During the tranSMART Annual Meeting 2015, Kees van Bochove, chair of the tranSMART Foundation Architecture Working Group, presented on the future roadmap for the tranSMART platform in a co-presentation with Keith Elliston, CEO of tranSMART Foundation.
The document summarizes the RISIS project, which aims to develop a distributed research infrastructure for science and innovation studies. It provides databases, analytical tools, and indicators to improve understanding. RISIS offers access to datasets and platforms through visits to research institutions, and provides training courses on using the data. It works to integrate databases by developing unique identifiers for organizations and matching data across sources.
Mapping of Terminology Standards, a Way for Interoperability (Position Paper)Sven Van Laere
Standards in medicine are essential to enable communication between healthcare providers. These standards can be used either for exchanging information, or for coding and documenting the health status of a patient. In this position paper we focus on the latter, namely terminology standards. However, the multidisciplinary field of medicine makes use of many different standards. We propose to invest in an interoperable electronic health record (EHR) that can be understood by all different levels of health care providers independent of the kind of terminology standard they use. To make this record interoperable, we suggest mapping standards in order to make uniform communication possible. We suggest using mappings between a reference
terminology (RT) and other terminology standards. By using this approach we limit the number of mappings that have to be provided. The Systematized Nomenclature of Medicine, Clinical Terms (SNOMED CT) can be used as a RT, because of its extensive character and the preserved semantics towards other terminology standards. Moreover, a lot of mappings from SNOMED CT to other standards are already defined previously.
This document discusses managing research data for open science based on the UK experience. It outlines key aspects of open science such as making research more open, global, collaborative and closer to society. The document discusses mandates for open research data from funding bodies in the UK and EU, including stipulations in Horizon 2020 and requirements from EPSRC. It defines what constitutes research data and examines challenges around research data management, including technology issues, people issues, policy issues and resources. The importance of data skills training for researchers and data professionals is also covered.
the OpenAIRE Research graph is a massive collection of metadata and links connecting research entities such as articles, datasets, software, and other research outputs
EU FP7 CarTarDis project overview April 2015Alain van Gool
The document describes CarTarDis, a 4-year public-private partnership with 13 partners from 8 countries and a budget of 8.0M Euros that began on October 1, 2013. The project aims to discover novel cardiovascular drug targets through a strong interdisciplinary team with expertise in cardiovascular disease biology, drug discovery, translational medicine, omics technologies, and more. CarTarDis will utilize unique human cohort data, biobanks, CVD models and samples to generate a candidate target database, review targets, validate a shortlist, and create online dossiers to share knowledge on selected targets. The goal is to prioritize 11 targets for further validation activities to identify new treatments for cardiovascular disease.
Open Research Gateway for the ELIXIR-GR Infrastructure (Part 2)OpenAIRE
OpenAIRE is a European infrastructure that helps stakeholders comply with open access policies by providing tools and services. It operates repositories, dashboards, and tools to help share and reuse research outputs in accordance with FAIR principles. OpenAIRE also coordinates activities through national open access desks and outreach to promote open science practices. Researchers can use OpenAIRE to publish open access works, deposit data, write data management plans, and link research outputs.
During the tranSMART Annual Meeting 2015, Kees van Bochove, chair of the tranSMART Foundation Architecture Working Group, presented on the future roadmap for the tranSMART platform in a co-presentation with Keith Elliston, CEO of tranSMART Foundation.
The document summarizes the RISIS project, which aims to develop a distributed research infrastructure for science and innovation studies. It provides databases, analytical tools, and indicators to improve understanding. RISIS offers access to datasets and platforms through visits to research institutions, and provides training courses on using the data. It works to integrate databases by developing unique identifiers for organizations and matching data across sources.
Mapping of Terminology Standards, a Way for Interoperability (Position Paper)Sven Van Laere
Standards in medicine are essential to enable communication between healthcare providers. These standards can be used either for exchanging information, or for coding and documenting the health status of a patient. In this position paper we focus on the latter, namely terminology standards. However, the multidisciplinary field of medicine makes use of many different standards. We propose to invest in an interoperable electronic health record (EHR) that can be understood by all different levels of health care providers independent of the kind of terminology standard they use. To make this record interoperable, we suggest mapping standards in order to make uniform communication possible. We suggest using mappings between a reference
terminology (RT) and other terminology standards. By using this approach we limit the number of mappings that have to be provided. The Systematized Nomenclature of Medicine, Clinical Terms (SNOMED CT) can be used as a RT, because of its extensive character and the preserved semantics towards other terminology standards. Moreover, a lot of mappings from SNOMED CT to other standards are already defined previously.
This document discusses managing research data for open science based on the UK experience. It outlines key aspects of open science such as making research more open, global, collaborative and closer to society. The document discusses mandates for open research data from funding bodies in the UK and EU, including stipulations in Horizon 2020 and requirements from EPSRC. It defines what constitutes research data and examines challenges around research data management, including technology issues, people issues, policy issues and resources. The importance of data skills training for researchers and data professionals is also covered.
the OpenAIRE Research graph is a massive collection of metadata and links connecting research entities such as articles, datasets, software, and other research outputs
EU FP7 CarTarDis project overview April 2015Alain van Gool
The document describes CarTarDis, a 4-year public-private partnership with 13 partners from 8 countries and a budget of 8.0M Euros that began on October 1, 2013. The project aims to discover novel cardiovascular drug targets through a strong interdisciplinary team with expertise in cardiovascular disease biology, drug discovery, translational medicine, omics technologies, and more. CarTarDis will utilize unique human cohort data, biobanks, CVD models and samples to generate a candidate target database, review targets, validate a shortlist, and create online dossiers to share knowledge on selected targets. The goal is to prioritize 11 targets for further validation activities to identify new treatments for cardiovascular disease.
Open Research Gateway for the ELIXIR-GR Infrastructure (Part 2)OpenAIRE
OpenAIRE is a European infrastructure that helps stakeholders comply with open access policies by providing tools and services. It operates repositories, dashboards, and tools to help share and reuse research outputs in accordance with FAIR principles. OpenAIRE also coordinates activities through national open access desks and outreach to promote open science practices. Researchers can use OpenAIRE to publish open access works, deposit data, write data management plans, and link research outputs.
The OpenAIRE project, in the vanguard of the open access and open data movements in Europe was commissioned by the EC to support their nascent Open Data policy by providing a catch-all repository for EC funded research. CERN, an OpenAIRE partner and pioneer in open source, open access and open data, provided this capability and Zenodo was launched in May 2013.
In support of its research programme CERN has developed tools for Big Data management and extended Digital Library capabilities for Open Data. Through Zenodo these Big Science tools could be effectively shared with the long-tail of research.
Unlocking Thesis Data - Stephen Grace, University of East LondonRepository Fringe
This document discusses unlocking thesis data by making it openly available online. It notes the benefits of doing so for students, funders, institutions, and researchers. It also provides examples of case studies from several universities that have assigned digital object identifiers (DOIs) to student theses to make them easily identifiable and citable. The document seeks feedback on what systems can be used to create and use persistent identifiers for thesis data and what type of data should or could be deposited online.
OpenAIRE Presentation @3AMconf - Supporting Research Analytics by OpenAIRE Us...OpenAIRE
Poster presentation at 3AM conference (Sept. 2016, Bucharest), by Dimitris Pierrakos, ATHENA Research & Innovation Center (poster co-authors: Jochen Schirrwagen, Bielefeld University; Pedro Príncipe, University of Minho).
Jisc on repositories unleashing data - Daniela DucaRepository Fringe
Jisc aims to make the UK the most digitally advanced education and research nation. It supports research through developing shared infrastructure, providing input to funders and publishers, and supporting standards. It is working on two relevant projects: the UK Research Data Discovery Service, which aims to make research data more discoverable by evaluating metadata models from Australia and Canada; and Research Data Metrics, which is scoping a tool to assess data usage and management systems through a proof of concept using the IRUS dataset.
OpenAIRE Content Providers Community Call, July 1st, 2020
This call was focused on Data Repositories namely the OpenAIRE Research Graph and Data Repositories, the OpenAIRE Content Acquisition Policy, and the Guidelines for Data Archive Managers.
Was also an opportunity to share the most recent updates and novelties in the OpenAIRE Content Provider Dashboard, and to get feedback from community.
Follow the Community activities at https://www.openaire.eu/provide-community-calls
Open data in ubi systems research data management plan (part 4)Heli Väätäjä
This slideset motivates to creating a data management plan and gives initial advice. Slides are from the seminar on Open Data in Ubiquitous Systems Research aimed for doctoral students in HCI and CS.
EOSC-hub and OpenAIRE-Advance collaboration (Presentation at RDA 11th plenary)OpenAIRE
Presentation by Paolo Manghi (CNR-ISTI and OpenAIRE) ath the RDA 11th plenary BoF meeting - EOSC-related European Projects getting Global: Engaging with the RDA.
Research data discovery in OpenAIRE (Presentation by Paolo Manghi at DI4R2018)OpenAIRE
"Research data discovery in OpenAIRE".
Presentation by Paolo Manghi from CNR-ISTI, at the Digital Infrastructures Conference 2018, Lisbon. Session: Building better collaborative national networks to support Open Science (Oct. 11, 2018)
The document discusses interest from researchers at other universities in Edinburgh's integration of electronic lab notebooks (ELNs) with research data management systems (RDMS). It summarizes the key benefits of RSpace, Edinburgh's ELN and RDMS, including its ability to capture, organize, and share data and files. It connects to Edinburgh's data storage systems and is integrated with their data repository and archive. This provides researchers an integrated research data management workflow.
Building data networks: exploring trust and interoperability between authoris...Repository Fringe
Building data networks: exploring trust and interoperability between authoris, repositories and journals. Varsha Khodiyar , Scientific Data; Neil Chue Hong, Journal of Open Research Software; Rachael Kotarski, DataCite, Peter McQuilton, BioSharing; Reza Salek, Metabolights. At Repository Fringe 2015
ChemAxon provides a suite of informatics tools and applications to help scientists manage chemical data. They have developed these tools together with customers and partners. ChemAxon is considered the market leader in mainstream chemical structure handling tools. Their portfolio offers the broadest range of solutions and good value. ChemAxon's tools allow for extraction of chemistry information from text documents and enable curation and visualization of chemical data.
Clinical Data Models - The Hyve - Bio IT World April 2019Kees van Bochove
Population genetics and genomics is an emerging topic for the application of machine learning methods in healthcare and biomedical sciences. Currently, several large genomics initiatives, such as Genomics England, UK Biobank, the All of Us Project, and Europe's 1 Million Genomes Initiative are all in the process of making both clinical and genomics data available from large numbers of patients to benefit biomedical research. However, a key challenge in these initiatives is the standardization of the clinical and outcomes data in such a way that machine learning methods can be effectively trained to discover useful medical and scientific insights. In this talk, we will look at what data is available at scale, and review some of examples of the application of common data and evidence models such as OMOP, FHIR, GA4GH etc. in order to achieve this, based on projects which The Hyve has executed with some of these initiatives to harmonize their clinical, genomics, imaging and wearables data and make it FAIR.
SciBite monitors drug discovery information on the internet 24/7 using text analytics tools. They provide free and paid services including a Twitter-like news feed for the biotech industry and a dashboard for analyzing the therapeutic landscape. Their text mining software, Termite, can identify topics in biomedical texts and is customized for challenges in the domain. SciBite also offers ontologies, APIs, and tools for augmenting enterprise searches.
GigaByte Chief Editor Scott Edmunds presents on how to prepare a data paper for the TDR and WHO sponsored call for data papers describing datasets on vectors of human diseases launched in Nov 2021. Presented at the GBIF webinar on 25th January 2022 and aimed at authors interested in submitting a manuscript submitted to the series.
2019-10-11 The value of FAIR data in health data networks - The Hyve - ELIXIR...Kees van Bochove
This presentation at the ELIXIR SME Innovation meeting on Personal Health Train and the distributed analysis of health data covered the value of data in health data networks. Slides attached for reference purposes.
#ELIXIR #SME #PHT #personalhealthtrain #healthdata
Business searching for engineering 185 fri am power point april 18 2014Michael Oppenheim
This document provides an overview of strategies and sources for locating business information. It discusses developing efficient research strategies, finding industry and company information, market and consumer information, and government regulations. Sample databases and resources are demonstrated, including IBISWorld, MarketLine, Business Source Complete, Factiva, MarketResearch.com, SimplyMap, American FactFinder, and government agency websites. Attendees are encouraged to follow up with the librarian presenter for any future research questions.
New ways to communicate in science: perspectives from biodiversity researchVince Smith
A presentation given at the co-ordination workshop on Open Access to Scientific Information on Wednesday 4th May 2011 at the EU DG Information Society & Media, Avenue de Beaulieu 25, Brussels.
mHealth Israel_Martin Hirsch_CEO_APHP_Greater Paris University Hospitals_Nov,...Levi Shapiro
Presentation for mHealth Israel by Martin Hirsch, CEO, l' APHP (Greater Paris University Hospitals), Nov 20, 2016. Includes an overview of the 39 hospitals in the system, IT processes and infrastructure, Clinical Data Warehouse, Genomics / bio-informatics platform
This document discusses opportunities for using the open source cBioPortal platform in a commercial setting. It summarizes The Hyve's experiences supporting cBioPortal for the Center for Translational Molecular Medicine's TraIT project. The Hyve provides professional support for open source bioinformatics software like cBioPortal through software development, data services, consultancy, and hosting. For translation projects, The Hyve employs a phased approach including definition, pilot, implementation, and evaluation phases to implement cBioPortal and demonstrate its capabilities for data integration and analysis.
Bio Data World - The promise of FAIR data lakes - The Hyve - 20191204Kees van Bochove
At the Bio Data World conference in Basel in December 2019, Kees van Bochove, Founder of The Hyve gave a talk on re-use of pharma R&D data, and what strategies could be used to realize operationalization of FAIR data at scale.
The OpenAIRE project, in the vanguard of the open access and open data movements in Europe was commissioned by the EC to support their nascent Open Data policy by providing a catch-all repository for EC funded research. CERN, an OpenAIRE partner and pioneer in open source, open access and open data, provided this capability and Zenodo was launched in May 2013.
In support of its research programme CERN has developed tools for Big Data management and extended Digital Library capabilities for Open Data. Through Zenodo these Big Science tools could be effectively shared with the long-tail of research.
Unlocking Thesis Data - Stephen Grace, University of East LondonRepository Fringe
This document discusses unlocking thesis data by making it openly available online. It notes the benefits of doing so for students, funders, institutions, and researchers. It also provides examples of case studies from several universities that have assigned digital object identifiers (DOIs) to student theses to make them easily identifiable and citable. The document seeks feedback on what systems can be used to create and use persistent identifiers for thesis data and what type of data should or could be deposited online.
OpenAIRE Presentation @3AMconf - Supporting Research Analytics by OpenAIRE Us...OpenAIRE
Poster presentation at 3AM conference (Sept. 2016, Bucharest), by Dimitris Pierrakos, ATHENA Research & Innovation Center (poster co-authors: Jochen Schirrwagen, Bielefeld University; Pedro Príncipe, University of Minho).
Jisc on repositories unleashing data - Daniela DucaRepository Fringe
Jisc aims to make the UK the most digitally advanced education and research nation. It supports research through developing shared infrastructure, providing input to funders and publishers, and supporting standards. It is working on two relevant projects: the UK Research Data Discovery Service, which aims to make research data more discoverable by evaluating metadata models from Australia and Canada; and Research Data Metrics, which is scoping a tool to assess data usage and management systems through a proof of concept using the IRUS dataset.
OpenAIRE Content Providers Community Call, July 1st, 2020
This call was focused on Data Repositories namely the OpenAIRE Research Graph and Data Repositories, the OpenAIRE Content Acquisition Policy, and the Guidelines for Data Archive Managers.
Was also an opportunity to share the most recent updates and novelties in the OpenAIRE Content Provider Dashboard, and to get feedback from community.
Follow the Community activities at https://www.openaire.eu/provide-community-calls
Open data in ubi systems research data management plan (part 4)Heli Väätäjä
This slideset motivates to creating a data management plan and gives initial advice. Slides are from the seminar on Open Data in Ubiquitous Systems Research aimed for doctoral students in HCI and CS.
EOSC-hub and OpenAIRE-Advance collaboration (Presentation at RDA 11th plenary)OpenAIRE
Presentation by Paolo Manghi (CNR-ISTI and OpenAIRE) ath the RDA 11th plenary BoF meeting - EOSC-related European Projects getting Global: Engaging with the RDA.
Research data discovery in OpenAIRE (Presentation by Paolo Manghi at DI4R2018)OpenAIRE
"Research data discovery in OpenAIRE".
Presentation by Paolo Manghi from CNR-ISTI, at the Digital Infrastructures Conference 2018, Lisbon. Session: Building better collaborative national networks to support Open Science (Oct. 11, 2018)
The document discusses interest from researchers at other universities in Edinburgh's integration of electronic lab notebooks (ELNs) with research data management systems (RDMS). It summarizes the key benefits of RSpace, Edinburgh's ELN and RDMS, including its ability to capture, organize, and share data and files. It connects to Edinburgh's data storage systems and is integrated with their data repository and archive. This provides researchers an integrated research data management workflow.
Building data networks: exploring trust and interoperability between authoris...Repository Fringe
Building data networks: exploring trust and interoperability between authoris, repositories and journals. Varsha Khodiyar , Scientific Data; Neil Chue Hong, Journal of Open Research Software; Rachael Kotarski, DataCite, Peter McQuilton, BioSharing; Reza Salek, Metabolights. At Repository Fringe 2015
ChemAxon provides a suite of informatics tools and applications to help scientists manage chemical data. They have developed these tools together with customers and partners. ChemAxon is considered the market leader in mainstream chemical structure handling tools. Their portfolio offers the broadest range of solutions and good value. ChemAxon's tools allow for extraction of chemistry information from text documents and enable curation and visualization of chemical data.
Clinical Data Models - The Hyve - Bio IT World April 2019Kees van Bochove
Population genetics and genomics is an emerging topic for the application of machine learning methods in healthcare and biomedical sciences. Currently, several large genomics initiatives, such as Genomics England, UK Biobank, the All of Us Project, and Europe's 1 Million Genomes Initiative are all in the process of making both clinical and genomics data available from large numbers of patients to benefit biomedical research. However, a key challenge in these initiatives is the standardization of the clinical and outcomes data in such a way that machine learning methods can be effectively trained to discover useful medical and scientific insights. In this talk, we will look at what data is available at scale, and review some of examples of the application of common data and evidence models such as OMOP, FHIR, GA4GH etc. in order to achieve this, based on projects which The Hyve has executed with some of these initiatives to harmonize their clinical, genomics, imaging and wearables data and make it FAIR.
SciBite monitors drug discovery information on the internet 24/7 using text analytics tools. They provide free and paid services including a Twitter-like news feed for the biotech industry and a dashboard for analyzing the therapeutic landscape. Their text mining software, Termite, can identify topics in biomedical texts and is customized for challenges in the domain. SciBite also offers ontologies, APIs, and tools for augmenting enterprise searches.
GigaByte Chief Editor Scott Edmunds presents on how to prepare a data paper for the TDR and WHO sponsored call for data papers describing datasets on vectors of human diseases launched in Nov 2021. Presented at the GBIF webinar on 25th January 2022 and aimed at authors interested in submitting a manuscript submitted to the series.
2019-10-11 The value of FAIR data in health data networks - The Hyve - ELIXIR...Kees van Bochove
This presentation at the ELIXIR SME Innovation meeting on Personal Health Train and the distributed analysis of health data covered the value of data in health data networks. Slides attached for reference purposes.
#ELIXIR #SME #PHT #personalhealthtrain #healthdata
Business searching for engineering 185 fri am power point april 18 2014Michael Oppenheim
This document provides an overview of strategies and sources for locating business information. It discusses developing efficient research strategies, finding industry and company information, market and consumer information, and government regulations. Sample databases and resources are demonstrated, including IBISWorld, MarketLine, Business Source Complete, Factiva, MarketResearch.com, SimplyMap, American FactFinder, and government agency websites. Attendees are encouraged to follow up with the librarian presenter for any future research questions.
New ways to communicate in science: perspectives from biodiversity researchVince Smith
A presentation given at the co-ordination workshop on Open Access to Scientific Information on Wednesday 4th May 2011 at the EU DG Information Society & Media, Avenue de Beaulieu 25, Brussels.
mHealth Israel_Martin Hirsch_CEO_APHP_Greater Paris University Hospitals_Nov,...Levi Shapiro
Presentation for mHealth Israel by Martin Hirsch, CEO, l' APHP (Greater Paris University Hospitals), Nov 20, 2016. Includes an overview of the 39 hospitals in the system, IT processes and infrastructure, Clinical Data Warehouse, Genomics / bio-informatics platform
This document discusses opportunities for using the open source cBioPortal platform in a commercial setting. It summarizes The Hyve's experiences supporting cBioPortal for the Center for Translational Molecular Medicine's TraIT project. The Hyve provides professional support for open source bioinformatics software like cBioPortal through software development, data services, consultancy, and hosting. For translation projects, The Hyve employs a phased approach including definition, pilot, implementation, and evaluation phases to implement cBioPortal and demonstrate its capabilities for data integration and analysis.
Bio Data World - The promise of FAIR data lakes - The Hyve - 20191204Kees van Bochove
At the Bio Data World conference in Basel in December 2019, Kees van Bochove, Founder of The Hyve gave a talk on re-use of pharma R&D data, and what strategies could be used to realize operationalization of FAIR data at scale.
The section provides an overview of the open science requirements and how to comply with them stipulated by selected funders and organizations: H2020 & ERC, FWO and Belspo by Emilie Hermans
Using Healthcare Data for Research @ The Hyve - Campus Party 2016Kees van Bochove
In this presentation, Kees van Bochove, founder & CEO of The Hyve, a services company in biomedical open source software, presents a number of different types of healthcare data. As an example, he also provides details of a project in which The Hyve participates and which uses that kind of data. Covered are: translational medicine data using tranSMART and cBioPortal, population health data using OMOP and OHDSI, and personal health data processing using open mHealth Shimmer and Apache Kafka.
As BioPharma adapts to incorporate nimble networks of suppliers, collaborators, and regulators the ability to link data is critical for dynamic interoperability. Adoption of linked data paradigm allows BioPharma to focus on core business: delivering valuable therapeutics in a timely manner.
Ontoforce: A Testimonial of a Start-up Companyimec
This document summarizes the testimonial of a startup company that has developed a data integration platform called DISQOVER to aggregate and link vast amounts of healthcare and life sciences data. The company has received over €770K in funding since 2012. It has grown its user base to over 100 users and integrated over 20 external databases. Its goals are to provide worldwide access to heterogeneous data for all researchers in an intuitive interface, and to ultimately make a difference for patients worldwide.
The document discusses open science and open innovation. It describes how open access to scientific data, publications, code, and workflows through online platforms is enabling new forms of collaborative scientific inquiry across traditional boundaries. Global collaboratories can now engage in research at unprecedented scales using open data. The benefits of open science include accelerating scientific discovery, empowering citizens and entrepreneurs to make new innovations based on open data and code, and transforming the nature of scientific research.
Open Insights Harvard DBMI - Personal Health Train - Kees van Bochove - The HyveKees van Bochove
In this talk, the Personal Health Train concept will be introduced, which enables running personalized medicine workflows as trains visiting data stations (e.g. hospital records, primary care records, clinical studies and registries, patient-held data from e.g. wearable sensors etc.) The Personal Health Train is a very powerful concept, which is however dependent on source medical data to be coded with appropriate metadata on consent, license, scope etc. of the data, and the data itself to be encoded using biomedical data standards, which is an ever growing field in biomedical informatics. In order to realize the Personal Health Train biomedical data will need to be FAIR, i.e. adopt the FAIR Guiding Principles. This talk will cover the emerging GO-FAIR international movement, and provide examples of how several European health data networks currently are adopting open standards based stacks, to enable routine health care data to be come accessible for research.
How 2019 became the year FAIR landed in biopharmaceutical R&DKees van Bochove
At the Pharma IT 2019 conference in London, Kees van Bochove, Founder of The Hyve gave a talk on how 2019 became the year in which many biopharmaceutical companies have operational programs to make data FAIR across the enterprise.
An open science introduction. Olinfer 18, La havana, Cuba 12-14 nov 2018pascal aventurier
Open Science is the practice of conducting science openly, where research data, lab notes and processes are freely available under terms of reuse. It promotes collaboration and contributions from others. The document discusses benefits like increased verification, reduced duplication and innovation. It also covers topics like open access, research data management, data repositories, and the FAIR principles. The goal of Open Science is greater efficiency, transparency and interdisciplinary work.
This presentation was provided by Violeta Ilik of Northwestern University during the NISO Virtual Conference held on Feb 15, 2017, entitled Institutional Repositories: Ensuring Yours is Populated, Useful and Thriving. The DOI for this presentation is http://dx.doi.org/10.18131/G3VP6R
Persistent Identifiers (PiDs) for research – why we have them, why there are so many PiD systems, how they work looking at a few examples (Handles, DOIs, ORCIDs), how to choose one, can PiD systems fail and what’s happening in the international PiD community
Training Experiences across Ris: OpenAIRE - Building a Trainers Community of ...EUDAT
1) The document discusses OpenAIRE's training experiences across Research Infrastructures (RIs) and building a community of practice for trainers. It promotes several OpenAIRE webinars during Open Access Week 2017 on topics like open science workflows, tools, and policies.
2) An upcoming workshop at the Open Science Fair conference is highlighted, where OpenAIRE, EGI, GEANT and other national e-infrastructures will discuss coordination opportunities around open scholarship, technical services, training and community engagement.
3) The webinars aim to target OpenAIRE stakeholders and focus on Horizon 2020 open access and data requirements using real project examples. Subjects are based on needs identified by national open access desks
Open Science: políticas e herramientas en Europa - Universidad de CantabriaPedro Príncipe
The document discusses open science policies and tools in Europe. It provides an overview of open access and open data policies in Horizon 2020, the European Union's research and innovation programme. Key points include:
- Horizon 2020 requires open access publication of research results and open data sharing where possible.
- OpenAIRE provides services and infrastructure to support open access, open data, and compliance with Horizon 2020 policies through depositing publications and research data.
- OpenAIRE offers discovery, reporting, and helpdesk services to help researchers and projects share results openly.
General introduction to Open Data Policies H2020, influence of OD policies on...Nancy Pontika
This document provides an overview of open data policies in Horizon 2020 (H2020) research projects. It discusses how H2020 mandates open access to peer-reviewed publications and research data generated by projects. Projects participating in the H2020 Open Research Data Pilot are required to make their data publicly available by depositing it in an open research data repository. Exceptions can be made if openly sharing the data would jeopardize commercialization, privacy, or the project's main goals. The document also outlines licensing options, metadata standards, and resources like Zenodo that can help researchers comply with H2020 open data requirements.
Let's work towards a #SaferWorldbyDesign - Knowledge-integrated Toxicology an...Barry Hardy
Let's work towards a #SaferWorldbyDesign - Knowledge-integrated Toxicology and Safety Assessment, Barry Hardy, OpenTox Asia 2019, Hyderabad, India. To make a good decision we need to bring both expertise and relevant information together to form the basis for a structured well-informed discussion leading to best judgement based on available evidence and opinions formed on it. Such a knowledge integration is required in many areas of toxicology and safety assessment based on scientific knowledge generated by a growing number of alternative testing research methods and initiatives. Integration may include evidence from in vitro or in silico methods, biology or chemistry, science and engineering, human health or environment-oriented, and requires both effective organisation of knowledge and communications to reach common understandings.
The requirements, context and format for applications may vary e.g., asking and answering scientific questions, carrying out a risk assessment on products, or performing a regulatory decision or submission. All applications however require a sound reproducible scientific basis and the use of good practices in characterising experiments, organising data and describing concepts in our ontology and knowledge framework.
There is a growing opportunity to develop knowledge integration based on combining emerging concepts and frameworks e.g., OpenTox for data integration and resource interoperability, adverse outcome pathways for mapping data to events, evidence-based methods including systematic review applied to weight of evidence and read across methods for combining evidence from chemical or biological mechanistic categories.
We also need community frameworks to bring different disciplines together for fruitful interactions and discussions.
In this seminar we will review recent developments related to integrated testing and assessment including applications to chemicals, cosmetic ingredients and nanotechnology and including 3Rs goals of reducing and replacing animal testing.
The document discusses policy, infrastructure, skills, and incentives related to data sharing in Africa. It provides information about the University of Botswana, including its faculties, research centers, and digital repository. It then discusses the upcoming International Data Week conference in Gaborone, Botswana, and themes related to digital science such as open data, data analysis, and data stewardship. Finally, it summarizes the proposed African Open Science Platform project to coordinate open science activities across Africa through a centralized initiative.
The document summarizes a research partnership between The Watershed Media Centre in Bristol and HP Labs Bristol that began in the mid-1990s and involved several collaborative projects using new digital technologies. It describes three key projects - Mobile Bristol, which explored uses of mobile technology in urban spaces; SE3D, an animation showcase that tested HP's rendering service; and various projects under the Interactive Building program that integrated interactive exhibits into Watershed's facilities. The partnership provided benefits to both organizations and helped foster innovative uses of emerging technologies.
Similar to The Hyve introduction TranSMART Annual Meeting 2015 Amsterdam (20)
Open science and medical evidence generation - Kees van Bochove - The HyveKees van Bochove
Presentation about open science, the FAIR principles, and medical evidence generation with the OHDSI COVID-19 study-a-thon as an example. I've used variations on this deck in a couple of classroom and online courses for PhD and master students early 2020.
Business context of FAIR health data networks - The Hyve - MEDINFO Lyon 2019Kees van Bochove
MedInfo Lyon 2019: FAIR Health Data Sharing Initiatives in Europe: Opportunities and Challenges for international cooperation (Ulli Prokosch, Thomas Ganslandt, Ulrich Sax, Christian Lovis, Carlos Luis Parra Calderón, Peter Rijnbeek, Nigel Hughes, Wiro Niessen, Barend Mons, Kees Van Bochove)
In the data-driven age of medical research many initiatives and projects focus on data linkage and functional integration as well as data reuse. Providing “FAIR data” is a common challenge for all of them. For this workshop leaders of six nation-wide and European initiatives/projects have joined in order to identify the major concepts, challenges and hurdles.
This presentation was used to provide the business context of FAIR data in health data networks.
https://www.youtube.com/watch?v=5YqAH3f9LiU
Digital Transformation is a key goal of many large and small companies, as well as of most research institutes today. However, a key prerequisite and enabler of digital transformation is computational accessibility and interoperability of data, as laid out in the FAIR Data principles. The Hyve has been involved in the FAIR Data movement since the start, and for this webinar, our CEO Kees van Bochove will be talking to a very special guest, Ruben Kok, director of DTL. DTL and its predecessor NBIC, as well as ‘spinoff’ GO-FAIR have spent an enormous amount of effort in the past years on outreach, training, tools and community building around the FAIR Data Principles. Where do we stand today? What can we expect to see in the coming years for FAIR and FAIR biomedical data (e.g. Personal Health Train) in particular?
https://youtu.be/C95pl11zdAs
Many countries around the world are starting to organise national health data research networks, investing hundreds of millions of dollars, euros, yuan, pounds, etc. in such initiatives. Some of these are organized by the government, such as the NIH All of Us Program in the U.S. and Genomics England, others are started by businesses such as PatientsLikeMe or by patient organizations such as DuchenneConnect. And then there are research-driven infrastructures such as ELIXIR and BBMRI and multi-stakeholder initiatives such as PCORI and HealthRI.
During this webinar, we are going to discuss the current technical practice of establishing health data research infrastructures, our experience in building them or advising on that, and the key elements of success that one should not overlook in order to build a healthy, long-lasting health data research network.
FAIR Data Experiences - Kees van Bochove - The HyveKees van Bochove
Talk at Bio IT World 2018 FAIR Data for Genomic Applications track.
Implementation of the FAIR Data Principles is a crucial step for all organizations pursuing a (biomedical) data-driven strategy, both to improve the effectiveness of scientists and doctors as well as computerized aides and autonomous programs. This talk will provide a number of concrete examples of how various customers of The Hyve, including large pharma companies, biobanks and registries and national health data sharing initiatives, have employed data FAIRification strategies to improve the (re)usability of their healthcare and biology data, and of the open source software tools and standards that are used and being further developed for that purpose.
SCOPE Summit - Applying the OMOP data model & OHDSI software to national Euro...Kees van Bochove
Talk from Kees van Bochove, The Hyve at SCOPE Summit, Real World Data track, Jan 26, 2017, Miami
A large open source initiative for standardisation and epidemiological analysis for real world data is OHDSI: Observational Health Data Sciences and Informatics. OHDSI leverages the OMOP common data model for observational data, and provides data analysis tools for a broad range of use cases. This talk will explain OMOP and OHDSI with case study IMI EMIF, in which health data from over 50 million patients from 13 national and regional European registries is brought together.
Usage of open source software for Real World Data Analysis in pharmaceutical ...Kees van Bochove
An upcoming area of interest for biopharmaceutical product development, as well as for public health and healthcare system evaluation, is the study of medical outcomes in so-called 'real world data'. This data can originate from electronic medical records in hospitals, general practitioners, pharmacies, insurance companies and even directly from patients, using forums or mobile health apps.
One of the largest open source initiatives for the standardisation and analysis for this type of data is called OHDSI: Observational Health Data Sciences and Informatics. OHDSI leverages the OMOP data model for observational data, and provides data analysis tools for a broad range of use cases. This talk will focus on a number of examples of the application of the OHDSI tooling for observational research, as well as provide a broader introduction of the topic and the use of open source software in pharmaceutical and healthcare context.
The presenter, Kees van Bochove, is founder and CEO of The Hyve, a company based in Utrecht, The Netherlands and Cambridge, MA, US that provides services around open source software in bioinformatics and translational research, such as OHDSI, tranSMART and cBioPortal.
During the tranSMART Annual Meeting 2015, Kees van Bochove, chair of the tranSMART Foundation Architecture Working Group, presented on current tranSMART development highlights, which illustrate how the tranSMART core database layer and APIs enables a range of varying translational research applications.
During the tranSMART Annual Meeting 2015, a hackathon will take place for developers to work an a few proof of concepts innovations around tranSMART, also preparing for the future 2.0 version of the platform. There will be two main topics during this hackathon, one catering to backend and one more to frontend developers.
The topics are:
building a POC around using SparkR on Amazon EC2 as a computational backend for tranSMART 1.3
improving the visual analytics in tranSMART, by updating or adding analytics workflows in the SmartR plugin
The reason for choosing these topics are:
For SparkR: Spark is the most active project in data science at the moment, with a lot of innovation and big names behind it. It makes sense to explore how we can optimally leverage this in the next version of the tranSMART platform. For this hackathon, a specific proposal has been prepared to use SparkR on top of the tranSMART core API to take advantage of the parallelization and lazy execution capabilities of Spark.
For Visual Analytics: the analytics in tranSMART are useful to get a quick overview of the data available in the platform, and one of the most visible and useful capabilities for early adopters to understand the value of the platform. The recently developed SmartR plugin (presented elsewhere in the meeting) provides already a few interactive analytics workflows, improving those and adding new ones is identified as a good opportunity for the hackathon.
Ideas for specific analytics workflows to work on are most welcome, and of course we are looking forward to welcome again both beginners and tranSMART developer ninja's in this years' sessions!
Open Source Collaboration in Drug Discovery in PharmaKees van Bochove
How pre-competitive collaboration in the pharmaceutical sector through open source platforms enables joint innovation of academics, pharma, SMEs and non-profits.
Explore the key differences between silicone sponge rubber and foam rubber in this comprehensive presentation. Learn about their unique properties, manufacturing processes, and applications across various industries. Discover how each material performs in terms of temperature resistance, chemical resistance, and cost-effectiveness. Gain insights from real-world case studies and make informed decisions for your projects.
2. 2
The Hyve
u Professional
support
for
open
source
so0ware
for
bioinforma4cs
and
transla4onal
research
so0ware,
such
as
tranSMART,
cBioPortal,
i2b2,
OHDSI,
Galaxy
and
ADAM
Mission
Enable
pre-‐compe44ve
collabora4on
in
life
science
R&D
by
leveraging
open
source
so,ware
Core
values
Share
Reuse
Specialize
Office
Loca5ons
Utrecht,
Netherlands
Cambridge,
MA,
United
States
Services
So0ware
development
Data
science
services
Consultancy
Hos4ng
/
SLAs
Fast-‐growing
Started
in
2012
32
people
by
now
3. Interdisciplinary team
so0ware
engineers,
data
scien4sts,
project
managers
&
staff;
exper4se
in
bioinforma4cs,
medical
informa4cs,
so0ware
engineering,
biosta4s4cs
etc.
3
6. Open Source
u Source code openly accessible and reusable for everyone
u Enables pre-competitive collaboration: both academics and
industry can use and enhance it à leverage public funding
u Transparency: verification (scientific as well as IT security) can be
done by anyone, no ‘black box’
Consumer market examples:
7. 7
Why open source?
u Leverage joint innovation power of academics, industry and SME’s
u Leverage public funding from EU and NIH
u Build a joint product roadmap and combine investments
u Proven model: works very well in cloud computing (Linux, OpenStack),
in web development and for data science in general (R, Spark etc.)
u Prerequisite: collaboration à community building
8. 8
Open Source in Precision Medicine
Study
design:
Biobanking:
Scientific compute:
Data visualisation:
Workflow / NGS:
Datawarehousing:
Imaging:
Clinical - eCRF & apps: