgBioData consortium is one example of international teams working together to expand the use of genetic and genomic databases, to prepare undergraduate and graduate level educational materials on FAIR databases and to encourage and support sustainable, robustly funded public and private partnerships in the use of integrated studies and large databases, including phenomics, with the sole purpose of expanding a robust, resilient, safe and plentiful food supply.