OpenAIRE: Open Science as-a-Service - presentation at #DI4R2016OpenAIRE
Presentation at the Digital Infrastructures for Research 2016 Conference (Sept 30). Title: OpenAIRE: Open Science as-a-Service, by Paolo Manghi, CNR-ISTI
Webinar: Data management and the Open Research Data Pilot in Horizon 2020OpenAccessBelgium
This webinar provides information about strategies for successful Research Data Management, resources to help manage data effectively, choosing where to store and deposit data, the EC H2020 Open Data Pilot and the basics of data management.
At the end of the session participants will be able to:
- Understand the basic principles and importance of RDM
- Set clear goals regarding data curation, preservation and sharing
- Comply with the requirements of the Research Data Pilot
- Draft a Data Management Plan
- Identify RDM resources and tools
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).
OpenAIRE: Open Science as-a-Service - presentation at #DI4R2016OpenAIRE
Presentation at the Digital Infrastructures for Research 2016 Conference (Sept 30). Title: OpenAIRE: Open Science as-a-Service, by Paolo Manghi, CNR-ISTI
Webinar: Data management and the Open Research Data Pilot in Horizon 2020OpenAccessBelgium
This webinar provides information about strategies for successful Research Data Management, resources to help manage data effectively, choosing where to store and deposit data, the EC H2020 Open Data Pilot and the basics of data management.
At the end of the session participants will be able to:
- Understand the basic principles and importance of RDM
- Set clear goals regarding data curation, preservation and sharing
- Comply with the requirements of the Research Data Pilot
- Draft a Data Management Plan
- Identify RDM resources and tools
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).
Scaling Usage Statistics across Repositories as an OpenAIRE Analytics Service...OpenAIRE
Presentation at the Open Repositories conference - 14 June 2016. Abstract:
Dimitris Pierrakos1, Jochen Schirrwagen2, Pedro Príncipe3, Ricardo Saraiva3
1ATHENA Research & Innovation Center, Greece; 2Bielefeld University; 3University of Minho
Usage metrics about scholarly output, such as publications and research data, are one of the measures to assess Open Access impact. The OpenAire 2020 [1] project aims to offer a service that monitors and analyzes usage information, as well as exploits usage metrics like views and downloads, which could be used as complements of bibliometrics and webometrics. In this paper, we present the first step towards the implementation of this service, manifested as a pilot run in a set of repositories, together with some initial results which illustrate the use of the applied methodology.
Research Data Management in GLAM: Managing Data for Cultural HeritageSarah Anna Stewart
Presentation given at the 'Open Science Infrastructures for Big Cultural Data' - Advanced International Masterclass in Plovdiv, Bulgaria. Dec. 13-15, 2018
Presented by by Luis Martinez-Uribe & Stuart Macdonald at IASSIST 2011, Simon Fraser University, Vancouver, 2 June 2011, http://www.rdl.sfu.ca/IASSIST/
Connecting the dots - e-Infra services for open scienceOpenAIRE
Starting from Open access towards services for open science, we present OpenAIRE, OpenMinTeD and OpenUP, three EU projects that build services to facilitate and accelerate open science.
The slides that supported the workshop "Accelerating data reuse: international initiatives? what role for the European Commission?" on February 27th, 2013, in Marseille, introducing the ENGAGE platform, and animated by Valerie BRASSE
Supporting Research Data Management in UK Universities: the Jisc Managing Res...L Molloy
Research data management in the UK: interventions by the Jisc Managing Research Data programme and the Digital Curation Centre. Specifies the importance of academic librarians for RDM. Includes links to openly available training resources. Presentation by L Molloy to ExLibris event, 'Excellence in Academic Knowledge Management', Utrecht, 29 October 2013.
Webinar about the Open Access mandate of the EC for Horizon 2020 projects.
* Open revisited & Open Access
* OA policy development in H2020
* Open Access in Horizon 2020
* What does OpenAIRE offer?
* How can OpenAIRE help?
Scaling Usage Statistics across Repositories as an OpenAIRE Analytics Service...OpenAIRE
Presentation at the Open Repositories conference - 14 June 2016. Abstract:
Dimitris Pierrakos1, Jochen Schirrwagen2, Pedro Príncipe3, Ricardo Saraiva3
1ATHENA Research & Innovation Center, Greece; 2Bielefeld University; 3University of Minho
Usage metrics about scholarly output, such as publications and research data, are one of the measures to assess Open Access impact. The OpenAire 2020 [1] project aims to offer a service that monitors and analyzes usage information, as well as exploits usage metrics like views and downloads, which could be used as complements of bibliometrics and webometrics. In this paper, we present the first step towards the implementation of this service, manifested as a pilot run in a set of repositories, together with some initial results which illustrate the use of the applied methodology.
Research Data Management in GLAM: Managing Data for Cultural HeritageSarah Anna Stewart
Presentation given at the 'Open Science Infrastructures for Big Cultural Data' - Advanced International Masterclass in Plovdiv, Bulgaria. Dec. 13-15, 2018
Presented by by Luis Martinez-Uribe & Stuart Macdonald at IASSIST 2011, Simon Fraser University, Vancouver, 2 June 2011, http://www.rdl.sfu.ca/IASSIST/
Connecting the dots - e-Infra services for open scienceOpenAIRE
Starting from Open access towards services for open science, we present OpenAIRE, OpenMinTeD and OpenUP, three EU projects that build services to facilitate and accelerate open science.
The slides that supported the workshop "Accelerating data reuse: international initiatives? what role for the European Commission?" on February 27th, 2013, in Marseille, introducing the ENGAGE platform, and animated by Valerie BRASSE
Supporting Research Data Management in UK Universities: the Jisc Managing Res...L Molloy
Research data management in the UK: interventions by the Jisc Managing Research Data programme and the Digital Curation Centre. Specifies the importance of academic librarians for RDM. Includes links to openly available training resources. Presentation by L Molloy to ExLibris event, 'Excellence in Academic Knowledge Management', Utrecht, 29 October 2013.
Webinar about the Open Access mandate of the EC for Horizon 2020 projects.
* Open revisited & Open Access
* OA policy development in H2020
* Open Access in Horizon 2020
* What does OpenAIRE offer?
* How can OpenAIRE help?
Archiving archaeological data in Austria, Edeltraud Aspöck, Anja Masur OREA/ÖAWariadnenetwork
This presentation on archiving archaeological data in Austria, given by Edeltraud Aspöck and Anja Masur of OREA/ÖAW, was part of a workshop focussing on the long-term preservation of digital data. The workshop looked at the topic from various angles and from the perspective of the needs of users in different fields of the Humanities. In their presentation, Aspöck and Masur talked aobut the archiving of archaeological research archives in Austria, and work within within the ARIADNE project to set up a metadata registry of such research archives.
Integrating archaeological data: The ARIADNE Infrastructure, Achille Felicett...ariadnenetwork
This presentation by Achille Felicetti of PIN (Università degli Studi di Firenze, Prato) on the work by the ARIADNE infrastructure to integrating archaeological data was given as part of a workshop organised by Digital Humanities Austria. The workshop focussed on the pressing question of long-term preservation of digital data from various angles, central being user needs specific to the different fields of the Humanities. Felicetti introduced the ARIADNE research infrastructure, which has been funded by the EC's FP7 programme, to integrate archaeological research datasets from across Europe and support their uses by researchers.
Open Data in Archaeology, Julian D. Richardsariadnenetwork
Open Data in Archaeology, presentation by Julian D Richards given at the Opening the Past 2013 conference, Pisa, 13 June 2013
Introduction to Open Data in Archaeology, the benefits and challenges. The Archaeology Data Service is presented as a case study of the UK's national research data infrastructure alongside examples from other countries, such as EDNA in the Netherlands, SND in Sweden, IANUS in Germany, Open Context and tDAR in the United States, Sustainable Archaeology in Canada, and FAIMS in Australia. The development of international frameworks in Europe from ARENA to ARIADNE are described.
http://www.ariadne-infrastructure.eu
Digital preservation and access in a European perspective: Introducing ARIADNEariadnenetwork
Préservation numérique et accès aux données
dans une perspective européenne:
Introduction à ARIADNE
Presentation in English and French
Présentation en anglais et en français
Julian Richards
Director, Archaeology Data Service, University of York, UK
Federico Nurra
Service Activités Internationales, DST, Inrap, France
Identity criteria and fundamental concepts in archaeology: the case of the ar...ariadnenetwork
Presentation by:
Sorin Hermon (STARC, The Cyprus Institute),
Franco Niccolucci (PIN),
Martin Doerr (ICS-FORTH)
and Gerald Hiebel (ICS-FORTH),
EAA 2013 in the 'New Digital Developments in Heritage Management and Research' session
Pilsen, Czech Republic
5 September 2013
A First Attempt at Describing, Disseminating and Reusing Methodological Knowl...ariadnenetwork
Presentation by Cesar Gonzalez-Perez, (Incipit) and Patricia Martín-Rodilla.
Spanish National Research Council (CSIC)
EAA 2013 in the 'New Digital Developments in Heritage Management and Research' session
Pilsen, Czech Republic
5 September 2013
Dalla pianificazione alla valorizzazione del patrimonio diffuso: co-design e ...ariadnenetwork
From planning to the enhancement of
widespread heritage : co - design and virtual museums
Sophia Pescarin, CNR ITABC, Roma
Landscape and Archaeology Conference
Faro, Italy
23-25 june 2016
Ariadne Booklet 2016: Building a research infrastructure for Digital Archaeol...ariadnenetwork
Authors:
Kate Fernie (PIN and 2Culture Associates Ltd)
Franco Niccolucci (PIN)
Julian Richards (University of York)
Contributors:
Achille Felicetti, Ilenia Galluccio and Paola Ronzino (PIN),
Bruno Fanini (ITABC CNR)
Carlo Meghini, Matteo Dellepiane and Roberto Scopigno (ISTI CNR)
Dimitris Gavrilis (Athena Research Centre)
Douglas Tudhope (University of South Wales)
Elizabeth Fentress (AIAC)
Guntram Geser (Salzburg Research)
Holly Wright (University of York)
Johan Fihn (SND)
Maria Theodoridou (ICS Forth)
Enabling better science - Results and vision of the OpenAIRE infrastructure a...Paolo Manghi
Enabling better science: presentation on the results and vision of the OpenAIRE infrastructure and RDA Publishing Data Services Working Group in this direction.
OpenAIRE services and tools - presentation at #DI4R2016OpenAIRE
Presentation at Digital Infrastrctures for Research Conference 2016 (Sept. 30). Title: Open Access and Open Data in Horizon 2020: for Research managers and Project Coordinators, by Pedro Príncipe (University of Minho)
Presentació a càrrec de Mireia Alcalá, tècnica de Recursos d'Informació al CSUC, duta a terme al workshop en línia "Research Data Management & Open Science" organitzat per l'IDIBELL el 2 de novembre de 2020.
OpenAIRE content in support of Open Science monitoring (Presentation by Paolo...OpenAIRE
"OpenAIRE content in support of Open Science monitoring".
Presentation by Paolo Manghi from Institute of Information Science and Technologies - CNR, at the Digital Infrastructures Conference 2018, Lisbon - OpenAIRE session: The Who and the How of Open Science: A user journey in Open Science through the lens of OpenAIRE (Oct. 10, 2018)
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)
Manage it locally to share it globally: RDM and Wikimedia CommonsNick Sheppard
Slides for Internet Librarian International 2018 about the Data Management Engagement Award, a first-ever competition launched to elicit new and imaginative ideas for engaging researchers in the practices of good Research Data Management (RDM) - http://www.rdmengagementaward.org/
A user journey in OpenAIRE services through the lens of repository managers -...OpenAIRE
A user journey in OpenAIRE services through the lens of repository managers (I – OpenAIRE interoperability guidelines, the content acquisition policy and the graph expansion)
Presentation on OpenAIRE infrastruture, EC Open Access Mandate, Zenodo repository, and Open Access developments in South Region Countries; by Pedro Príncipe - University of Minho (OpenAIRE Region South Coordinator.
OpenAIRE Content Providers Community Call, November 4th, 2020
This call was focused on the PROVIDE future developments, functionalities wishlist and PROVIDE service in EOSC.
Was also an opportunity to share the most recent updates and novelties in the OpenAIRE Content Provider Dashboard, and to get feedback from community.
Recordings: https://youtu.be/wY4fOS767Us
Follow the Community activities at https://www.openaire.eu/provide-community-calls
OpenAIRE in the European Open Science Cloud (EOSC)OpenAIRE
Openness is the success factor for EOSC. OpenAIRE has been working in delivering an open access scholarly communication in Europe for the past 10 years and we now present how our work fits into the EOSC core developments
OpenAIRE Content Providers Community Call, October 7th, 2020
This call was focused on the OpenAIRE Broker Service, specifying how the service works to deploy the enrichment events to the Content Providers 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.
Recording: https://youtu.be/3sF4B58EGcs
Follow the Community activities at https://www.openaire.eu/provide-community-calls
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
OpenAIRE Content Providers Community Call. May 6th, 2020.
This Call focused the presentation of the new User Interface of Provide Dashboard and the presentation of 4 use cases using the Provide service.
Was also an opportunity to share the most recent updates and novelties in the OpenAIRE Content Provider Dashboard, and to get feedback from community.
Recording available here: https://youtu.be/J4m_ryRxtnY
20200504_OpenAIRE Legal Policy Webinar: GDPR and Sharing DataOpenAIRE
Presentation by Jacques Flores Dourojeanni (Research Data Management Consultant Utrecht University Library), as delivered during the OpenAIRE Legal Policy Webinar series on May 4th 2020.
More information and recordings: https://www.openaire.eu/item/openaire-legal-policy-webinars
20200504_Research Data & the GDPR: How Open is Open?OpenAIRE
Presentation by Prodromos Tsiavos (Senior Legal Advisor - ARC/ Director - Onassis Group) as delivered during the OpenAIRE Legal Policy Webinar series on May 4th 2020.
More information and recordings: https://www.openaire.eu/item/openaire-legal-policy-webinars
20200504_Data, Data Ownership and Open ScienceOpenAIRE
Presentation by Thomas Margoni (Senior Lecturer in Intellectual Property and Internet Law, Co-director, CREATe, University of Glasgow) as delivered during the OpenAIRE Legal Policy Webinar series on May 4th 2020.
More information and recordings: https://www.openaire.eu/item/openaire-legal-policy-webinars
20200429_Research Data & the GDPR: How Open is Open? (updated version)OpenAIRE
Presentation by Prodromos Tsiavos (Senior Legal Advisor - ARC/ Director - Onassis Group) as delivered during the OpenAIRE Legal Policy Webinar series on April 29th 2020.
More information and recordings: https://www.openaire.eu/item/openaire-legal-policy-webinars
20200429_Data, Data Ownership and Open ScienceOpenAIRE
Presentation by Thomas Margoni (Senior Lecturer in Intellectual Property and Internet Law, Co-director, CREATe, University of Glasgow) as delivered during the OpenAIRE Legal Policy Webinar series on April 29th 2020.
More information and recordings: https://www.openaire.eu/item/openaire-legal-policy-webinars
20200429_OpenAIRE Legal Policy Webinar: GDPR and Sharing DataOpenAIRE
Presentation by Jacques Flores Dourojeanni (Research Data Management Consultant Utrecht University Library), as delivered during the OpenAIRE Legal Policy Webinar series on April 29th 2020.
More information and recordings: https://www.openaire.eu/item/openaire-legal-policy-webinars
COVID-19: Activities, tools, best practice and contact points in GreeceOpenAIRE
Presentation from the webinar organized by the Greek OpenAIRE and RDA Nodes (Athena RC) and Elixir-GR to inform participants of EU and national efforts, in collaboration with the following research organizations: Flemming, CERTH, HEAL-Link, Demokritos, Univ. of Athens (Medical School).
Presentation of the 2nd Content Providers Community Call, targeting the following topics: 1) OpenAIRE Content provider dashboard updates; Main topic: DSpace-CRIS for OpenAIRE: implementation of the CRIS guidelines and beyond; 3) Community questions & comments.
Presentation of the 2nd Content Providers Community Call, targeting the following topics: 1) OpenAIRE Content provider dashboard updates;
2) OpenAIRE aggregation and enrichment processes: specifications and good practices;
3) Community questions & comments.
Introduction:
RNA interference (RNAi) or Post-Transcriptional Gene Silencing (PTGS) is an important biological process for modulating eukaryotic gene expression.
It is highly conserved process of posttranscriptional gene silencing by which double stranded RNA (dsRNA) causes sequence-specific degradation of mRNA sequences.
dsRNA-induced gene silencing (RNAi) is reported in a wide range of eukaryotes ranging from worms, insects, mammals and plants.
This process mediates resistance to both endogenous parasitic and exogenous pathogenic nucleic acids, and regulates the expression of protein-coding genes.
What are small ncRNAs?
micro RNA (miRNA)
short interfering RNA (siRNA)
Properties of small non-coding RNA:
Involved in silencing mRNA transcripts.
Called “small” because they are usually only about 21-24 nucleotides long.
Synthesized by first cutting up longer precursor sequences (like the 61nt one that Lee discovered).
Silence an mRNA by base pairing with some sequence on the mRNA.
Discovery of siRNA?
The first small RNA:
In 1993 Rosalind Lee (Victor Ambros lab) was studying a non- coding gene in C. elegans, lin-4, that was involved in silencing of another gene, lin-14, at the appropriate time in the
development of the worm C. elegans.
Two small transcripts of lin-4 (22nt and 61nt) were found to be complementary to a sequence in the 3' UTR of lin-14.
Because lin-4 encoded no protein, she deduced that it must be these transcripts that are causing the silencing by RNA-RNA interactions.
Types of RNAi ( non coding RNA)
MiRNA
Length (23-25 nt)
Trans acting
Binds with target MRNA in mismatch
Translation inhibition
Si RNA
Length 21 nt.
Cis acting
Bind with target Mrna in perfect complementary sequence
Piwi-RNA
Length ; 25 to 36 nt.
Expressed in Germ Cells
Regulates trnasposomes activity
MECHANISM OF RNAI:
First the double-stranded RNA teams up with a protein complex named Dicer, which cuts the long RNA into short pieces.
Then another protein complex called RISC (RNA-induced silencing complex) discards one of the two RNA strands.
The RISC-docked, single-stranded RNA then pairs with the homologous mRNA and destroys it.
THE RISC COMPLEX:
RISC is large(>500kD) RNA multi- protein Binding complex which triggers MRNA degradation in response to MRNA
Unwinding of double stranded Si RNA by ATP independent Helicase
Active component of RISC is Ago proteins( ENDONUCLEASE) which cleave target MRNA.
DICER: endonuclease (RNase Family III)
Argonaute: Central Component of the RNA-Induced Silencing Complex (RISC)
One strand of the dsRNA produced by Dicer is retained in the RISC complex in association with Argonaute
ARGONAUTE PROTEIN :
1.PAZ(PIWI/Argonaute/ Zwille)- Recognition of target MRNA
2.PIWI (p-element induced wimpy Testis)- breaks Phosphodiester bond of mRNA.)RNAse H activity.
MiRNA:
The Double-stranded RNAs are naturally produced in eukaryotic cells during development, and they have a key role in regulating gene expression .
(May 29th, 2024) Advancements in Intravital Microscopy- Insights for Preclini...Scintica Instrumentation
Intravital microscopy (IVM) is a powerful tool utilized to study cellular behavior over time and space in vivo. Much of our understanding of cell biology has been accomplished using various in vitro and ex vivo methods; however, these studies do not necessarily reflect the natural dynamics of biological processes. Unlike traditional cell culture or fixed tissue imaging, IVM allows for the ultra-fast high-resolution imaging of cellular processes over time and space and were studied in its natural environment. Real-time visualization of biological processes in the context of an intact organism helps maintain physiological relevance and provide insights into the progression of disease, response to treatments or developmental processes.
In this webinar we give an overview of advanced applications of the IVM system in preclinical research. IVIM technology is a provider of all-in-one intravital microscopy systems and solutions optimized for in vivo imaging of live animal models at sub-micron resolution. The system’s unique features and user-friendly software enables researchers to probe fast dynamic biological processes such as immune cell tracking, cell-cell interaction as well as vascularization and tumor metastasis with exceptional detail. This webinar will also give an overview of IVM being utilized in drug development, offering a view into the intricate interaction between drugs/nanoparticles and tissues in vivo and allows for the evaluation of therapeutic intervention in a variety of tissues and organs. This interdisciplinary collaboration continues to drive the advancements of novel therapeutic strategies.
Observation of Io’s Resurfacing via Plume Deposition Using Ground-based Adapt...Sérgio Sacani
Since volcanic activity was first discovered on Io from Voyager images in 1979, changes
on Io’s surface have been monitored from both spacecraft and ground-based telescopes.
Here, we present the highest spatial resolution images of Io ever obtained from a groundbased telescope. These images, acquired by the SHARK-VIS instrument on the Large
Binocular Telescope, show evidence of a major resurfacing event on Io’s trailing hemisphere. When compared to the most recent spacecraft images, the SHARK-VIS images
show that a plume deposit from a powerful eruption at Pillan Patera has covered part
of the long-lived Pele plume deposit. Although this type of resurfacing event may be common on Io, few have been detected due to the rarity of spacecraft visits and the previously low spatial resolution available from Earth-based telescopes. The SHARK-VIS instrument ushers in a new era of high resolution imaging of Io’s surface using adaptive
optics at visible wavelengths.
Richard's entangled aventures in wonderlandRichard Gill
Since the loophole-free Bell experiments of 2020 and the Nobel prizes in physics of 2022, critics of Bell's work have retreated to the fortress of super-determinism. Now, super-determinism is a derogatory word - it just means "determinism". Palmer, Hance and Hossenfelder argue that quantum mechanics and determinism are not incompatible, using a sophisticated mathematical construction based on a subtle thinning of allowed states and measurements in quantum mechanics, such that what is left appears to make Bell's argument fail, without altering the empirical predictions of quantum mechanics. I think however that it is a smoke screen, and the slogan "lost in math" comes to my mind. I will discuss some other recent disproofs of Bell's theorem using the language of causality based on causal graphs. Causal thinking is also central to law and justice. I will mention surprising connections to my work on serial killer nurse cases, in particular the Dutch case of Lucia de Berk and the current UK case of Lucy Letby.
The increased availability of biomedical data, particularly in the public domain, offers the opportunity to better understand human health and to develop effective therapeutics for a wide range of unmet medical needs. However, data scientists remain stymied by the fact that data remain hard to find and to productively reuse because data and their metadata i) are wholly inaccessible, ii) are in non-standard or incompatible representations, iii) do not conform to community standards, and iv) have unclear or highly restricted terms and conditions that preclude legitimate reuse. These limitations require a rethink on data can be made machine and AI-ready - the key motivation behind the FAIR Guiding Principles. Concurrently, while recent efforts have explored the use of deep learning to fuse disparate data into predictive models for a wide range of biomedical applications, these models often fail even when the correct answer is already known, and fail to explain individual predictions in terms that data scientists can appreciate. These limitations suggest that new methods to produce practical artificial intelligence are still needed.
In this talk, I will discuss our work in (1) building an integrative knowledge infrastructure to prepare FAIR and "AI-ready" data and services along with (2) neurosymbolic AI methods to improve the quality of predictions and to generate plausible explanations. Attention is given to standards, platforms, and methods to wrangle knowledge into simple, but effective semantic and latent representations, and to make these available into standards-compliant and discoverable interfaces that can be used in model building, validation, and explanation. Our work, and those of others in the field, creates a baseline for building trustworthy and easy to deploy AI models in biomedicine.
Bio
Dr. Michel Dumontier is the Distinguished Professor of Data Science at Maastricht University, founder and executive director of the Institute of Data Science, and co-founder of the FAIR (Findable, Accessible, Interoperable and Reusable) data principles. His research explores socio-technological approaches for responsible discovery science, which includes collaborative multi-modal knowledge graphs, privacy-preserving distributed data mining, and AI methods for drug discovery and personalized medicine. His work is supported through the Dutch National Research Agenda, the Netherlands Organisation for Scientific Research, Horizon Europe, the European Open Science Cloud, the US National Institutes of Health, and a Marie-Curie Innovative Training Network. He is the editor-in-chief for the journal Data Science and is internationally recognized for his contributions in bioinformatics, biomedical informatics, and semantic technologies including ontologies and linked data.
Cancer cell metabolism: special Reference to Lactate PathwayAADYARAJPANDEY1
Normal Cell Metabolism:
Cellular respiration describes the series of steps that cells use to break down sugar and other chemicals to get the energy we need to function.
Energy is stored in the bonds of glucose and when glucose is broken down, much of that energy is released.
Cell utilize energy in the form of ATP.
The first step of respiration is called glycolysis. In a series of steps, glycolysis breaks glucose into two smaller molecules - a chemical called pyruvate. A small amount of ATP is formed during this process.
Most healthy cells continue the breakdown in a second process, called the Kreb's cycle. The Kreb's cycle allows cells to “burn” the pyruvates made in glycolysis to get more ATP.
The last step in the breakdown of glucose is called oxidative phosphorylation (Ox-Phos).
It takes place in specialized cell structures called mitochondria. This process produces a large amount of ATP. Importantly, cells need oxygen to complete oxidative phosphorylation.
If a cell completes only glycolysis, only 2 molecules of ATP are made per glucose. However, if the cell completes the entire respiration process (glycolysis - Kreb's - oxidative phosphorylation), about 36 molecules of ATP are created, giving it much more energy to use.
IN CANCER CELL:
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
Unlike healthy cells that "burn" the entire molecule of sugar to capture a large amount of energy as ATP, cancer cells are wasteful.
Cancer cells only partially break down sugar molecules. They overuse the first step of respiration, glycolysis. They frequently do not complete the second step, oxidative phosphorylation.
This results in only 2 molecules of ATP per each glucose molecule instead of the 36 or so ATPs healthy cells gain. As a result, cancer cells need to use a lot more sugar molecules to get enough energy to survive.
introduction to WARBERG PHENOMENA:
WARBURG EFFECT Usually, cancer cells are highly glycolytic (glucose addiction) and take up more glucose than do normal cells from outside.
Otto Heinrich Warburg (; 8 October 1883 – 1 August 1970) In 1931 was awarded the Nobel Prize in Physiology for his "discovery of the nature and mode of action of the respiratory enzyme.
WARNBURG EFFECT : cancer cells under aerobic (well-oxygenated) conditions to metabolize glucose to lactate (aerobic glycolysis) is known as the Warburg effect. Warburg made the observation that tumor slices consume glucose and secrete lactate at a higher rate than normal tissues.
Nutraceutical market, scope and growth: Herbal drug technologyLokesh Patil
As consumer awareness of health and wellness rises, the nutraceutical market—which includes goods like functional meals, drinks, and dietary supplements that provide health advantages beyond basic nutrition—is growing significantly. As healthcare expenses rise, the population ages, and people want natural and preventative health solutions more and more, this industry is increasing quickly. Further driving market expansion are product formulation innovations and the use of cutting-edge technology for customized nutrition. With its worldwide reach, the nutraceutical industry is expected to keep growing and provide significant chances for research and investment in a number of categories, including vitamins, minerals, probiotics, and herbal supplements.
Nutraceutical market, scope and growth: Herbal drug technology
Moving content across the OpenAIRE infrastructure boundaries (6th RDA Plenary)
1. Moving content across the
OpenAIRE infrastructure
boundaries
RDA Plenary
Data and computing infrastructures for open scholarship
Workshop
Session 2: Linking up science: Interoperability aspects and
services
22nd of September, 2015 - Paris
Paolo Manghi
National Research Council (IT)
1
2. • NOADS: National Open Access Desks
• Monitor and foster the adoption of Open
Access policies at the local level
• Support researchers at the
implementation of the Data Pilot
• Gold OA: FP7 post grant APCs Pilot
• e-infrastructure for monitoring impact of
OA mandates and research projects
• OpenAIRE guidelines for metadata
exchange
• Zenodo Repository for the deposition of
research products
DonatellaCastelliandAlessiaBardi,September2015,bardi@isti.cnr.it
OPEN ACCESS INFRASTRUCTURE
FOR RESEARCH IN EUROPE
The point of reference for
Open Access in Europe
Human Network e-infrastructure
50 Partners: EC countries, data centers, universities, libraries, repositories
3. Get support
(NOADs)
Linked Content
Statistics
Search & Browse
Feedback
Claim/deposit
Publications
& data
Research impact
Citations, usage statistics
+++
Data
repositories/aggregator
s
Data Journals
Metadata
on data
Publication
repositories/aggregators
Institutional & Thematic
Open Access Journals/Publishers
Usage data
Metadata
And pdfs
National funding
EC funding
Guidelines for use services
Institutional
CRIS
Systems
CERN/OpenAIRE “catch-all” repository
Guidelines for data interoperability
OpenDOAR
re3data
Validation
Cleaning &
Transformation
De-duplication
Enrichment by
metadata and
text mining
APIs: OAI-PMH, LOD, REST
search
Repository
Notification Broker
5. Data
Sources
Metadata
records
files
cleaned
records
files
Native
De-duplicated
De-duplicated
and enriched
Transform
Mine
Identify
duplicates
ActionSet
(Similarity rels)
Aggregation sub-system
De-duplication
sub-system
Information
Inference
sub-system
Data provision
sub-system
Full-text
Index
OAI-PMH
StatsDB
Collect
Populate Merge Enrich
ActionSet
(inferred
information)
Publish
LOD
End-user
feedback
www.d-net.research-infrastructures.eu
OpenAIRE infrastructure machinery: a
view from the moon
Literature
Broker
Provision
Services
Portal Search
and stats
Deduplication/Data
provision cluster
• 15 servers
• 90 CPU cores
• 236 GB ram
• 12,300 GB disk
Mining Cluster
• 14 servers
• 98 CPU cores
• 514 GB ram
• 18,458 GB disk
Provision
APIs
Aggregation/APIs
/Services
• 44 CPU cores
• 84 GB of RAM
• 3,998 GB disk
6. Feeding the OpenAIRE
information space
• Collection of metadata and files from data sources
• OpenAIRE Guidelines (http://guidelines.openaire.eu): Literature
Repositories (enriched qualified DC, in cooperation with SHARE-US, La
Referencia-South America, JISC-UK), Data Archive (enriched qualified
DataCite), CRIS systems (OpenAIRE/CERIF-XML)
• Cleaning, de-duplication, enrichment by inference: guidelines are not
enough….
• End-users
• Claims: publications related to projects (e.g. EC project coordinators),
links between projects, datasets, and publications
• Deposition in Zenodo: articles, datasets, software linked to projects
6
8. OpenAIRE’s
http://www.zenodo.org
• Zenodo repository (production)
• Deposition of publications, datasets, software
• DOI minting and metadata curation
• Community support
• Much more…
• FREE
• Numbers
• Publications 16,240
• Datasets 1,477
• Software 4,456
• Other products
1,400+
9. OpenAIRE information space
numbers (September 2015)
• 12M+ publications (de-duplicated)
• 200,000+ links publication-project from 5 funders
• 9,000+ datasets linked to publications or projects
• 34,000+ organizations (de-duplicated)
10. How to access the OpenAIRE
information space
• OpenAIRE APIs, programmatic access: http://api.openaire.eu
• OAI-PMH (production ready)
• REST Search (production ready)
• Linked Open Data (delivery 2015, 2016)
• OpenAIRE Services
• Portal search and statistics (production ready)
• Literature Repository Notification Broker Service (delivery 2016)
• Data-Literature Interlinking Service (BETA ready, integration in
OpenAIRE to be planned)
10
11. Linked Open Data
• Specified an RDF vocabulary
• Based on the OpenAIRE entity-relationship data model
• Skipping complicated and unnecessary attributes of entities
• Reused common vocabularies, e.g. CERIF, FOAF, BIBO, DC, …
• Data conforming to LOD best practices to be published in BETA end of
2015
• Entity descriptions downloadable from URIs + dumps + SPARQL endpoint
• Integration in OpenAIRE data provision workflow in 2016
11
…
MapReduce job
Read Rules
Generates RDF
HBase
Number of input rows 20,985,097
Number of output rows ~
655,000,000
Time of indexing(s) 1.043
Virtuoso
12. OpenAIRE RDF Graph:
integration into the cloud
Identified Datasets to be
interlinked to:
DBLP, CiteSeer, CEUR-
WS.org, and others
13. Literature Repository Notification
Broker Service
• Literature repository subscriptions based on configurable criteria of
publication-repository “closeness”
• From repositories (and other data sources) to institutional repositories
• For example, from journals or thematic repositories to institutional repositories
13
Service design in
cooperation/alignment with
SHARE US, JISC-UK, La
Referencia (South America)
14. Literature Repository Notification
Broker Service
Publication-repository “closeness”, relationships:
• publication-author-organization-repository
• Inferred by mining PDF for affiliations and deduplicating organizations
• publication-author-repository
• Inferred from occurrences of author articles within repositories
• publication-project-organization-repository
• Inferred from deduplicating organizations
14
15. Data-Literature Interlinking
Service
• In cooperation with RDA/WDS Publishing Data Service Working
Group, to create: “an open, freely accessible, web based service
that enables its users to identify datasets that are associated with a
given article, and vice versa”
• Major scholarly communication stakeholders involved at different
levels: providers, users, requirements
15
16. PDS-WG Stakeholders
Harkan Grudd
Siddeswara Guru
Laure Haak (ORCID)
John Helly
Francisco Hernandez
Simon Hodson
Richard Kidd (RSc)
Hylke Koers (Elsevier) – co-chair
Paolo Manghi (OpenAire)
Haralambos Marmanis
Caroline Martin
Jo McEntyre (EMBL - EBI)
Yolanda Meleco
Sheila Morrissey
Lyubomir Penev
Mohan Ramamurthy
Howard Ratner
Nigel Robinson (Thomson Reuters)
Sergio Ruiz (DataCite)
Uwe Schindler (PANGAEA)
Johanna Schwarz (Springer)
Martina Stockhause
Carly Strasser
Eefke Smit (STM)
Jonathan Tedds
Joachim Wackerow
Juanle Wang
Hua Xu
Eva Zanzerkia
Carol Goble
Jeffrey Grethe
Claire Austin
David Arctur
Amir Aryani (ANDS)
Geoff Bilder (CrossRef)
Timea Biro
Adrian Burton (ANDS) - co-chair
Ian Bruno (CCDC)
Sarah Callaghan
David Carlson
Jamus Collier (PANGAEA)
Suenje Dallmeier-Thiessen
Tim DiLauro
Ingrid Dillo
Rorie Edmunds
Janine Felden
17. System development and operation:
OpenAIRE and PANGAEA
Links collection
…
Harmonizing
PID resolution
De-duplicating
Information Space
Web Portal
Core Data Model
Data Sources
OAI-PMHSearch APIs
Examples:
• Pairs of DOIs
• DataCite records
• PANGAEA records
OAI-PMH
intersection
20. Lessons learnt from
OpenAIRE
• Homogeneity: “they all want it, but it is not for free”
• Guidelines are hard to be adopted: lack of funds, legacy content, old
practices, multiple guidelines, discipline/community requirements, etc.
• Mining: lack of access to the payload (articles, datasets,
experiment)
• Open Access is definitely taking off, but still it is not the rule
• PDFs are not often available
• Products of science live in disconnected silos
• Articles, datasets, software are deposited in disconnected repositories
• Funders lack policies enabling impact measurement
• No rigorous guidelines on how to link products to funding (H2020 drives 20
21. Lessons learnt from
OpenAIRE
• Literature repositories find it hard to keep up with the
demands of Open Scholarship in the digital era
• Supporting interlinking with other products of science, e.g. datasets
and experiments (e.g. software, services, workflows), alternative
products
• Supporting modern ways to export/exchange content (metadata and
files) with publishers, other repositories, or third-party services
• Advocate and support novel forms of research products and
evaluation: readers feedbacks, downloads, etc.
21
22. Lessons learnt from
OpenAIRE
• The “infrastructural” elements necessary to enable
Open Scholarship are still missing
• Beyond the PDF (sharing and citation): lack of metadata
standards for several research-related entities: e.g. experiments
(e.g. software, workflows, services), authors, funding, projects,
etc.
• Contextualization: Lack of standards for interlinking datasets,
articles, and experiments
• Identification: Coexistence of several persistent identifier
schemes
• Scientific reward: Lack of evaluation schemes for products
22
23. Lessons learnt from
OpenAIRE
• Articles: cross-community
• Datasets: community-oriented
• Experiments: community or research groups oriented
23
Community e-
infrastructure
Community e-
infrastructure
Community e-
infrastructure
Literature
Research data Research data
Experi
ments
Experi
ments
Scientific
Communication
workflows
Scientific
Reward
practices
Missing
Established
?
??
24. Vision: scholarly
communication infrastructures
• Collective approach (community building and trust): round table of
policy makers, funders, publishers, research organizations, data
centres, scientists, general public and companies
• OA mandates, OA data pilot
• Policies: making synergies on how science should be openly shared,
communicated, reused, and evaluated
• OpenAIRE guidelines, OA mandates and data pilot advocacy
• Services: can provide infrastructural support where it is missing
(economy of scale approach) and enable realization of other services
• LOD, DLI service, Notification Broker, inference of links
24
Publications from OA repositories
Links to any funding information
Links them to data repositories
Integrating national research systems
Produces new knowledge / service
Monitoring for research administrators