Enhancing the Human Phenotype Ontology for Use by the Layperson
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The document describes efforts to enhance the Human Phenotype Ontology (HPO) by adding layperson synonyms to make it more useful and accessible for patients. The workflow involved systematically reviewing over 12,000 HPO classes, searching external sources to identify potential layperson synonyms, assigning the synonyms and validating their use, and integrating the new synonyms into the HPO ontology. As a result, 44% of existing HPO synonyms are now classified as layperson terms, increasing the usability and interoperability of HPO for patients, clinicians and researchers.
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a University of Nevada, Reno, NV, United States of America
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c Binghamton University, Binghamton, NY, United States of America
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• There has been a historical breach between evolutionary science and clinical psychology.
• The expansion of evolutionary science beyond genetic evolution makes it more relevant to applied psychology than in the past.
• A multi-dimensional and multi-level extended evolutionary synthesis can bring consilience to clinical psychology as a field.
• Learning, behavior, symbolic thought, consciousness and culture are central to an extended evolutionary synthesis.
A R T I C L E I N F O
Keywords:
Evolution
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Selection
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Extended evolutionary synthesis
Conscious evolution
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connection to evolutionary science is historically limited. A few min-
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This document summarizes Nicole Vasilevsky's presentation on teaching data science to undergraduate students. It discusses the need for data science training, the open educational resources (OERs) developed by OHSU Library to address this need, and workshops offered including "Data and Donuts". The OERs cover the entire research process, from finding data to analysis to sharing results. Workshops are hands-on and interactive. Future plans include continuing "Data and Donuts" and potentially a larger OHSU Library Data Science Institute. The overall goal is to provide accessible data science training to address the growing demand.
Improving Knowledge Discovery Through Development of Big Data to Knowledge S...
Poster presentation at the Oregon Health & Science University (OHSU) BICC 25 year anniversary celebration.
Empowering patients by increasing accessibility to clinical terminology
Flash talk at Medical Library Association Pacific Northwest Chapter meeting in Portland, OR on October 18, 2016.
http://pnc-mla.cloverpad.org/annual2016
Authors: Erin Foster, Mark Engelstad, Chris Mungall, Peter Robinson, Sebastian Kohler, Melissa Haendel and Nicole Vasilevsky
Data science education resources for everyone
The document summarizes data science education resources developed by researchers at Oregon Health & Science University. It describes the challenges of managing vast amounts of biomedical data and the goal of providing training to address this issue. The team developed skills courses and open educational resources (OERs) on topics across the data science life cycle. Courses included introductory, advanced, and targeted workshops. OER modules covered a range of data science topics and mapped to competencies for health sciences librarians. The team seeks to disseminate the resources broadly while addressing challenges around customization for different users and protection of intellectual property.
Enhancing the Human Phenotype Ontology for Use by the Layperson
Presentation at the International Conference on Biological Ontology & BioCreative, August 1-4, 2016, Corvallis, Oregon, USA.
Abstract
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 (i.e., 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.
Couture Curricula - BD2K Data Science Tailored to Your Needs
Poster presentation at Force2016 (https://www.force11.org/meetings/force2016) describing Big Data to Science (BD2K) efforts at Oregon Health & Science University.
Acrl march2015 final
This document summarizes roles for libraries in providing research data management services. It describes data services at the University of Oregon Library including consultations, education workshops, and developing data management web pages. It discusses support for documentation provided by the University of Idaho Library through instruction sessions, research consultations, and emphasizing good documentation practices. It outlines data management trainings provided by Oregon Health & Science University Library including workshops with researchers, individual consultations, and developing new data services.
The Role of Libraries in Data Management and Curation
The Role of Libraries in Data Management and Curation, presented at the American Library Association conference in Las Vegas, NV, 07/29/14.
Abstract:
As increasing amounts of data are being generated, applying best practices in handling data is important, and librarians are well poised to assist users. During this session, we will discuss the role of libraries in assisting with data management, application of metadata, ontologies, data standards, and the publication of data in repositories and on the Semantic Web. This talk will describe best data practices and engage the attendees in interactive activities to demonstrate these principles.
Resource Identification Initiative_RDA_March2014
Poster presentation about the Resource Identification Initiative (http://www.force11.org/Resource_identification_initiative) at the Research Data Alliance meeting in Dublin, Ireland in March 2014 (https://rd-alliance.org/rda-third-plenary-meeting.html).
On the Reproducibility of Science: Unique Identification of Research Resourc...
Poster presentation at the Data Information Literacy Symposium at Purdue University in Indiana, Sept. 2013. This study is published here: https://peerj.com/articles/148/
Research resources: curating the new eagle-i discovery system
Poster presentation at the International Society for Biocuration Conference in Washington, DC in 2012.
More from Nicole Vasilevsky (13)
Improving Knowledge Discovery Through Development of Big Data to Knowledge S...
Improving Knowledge Discovery Through Development of Big Data to Knowledge S...
Empowering patients by increasing accessibility to clinical terminology
Empowering patients by increasing accessibility to clinical terminology
Enhancing the Human Phenotype Ontology for Use by the Layperson
Enhancing the Human Phenotype Ontology for Use by the Layperson
Couture Curricula - BD2K Data Science Tailored to Your Needs
Couture Curricula - BD2K Data Science Tailored to Your Needs
The Role of Libraries in Data Management and Curation
The Role of Libraries in Data Management and Curation
On the Reproducibility of Science: Unique Identification of Research Resourc...
On the Reproducibility of Science: Unique Identification of Research Resourc...
Research resources: curating the new eagle-i discovery system
Research resources: curating the new eagle-i discovery system
Recently uploaded
Randomised Optimisation Algorithms in DAPHNE
Slides from talk:
Aleš Zamuda: Randomised Optimisation Algorithms in DAPHNE .
Austrian-Slovenian HPC Meeting 2024 – ASHPC24, Seeblickhotel Grundlsee in Austria, 10–13 June 2024
https://ashpc.eu/
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...University of Maribor
Slides from talk:
Aleš Zamuda: Remote Sensing and Computational, Evolutionary, Supercomputing, and Intelligent Systems.
11th International Conference on Electrical, Electronics and Computer Engineering (IcETRAN), Niš, 3-6 June 2024
Inter-Society Networking Panel GRSS/MTT-S/CIS Panel Session: Promoting Connection and Cooperation
https://www.etran.rs/2024/en/home-english/Immersive Learning That Works: Research Grounding and Paths Forward
We will metaverse into the essence of immersive learning, into its three dimensions and conceptual models. This approach encompasses elements from teaching methodologies to social involvement, through organizational concerns and technologies. Challenging the perception of learning as knowledge transfer, we introduce a 'Uses, Practices & Strategies' model operationalized by the 'Immersive Learning Brain' and ‘Immersion Cube’ frameworks. This approach offers a comprehensive guide through the intricacies of immersive educational experiences and spotlighting research frontiers, along the immersion dimensions of system, narrative, and agency. Our discourse extends to stakeholders beyond the academic sphere, addressing the interests of technologists, instructional designers, and policymakers. We span various contexts, from formal education to organizational transformation to the new horizon of an AI-pervasive society. This keynote aims to unite the iLRN community in a collaborative journey towards a future where immersive learning research and practice coalesce, paving the way for innovative educational research and practice landscapes.
ESR spectroscopy in liquid food and beverages.pptx
With increasing population, people need to rely on packaged food stuffs. Packaging of food materials requires the preservation of food. There are various methods for the treatment of food to preserve them and irradiation treatment of food is one of them. It is the most common and the most harmless method for the food preservation as it does not alter the necessary micronutrients of food materials. Although irradiated food doesn’t cause any harm to the human health but still the quality assessment of food is required to provide consumers with necessary information about the food. ESR spectroscopy is the most sophisticated way to investigate the quality of the food and the free radicals induced during the processing of the food. ESR spin trapping technique is useful for the detection of highly unstable radicals in the food. The antioxidant capability of liquid food and beverages in mainly performed by spin trapping technique.
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...
Travis Hills of Minnesota developed a method to convert waste into high-value dry fertilizer, significantly enriching soil quality. By providing farmers with a valuable resource derived from waste, Travis Hills helps enhance farm profitability while promoting environmental stewardship. Travis Hills' sustainable practices lead to cost savings and increased revenue for farmers by improving resource efficiency and reducing waste.
The binding of cosmological structures by massless topological defects
Assuming spherical symmetry and weak field, it is shown that if one solves the Poisson equation or the Einstein field
equations sourced by a topological defect, i.e. a singularity of a very specific form, the result is a localized gravitational
field capable of driving flat rotation (i.e. Keplerian circular orbits at a constant speed for all radii) of test masses on a thin
spherical shell without any underlying mass. Moreover, a large-scale structure which exploits this solution by assembling
concentrically a number of such topological defects can establish a flat stellar or galactic rotation curve, and can also deflect
light in the same manner as an equipotential (isothermal) sphere. Thus, the need for dark matter or modified gravity theory is
mitigated, at least in part.
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...
Context. With a mass exceeding several 104 M⊙ and a rich and dense population of massive stars, supermassive young star clusters
represent the most massive star-forming environment that is dominated by the feedback from massive stars and gravitational interactions
among stars.
Aims. In this paper we present the Extended Westerlund 1 and 2 Open Clusters Survey (EWOCS) project, which aims to investigate
the influence of the starburst environment on the formation of stars and planets, and on the evolution of both low and high mass stars.
The primary targets of this project are Westerlund 1 and 2, the closest supermassive star clusters to the Sun.
Methods. The project is based primarily on recent observations conducted with the Chandra and JWST observatories. Specifically,
the Chandra survey of Westerlund 1 consists of 36 new ACIS-I observations, nearly co-pointed, for a total exposure time of 1 Msec.
Additionally, we included 8 archival Chandra/ACIS-S observations. This paper presents the resulting catalog of X-ray sources within
and around Westerlund 1. Sources were detected by combining various existing methods, and photon extraction and source validation
were carried out using the ACIS-Extract software.
Results. The EWOCS X-ray catalog comprises 5963 validated sources out of the 9420 initially provided to ACIS-Extract, reaching a
photon flux threshold of approximately 2 × 10−8 photons cm−2
s
−1
. The X-ray sources exhibit a highly concentrated spatial distribution,
with 1075 sources located within the central 1 arcmin. We have successfully detected X-ray emissions from 126 out of the 166 known
massive stars of the cluster, and we have collected over 71 000 photons from the magnetar CXO J164710.20-455217.
SAR of Medicinal Chemistry 1st by dk.pdf
In this presentation include the prototype drug SAR on thus or with their examples .
Syllabus of Second Year B. Pharmacy
2019 PATTERN.
Authoring a personal GPT for your research and practice: How we created the Q...
Thematic analysis in qualitative research is a time-consuming and systematic task, typically done using teams. Team members must ground their activities on common understandings of the major concepts underlying the thematic analysis, and define criteria for its development. However, conceptual misunderstandings, equivocations, and lack of adherence to criteria are challenges to the quality and speed of this process. Given the distributed and uncertain nature of this process, we wondered if the tasks in thematic analysis could be supported by readily available artificial intelligence chatbots. Our early efforts point to potential benefits: not just saving time in the coding process but better adherence to criteria and grounding, by increasing triangulation between humans and artificial intelligence. This tutorial will provide a description and demonstration of the process we followed, as two academic researchers, to develop a custom ChatGPT to assist with qualitative coding in the thematic data analysis process of immersive learning accounts in a survey of the academic literature: QUAL-E Immersive Learning Thematic Analysis Helper. In the hands-on time, participants will try out QUAL-E and develop their ideas for their own qualitative coding ChatGPT. Participants that have the paid ChatGPT Plus subscription can create a draft of their assistants. The organizers will provide course materials and slide deck that participants will be able to utilize to continue development of their custom GPT. The paid subscription to ChatGPT Plus is not required to participate in this workshop, just for trying out personal GPTs during it.
Sharlene Leurig - Enabling Onsite Water Use with Net Zero Water
Sharlene Leurig - Enabling Onsite Water Use with Net Zero WaterTexas Alliance of Groundwater Districts
Presented at June 6-7 Texas Alliance of Groundwater Districts Business MeetingDeep Software Variability and Frictionless Reproducibility
Deep Software Variability and Frictionless ReproducibilityUniversity of Rennes, INSA Rennes, Inria/IRISA, CNRS
The ability to recreate computational results with minimal effort and actionable metrics provides a solid foundation for scientific research and software development. When people can replicate an analysis at the touch of a button using open-source software, open data, and methods to assess and compare proposals, it significantly eases verification of results, engagement with a diverse range of contributors, and progress. However, we have yet to fully achieve this; there are still many sociotechnical frictions.
Inspired by David Donoho's vision, this talk aims to revisit the three crucial pillars of frictionless reproducibility (data sharing, code sharing, and competitive challenges) with the perspective of deep software variability.
Our observation is that multiple layers — hardware, operating systems, third-party libraries, software versions, input data, compile-time options, and parameters — are subject to variability that exacerbates frictions but is also essential for achieving robust, generalizable results and fostering innovation. I will first review the literature, providing evidence of how the complex variability interactions across these layers affect qualitative and quantitative software properties, thereby complicating the reproduction and replication of scientific studies in various fields.
I will then present some software engineering and AI techniques that can support the strategic exploration of variability spaces. These include the use of abstractions and models (e.g., feature models), sampling strategies (e.g., uniform, random), cost-effective measurements (e.g., incremental build of software configurations), and dimensionality reduction methods (e.g., transfer learning, feature selection, software debloating).
I will finally argue that deep variability is both the problem and solution of frictionless reproducibility, calling the software science community to develop new methods and tools to manage variability and foster reproducibility in software systems.
Exposé invité Journées Nationales du GDR GPL 2024
3D Hybrid PIC simulation of the plasma expansion (ISSS-14)
3D Particle-In-Cell (PIC) algorithm,
Plasma expansion in the dipole magnetic field.
如何办理(uvic毕业证书)维多利亚大学毕业证本科学位证书原版一模一样
原版纸张【微信：741003700 】【(uvic毕业证书)维多利亚大学毕业证】【微信：741003700 】学位证，留信认证（真实可查，永久存档）offer、雅思、外壳等材料/诚信可靠,可直接看成品样本，帮您解决无法毕业带来的各种难题！外壳，原版制作，诚信可靠，可直接看成品样本。行业标杆！精益求精，诚心合作，真诚制作！多年品质 ,按需精细制作，24小时接单,全套进口原装设备。十五年致力于帮助留学生解决难题，包您满意。
本公司拥有海外各大学样板无数，能完美还原海外各大学 Bachelor Diploma degree, Master Degree Diploma
1:1完美还原海外各大学毕业材料上的工艺：水印，阴影底纹，钢印LOGO烫金烫银，LOGO烫金烫银复合重叠。文字图案浮雕、激光镭射、紫外荧光、温感、复印防伪等防伪工艺。材料咨询办理、认证咨询办理请加学历顾问Q/微741003700
留信网认证的作用:
1:该专业认证可证明留学生真实身份
2:同时对留学生所学专业登记给予评定
3:国家专业人才认证中心颁发入库证书
4:这个认证书并且可以归档倒地方
5:凡事获得留信网入网的信息将会逐步更新到个人身份内，将在公安局网内查询个人身份证信息后，同步读取人才网入库信息
6:个人职称评审加20分
7:个人信誉贷款加10分
8:在国家人才网主办的国家网络招聘大会中纳入资料，供国家高端企业选择人才
bordetella pertussis.................................ppt
Bordettela is a gram negative cocobacilli spread by air born drop let
The debris of the ‘last major merger’ is dynamically young
The Milky Way’s (MW) inner stellar halo contains an [Fe/H]-rich component with highly eccentric orbits, often referred to as the
‘last major merger.’ Hypotheses for the origin of this component include Gaia-Sausage/Enceladus (GSE), where the progenitor
collided with the MW proto-disc 8–11 Gyr ago, and the Virgo Radial Merger (VRM), where the progenitor collided with the
MW disc within the last 3 Gyr. These two scenarios make different predictions about observable structure in local phase space,
because the morphology of debris depends on how long it has had to phase mix. The recently identified phase-space folds in Gaia
DR3 have positive caustic velocities, making them fundamentally different than the phase-mixed chevrons found in simulations
at late times. Roughly 20 per cent of the stars in the prograde local stellar halo are associated with the observed caustics. Based
on a simple phase-mixing model, the observed number of caustics are consistent with a merger that occurred 1–2 Gyr ago.
We also compare the observed phase-space distribution to FIRE-2 Latte simulations of GSE-like mergers, using a quantitative
measurement of phase mixing (2D causticality). The observed local phase-space distribution best matches the simulated data
1–2 Gyr after collision, and certainly not later than 3 Gyr. This is further evidence that the progenitor of the ‘last major merger’
did not collide with the MW proto-disc at early times, as is thought for the GSE, but instead collided with the MW disc within
the last few Gyr, consistent with the body of work surrounding the VRM.
Applied Science: Thermodynamics, Laws & Methodology.pdf
When I was asked to give a companion lecture in support of ‘The Philosophy of Science’ (https://shorturl.at/4pUXz) I decided not to walk through the detail of the many methodologies in order of use. Instead, I chose to employ a long standing, and ongoing, scientific development as an exemplar. And so, I chose the ever evolving story of Thermodynamics as a scientific investigation at its best.
Conducted over a period of >200 years, Thermodynamics R&D, and application, benefitted from the highest levels of professionalism, collaboration, and technical thoroughness. New layers of application, methodology, and practice were made possible by the progressive advance of technology. In turn, this has seen measurement and modelling accuracy continually improved at a micro and macro level.
Perhaps most importantly, Thermodynamics rapidly became a primary tool in the advance of applied science/engineering/technology, spanning micro-tech, to aerospace and cosmology. I can think of no better a story to illustrate the breadth of scientific methodologies and applications at their best.
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Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...
Remote Sensing and Computational, Evolutionary, Supercomputing, and Intellige...
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ESR spectroscopy in liquid food and beverages.pptx
ESR spectroscopy in liquid food and beverages.pptx
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...
Travis Hills' Endeavors in Minnesota: Fostering Environmental and Economic Pr...
The binding of cosmological structures by massless topological defects
The binding of cosmological structures by massless topological defects
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...
EWOCS-I: The catalog of X-ray sources in Westerlund 1 from the Extended Weste...
Authoring a personal GPT for your research and practice: How we created the Q...
Authoring a personal GPT for your research and practice: How we created the Q...
Sharlene Leurig - Enabling Onsite Water Use with Net Zero Water
Sharlene Leurig - Enabling Onsite Water Use with Net Zero Water
Deep Software Variability and Frictionless Reproducibility
Deep Software Variability and Frictionless Reproducibility
3D Hybrid PIC simulation of the plasma expansion (ISSS-14)
3D Hybrid PIC simulation of the plasma expansion (ISSS-14)
aziz sancar nobel prize winner: from mardin to nobel
aziz sancar nobel prize winner: from mardin to nobel
bordetella pertussis.................................ppt
bordetella pertussis.................................ppt
The debris of the ‘last major merger’ is dynamically young
The debris of the ‘last major merger’ is dynamically young
Applied Science: Thermodynamics, Laws & Methodology.pdf
Applied Science: Thermodynamics, Laws & Methodology.pdf
Enhancing the Human Phenotype Ontology for Use by the Layperson
- 1. Enhancing the Human Phenotype Ontology for use by the Layperson Introduction Nicole Vasilevsky1, Mark Engelstad1, Erin Foster1, Chris Mungall3, Peter Robinson2, Sebastian Köhler2, Melissa Haendel1 1Ontology Development Group, Oregon Health & Science University, Portland, OR, USA 2Charité - Universitätsmedizin, Berlin, Germany, 3Lawrence Berkeley National Laboratory, Berkeley, CA, USA Enhancing the Human Phenotype Ontology for Use by the Layperson Human Phenotype Ontology Workflow Outcomes Many diseases present with distinct phenotypes, making computational description critical for diagnostics Patients are a good source of phenotypic information and need to participate in their diagnostic odyssey The Human Phenotype Ontology can be used to capture structured information about patient phenotypes § Contains over 12,000 classes describing human phenotypic features § Used for clinical “deep phenotyping” § HPO annotations utilized in semantic similarity analysis within and across species for rare disease diagnostics 4 | Synonym classification Exact synonyms: precise alternatives to the HPO term Broad synonyms: more general than the HPO term Narrow synonyms: more specific than HPO term Related synonyms: associated with the HPO term. 3 | Assign synonyms Assign synonyms to existing classes or mark existing synonyms as layperson § Wikipedia § MedlinePlus § Mayo Clinic § OMIM § Uberon § Elements of Morphology § SNOMED CT Browsers § Specialty texts 1 | Systematic review of HPO classes Challenges Use of HPO The inclusion of plain language synonyms will support patient-driven applications for deep phenotyping, that can be utilized clinical and computationally 44% of synonyms in HPO are layperson HPO can be integrated into patient registries and other platforms such as the following: § Recognizing when an HPO class did not have an equivalent layperson synonym e.g., joint contracture § Aligning synonyms with definition of HPO classes e.g., Neoplasm of breast ≠ Breast cancer § Applying synonyms consistently across HPO classes and subclasses e.g., “Yellowing of skin” à Jaundice, Intermittent jaundice, Prolonged neonatal jaundice § Continuous review of HPO OWL file for quality assurance § Valid character-encoding § Check for duplicated synonyms § Title case forma?ng § Check annotation consistency between similar terms § Reviewed by 3 curators 6 | Quality Assurance All synonyms in HPO Synonyms marked as lay All synonyms 14,253 6,240 Exact 12,167 5,357 Broad 441 298 Related 1,236 419 Narrow 409 166 On the left is a mouse phenotypic profile using the Mammalian Phenotype Ontology; on the right, a disease profile using HPO. In the center are shown the phenotypes in common based semantic similarity matching. Goal Add new layperson synonyms to terms to increase the usability of the HPO, and make it useful for data interoperability for patients, clinicians, and researchers 5 | Script in new synonyms to HPO OWL file § Initial review in HPO OWL files in the ontology editing tool, Protégé § HPO terms and synonyms were downloaded to a spreadsheet to allow sorting and grouping of terms § HPO curation team, with clinical and biocuration expertise, cross-reviewed each class 2 | Search for synonyms Acknowledgements This work is supported by NIH Office of Director grant: 1R24OD011883. Thank you to Tudor Groza and Julie McMurry for their help. Apert’s syndrome image credits available from monarchinitiative.org Contact Nicole Vasilevsky: vasilevs@ohsu.edu, @N_Vasilevsky Sebastian Köhler: sebastian.koehler@charite.de Monarch Initiative: @MonarchInit File available at: www.purl.obolibrary.org/obo/hp.owl Community contributions welcome! https://github.com/obophenotype/human- phenotype-ontology @hp_ontology