This document discusses improving the relationship between scientists and Wikipedia. It notes that Wikipedia often lacks basic biographical information about notable scientists. A Wikipedian in Residence program was established at the Royal Society to address this issue through edit-a-thons and releasing portraits and data under open licenses. This led to improved coverage of Fellows of the Royal Society on Wikipedia. The document advocates for expanding such programs to other scientific organizations to increase representation of scientists on Wikipedia.
Bibliography 2.0: A citeulike case study from the Wellcome Trust Genome CampusDuncan Hull
Abstract: This talk will describe the use of http://www.citeulike.org to manage and share bibliographic references among 1300 scientists and engineers working at the Sanger Institute (http://www.sanger.ac.uk) and European Bioinformatics Insitute (http://www.ebi.ac.uk) based on the Wellcome Trust Genome Campus in Cambridge, UK. Using data from references shared so far, we will illustrate the costs, benefits and adoption of citeulike to create and share bibliographic data on the web.
Presentation from The Influence and Impact of Web 2.0 on Various Applications at the National e-Science Centre, Edinburgh, UK.
Slides from the "Author Identity – Creating a new kind of reputation online" session at Science Online London (solo09) with Duncan Hull, Geoffrey Bilder, Michael Habib, Reynold Guida
ResearcherID, Contributor ID, Scopus Author ID, etc. help to connect your scientific record. How do these tools connect to your online identity, and how can OpenID and other tools be integrated? How can we build an online reputation and when should we worry about our privacy?
Jean-Claude Bradley was a pioneer of doing Open Science and on 2014-07-14 we held a memorial meeting in Cambridge (see also http://inmemoriamjcb.wikispaces.com/Jean-Claude+Bradley+Memorial+Symposium)
Open Data and Open Science presented in Rio for Open Science 2014-08-22. I argue that Open Notebook Science is the way forward and will lead to great benefits
Scientific information is often hidden or not published properly. The ContentMine is a Social Machine consisting of semantic software and communities of domain expertise; it aims to liberate all scientific facts from the published literature on a daily basis.
The talk , delivered to the Computational Institute, will be /was followed by a hands-on workshop learning how to use the technology and work as a community.
Copyright is one of the greatest barrier to Open Data. This presentation for insidegovernment UK shows the struggle between those who want to reform copyright and those opposed to reform
Bibliography 2.0: A citeulike case study from the Wellcome Trust Genome CampusDuncan Hull
Abstract: This talk will describe the use of http://www.citeulike.org to manage and share bibliographic references among 1300 scientists and engineers working at the Sanger Institute (http://www.sanger.ac.uk) and European Bioinformatics Insitute (http://www.ebi.ac.uk) based on the Wellcome Trust Genome Campus in Cambridge, UK. Using data from references shared so far, we will illustrate the costs, benefits and adoption of citeulike to create and share bibliographic data on the web.
Presentation from The Influence and Impact of Web 2.0 on Various Applications at the National e-Science Centre, Edinburgh, UK.
Slides from the "Author Identity – Creating a new kind of reputation online" session at Science Online London (solo09) with Duncan Hull, Geoffrey Bilder, Michael Habib, Reynold Guida
ResearcherID, Contributor ID, Scopus Author ID, etc. help to connect your scientific record. How do these tools connect to your online identity, and how can OpenID and other tools be integrated? How can we build an online reputation and when should we worry about our privacy?
Jean-Claude Bradley was a pioneer of doing Open Science and on 2014-07-14 we held a memorial meeting in Cambridge (see also http://inmemoriamjcb.wikispaces.com/Jean-Claude+Bradley+Memorial+Symposium)
Open Data and Open Science presented in Rio for Open Science 2014-08-22. I argue that Open Notebook Science is the way forward and will lead to great benefits
Scientific information is often hidden or not published properly. The ContentMine is a Social Machine consisting of semantic software and communities of domain expertise; it aims to liberate all scientific facts from the published literature on a daily basis.
The talk , delivered to the Computational Institute, will be /was followed by a hands-on workshop learning how to use the technology and work as a community.
Copyright is one of the greatest barrier to Open Data. This presentation for insidegovernment UK shows the struggle between those who want to reform copyright and those opposed to reform
PhD Theses are normally locked away digitally. They cost 20 billion dollars to create and we waste much of this value. By making them open we can use software to read, index, reuse, compute and add massive value
This is a keynote presentation to "Open science, transparence et evaluation. Perspectives et enjeux pour les chercheurs.' Held at Urfist de Bordeaux, France, 4 April 2017
https://sygefor.reseau-urfist.fr/#!/training/6701/7159/?from=true
ABSTRACT: The way research is disseminated has changed immeasurably since the advent of the internet, yet we still reward researchers in the same way - for publication of novel results in high impact journals. This talk will start with a brief discussion of some of the big challenges the research sector is facing as a result and describe how Open Science can address these. The talk will then focus on the difficulty of introducing and implementing Open Science solutions. Open Science questions the status quo, and potentially threatens the established reputation of both institutions and individuals. It is not an easy concept to implement. While the discipline of Scholarly Communication takes a 'meta' view of the whole research ecosystem, most players in that system are working within a narrow view. It is very rare for individuals to be able to see beyond their own experience. Challenges for people trying to implement Open Science initiatives range from practical issues in implementing change, through to the people skills and negotiations required to convince individuals and institutions that this change is necessary.
An overview of ContentMining for JISC (the infrastructure provider of UK academia). Examples, details leading to hands-on exercise (http://contentmine.org/workflow
What works and doesn't work in research disseminationtbirdcymru
Is 'closed' more effective than 'open' in research knowledge creation and dissemination? This paper argues that open is more efficient and effective, and makes better scholarship as well as academic profile for the researcher.
The Year of Blogging Dangerously: Lessons from the "Blogosphere". This talk will describe how to build an institutional repository using free (or cheap) web-based and blogging tools including flickr.com, slideshare.net, citeulike.org, wordpress.com, myexperiment.org and friendfeed.com. We will discuss some strengths and limitations of these tools and what Institutional Repositories can learn from them.
Open access for researchers, policy makers and research managers, librariesIryna Kuchma
Open access for researchers: enlarged audience and citation impact, tenure and promotion. Open access for policy makers and research managers: new tools to manage a university’s image and impact. Open access for libraries. Maintaining digital repository as a key function for research libraries.
Demystifying & Integrating Web 2.0 at the Metropolitan Museum of ArtJennie Pu
This session focuses on successful strategies for experimenting with, trusting, and integrating Web 2.0 tools in an organization’s daily work. It covers marketing strange new tools to an idiosyncratic group of library users with extremely specific needs and whose discipline, art history, has typically relied on more traditional resources. Speakers demonstrate how the library staff quickly adopted Web 2.0 tools, created winning presentations for all museum staff dealing with the relevancy of these tools to scholarly research, the concern with authority and security.
Open access for researchers and research managersIryna Kuchma
Presented at “Gaining the momentum: Open Access and advancement of science and research” workshop, African Digital Scholarship & Curation 2009, Thursday 14 May 2009, CSIR Conference Centre, Pretoria, South Africa. About enlarged audience and citation impact, tenure and promotion. Advanced and enhanced metrics. The evidences that Open Access leads to advancement of science and research.
Leveraging the ETD as a pathway to broader discussions about openness in a un...Danny Kingsley
Workshop held as part of ETD2021 https://conferences.uaeu.ac.ae/etd2021/en/index.shtml on 15 November 2021
This workshop will explore different challenges to making ETDs openly available and how they can be used within an institution to engage with faculty in relation to open research practices. Example considerations include the use of third party copyright, whether a data management plan is required as part of the PhD research process and how the ethical approval process can be a natural point for considering and formalizing research integrity issues. Through these processes, universities have an opportunity to not only ensure the next generation of scholars are working with a high level of research integrity, but also to update the skills and knowledge of those who supervise PhD students.
Opportunities and Challenges of establishing Open Access Repositories: A case...Sukhdev Singh
National Informatics Centre had established a subject repository in May 2005. It is meant for Medical and Allied Sciences and named as OpenMED@NIC . It has MeSH® based subject categorization and this makes it one of its own kind. Taking OpenMED@NIC as a case – this paper discusses key issues in establishing and maintaining an open access repository. Librarians and information science professionals can play active role in providing access and exposure to quality research and academic content generated in their institutions. Mature and standard open sources softwares are now available for setting up repositories. Libraries can install one of these on existing institutional or library servers to setup repositories. However to ensure better access and faster response time dedicated hardware and reliable connectivity would be required. Librarians and information science professional can play important role in exposing intellectual content produced by their organizations. They can take of various roles like – generating awareness among staff, researchers and students about benefits of self arching in institutional or subject repositories; training them in uploading their articles and other documents in such repositories; acting as meta-data editors and repositories managers. Establishing a repository, administrating and inviting authors to deposit their articles and other works in it is golden opportunity available to librarians and information science professionals. This opportunity should be grabbed with open hands.
This presentation is from the talk I gave at the Museum Computer Network 2014 in Dallas, TX. Here is the description:
An editathon is an ideal first step in beginning a collaboration between your museum and Wikipedians. Starting small with an editathon can open up a whole world of opportunities to co-create knowledge about collections with your community. This presentation is your chance to hear about organizing and leading Wikipedia editathons, with the hope that you will leave with the practical skills necessary to host such an event. The talk will sketch a typical editathon and answer beginners' questions such as "What is it? (and what is it not?)" and "Why we do it?" Examples, especially from successful Smithsonian editathons, will support a step-by-step guide to planning and executing an editathon.
PhD Theses are normally locked away digitally. They cost 20 billion dollars to create and we waste much of this value. By making them open we can use software to read, index, reuse, compute and add massive value
This is a keynote presentation to "Open science, transparence et evaluation. Perspectives et enjeux pour les chercheurs.' Held at Urfist de Bordeaux, France, 4 April 2017
https://sygefor.reseau-urfist.fr/#!/training/6701/7159/?from=true
ABSTRACT: The way research is disseminated has changed immeasurably since the advent of the internet, yet we still reward researchers in the same way - for publication of novel results in high impact journals. This talk will start with a brief discussion of some of the big challenges the research sector is facing as a result and describe how Open Science can address these. The talk will then focus on the difficulty of introducing and implementing Open Science solutions. Open Science questions the status quo, and potentially threatens the established reputation of both institutions and individuals. It is not an easy concept to implement. While the discipline of Scholarly Communication takes a 'meta' view of the whole research ecosystem, most players in that system are working within a narrow view. It is very rare for individuals to be able to see beyond their own experience. Challenges for people trying to implement Open Science initiatives range from practical issues in implementing change, through to the people skills and negotiations required to convince individuals and institutions that this change is necessary.
An overview of ContentMining for JISC (the infrastructure provider of UK academia). Examples, details leading to hands-on exercise (http://contentmine.org/workflow
What works and doesn't work in research disseminationtbirdcymru
Is 'closed' more effective than 'open' in research knowledge creation and dissemination? This paper argues that open is more efficient and effective, and makes better scholarship as well as academic profile for the researcher.
The Year of Blogging Dangerously: Lessons from the "Blogosphere". This talk will describe how to build an institutional repository using free (or cheap) web-based and blogging tools including flickr.com, slideshare.net, citeulike.org, wordpress.com, myexperiment.org and friendfeed.com. We will discuss some strengths and limitations of these tools and what Institutional Repositories can learn from them.
Open access for researchers, policy makers and research managers, librariesIryna Kuchma
Open access for researchers: enlarged audience and citation impact, tenure and promotion. Open access for policy makers and research managers: new tools to manage a university’s image and impact. Open access for libraries. Maintaining digital repository as a key function for research libraries.
Demystifying & Integrating Web 2.0 at the Metropolitan Museum of ArtJennie Pu
This session focuses on successful strategies for experimenting with, trusting, and integrating Web 2.0 tools in an organization’s daily work. It covers marketing strange new tools to an idiosyncratic group of library users with extremely specific needs and whose discipline, art history, has typically relied on more traditional resources. Speakers demonstrate how the library staff quickly adopted Web 2.0 tools, created winning presentations for all museum staff dealing with the relevancy of these tools to scholarly research, the concern with authority and security.
Open access for researchers and research managersIryna Kuchma
Presented at “Gaining the momentum: Open Access and advancement of science and research” workshop, African Digital Scholarship & Curation 2009, Thursday 14 May 2009, CSIR Conference Centre, Pretoria, South Africa. About enlarged audience and citation impact, tenure and promotion. Advanced and enhanced metrics. The evidences that Open Access leads to advancement of science and research.
Leveraging the ETD as a pathway to broader discussions about openness in a un...Danny Kingsley
Workshop held as part of ETD2021 https://conferences.uaeu.ac.ae/etd2021/en/index.shtml on 15 November 2021
This workshop will explore different challenges to making ETDs openly available and how they can be used within an institution to engage with faculty in relation to open research practices. Example considerations include the use of third party copyright, whether a data management plan is required as part of the PhD research process and how the ethical approval process can be a natural point for considering and formalizing research integrity issues. Through these processes, universities have an opportunity to not only ensure the next generation of scholars are working with a high level of research integrity, but also to update the skills and knowledge of those who supervise PhD students.
Opportunities and Challenges of establishing Open Access Repositories: A case...Sukhdev Singh
National Informatics Centre had established a subject repository in May 2005. It is meant for Medical and Allied Sciences and named as OpenMED@NIC . It has MeSH® based subject categorization and this makes it one of its own kind. Taking OpenMED@NIC as a case – this paper discusses key issues in establishing and maintaining an open access repository. Librarians and information science professionals can play active role in providing access and exposure to quality research and academic content generated in their institutions. Mature and standard open sources softwares are now available for setting up repositories. Libraries can install one of these on existing institutional or library servers to setup repositories. However to ensure better access and faster response time dedicated hardware and reliable connectivity would be required. Librarians and information science professional can play important role in exposing intellectual content produced by their organizations. They can take of various roles like – generating awareness among staff, researchers and students about benefits of self arching in institutional or subject repositories; training them in uploading their articles and other documents in such repositories; acting as meta-data editors and repositories managers. Establishing a repository, administrating and inviting authors to deposit their articles and other works in it is golden opportunity available to librarians and information science professionals. This opportunity should be grabbed with open hands.
This presentation is from the talk I gave at the Museum Computer Network 2014 in Dallas, TX. Here is the description:
An editathon is an ideal first step in beginning a collaboration between your museum and Wikipedians. Starting small with an editathon can open up a whole world of opportunities to co-create knowledge about collections with your community. This presentation is your chance to hear about organizing and leading Wikipedia editathons, with the hope that you will leave with the practical skills necessary to host such an event. The talk will sketch a typical editathon and answer beginners' questions such as "What is it? (and what is it not?)" and "Why we do it?" Examples, especially from successful Smithsonian editathons, will support a step-by-step guide to planning and executing an editathon.
Open Monuments Project at GLAM Wiki Conference 2015Aleksandra Janus
How GLAM WIKI could be helpful or inspirational for social projects or change is more commons questions than what is there still missed. In order to reconsider idea for GLAM WIKI and make some improvements we would like to take a closer look at situations where and how GLAM WIKI has some limitations. When it could not be a good solution and why?
Why didn’t we decided to base our project on Wikipedia? How are the other examples of such projects? Is it only the example of monuments? What should be done in order to make Wikipedia more universal way of opening GLAM?
Children's songs are universal. They are part of our cultural heritage. As you might know, there are a melodies that are sung in different languages. Sometimes with the same meaning, but sometimes they have total different lyrics and meaning. They illustrate how we are globally connected to each other. In a time where copyright dominates the music industry, we think it is important that the knowledge about songs like these is accessible. Not only the lyrics and their meaning, but also what they sound like. The wikis are a great place to collect this knowledge, just like the way these songs are taught to children around the world.
This presentation was used for a music scoring workshop. This workshop was an assignment for the Training for Trainers program at Wikimedia UK in August 2014.
Wikimedia Strategy - making it impactful, measuring impact, and thinking abou...Simon Knight
Slides from 3 sessions (on strategy (1), evaluation (2), and tech (3) with some overlap. The last isn't much thought out yet, and isn't one I'm presenting at wmcon.
Making the strategy impactful
From Strategy to Impact Measurement
Measuring impact – co-ordination, and localisationMaking the most of tech?
Check image attributions for licenses, otherwise CC-By with Wikimedia UK mark under a restricted license.
Philippe Beaudette - How To Motivate Legions of VolunteersFeverBee Limited
Philippe Beaudette, the director of community at Wikimedia, explains how Wikipedia uses various methods of persuasion to build a legion of volunteers to help edit their articles.
Presentation of the photo competition "Wiki Loves Earth 2016 in Bulgaria", given in the lecture panel of Bulgarian Foundation Biodiversity in the Biological Faculty of Sofia University.
Date: 1 June 2016
Authors: Spasimir Pilev and Vassia Atanassova
Intro to Editing Wikipedia - SCOTUS Editathon at NARASara Snyder
Introduction to editing Wikipedia. Part of the December 11, 2015 editathon on the Supreme Court of the United States, held at the National Archives and Records Administration's Innovation Hub #ArchivesInnovHub
Presentation delivered as part of OpenFest Online Symposium at the University of Sheffield on 7th September 2023.
Abstract:
Google something, anything. What are the top ten results? Whether a scientific concept, political theory or research methodology, Wikipedia will almost certainly be near the top, if not the very first result.
As a large-scale collaborative platform funded through charitable donations, with a mission to provide universal free access to knowledge as a public good, Wikipedia is one of the most popular websites in the world and a primary source of information on the web, especially for people outside academia.
This presentation will explore the role of Wikipedia in the information ecosystem, where it occupies a unique role as a bridge between informal discussion and scholarly publication. We explore how it relates to the broader Wikimedia ecosystem, through structured data on Wikidata for instance, and openly licensed media on Wikimedia Commons. We consider the potential for universities to engage strategically with Wikimedia and the benefits of doing so, in the areas of information literacy and research impact, sharing openly licensed text and images to improve Wikipedia, for example, and linking Wikipedia citations to open access repositories.
We will discuss our Wikimedia Champions project at the University of Leeds, which has recruited PGRs to examine Wikipedia in their subject area, identifying areas of need and making contributions. The project has been an opportunity to explore ways of sharing University research with a wider audience in an open and accessible way and thereby contribute to the global commons.
Presented by Samara Carter and Monique Clark at the 2013 Power Up Your Pedagogy Conference held at the Annandale campus of Northern Virginia Community College.
Contributing to the global commons: Repositories and WikimediaNick Sheppard
There is huge potential for universities and their libraries to leverage Wikimedia in order to expose research outputs and collections. Wikimedia comprises sixteen projects in total, including Wikipedia, Wikimedia Commons and Wikidata. At the University of Leeds, the Research Data Management Service have successfully run a project that focuses on linking research data with the Wikimedia suite of tools via a series of ‘editathons’, in order to increase the visibility of research data and enable reuse on Wikipedia and elsewhere. The project - "Manage it locally to share it globally: RDM and Wikimedia Commons" - was the winning submission to a competition launched in May 2018 and sponsored by SPARC Europe, Jisc and the University of Cambridge, called the "Data Management Engagement Award", which aimed to address cultural challenges involved in promoting effective research data practices.
The project has served as a springboard to further explore Wikimedia strategically, both at the University of Leeds and across the White Rose Consortium. For example we are collaborating on a new project looking at Wikipedia citations of research from York, Sheffield and Leeds, and the proportion of these that are open access. The long term goal might be to establish a "Wikimedian in Residence" across the consortium. In this talk, we will present the project's outputs - including a toolkit that will enable other institutions to apply the same methodology. In addition we will explore the potential of Wikidata to link up repositories and other data silos in a manner that enables reuse and increases impact.
Working with Wikipedia: Leveraging the Online Encyclopedia to Serve Your Patr...Don Boozer
For almost fourteen years, Wikipedia has stirred strong emotions among librarians and educators - both pro and con. Regardless of any controversy students, patrons, and - yes - librarians are using Wikipedia, and it remains steadfastly in the top ten most-visited sites on the Internet. If patrons are going to be using Wikipedia, it is in librarians' interest to understand both its strengths and weaknesses and be able to communicate these to local patrons, students, and educators. This presentation will address these concerns and also look at how librarians can use the online encyclopedia to share their expertise and highlight their local resources. Presented at the Ohio Library Council
The Future of Knowledge in the Age of Wikipedia - REMIXNYC 2014Andrew Lih
The Future of Knowledge in the Age of Wikipedia, talks about the history of the world's most popular reference work, how galleries, libraries, archives and museums (GLAM) have come to work with it, and the challenges to Wikipedia's growth. We also describe how Wikipedia solves the "knowledge gap" problem by being the unusual blend of speed, depth and accuracy.
Subjects discussed: Smithsonian, British Museum, National Archives, VOX, Ezra Klein, Wikidata, Histropedia, Wikipedia, mobiles, Jimmy Wales, Ward Cunningham, Larry Sanger.
By: Andrew Lih of American University and author of The Wikipedia Revolution: How a bunch of nobodies created the world's greatest encyclopedia.
Free for All: Wikipedia, Wikimedia, and the Future of HistoryAndrew Lih
Free for All: Wikipedia, Wikimedia, and the Future of History
Chautauqua Institution, Week 4
Future of History
Andrew Lih, July 20, 2022
https://chqdaily.com/2022/07/tech-journalist-smithsonians-wikimedian-at-large-lih-to-trace-wikipedias-power-in-cultural-heritage/
https://chqdaily.com/2022/07/digital-strategist-andrew-lih-traces-past-present-future-of-information-knowledge-through-lens-of-wikipedia/
Digital Transformation and Data - the Wikimedia Residency at the University o...Ewan McAndrew
Digital Transformation and Data — The Wikimedia Residency at the University of Edinburgh
This presentation took place at SCURL’s ‘Libraries, Literacies & Learning’ event 23 March 2018.
MCG’s Museums+Tech 2016 presentation
All afternoonn lightning sessions
1. Russell Dornan, Wellcome Collection - Sleep Stories: crowdsourcing a patchwork of meaningful stories online and in person
2. Jason Evans, National Library of Wales - Sharing digital content with Wikimedia
3. Chloe Roberts, Wellcome Collection - Adaptive evolution with A/B testing
4. Anna Lowe, SMARTIFY - An Audioguide for the Digital Age
5. Sarah Cole, TIME/IMAGE - Poetic Places: making a geolocation app with little time, less money and no coding
6. Andrew Larking, Deeson - The naked bot
7. James Lloyd, Ure Museum of Greek Archaeology - Objects in the Round: photogrammetry for engagement and education
How I Learned How To Stop Worrying And Learned To Love Wikipedia
Brian C. Housand, PhD
North Carolina Gifted Conference (NCAGT)
Winston-Salem, NC
March 26, 2009
Slides used by Martin Poulter in two sessions of the EduWiki Conference, 1 November 2013 in Cardiff. The first 5 slides relate to the opening session titled "Where's the edit button on this textbook?". The rest are from a session on "Linking Research Impact and Open Education". These slides are also available on Wikimedia Commons, with a list of works it is derived from, at https://commons.wikimedia.org/wiki/File:EduWiki_2013_Poulter_Slides.pdf .
Wikiconference USA 2015 - What Wikipedia Must DoAndrew Lih
By Andrew Lih, Keynote address on October 9, 2015 at the US National Archives and Records Administration, Wikiconference USA 2015 - What Wikipedia Must Do
Presentada en la Jornada Internacional sobre Archivos Web y Depósito Legal Electrónico, en la Biblioteca Nacional de España (BNE), el día 9 de julio de 2013.
Similar to Improving the troubled relationship between Scientists and Wikipedia (20)
Wikipedia at the Royal Society: The Good, the Bad and the UglyDuncan Hull
Wikipedia has a troubled relationship with scientists and their science. Many scientists are wary of editing Wikipedia and reluctant to contribute their knowledge to it, despite its global reach. Consequently, Wikipedia's coverage of Science is very variable with many notable scientists work either completely absent or poorly described.
There are several WikiProjects that are tackling these problems across Science, including in Computational Biology, Medicine, Cell Biology, Physiology and Women Scientists.
This talk will describe how the WikiProject Royal Society has addressed these issues, through its Wikipedian in Residence scheme. We will examine the outcomes of the project as well as the challenges that remain for this ongoing collaboration between the Royal Society and Wikimedia UK.
We will discuss the good, bad and "ugly" aspects of scientists Wiki-biographies (quick biographies in Wikipedia) and draw conclusions about improving coverage of Scientists, and their Science in Wikipedia using the resources of a learned academic society.
Speaker biography: Dr. Duncan Hull is a lecturer in the School of Computer Science at the University of Manchester who started editing Wikipedia in 2004. He helped setup the Wikipedian in Residence scheme at the Royal Society in 2012.
Part of a joint presentation with Midori Harris comparing OWL (Web Ontology Language) and OBO (Open Biomedical Ontologies) as ontology languages, This presentation concentrates on OWL, Midori Harris presented OBO.
Accessing small molecule data using ChEBIDuncan Hull
Presentation on Chemical Entities of Biological Interest (ChEBI) for the Programmatic Access to Biological Databases (Perl) course
22-26 February 2010 @ EBI
Digital Identity is fundamental to collaboration in bioinformatics research and development because it enables attribution, contribution, publication to be recorded and quantified.
However, current models of identity are often obsolete and have problems capturing both small contributions "microattribution" and large contributions "mega-attribution" in Science. Without adequate identity mechanisms, the incentive for collaboration can be reduced, and the utility of collaborative social tools hindered.
Using examples of metabolic pathway analysis with the taverna workbench and myexperiment.org, this talk will illustrate problems and solutions to identifying scientists accurately and effectively in collaborative bioinformatics networks on the Web.
Defrosting the Digital Library: A survey of bibliographic tools for the next ...Duncan Hull
After centuries with little change, scientific libraries have recently experienced massive upheaval. From being almost entirely paper-based, most libraries are now almost completely digital. This information revolution has all happened in less than 20 years and has created many novel opportunities and threats for scientists, publishers and libraries.
Today, we are struggling with an embarassing wealth of digital knowledge on the Web. Most scientists access this knowledge through some kind of digital library, however these places can be cold, impersonal, isolated, and inaccessible places. Many libraries are still clinging to obsolete models of identity, attribution, contribution, citation and publication.
Based on a review published in PLoS Computational Biology, http://pubmed.gov/18974831 this talk will discuss the current chilly state of digital libraries for biologists, chemists and informaticians, including PubMed and Google Scholar. We highlight problems and solutions to the coupling and decoupling of publication data and metadata, with a tool called http://www.citeulike.org. This software tool exploits the Web to make digital libraries “warmer”: more personal, sociable, integrated, and accessible places.
Finally issues that will help or hinder the continued warming of libraries in the future, particularly the accurate identity of authors and their publications, are briefly introduced. These are discussed in the context of the BBSRC funded REFINE project, at the National Centre for Text Mining (NaCTeM.ac.uk), which is linking biochemical pathway data with evidence for pathways from the PubMed database.
Seminar of U.V. Spectroscopy by SAMIR PANDASAMIR PANDA
Spectroscopy is a branch of science dealing the study of interaction of electromagnetic radiation with matter.
Ultraviolet-visible spectroscopy refers to absorption spectroscopy or reflect spectroscopy in the UV-VIS spectral region.
Ultraviolet-visible spectroscopy is an analytical method that can measure the amount of light received by the analyte.
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.
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 .
Professional air quality monitoring systems provide immediate, on-site data for analysis, compliance, and decision-making.
Monitor common gases, weather parameters, particulates.
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.
Cancer cell metabolism: special Reference to Lactate Pathway
Improving the troubled relationship between Scientists and Wikipedia
1. Improving the troubled relationship
between Scientists & Wikipedia
Duncan Hull @dullhunk
University of Manchester
& John Byrne User:Johnbod
Wikipedian in Residence
Royal Society & CRUK
Wikipedia Science Conference @WellcomeTrust
London 2nd & 3rd September 2015
6. The “distorted mirror of Wikipedia”…
“Wikipedia failed in covering notable scholars properly ...
might be producing an inaccurate image
of academics on the front end of science.”
Samoilenko & Yasseri (2014) Quantitative analysis of Wikipedia
coverage, EPJ Data Science http://doi.org/66r via the Oxford
Internet Institute (OII)
7. …typically lack very basic information
1. Education? no X
2. Research? nada X
3. Career? nope X
4. Funding? E.g. orcid.org non X
5. Publications? [Citation-needed] doi.org naw X
6. Collaborators, PhD students & postdocs? nein X
7. Pictures? (CC-BY / CC-BY-SA license) null X
If wiki-biographies exist…
8. Credit: Randall Munroe https://xkcd.com/773/
Universities typically don’t provide this information…
11. Wikipedia loves
celebrities…
e.g. every tiny detail
of Beckham’s life is
documented at
http://enwp.org/Dav
id_Beckham
yet it has nothing to
say about equivalent
scientists
12. Many notable scientists are
Fellows of the Royal Society (FRS)
Darwin Newton Turing Hodgkin Einstein
Hawking Berners-Lee Geim Ramakrishnan Blackburn
13. Many notable scientists are
Fellows of the Royal Society (FRS)
Darwin Newton Turing Hodgkin Einstein
Hawking Berners-Lee Geim Ramakrishnan Blackburn
approx:
50 new Fellows / year for 350 years
8000 Fellows (since 1660)
1400 Living (FRS)
160 Foreign (ForMemRS)
160 Women
280 Nobels ( )
14. “Recognise, promote and
support excellence in
science and to encourage
the development and use of
science for the benefit of
humanity”
“… every single person
on the planet is given free
access to the sum of all human
knowledge”
Note significant overlap
15. How about a Wikipedian in
Residence @RoyalSociety?
16. How about a Wikipedian in
Residence @RoyalSociety?
YES!
18. Results: Edit-a-thons
• 3 public edit-a-thons, focused on diversity particularly
Women in Wikipedia
• Internal training sessions ran at the Royal Society
http://enwp.org/Wikipedia:WikiProject_Royal_Society
• Ongoing relationship and understanding between
Royal Society and Wikipedia editors
19. Results: Data published
• 118 high quality, high-resolution portraits
published CC-BY-SA (2014 & 2015)
• https://commons.wikimedia.org/wiki/Category:Images
_released_by_the_Royal_Society
• Biographical data published at
http://www.royalsociety.org released CC-BY-SA
allowing easier re-use on Wikipedia and elsewhere
• Journal subscription offer renewed & extended to 75
subscriptions
http://enwp.org/Wikipedia:Royal_Society_Journals
20. Results: FRS coverage
100% of Female Fellows and FRS from 2014/5
have wiki-biographes
On average, 30% of 1000 fellows elected in
last 20 years have no wiki-biography at all
(300 total)
21. Results: Impact
• Images (e.g. in 22 different
languageshttps://commons.wikime
dia.org/wiki/File:Professor_Martin_Hair
er_FRS.jpg )
• Data widely re-used and
highly visible & accessible
22. Results: Impact
Data from
1. http://stats.grok.se/
2. https://tools.wmflabs.org/glamtools/baglama2/
3. https://blog.wikimedia.org/2014/09/11/new-images-released-are-quickly-put-to-use/
• Images: about 40k page views a month, biggest spike 100k views (due to Fields Medal)
• Biography pages: ~1k page views per month (for http://en.wikipedia.org/wiki )
23.
24. via Google’s Knowledge Graph
using data from Wikipedia
Wiki-biographies rank highly in
search results, often top result
or on the first page
25. Where next?
• We need more scientist editors to help…
– Better reflect Scientists (and Science) in Wikipedia
– Create new biographies that don’t exist yet
– Improve existing biographies
• Maybe if Wikipedia loved scientist a bit more, they might be more
inclined to edit it?
• More pictures available under CC-BY license e.g.
– royalsociety.org/library/collections
– https://pictures.royalsociety.org
• More learned societies (and funding bodies) to employ wikipedians
in residence
26. Where next?
Wikipedians in residence at European Molecular Biology Organization (EMBO), Academy
of Medical Sciences, Royal Academy of Engineering, Zoological Society of London, Institute
of Physics, Linnean Society, IET, Royal Astronomical Society, Royal Society of Biology… etc
27. web wiki-loves-scientists.org.uk
twitter @wikiscientists
• Wikipedia pages (and data) are used by
thousands of people (and machines) around the
globe: 26 million page views per hour*
• Entertaining to edit biographies
of scientists you don’t know personally for
Neutral Point of View (NPOV)
• Might encourage more scientist editors?
*According to
https://wikimania2015.wikime
dia.org/wiki/Submissions/The
_next_million_articles_in_Wik
ipedia
28. Acknowledgements
• Paul Nurse @TheCrick, Francis Bacon, Emma
Tennant, David Silverthorne, Aosaf Afzal
@RoyalSociety
• Martin Poulter, University of Bristol
@mlpoulter
• Wikimedia UK @WikimediaUK
• All the contributors to wiki-biographies (too
numerous to mention here)
If wikipedia biographies exist they tend to commit at least one of seven deadly sins of omission.
Where was the scientists educated?
What is their research about?
What has their career been and how did they become wikipedia notable?
Where did they get their funding from? (can be millions from taxpayers)
Where are the publications and results?
Who are their collaborators? Who were their PhD students and postdocs?
Last but not least, no high quality image of scientist available under an appropriate license
You might say, so what? Let the Universities provide this information. But Universities often do a bad job of providing this information… as pointed out by Randall Munroe of XKCD
You’ll be lucky if you can find basic information on a university website
You might also say, leave the scientists to desribe themselves to the world on their academic homepage.
But this are typically very dated and not written from a very neutral point of view (NPOV)
Compare the situation with how wikipedia LOVES celebrities.
The encyclopedia tells you all about EVERY goal David Beckham scored for Manchester United because it CELEBRATES celebrities
BUT has NOTHING to say about many leading scientists – this needs to change.
Where can we go to find notable scientists? The Royal Society. Many distinguished members, nobel laureates from the last 350 years to the present day (not just UK)
Where can we go to find notable scientists? The Royal Society. Many distinguished members, nobel laureates from the last 350 years to the present day (not just UK)
The royal society and wikipedia have similar goals (although their approaches are very different)
I put this to Paul Nurse via an email (never seriously expected a reply)
Thankfully he agreed and they employed a part-time wikipedian in residence for 6(?) months