Browsing by Author "Foster, Erin D."
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Item Agitation and impulsivity in mid and late life as possible risk markers for incident dementia(Wiley, 2020-09-06) Bateman, Daniel R.; Gill, Sascha; Hu, Sophie; Foster, Erin D.; Ruthirakuhan, Myuri T.; Sellek, Allis F.; Mortby, Moyra E.; Matušková, Veronika; Ng, Kok Pin; Tarawneh, Rawan M.; Freund‐Levi, Yvonne; Kumar, Sanjeev; Gauthier, Serge; Rosenberg, Paul B.; Oliveira, Fabricio Ferreira de; Devanand, D. P.; Ballard, Clive; Ismail, Zahinoor; Psychiatry, School of MedicineTo identify knowledge gaps regarding new‐onset agitation and impulsivity prior to onset of cognitive impairment or dementia the International Society to Advance Alzheimer's Research and Treatment Neuropsychiatric Syndromes (NPS) Professional Interest Area conducted a scoping review. Extending a series of reviews exploring the pre‐dementia risk syndrome Mild Behavioral Impairment (MBI), we focused on late‐onset agitation and impulsivity (the MBI impulse dyscontrol domain) and risk of incident cognitive decline and dementia. This scoping review of agitation and impulsivity pre‐dementia syndromes summarizes the current biomedical literature in terms of epidemiology, diagnosis and measurement, neurobiology, neuroimaging, biomarkers, course and prognosis, treatment, and ongoing clinical trials. Validations for pre‐dementia scales such as the MBI Checklist, and incorporation into longitudinal and intervention trials, are needed to better understand impulse dyscontrol as a risk factor for mild cognitive impairment and dementia.Item Building a community of practice: Situating data management in the transition to electronic lab notebooks(2019-05) Coates, Heather L.; Foster, Erin D.; Whipple, Elizabeth C.This poster will describe an information management initiative sponsored by the School of Medicine Research Administration. The 4-month pilot involved the rollout of an electronic lab notebook (ELN) system alongside tailored support for developing operational data management plans. Administrative drivers included improving lab efficiency and reducing institutional liability. The pilot primarily focused on the benefits of ELN use and formalizing data management practices. A key goal was to improve the collection of and access to experimental information and improve information management workflows. Integrating data management plan support as part of the ELN pilot contextualizes how the ELN fits into, and can potentially improve, existing lab workflows and highlights the unique information management needs of each research lab.Item Enhancing the Human Phenotype Ontology for Use by the Layperson(2016) Vasilevsky, Nicole A.; Engelstad, Mark; Foster, Erin D.; Mungall, Christopher J.; Robinson, Peter N.; Köhler, Sebastian; Haendel, Melissa A.In rare or undiagnosed diseases, physicians rely upon genotype and phenotype information in order to compare abnormalities to other known cases and to inform diagnoses. Patients are often the best sources of information about their symptoms and phenotypes. The Human Phenotype Ontology (HPO) contains over 12,000 terms describing abnormal human phenotypes. However, the labels and synonyms in the HPO primarily use medical terminology, which can be difficult for patients and their families to understand. In order to make the HPO more accessible to non-medical experts, we systematically added new synonyms using non-expert terminology (ie, layperson terms) to the existing HPO classes or tagged existing synonyms as layperson. As a result, the HPO contains over 6,000 classes with layperson synonyms.Item Finding common ground and identifying opportunities: Case study in data policy at an academic medical school(IUPUI University Library, 2023-11-21) Foster, Erin D.; Coates, Heather L.We present this paper to our colleagues as a case study of a well supported effort by a large medical school to actively engage researchers in data management by requiring the completion of data management plans. We will outline the people and roles involved in this initiative, the efforts to scope and adjust the mandate over the past three years, the communication and work to change research culture, the infrastructure used to create these plans, and the training and support provided throughout to the research community. We hope this work offers insight and proves useful in advocating for and/or engaging with research data management work at your respective institutions.Item The Human Phenotype Ontology in 2017(Oxford Journals, 2016-11-24) Köhler, Sebastian; Vasilevsky, Nicole A.; Engelstad, Mark; Foster, Erin D.; McMurry, Julie A.; Aymé, Ségolène; Baynam, Gareth; Bello, Susan M.; Boerkoel, Cornelius F.; Boycott, Kym M.; Brudno, Michael; Buske, Orion J.; Chinnery, Patrick F.; Cipriani, Valentina; Connell, Laureen E.; Dawkins, Hugh J.S.; DeMare, Laura E.; Devereau, Andrew D.; de Vries, Bert B.A.; Firth, Helen V.; Freson, Kathleen; Greene, Daniel; Hamosh, Ada; Helbig, Ingo; Hum, Courtney; Jähn, Johanna A.; James, Roger; Krause, Roland; Laulederkind, Stanley J. F.; Lochmüller, Hanns; Lyon, Gholson J.; Ogishima, Soichi; Olry, Annie; Ouwehand, Willem H.; Pontikos, Nikolas; Rath, Ana; Schaefer, Franz; Scott, Richard H.; Segal, Michael; Sergouniotis, Panagiotis I.; Sever, Richard; Smith, Cynthia L.; Straub, Volker; Thompson, Rachel; Turner, Catherine; Turro, Ernest; Veltman, Marijcke W.M.; Vulliamy, Tom; Yu, Jing; von Ziegenweidt, Julie; Zankl, Andreas; Züchner, Stephan; Zemojtel, Tomasz; Jacobsen, Julius O.B.; Groza, Tudor; Smedley, Damian; Mungall, Christopher J.; Haendel, Melissa A.; Robinson, Peter N.Deep phenotyping has been defined as the precise and comprehensive analysis of phenotypic abnormalities in which the individual components of the phenotype are observed and described. The three components of the Human Phenotype Ontology (HPO; www.human-phenotype-ontology.org) project are the phenotype vocabulary, disease-phenotype annotations and the algorithms that operate on these. These components are being used for computational deep phenotyping and precision medicine as well as integration of clinical data into translational research. The HPO is being increasingly adopted as a standard for phenotypic abnormalities by diverse groups such as international rare disease organizations, registries, clinical labs, biomedical resources, and clinical software tools and will thereby contribute toward nascent efforts at global data exchange for identifying disease etiologies. This update article reviews the progress of the HPO project since the debut Nucleic Acids Research database article in 2014, including specific areas of expansion such as common (complex) disease, new algorithms for phenotype driven genomic discovery and diagnostics, integration of cross-species mapping efforts with the Mammalian Phenotype Ontology, an improved quality control pipeline, and the addition of patient-friendly terminology.Item Implementing an institution-wide electronic lab notebook initiative(Pitt Open Library Publishing, 2022) Foster, Erin D.; Whipple, Elizabeth C.; Rios, Gabriel R.; Ruth Lilly Medical Library, School of MedicineBackground: To strengthen institutional research data management practices, the Indiana University School of Medicine (IUSM) licensed an electronic lab notebook (ELN) to improve the organization, security, and shareability of information and data generated by the school's researchers. The Ruth Lilly Medical Library led implementation on behalf of the IUSM's Office of Research Affairs. Case presentation: This article describes the pilot and full-scale implementation of an ELN at IUSM. The initial pilot of the ELN in late 2018 involved fifteen research labs with access expanded in 2019 to all academic medical school constituents. The Ruth Lilly Medical Library supports researchers using the electronic lab notebook by (1) delivering trainings that cover strategies for adopting an ELN and a hands-on demo of the licensed ELN, (2) providing one-on-one consults with research labs or groups as needed, and (3) developing best practice guidance and template notebooks to assist in adoption of the ELN. The library also communicates availability of the ELN to faculty, students, and staff through presentations delivered at department meetings and write-ups in the institution's newsletter as appropriate. Conclusion: As of August 2021, there are 829 users at IUSM. Ongoing challenges include determining what support to offer beyond the existing training, sustaining adoption of the ELN within research labs, and defining "successful" adoption at the institution level. By leading the development of this service, the library is more strongly integrated and visible in the research activities of the institution, particularly as related to information and data management.Item Increasing Visibility of Research in IUPUI ScholarWorks through NCBI LinkOut(Medical Library Association, 2019-05-05) Foster, Erin D.; Polley, David E.; Anne, H. Varsha; Odell, Jere D.Background : To increase the visibility and access to an academic university’s institutional repository content by participating in the National Center for Biotechnology Information (NCBI) “Institutional Repository LinkOut” program. Description : The authors used R, an open source programming language, and an R package called ‘rentrez’ to a) identify those articles in the university's repository that were in PubMed and b) determine of those, which ones did not already have full-text available via PubMed Central. Identifying articles in PubMed that are not in PubMed Central is required by NCBI in order to participate in the “Institutional Repository LinkOut” program. Using the R package, a set of 4,400 open access items from the repository were processed, 557 eligible records were identified, and were sent to NCBI. In June 2018, the R scripts were revised to further streamline the process--at the beginning of July 2018 a total of 2,129 repository items were processed and 434 eligible records were identified for inclusion in the LinkOut program. Conclusion : The university’s institutional repository experienced a significant increase in visibility due to its participation in the NCBI’s “Institutional Repository LinkOut” program. In its first implementation (July 2017), this automated solution was estimated to save over 30 hours of manual work on the part of the library staff. The LinkOut program has resulted in a 9% annual increase in web traffic to the repository and PubMed is now the third most frequent referral site to the repository. The R script and implementation process are publicly available, via GitHub, to help other institutions reduce the barriers for participating in the LinkOut program.Item Introducing First Year Medical Students to Personalized Medicine Concepts in a Small Group Activity(2020-03-06) Harrington, Maureen A.; Blevins, Amy E.; Foster, Erin D.; Pratt, Vickie; Sharpe, StephanieAn individuals’ genetic profile is becomingly an increasingly important parameter in healthcare decisions. This small group activity was developed to introduce first year medical students in the Molecules to Cells and Tissues course to the concept and significance of Pharmacogenomics and personalized medicine. Additionally, this activity provided students with an opportunity to work with a large dataset and use the information to impact clinical decision making. This activity has two cases, takes student groups approximately 2 hours to complete, and requires internet access. Case materials are available through the learning management system Canvas, and include open-ended questions to guide students through the cases. In these cases students explore the functional significance of different alleles of a panel of cytochrome P450 genes. The group activity has the students examine a large data set of cytochrome P450 genes and cognate alleles to determine their prevalence in the local population and calculate the individuals’ gene scores. The students are then asked to explain the impact of the genotype (or gene score) on the resulting patient phenotype (i.e. the functional significance of the genotype). The first case involves a breast cancer survivor support group in which patients taking Taxol discuss lack of adequate pain relief from opioids and the potential impact of concomitant use of natural compounds/supplements on drug metabolism. The second case involves a patient presenting with recurrent stroke-like symptoms despite being on the anticoagulant medication clopidogrel. The patient is initially suspected to be non-compliant, but is later determined to be a poor metabolizer of the anticoagulant clopidogrelto its active form thus decreasing its efficacy. The expertise of the IUSM Medical Genetics research faculty was leveraged to provide a large data set of cytochrome P450 genes and cognate alleles. The selection of cytochrome P450 was based upon delivering content focused on the biochemistry of the enzyme system and provided an opportunity to highlight the drug interaction database available through IUSM Clinical Pharmacology (The FlockhartTable™ ; https://drug-interactions.medicine.iu.edu/). The addition of natural compounds was to draw students’ attention to the Natural Medicines database, which is the recommended source for evidence-based data on complementary and alternative medicine. Natural Medicines is available through the Ruth Lilly Medical Library and can be searched by substance or condition. It provides both a summary of the literature available on substances as well as the level of evidence or quality of studies done on the substance.Item Kick starting use of electronic lab notebooks at IU School of Medicine(2020-08-10) Foster, Erin D.; Whipple, Elizabeth C.; Craven, Hannah J.Item Love Data Week website 2016 - 2020(2020-06) Coates, Heather L.; Atwood, Thea; Bass, Michelle; Condon, Patricia; Foster, Erin D.; Graebner, Carla; Ippoliti, Cynthia; Julian, Renaine; Karcher, Sebastian; Kouper, Inna; Neeser, Amy; Ratajeski, Melissa; Beke-Harrigan, Heidi; Hardeman, Megan; Vecchio, Julie; Wright, Stephanie; Yin, Wei; Glusker, Ann; Sahadath, Catie; Chaput, Jennifer; Hannan, Katie; Woodbrook, Rachel; Adamus, TrishaAll pages from the Love Data Week event website are archived here in PDF. Love Data Week was established in 2016 as Love Your Data week. Originally created in the USA, it quickly grew to an international event in which a wide range of institutions, organizations, scholars, students, and other data lovers could celebrate their data. Coordinated by Heather Coates, the planning committee developed themes, wrote, curated content, developed activities, all to celebrate data in all its forms, promote good research data management strategies, ask hard questions about the role of data in our lives, and share data success and horror stories. Though the website is defunct, the event lives on, driven by the community.