Cohort studies, which recruit groups of individuals who share common characteristics and follow them over a period of time, are a robust and essential method in biomedical research for understanding the links between risk factors and diseases. Through questionnaires, medical assessments, and other interactions, voluminous and complex data are collected about the study participants. While cohort studies present a treasure trove of data, the data is often not FAIR (findable, accessible, interoperable and reusable). First, due to the sensitive and private nature of medical information, cohort data are often access controlled. Due to the lack of information about the studies (metadata), often one needs to dig deep to know what data is available in a cohort study. Therefore, many cohort datasets suffer from the findable and accessible issues. Second, often data collection is performed with instruments and data specifications tailored to the study. As a result, combining data across cohorts, even ones with similar characteristics, is difficult, making interoperability and reusability a challenge. In this presentation, we will explore several informatics techniques, such as the use of ontology, to make cohort data more FAIR. We will also consider the implications of making cohort data more open and the ethical and governance issues associated with open science benefit sharing.
This webinar is part of the “How FAIR are you” webinar series and hackathon, which aim at increasing and facilitating the uptake of FAIR approaches into software, training materials and cohort data, to facilitate responsible and ethical data and resource sharing and implementation of federated applications for data analysis.
The CINECA webinar series aims to discuss ways to address common challenges and share best practices in the field of cohort data analysis, as well as distribute CINECA project results. All CINECA webinars include an audience Q&A session during which attendees can ask questions and make suggestions. Please note that all webinars are recorded and available for posterior viewing. CINECA webinars include an audience Q&A session during which attendees can ask questions and make suggestions.
This webinar took place on 17th February 2021 and is part of the CINECA webinar series.
For previous and upcoming CINECA webinars see:
https://www.cineca-project.eu/webinars
CINECA webinar slides: Open science through fair health data networks dream o...CINECAProject
Since the FAIR data principles were published in 2016, many organizations including science funders and governments have adopted these principles to promote and foster true open science collaborations. However, to define a vision and create a video of a Personal Health Train that leverages worldwide FAIR health data in a federated manner is one step. To actually make this happen at scale and be able to show new scientific and medical insights for it is quite another!
In this webinar, we will dive into the basics of FAIR health data, but also take stock of the current situation in health data networks: after a year of frantic research and collaborations and many open datasets and hackathons on COVID-19, has the situation actually improved? Are we sharing health data on a global scale to improve medical practice, or is quality medical data still only accessible to researchers with the right credentials and deep pockets?
This webinar is part of the “How FAIR are you” webinar series and hackathon, which aim at increasing and facilitating the uptake of FAIR approaches into software, training materials and cohort data, to facilitate responsible and ethical data and resource sharing and implementation of federated applications for data analysis.
The CINECA webinar series aims to discuss ways to address common challenges and share best practices in the field of cohort data analysis, as well as distribute CINECA project results. All CINECA webinars include an audience Q&A session during which attendees can ask questions and make suggestions. Please note that all webinars are recorded and available for posterior viewing. CINECA webinars include an audience Q&A session during which attendees can ask questions and make suggestions.
This webinar took place on 21st January 2021 and is part of the CINECA webinar series.
For previous and upcoming CINECA webinars see:
https://www.cineca-project.eu/webinars
Increasing transparency in Medical Education through Open Data Rebecca Grant
Slides presented at the AMEE Virtual Conference 2021, introducing the MedEdPublish platform and data policies. Approaches to sharing sensitive human data, and particulary qualitative data, are discussed.
Research in the time of Covid: Surveying impacts on Early Career ResearchersRebecca Grant
Based on a survey of over 4,500 researchers published in the white paper The State of Open Data 2020, this session will explore the impacts of the pandemic on early career reearchers (ECRs), their research practice, and how they interact with open data. We will discuss the specific challenges reported by ECRs, as well as the gaps in training and support that they have identified that would encourage their sharing and reuse of research data.
Presentation at the E-ARMA conference 2021.
Presentation about OHSL's new initiative, Mycroft Cognitive Assistant®, which is intended to streamline the operational aspects of research using IBM Watson cognitive computing capabilities.
CINECA webinar slides: Open science through fair health data networks dream o...CINECAProject
Since the FAIR data principles were published in 2016, many organizations including science funders and governments have adopted these principles to promote and foster true open science collaborations. However, to define a vision and create a video of a Personal Health Train that leverages worldwide FAIR health data in a federated manner is one step. To actually make this happen at scale and be able to show new scientific and medical insights for it is quite another!
In this webinar, we will dive into the basics of FAIR health data, but also take stock of the current situation in health data networks: after a year of frantic research and collaborations and many open datasets and hackathons on COVID-19, has the situation actually improved? Are we sharing health data on a global scale to improve medical practice, or is quality medical data still only accessible to researchers with the right credentials and deep pockets?
This webinar is part of the “How FAIR are you” webinar series and hackathon, which aim at increasing and facilitating the uptake of FAIR approaches into software, training materials and cohort data, to facilitate responsible and ethical data and resource sharing and implementation of federated applications for data analysis.
The CINECA webinar series aims to discuss ways to address common challenges and share best practices in the field of cohort data analysis, as well as distribute CINECA project results. All CINECA webinars include an audience Q&A session during which attendees can ask questions and make suggestions. Please note that all webinars are recorded and available for posterior viewing. CINECA webinars include an audience Q&A session during which attendees can ask questions and make suggestions.
This webinar took place on 21st January 2021 and is part of the CINECA webinar series.
For previous and upcoming CINECA webinars see:
https://www.cineca-project.eu/webinars
Increasing transparency in Medical Education through Open Data Rebecca Grant
Slides presented at the AMEE Virtual Conference 2021, introducing the MedEdPublish platform and data policies. Approaches to sharing sensitive human data, and particulary qualitative data, are discussed.
Research in the time of Covid: Surveying impacts on Early Career ResearchersRebecca Grant
Based on a survey of over 4,500 researchers published in the white paper The State of Open Data 2020, this session will explore the impacts of the pandemic on early career reearchers (ECRs), their research practice, and how they interact with open data. We will discuss the specific challenges reported by ECRs, as well as the gaps in training and support that they have identified that would encourage their sharing and reuse of research data.
Presentation at the E-ARMA conference 2021.
Presentation about OHSL's new initiative, Mycroft Cognitive Assistant®, which is intended to streamline the operational aspects of research using IBM Watson cognitive computing capabilities.
Managing Ireland's Research Data - 3 Research MethodsRebecca Grant
Slides providing an overview of the research methods used in the author's thesis, "Managing Ireland's Research Data: Recognising Roles for Recordkeepers". The methods discussed are online surveys, comparative case studies, and autoethnography.
Licensed as CC-BY.
Do Open data badges influence author behaviour? A case study at Springer NatureRebecca Grant
Digital badges have previously been shown to incentivise journal authors to share their data openly. In this paper we introduce an Open data badging project at the Springer Nature journal BMC Microbiology. The development of the Open data badge is described, as well as the challenges of developing standard badging criteria and ensuring authors’ awareness of the badges. Next steps for the badging project are outlined, which are based on the experiences of the team assessing the badges, the number of badges awarded at the journal to date, and the results of an author survey.
dkNET Webinar: Creating and Sustaining a FAIR Biomedical Data Ecosystem 10/09...dkNET
Abstract
In this presentation, Susan Gregurick, Ph.D., Associate Director of Data Science and Director, Office of Data Science Strategy at the National Institutes of Health, will share the NIH’s vision for a modernized, integrated FAIR biomedical data ecosystem and the strategic roadmap that NIH is following to achieve this vision. Dr. Gregurick will highlight projects being implemented by team members across the NIH’s 27 institutes and centers and will ways that industry, academia, and other communities can help NIH enable a FAIR data ecosystem. Finally, she will weave in how this strategy is being leveraged to address the COVID-19 pandemic.
Presenter: Susan Gregurick, Ph.D., Associate Director of Data Science and Director, Office of Data Science Strategy at the National Institutes of Health
dkNET Webinar Information: https://dknet.org/about/webinar
"Open Science, Open Data" training for participants of Software Writing Skills for Your Research - Workshop for Proficient, Helmholtz Centre Potsdam - GFZ German Research Centre for Geosciences, Telegrafenberg, December 16, 2015
Methodologies for Addressing Privacy and Social Issues in Health Data: A Case...Trilateral Research
Huge quantities of complex and diverse data are generated everyday in healthcare institutions, including clinical documentation (diagnostics, lab data, imaging data, etc.), administrative data, activities and cost data, and R&D data from clinical trials.
A Lightning Round presentation for the University of Michigan's Emergent Research Series, July 23, 2016, presenting recent work from the MLA Systematic Review Team 6 on Emerging Technologies.
Presentation by Dr Steve McEachern, ADA, to the 'Unlocking value from publicly funded Clinical Research Data' workshop, cohosted by ARDC and CSIRO at ANU on 6 March 2019.
The Challenges of Making Data Travel, by Sabina LeonelliLEARN Project
1st LEARN Workshop. Embedding Research Data as part of the research cycle. 29 Jan 2016. Presentation by Sabina Leonelli, Exeter Centre for the Study of Life Sciences (Egenis) & Department of Sociology, Philosophy and Anthropology, University of Exeter
Genome sharing projects around the world nijmegen oct 29 - 2015Fiona Nielsen
Genome sharing projects across the world
Did you ever wonder what happened to the exponential increase in genome sequencing data? It is out there around the world and a lot of it is consented for research use. This means that if you just know where to find the data, you can potentially analyse gigabytes of data to power your research.
In this talk Fiona will present community genome initiatives, the genome sharing projects across the world, how you can benefit from this wealth of data in your work, and how you can boost your academic career by sharing and collaboration.
by Fiona Nielsen, Founder and CEO of DNAdigest and Repositive
With a background in software development Fiona pursued her career in bioinformatics research at Radboud University Nijmegen. Now a scientist-turned-entrepreneur Fiona founded DNAdigest and its social enterprise spin-out Repositive Ltd. Both the charity and company focus on efficient and ethical sharing of genetics data for research to accelerate diagnostics and cures for genetic diseases.
CINECA webinar slides: Ethics/ELSI considerations - From FAIR to fair data sh...CINECAProject
The FAIR principles – standing for Findability, Accessibility, Interoperability, and Reusability – have become the guiding principles for the wider sharing of research data in the life sciences. While FAIR provides guidance for the management of data as well as tools and workflows, the institutional conditions and organizational challenges associated with data sharing need to be taken into account to ensure responsible and fair data practices. This requires considering the context of legal requirements, for instance the principle of fairness and transparency in GDPR, expectations of research participants/data subjects, societal aspects and the “ethics work” that is an integral part of data flows, as well as fairness, equity and benefit sharing within transnational collaborations, which is of utmost importance. This webinar will, from the perspective of ethical, legal and societal implications (ELSI), discuss this broader context of responsible and fair data sharing associated with FAIR.
The “How FAIR are you” webinar series and hackathon aim at increasing and facilitating the uptake of FAIR approaches into software, training materials and cohort data, to facilitate responsible and ethical data and resource sharing and implementation of federated applications for data analysis.
The CINECA webinar series aims to discuss ways to address common challenges and share best practices in the field of cohort data analysis, as well as distribute CINECA project results. All CINECA webinars include an audience Q&A session during which attendees can ask questions and make suggestions. Please note that all webinars are recorded and available for posterior viewing.
This webinar took place on 15th April 2021 and is part of the CINECA webinar series.
For previous and upcoming CINECA webinars see:
https://www.cineca-project.eu/webinars
Managing Ireland's Research Data - 3 Research MethodsRebecca Grant
Slides providing an overview of the research methods used in the author's thesis, "Managing Ireland's Research Data: Recognising Roles for Recordkeepers". The methods discussed are online surveys, comparative case studies, and autoethnography.
Licensed as CC-BY.
Do Open data badges influence author behaviour? A case study at Springer NatureRebecca Grant
Digital badges have previously been shown to incentivise journal authors to share their data openly. In this paper we introduce an Open data badging project at the Springer Nature journal BMC Microbiology. The development of the Open data badge is described, as well as the challenges of developing standard badging criteria and ensuring authors’ awareness of the badges. Next steps for the badging project are outlined, which are based on the experiences of the team assessing the badges, the number of badges awarded at the journal to date, and the results of an author survey.
dkNET Webinar: Creating and Sustaining a FAIR Biomedical Data Ecosystem 10/09...dkNET
Abstract
In this presentation, Susan Gregurick, Ph.D., Associate Director of Data Science and Director, Office of Data Science Strategy at the National Institutes of Health, will share the NIH’s vision for a modernized, integrated FAIR biomedical data ecosystem and the strategic roadmap that NIH is following to achieve this vision. Dr. Gregurick will highlight projects being implemented by team members across the NIH’s 27 institutes and centers and will ways that industry, academia, and other communities can help NIH enable a FAIR data ecosystem. Finally, she will weave in how this strategy is being leveraged to address the COVID-19 pandemic.
Presenter: Susan Gregurick, Ph.D., Associate Director of Data Science and Director, Office of Data Science Strategy at the National Institutes of Health
dkNET Webinar Information: https://dknet.org/about/webinar
"Open Science, Open Data" training for participants of Software Writing Skills for Your Research - Workshop for Proficient, Helmholtz Centre Potsdam - GFZ German Research Centre for Geosciences, Telegrafenberg, December 16, 2015
Methodologies for Addressing Privacy and Social Issues in Health Data: A Case...Trilateral Research
Huge quantities of complex and diverse data are generated everyday in healthcare institutions, including clinical documentation (diagnostics, lab data, imaging data, etc.), administrative data, activities and cost data, and R&D data from clinical trials.
A Lightning Round presentation for the University of Michigan's Emergent Research Series, July 23, 2016, presenting recent work from the MLA Systematic Review Team 6 on Emerging Technologies.
Presentation by Dr Steve McEachern, ADA, to the 'Unlocking value from publicly funded Clinical Research Data' workshop, cohosted by ARDC and CSIRO at ANU on 6 March 2019.
The Challenges of Making Data Travel, by Sabina LeonelliLEARN Project
1st LEARN Workshop. Embedding Research Data as part of the research cycle. 29 Jan 2016. Presentation by Sabina Leonelli, Exeter Centre for the Study of Life Sciences (Egenis) & Department of Sociology, Philosophy and Anthropology, University of Exeter
Genome sharing projects around the world nijmegen oct 29 - 2015Fiona Nielsen
Genome sharing projects across the world
Did you ever wonder what happened to the exponential increase in genome sequencing data? It is out there around the world and a lot of it is consented for research use. This means that if you just know where to find the data, you can potentially analyse gigabytes of data to power your research.
In this talk Fiona will present community genome initiatives, the genome sharing projects across the world, how you can benefit from this wealth of data in your work, and how you can boost your academic career by sharing and collaboration.
by Fiona Nielsen, Founder and CEO of DNAdigest and Repositive
With a background in software development Fiona pursued her career in bioinformatics research at Radboud University Nijmegen. Now a scientist-turned-entrepreneur Fiona founded DNAdigest and its social enterprise spin-out Repositive Ltd. Both the charity and company focus on efficient and ethical sharing of genetics data for research to accelerate diagnostics and cures for genetic diseases.
CINECA webinar slides: Ethics/ELSI considerations - From FAIR to fair data sh...CINECAProject
The FAIR principles – standing for Findability, Accessibility, Interoperability, and Reusability – have become the guiding principles for the wider sharing of research data in the life sciences. While FAIR provides guidance for the management of data as well as tools and workflows, the institutional conditions and organizational challenges associated with data sharing need to be taken into account to ensure responsible and fair data practices. This requires considering the context of legal requirements, for instance the principle of fairness and transparency in GDPR, expectations of research participants/data subjects, societal aspects and the “ethics work” that is an integral part of data flows, as well as fairness, equity and benefit sharing within transnational collaborations, which is of utmost importance. This webinar will, from the perspective of ethical, legal and societal implications (ELSI), discuss this broader context of responsible and fair data sharing associated with FAIR.
The “How FAIR are you” webinar series and hackathon aim at increasing and facilitating the uptake of FAIR approaches into software, training materials and cohort data, to facilitate responsible and ethical data and resource sharing and implementation of federated applications for data analysis.
The CINECA webinar series aims to discuss ways to address common challenges and share best practices in the field of cohort data analysis, as well as distribute CINECA project results. All CINECA webinars include an audience Q&A session during which attendees can ask questions and make suggestions. Please note that all webinars are recorded and available for posterior viewing.
This webinar took place on 15th April 2021 and is part of the CINECA webinar series.
For previous and upcoming CINECA webinars see:
https://www.cineca-project.eu/webinars
Making Data FAIR (Findable, Accessible, Interoperable, Reusable)Tom Plasterer
What to do About FAIR…
In the experience of most pharma professionals, FAIR remains fairly abstract, bordering on inconclusive. This session will outline specific case studies – real problems with real data, and address opportunities and real concerns.
·
Why making data Findable, Actionable, Interoperable and Reusable is important.
Talk presented at the Data Driven Drug Development (D4) conference on March 20th, 2019.
Digital transformation to enable a FAIR approach for health data scienceVarsha Khodiyar
Invited talk for ConTech Pharma on 1st March 2022
Abstract
Health Data Research UK is the UK’s national institute for health data science, with a mission to unite the UK’s health data to enable discoveries that improve people’s lives. In this talk, Dr Varsha Khodiyar will outline how HDR UK is bringing together disparate health data from all four countries of the United Kingdom, creating the infrastructure to enable discovery of and access to health data, and the convening standards making bodies to improve data linkage and data reuse. Varsha will also discuss how HDR UK is moving beyond the traditional confines of FAIR data to also ensure that data sharing and data use is transparent and ‘fair’ for the patients and lay public who are the subjects of these datasets.
Susanna Sansone's talk at the "Beyond Open" Knowledge Dialogues/Open Data Hong Kong event on research data, hosted at the Hong Kong Innocentre on Monday 20 November 2017.
Presentation during the 14th Association of African Universities (AAU) Conference and African Open Science Platform (AOSP)/Research Data Alliance (RDA) Workshop in Accra, Ghana, 7-8 June 2017.
Clinical Research Informatics Year-in-Review 2024Peter Embi
Peter Embi, MD's presentation of Clinical Research Informatics year-in-review presented at the 2024 AMIA Informatics Summit in Boston, MA on March 20, 2024.
International perspective for sharing publicly funded medical research dataARDC
Presentation by Olivier Salvado, CSIRO, to the 'Unlocking value from publicly funded Clinical Research Data' workshop, cohosted by ARDC and CSIRO at ANU on 6 March 2019.
David Van Enckevort - FAIR sample and data access DataSciSIG
David van Enckevort from the University of Groningen describes FAIR Sample and Data Access in Biobanking and Biorepositories.
This talk was sponsored by the NIH Data Science Special Interest Group and part of a webinar panel on June 23, 2017 on Global Biobanking and Access to Specimens.
CINECA webinar slides: H3ABioNet Experiences in Phenotype Data Harmonisation ...CINECAProject
H3ABioNet supports the H3Africa Consortium in their research data collection and analysis efforts. This includes both genomic and phenotypic data. With the completion of data collection from some of the projects in H3Africa cycle 1 of funding it become clear midway that some data standardisation/harmonisation would be needed to facilitate meta-analyses of data especially with regards to the clinical data collected by the various studies. H3ABioNet working with the H3Africa Phenotype Harmonisation Working Group have developed an H3Africa Standard CRF which newer studies in cycle 2 of funding having taken up to use for their clinical data collection and we have also supported post data collection harmonisation effort for the H3Africa Cardiovascular Disease Working Group assisting with harmonising data across 6 different studies. We will be talking about experiences in both standards development in Africa and data harmonisation methods used.
CINECA (Common Infrastructure for National Cohorts in Europe, Canada, and Africa) project, aims to develop a federated cloud enabled infrastructure to make population scale genomic and biomolecular data accessible across international borders, to accelerate research, and improve the health of individuals across continents. CINECA will leverage international investment in human cohort studies from Europe, Canada, and Africa to deliver a paradigm shift of federated research and clinical applications.
This webinar took place on 12th December 2019. Recording of the webinar is available through the CINECA website.
https://www.cineca-project.eu/news-events-all/h3abionet-experiences-in-phenotype-data-harmonisation-and-standards-development
For upcoming CINECA webinars see:
https://www.cineca-project.eu/webinars
CINECA webinar slides: Modular and reproducible workflows for federated molec...CINECAProject
Genetic analysis of molecular traits such as gene expression, splicing and chromatin accessibility requires a number of complex analysis steps that can easily take weeks or months for a analyst to implement from scratch. In the CINECA project, we have developed a number of modular Nextflow workflows that standardise and automate these steps. In this webinar, we will give an overview of the CINECA workflows for genotype imputation, gene expression and splicing quantification, data normalisation and association testing, and demonstrate how these workflows can be used in a federated setting without transferring identifiable personal data between partners.
The CINECA webinar series aims to discuss ways to address common challenges and share best practices in the field of cohort data analysis, as well as distribute CINECA project results. All CINECA webinars include an audience Q&A session during which attendees can ask questions and make suggestions. Please note that all webinars are recorded and available for posterior viewing.
This webinar took place on 10th November 2020 and is part of the CINECA webinar series.
For previous and upcoming CINECA webinars see:
https://www.cineca-project.eu/webinars
Beacon v2 Reference Implementation: An OverviewCINECAProject
The Beacon v2 Reference Implementation (B2RI) is a free open source Linux-based software created by the Centre for Genomic Regulation (Barcelona, Spain) that allows lighting up a Beacon v2 out-of-the-box.In this training session, a B2RI developer will give an overview on how to use the software to “beaconize” your data (from the user’s perspective).
At the end of this training session, participants will be familiarized with the input and output requirements of the B2RI, as well as with the type of queries allowed.
This training session was delivered on 17 February 2022 as part of the CINECA GA4GH Beacon series.
You can learn about the CINECA project on https://www.cineca-project.eu/
Lighting a Beacon: training for (future) implementersCINECAProject
The Beacon project has received a lot of attention and can already count with implementations (e.g., CINECA cohorts, Beacon+). Beacon purposely leaves a lot of room for freedom on the options to be implemented, and its versatility is part of its success. It also means that implementing Beacon can sometimes be quite challenging: this training session presents the steps for a Beacon implementation in general ways, and leaves room for an extended Q&A session from the audience. The questions might be sent in advance so the use cases can turn into training exercises.
At the end of this training session, participants should have the tools to get started with the implementation autonomously, and have identified the resource persons to answer their questions during the implementation process.
This training session was delivered on 15 February 2022 as part of the CINECA GA4GH Beacon series.
You can learn about the CINECA project on https://www.cineca-project.eu/
CINECA webinar slides: How to make training FAIRCINECAProject
There is a wealth of training content developed and delivered across the globe each year, there will be many similar sessions on similar topics all delivered to similar audiences. At the same time, there will be trainers looking for inspiration and ideas on how to approach new topics or on new ways to teach old topics; as well as trainees looking for materials to further their own knowledge. Many trainers (or lecturers/educators etc) do not share their materials, or if materials are shared they are not easily found or re-used by others.
During this webinar, we will give you some tips and suggestions on how you can make more of the training materials you produce and encourage others to do the same. FAIR is not just for data - we can make our training materials FAIR too. Join us to find out the benefits of sharing your FAIR materials and some simple ways you can make it easy for others to use your materials in their teaching, or as aids for individuals to learn more.
The “How FAIR are you” webinar series and hackathon aim at increasing and facilitating the uptake of FAIR approaches into software, training materials and cohort data, to facilitate responsible and ethical data and resource sharing and implementation of federated applications for data analysis.
The CINECA webinar series aims to discuss ways to address common challenges and share best practices in the field of cohort data analysis, as well as distribute CINECA project results. All CINECA webinars include an audience Q&A session during which attendees can ask questions and make suggestions. Please note that all webinars are recorded and available for posterior viewing.
This webinar took place on 18th March 2021 and is part of the CINECA webinar series.
For previous and upcoming CINECA webinars see:
https://www.cineca-project.eu/webinars
This webinar will focus on practical applications of the FAIR data principles, particularly in the context of clinical bioinformatics. We will highlight several example projects that have put the FAIR principles in practice, and discuss the advantages and some of the challenges involved. ELIXIR Galaxy community (elixir-europe.org/communities/galaxy) promotes the use of Galaxy projects that enhance the FAIRness in data analysis. We will demonstrate the Galaxy services that deliver practical FAIR data analysis with “Single Sign-On” capability provided by ELIXIR-AAI. The aim is to provide (medical) researchers with the practicalities of implementing and using FAIR principles in the context of the CINECA project as applied to translational research at Erasmus University Medical Center.
The “How FAIR are you” webinar series and hackathon aim at increasing and facilitating the uptake of FAIR approaches into software, training materials and cohort data, to facilitate responsible and ethical data and resource sharing and implementation of federated applications for data analysis.
The CINECA webinar series aims to discuss ways to address common challenges and share best practices in the field of cohort data analysis, as well as distribute CINECA project results. All CINECA webinars include an audience Q&A session during which attendees can ask questions and make suggestions. Please note that all webinars are recorded and available for posterior viewing.
This webinar took place on 4th March 2021 and is part of the CINECA webinar series.
For previous and upcoming CINECA webinars see:
https://www.cineca-project.eu/webinars
In this talk, I will discuss the importance of the FAIR principles for the software tools we use to process data. Ranging from small analysis scripts to full fledged data processing pipelines, software needs to be FAIR to enable other researchers to reproduce our own experiments and reuse our software. However software and data are fundamentally different – software is executable in nature and may have intricate dependencies. FAIR principles apply differently to software than they do to data and we must be aware of these differences. Existing initiatives such as the RDA FAIR for Research Software (FAIR4RS) working group (https://www.rd-alliance.org/groups/fair-4-research-software-fair4rs-wg) and http://fair-software.eu/ are already focused on addressing these differences and raising awareness of the importance of FAIR for software.
The “How FAIR are you” webinar series and hackathon aim at increasing and facilitating the uptake of FAIR approaches into software, training materials and cohort data, to facilitate responsible and ethical data and resource sharing and implementation of federated applications for data analysis.
The CINECA webinar series aims to discuss ways to address common challenges and share best practices in the field of cohort data analysis, as well as distribute CINECA project results. All CINECA webinars include an audience Q&A session during which attendees can ask questions and make suggestions. Please note that all webinars are recorded and available for posterior viewing.
This webinar took place on 24th February 2021 and is part of the CINECA webinar series.
For previous and upcoming CINECA webinars see:
https://www.cineca-project.eu/webinars
CINECA webinar slides: Data Gravity in the Life Sciences: Lessons learned fro...CINECAProject
We live in an era of cloud computing. Many of the services in the life sciences are keenly planning cloud transformations, seeking to create globally distributed ecosystems of harmonised data based on standards from organisations like GA4GH. CINECA faces similar challenges, gathering cohort datasets from all over the globe, many of which are pinned in place, due to their size, legal restrictions, or other considerations. But is “bringing compute to the data” always the right choice? In this webinar, based on experiences from the Human Cell Atlas Data Coordination Platform and other projects from EMBL-EBI, we will explore the concept of “data gravity”: The idea that whilst there are forces that may hold data in one place, there are others that require it to be mobile. We’ll consider how effectively planning a cloud strategy requires consideration of the gravity of datasets, and the impact it may have on team skills required, incentives for good practice, and storage and compute costs.
The CINECA webinar series aims to discuss ways to address common challenges and share best practices in the field of cohort data analysis, as well as distribute CINECA project results. All CINECA webinars include an audience Q&A session during which attendees can ask questions and make suggestions. Please note that all webinars are recorded and available for posterior viewing. CINECA webinars include an audience Q&A session during which attendees can ask questions and make suggestions.
This webinar took place on 12th November 2020 and is part of the CINECA webinar series.
For previous and upcoming CINECA webinars see:
https://www.cineca-project.eu/webinars
CINECA webinar slides: Status Update Code of Conduct: Teaming up & Talking ab...CINECAProject
Committed to the drafting of a Code of Conduct for the sector of health research according to Art. 40 GDPR, our initiative is advancing slowly but steadily. Throughout Europe, national jurisdictions differ to a great deal in their interpretations of the GDPR, especially in regard to its application in health research. This is due to some quite vague provisions (public interest, not incompatible clause) as wells as to numerous exemption/derogation clauses concerning the use of health data for research purposes, which encourage States to set up national rules – enhancing fragmentation. Notably, a Code of Conduct can help to bridge the harmonization gaps that may exist between Member States in their application of data protection law. On a practical level, a code is potentially a cost-effective method to achieve greater levels of consistency of protection as well as a mechanism to demonstrate compliance with the GDPR. By spring 2020, several hundred individuals representing around 90 organizations in the field of health research have indicated their interest and support for the Code of Conduct for Health Research. At this stage, this does not yet indicate an endorsement but means that they see a benefit in the development of such a code and are interested in partaking in the process. Additionally, several exchanges take place with national and sectoral codes in order to use synergies and finds ways for collaboration. This webinar is intended to inform you about the latest results.
The CINECA webinar series aims to discuss ways to address common challenges and share best practices in the field of cohort data analysis, as well as distribute CINECA project results. All CINECA webinars include an audience Q&A session during which attendees can ask questions and make suggestions. Please note that all webinars are recorded and available for posterior viewing. CINECA webinars include an audience Q&A session during which attendees can ask questions and make suggestions.
This webinar took place on 1st October 2020 and is part of the CINECA webinar series. It is best viewed in full screen mode using Google Chrome.
For previous and upcoming CINECA webinars see:
https://www.cineca-project.eu/webinars
CINECA webinar slides: Ethical, legal and societal issues in international da...CINECAProject
The CINECA webinar series continues with a presentation by Dr. Éloïse Gennet (INSERM) and Dr. Melanie Goisauf (BBMRI-ERIC) on Ethical, Legal and Societal Issues in international data sharing.
The goal of this webinar will be to present the first findings of the ELSI activities in the CINECA project, ranging from questions of ethics of data sharing across continents to legal basis of secondary processing of personal data, consent requirements and vulnerable groups or public and stakeholders’ attitudes toward sharing of genomic and health related data for research.
CINECA (Common Infrastructure for National Cohorts in Europe, Canada, and Africa) project, aims to develop a federated cloud enabled infrastructure to make population scale genomic and biomolecular data accessible across international borders, to accelerate research, and improve the health of individuals across continents. CINECA will leverage international investment in human cohort studies from Europe, Canada, and Africa to deliver a paradigm shift of federated research and clinical applications.
This webinar took place on 24th January 2020. Recording of the webinar is available through the CINECA website.
https://www.cineca-project.eu/news-events-all/ethical-legal-and-societal-issues-in-international-data-sharing
For upcoming CINECA webinars see:
https://www.cineca-project.eu/webinars
ARTIFICIAL INTELLIGENCE IN HEALTHCARE.pdfAnujkumaranit
Artificial intelligence (AI) refers to the simulation of human intelligence processes by machines, especially computer systems. It encompasses tasks such as learning, reasoning, problem-solving, perception, and language understanding. AI technologies are revolutionizing various fields, from healthcare to finance, by enabling machines to perform tasks that typically require human intelligence.
Flu Vaccine Alert in Bangalore Karnatakaaddon Scans
As flu season approaches, health officials in Bangalore, Karnataka, are urging residents to get their flu vaccinations. The seasonal flu, while common, can lead to severe health complications, particularly for vulnerable populations such as young children, the elderly, and those with underlying health conditions.
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Knee anatomy and clinical tests 2024.pdfvimalpl1234
This includes all relevant anatomy and clinical tests compiled from standard textbooks, Campbell,netter etc..It is comprehensive and best suited for orthopaedicians and orthopaedic residents.
Tom Selleck Health: A Comprehensive Look at the Iconic Actor’s Wellness Journeygreendigital
Tom Selleck, an enduring figure in Hollywood. has captivated audiences for decades with his rugged charm, iconic moustache. and memorable roles in television and film. From his breakout role as Thomas Magnum in Magnum P.I. to his current portrayal of Frank Reagan in Blue Bloods. Selleck's career has spanned over 50 years. But beyond his professional achievements. fans have often been curious about Tom Selleck Health. especially as he has aged in the public eye.
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Introduction
Many have been interested in Tom Selleck health. not only because of his enduring presence on screen but also because of the challenges. and lifestyle choices he has faced and made over the years. This article delves into the various aspects of Tom Selleck health. exploring his fitness regimen, diet, mental health. and the challenges he has encountered as he ages. We'll look at how he maintains his well-being. the health issues he has faced, and his approach to ageing .
Early Life and Career
Childhood and Athletic Beginnings
Tom Selleck was born on January 29, 1945, in Detroit, Michigan, and grew up in Sherman Oaks, California. From an early age, he was involved in sports, particularly basketball. which played a significant role in his physical development. His athletic pursuits continued into college. where he attended the University of Southern California (USC) on a basketball scholarship. This early involvement in sports laid a strong foundation for his physical health and disciplined lifestyle.
Transition to Acting
Selleck's transition from an athlete to an actor came with its physical demands. His first significant role in "Magnum P.I." required him to perform various stunts and maintain a fit appearance. This role, which he played from 1980 to 1988. necessitated a rigorous fitness routine to meet the show's demands. setting the stage for his long-term commitment to health and wellness.
Fitness Regimen
Workout Routine
Tom Selleck health and fitness regimen has evolved. adapting to his changing roles and age. During his "Magnum, P.I." days. Selleck's workouts were intense and focused on building and maintaining muscle mass. His routine included weightlifting, cardiovascular exercises. and specific training for the stunts he performed on the show.
Selleck adjusted his fitness routine as he aged to suit his body's needs. Today, his workouts focus on maintaining flexibility, strength, and cardiovascular health. He incorporates low-impact exercises such as swimming, walking, and light weightlifting. This balanced approach helps him stay fit without putting undue strain on his joints and muscles.
Importance of Flexibility and Mobility
In recent years, Selleck has emphasized the importance of flexibility and mobility in his fitness regimen. Understanding the natural decline in muscle mass and joint flexibility with age. he includes stretching and yoga in his routine. These practices help prevent injuries, improve posture, and maintain mobilit
MANAGEMENT OF ATRIOVENTRICULAR CONDUCTION BLOCK.pdfJim Jacob Roy
Cardiac conduction defects can occur due to various causes.
Atrioventricular conduction blocks ( AV blocks ) are classified into 3 types.
This document describes the acute management of AV block.
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Report Back from SGO 2024: What’s the Latest in Cervical Cancer?bkling
Are you curious about what’s new in cervical cancer research or unsure what the findings mean? Join Dr. Emily Ko, a gynecologic oncologist at Penn Medicine, to learn about the latest updates from the Society of Gynecologic Oncology (SGO) 2024 Annual Meeting on Women’s Cancer. Dr. Ko will discuss what the research presented at the conference means for you and answer your questions about the new developments.
Basavarajeeyam is an important text for ayurvedic physician belonging to andhra pradehs. It is a popular compendium in various parts of our country as well as in andhra pradesh. The content of the text was presented in sanskrit and telugu language (Bilingual). One of the most famous book in ayurvedic pharmaceutics and therapeutics. This book contains 25 chapters called as prakaranas. Many rasaoushadis were explained, pioneer of dhatu druti, nadi pareeksha, mutra pareeksha etc. Belongs to the period of 15-16 century. New diseases like upadamsha, phiranga rogas are explained.
Ozempic: Preoperative Management of Patients on GLP-1 Receptor Agonists Saeid Safari
Preoperative Management of Patients on GLP-1 Receptor Agonists like Ozempic and Semiglutide
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CINECA webinar slides: Making cohort data FAIR
1. This project has received funding from the European Union’s Horizon 2020 research and
Innovation programme under grant agreement No. 825775
Making Cohort data FAIR
Presenter: William Hsiao (Simon Fraser University)
Host: Marta Lloret Llinares (EMBL-EBI)
4. The challenges:
Stay
informed
@CinecaProject
www.cineca-project.eu
Common Infrastructure for National Cohorts
in Europe, Canada and Africa
This project has received funding from the European Union’s Horizon 2020 research and
Innovation programme under grant agreement No. 825775
Accelerating disease research and
improving health by facilitating
transcontinental human data exchange
The vision:
This project has received funding from the Canadian Institute of Health
Research under grant agreement #404896
5. Context for the webinar
• CINECA “How FAIR are you?” webinar series and hackathon:
• https://www.cineca-project.eu/news-events-all/how-fair-are-you-
webinar-series-and-hackathon
• Webinar series Jan-April
• Making cohort data FAIR
• FAIR software tools
• Practically FAIR
• How to make training FAIR
• Ethics/ELSI considerations
• Hackathon 28-29th April 4 hours per day
• 3 streams: cohort data, software, training materials
6. Today’s presenter
Dr. William Hsiao joined the Faculty of Health Sciences at Simon Fraser University as an
associate professor in September 2020. He is also an affiliated scientist at the BC Centre for
Disease Control Public Health Laboratory (BCCDC PHL) and at Canada’s Michael Smith Genome
Sciences Centre.
Prior to joining FHS, Dr. Hsiao was the chief bioinformatician and a senior scientist at the
BCCDC PHL for 8 years and a clinical associate professor at the University of British Columbia.
Dr. Hsiao obtained his PhD in the Department of Molecular Biology and Biochemistry at Simon
Fraser University followed by a postdoctoral fellowship at the Institute for Genome Sciences at
University of Maryland School of Medicine. His research focused on microbial genomics and
metagenomics.
At the BCCDC PHL, he incorporated data science and knowledge engineering into his research and developed expertise in
public health data sharing, integration, and harmonization. With experience conducting and applying genomics and data
science research both in academia and in government laboratories, Dr. Hsiao has developed a special perspective on
integrating basic and applied research to improve our public health system.
7. This project has received funding from the European Union’s Horizon 2020 research and
Innovation programme under grant agreement No. 825775
Making Cohort data FAIR
William Hsiao, PhD
Associate Professor, Faculty of Health Sciences
Simon Fraser University
8. Cohort Studies
• A cohort is a group of people who share a common characteristics or
experience within a defined period
• A cohort study typically is observational in nature and follows a large
number of participants over a long period of time (longitudinal)
• Useful when intervention (e.g. RCT) is not possible or not ethical
• Exposure to risk factors are measured or collected
• Multiple outcomes can be observed (e.g. from large population-based
cohort)
• Valuable for scientific understanding of disease causation
• In CINECA, ~10 cohorts are part of the consortium
• A goal of CINECA is to enable federated queries and analyses of the varying
and wide-ranging datasets from the 10 CINECA cohorts.
9. Construction of Cohorts
• Define study question(s)/scope and identify and consent the study
subjects (cohort)
• Obtain baseline data on the exposure(s) to the risk factor(s) of
interest (e.g. obese vs. lean, genetic allelic variation)
• Subclassify the cohorts into groups with or without (or less) of the
risk factor(s)
• Follow-up with the participants to measure the outcomes using data
collection instruments (questionnaire, physical measures, cognitive
measures, biosamples, etc.)
• Analyze the data to see if outcome correlated to risk factor(s); infer
causality
10. Examples of Cohorts in CINECA
• CHILD: The CHILD Cohort Study is a prospective longitudinal birth
cohort study in Canada; ~3000 participating families (trios);
multidisciplinary; multi-modal (questionnaires, biological samples,
home assessments, clinical assessments)
• UK-Biobank: population based biomedical database; 500,000
participants from UK (national cohort); able to mobilize for COVID-19
related research by linking host genetics to disease status
• H3Africa: a pan-African consortium to build research program and
infrastructure in genomic medicine on the African continent;
biospecimens and data collection for research
11. Challenges with Cohort Studies
• Due to the (usually) prospective, large sample-size, and longitudinal
nature, cohort studies can be expensive and labour-intensive
• Data collection instruments and variables are usually specific to a
study, and data may not be interoperable and machine readable (e.g.
free text, custom pick-list, non-standardized units)
• Most valuable data is often the most sensitive and access controlled
• Consent process may restrict the re-use of cohort data
• Broad consents are encouraged as long as they are informed consents and
allow withdrawal of the consents at any time
12. Discovery of Cohort Database Content (F/A)
• Cohort Profiles are often in descriptive text that are human but not
machine readable
• Similarly, data fields and study protocols are accessible openly but
only in human readable formats (free text or tables)
Cohort profile – CHILD Cohort Study (childstudy.ca)
13. Access to Data is controlled to protect
privacy
Data access – CHILD Cohort Study (childstudy.ca)
14. Minimal Metadata for Cohorts
• One solution is to make cohort metadata and aggregated data
researchable by machines by encoding the data in common formats
• E.g. GO FAIR’s Framework for FAIRification has a Metadata for
Machines (M4M) component
• Assess community specific metadata practices
• Using the FAIR principles to define metadata elements
• Formulate these decisions as machine-actionable templates
• Register these templates so they are FAIR and accessible by
machine API
• Result in domain-specific, community built, FAIR metadata schema
Metadata for Machines - GO FAIR (go-fair.org)
15. A Minimal Metadata Model for
CINECA
• A minimal metadata model is being developed for CINECA
• Based on surveys of common data fields in 10 cohort studies (no assessment of
actual data, but consulted data dictionaries to capture acceptable data values)
• Supplemented with common data fields from additional data catalogues
• Supplemented with “use cases”
• Each variable grouped into a broad category (e.g. socio-demographic and economic
characteristics, diseases, and lifestyle and behaviours)
• Maelstrom Research data standards were used as the basis for the categorization –
promote compatibility with existing data catalogues
• Each variables is mapped to an ontology term (work in progress)
• Metadata model encoded as a new ”application ontology” called GEKCO (Genomics
Cohorts Knowledge Ontology) - http://www.obofoundry.org/ontology/gecko.html
17. Harmonization of metadata (-IR)
• Data collection instruments are usually developed in silos (only
considering the study scope and current research needs)
• This leads to incompatibilities when trying to aggregate datasets
across studies at both the cohort level (study attributes) and at the
individual data (participant attributes)
• As a result, data are:
• Not Interoperable
• Not (easily) reusable
18. Similar Epi/Clinical data needs across agencies
Questions re: diseases, symptoms, clinical events, dates of onset
CDC Atlanta,
BC CDC, WHO
18
22. Maelstrom Data Harmonization Guideline
Fortier, Isabel, et al. "Maelstrom Research guidelines for rigorous retrospective data harmonization." International journal of epidemiology (2017) 46 (1): 103-105.
23. Semantic Web and Ontology
• Semantic Web term refers to set of standards and best practice for
sharing data and the semantic (Meanings) of that data over the web by
using application. Semantic web can be processed directly or indirectly
from machines, so basically human and computers can work in
cooperation.
• Ontology is a way to structure knowledge in a machine readable way with
defined terms and relationships.
• In ontology, one can provide a set of vocabularies that can be used to
model a domain, which is types of objects and concepts that are exist in
specific area and the relationship between them (Gruber TR, 1993).
24. Ontology
● Ontologies provide standard and linkable IDs for
○ names for form and tabular data fields
○ terms (choices) for categorical variables
● Modelling processes into data structures may be subjective: Who is the
model for, and to what granularity?
● Upper level ontologies (e.g. BFO) bring some harmony but do not
guarantee full interoperability
25. Ontology Creation and Re-use
● No silo = build the ontology as a suite of interoperable modules
structured to provide berths for future ontologies as needed
● No short half-life = start not with data (which changes rapidly) but
with the entities (things, processes, attributes, ...) the data are used
to describe
● No reinvent the wheel = follow a method tested in over 300
ontology-building initiatives and documented in ISO 21838,
(https://www.iso.org/standard/71954.html) leveraging existing
resources wherever possible
● E.g. GECKO ontology reuse terms whenever possible
26. • Formal representation of objects, concepts and relationships among
them
• Shared understanding [language] for communicating cohort information
• Overcome the semantic heterogeneity
• Ontologies are interpretable by humans and by computer programs.
• Information integration - Multiple information resources are combined
using ontologies to match concepts with similar meaning.
• Ontology embedded into software - Object-oriented implementation
(e.g. Java classes) generated from classes in the ontology…
Strength of Ontology and Semantic web
26
27. 27
GEEM: platform for building ontology-based data
specifications
http://genepio.org/geem/form.html#GENEPIO:0002083
28. Challenges with Harmonization
• balance between accepting only precisely uniform variables that
render pooling straightforward (e.g. exact question or standard
operating procedures) but limit the potential to integrate multiple
studies; and accepting a certain level of heterogeneity across
participating studies providing similar but not necessarily identical
data
• E.g. broader terms used to aggregate more detailed terms
• E.g. same term used for different scales
https://www.maelstrom-research.org/about-harmonization/guidelines/data-processing-methods
29. Benefit Sharing and Privacy Concerns
• Making Cohort Data FAIR can mean broader and easier access to data
• However, usually the HICs (more research capacity) can take better
advantages of such broader access than LMICs
• Food for Thought (discussion): how to we protect the interests of
study participants and enable benefit sharing?
30. Questions?
Title: Making Cohort data FAIR
Presenter: William Hsiao
Please write your questions in the
questions window of the GoToWebinar
application
31. Next CINECA webinars
Title: FAIR Software tools
Presenter: Carlos Martinez
Date: Wed 24th February 2021
Time: 3:00 PM GMT / 4:00 PM CET
Registration and details:
https://www.cineca-project.eu/news-
events-all/fair-software-tools
Title: Practically Fair
Presenter: Andrew Stubbs
Date: Thurs 4th March 2021
Time: 3:00 PM GMT / 4:00 PM CET
Registration and details:
https://www.cineca-project.eu/news-
events-all/practically-fair