xhttp://www.escience2009.org/ Web Semantics in Action: Web 3.0 in e-Science 11:50 – 12:15 Annamaria Carusi & Anita de Waard: Changing Modes of Scientific Discourse Analysis, Changing Perceptions of Science
Connecting life sciences data at the European Bioinformatics InstituteConnected Data World
Tony Burdett's slides from his talk at Connected Data London. Tony is a Senior Software Engineer at The European Bioinformatics Institute. He presented the complexity of data at the EMBL-EBI and what is their solution to make sense of all this data.
The information revolution has transformed many business sectors over the last decade and the pharmaceutical industry is no exception. Developments in scientific and information technologies have unleashed an avalanche of content on research scientists who are struggling to access and filter this in an efficient manner. Furthermore, this domain has traditionally suffered from a lack of standards in how entities, processes and experimental results are described, leading to difficulties in determining whether results from two different sources can be reliably compared. The need to transform the way the life-science industry uses information has led to new thinking about how companies should work beyond their firewalls. In this talk we will provide an overview of the traditional approaches major pharmaceutical companies have taken to knowledge management and describe the business reasons why pre-competitive, cross-industry and public-private partnerships have gained much traction in recent years. We will consider the scientific challenges concerning the integration of biomedical knowledge, highlighting the complexities in representing everyday scientific objects in computerised form. This leads us to discuss how the semantic web might lead us to a long-overdue solution. The talk will be illustrated by focusing on the EU-Open PHACTS initiative (openphacts.org), established to provide a unique public-private infrastructure for pharmaceutical discovery. The aims of this work will be described and how technologies such as just-in-time identity resolution, nanopublication and interactive visualisations are helping to build a powerful software platform designed to appeal to directly to scientific users across the public and private sectors.
Connecting life sciences data at the European Bioinformatics InstituteConnected Data World
Tony Burdett's slides from his talk at Connected Data London. Tony is a Senior Software Engineer at The European Bioinformatics Institute. He presented the complexity of data at the EMBL-EBI and what is their solution to make sense of all this data.
The information revolution has transformed many business sectors over the last decade and the pharmaceutical industry is no exception. Developments in scientific and information technologies have unleashed an avalanche of content on research scientists who are struggling to access and filter this in an efficient manner. Furthermore, this domain has traditionally suffered from a lack of standards in how entities, processes and experimental results are described, leading to difficulties in determining whether results from two different sources can be reliably compared. The need to transform the way the life-science industry uses information has led to new thinking about how companies should work beyond their firewalls. In this talk we will provide an overview of the traditional approaches major pharmaceutical companies have taken to knowledge management and describe the business reasons why pre-competitive, cross-industry and public-private partnerships have gained much traction in recent years. We will consider the scientific challenges concerning the integration of biomedical knowledge, highlighting the complexities in representing everyday scientific objects in computerised form. This leads us to discuss how the semantic web might lead us to a long-overdue solution. The talk will be illustrated by focusing on the EU-Open PHACTS initiative (openphacts.org), established to provide a unique public-private infrastructure for pharmaceutical discovery. The aims of this work will be described and how technologies such as just-in-time identity resolution, nanopublication and interactive visualisations are helping to build a powerful software platform designed to appeal to directly to scientific users across the public and private sectors.
Specimen-level mining: bringing knowledge back 'home' to the Natural History ...Ross Mounce
A talk given at the Geological Society of London, UK on 2016/03/09 as part of the Lyell meeting on Palaeoinformatics. http://www.geolsoc.org.uk/lyell16 #lyell16
Current advances to bridge the usability-expressivity gap in biomedical seman...Maulik Kamdar
I presented a talk at the Protege research meeting on the 'Current advances to bridge the usability-expressivity gap in biomedical semantic search (and visualizing linked data)' https://sites.google.com/site/protegeresearchmeeting/meeting-materials/current-advances-to-bridge-the-usability-expressivity-gap-in-semantic-search
The Seven Deadly Sins of BioinformaticsDuncan Hull
Keynote talk at Bioinformatics Open Source Conference (BOSC) Special Interest Group at the 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2007) in Vienna, July 2007 by Carole Goble, University of Manchester.
Web-scale Discovery Tools and the Backgrounding of Government InformationChristopher Brown
Brown, Christopher. C. “Web-scale Discovery Tools and the Backgrounding of Government Information.” Presentation given at the Electronic Resources & Libraries Conference, 23 February 2015, Austin, TX.
Web-scale discovery tools have opened up new realms of discovery for libraries and their electronic resources. However, government information is being short-changed and backgrounded in these tools. Find out why this is happening, the diagnostic tests to show that this is so, and what we can do about it.
An overview of Text and Data Mining (ContentMining) including live demonstrations. The fundamentals: discover, scrape, normalize , facet/index, analyze, publish are exemplified using the recent Zika outbreak. Mining covers textual and non-textual content and examples of chemistry and phylogenetic tress are given.
Slides for a talk given by Norman Meuschke at the National Institute of Informatics Tokyo in June 2018.
The talk gives an overview of the research of the Information Science group and presents recent work of Norman on analyzing nontextual content features to improve the detection capabilities for academic plagiarism. Identifying academic plagiarism is an important task for educational and research institutions, publishers, and funding agencies. Current plagiarism detection systems reliably find instances of copied and moderately reworded text. However, reliably detecting instances of concealed plagiarism, such as strong paraphrases, translations, and the reuse of nontextual content and ideas, is an open research problem. Norman’s research focuses on analyzing nontextual features of academic documents, such as citations, images, and mathematical expressions, to complement the well-performing text-based detection methods. His goal is to devise a hybrid detection approach that analyzes textual and nontextual content features in academic documents to best possibly cover the wide range of plagiarism forms. More information on the Information Science research group and Norman can be found at: www.isg.uni.kn and www.meuschke.org
Overview of scientific discourse annotatoinAnita de Waard
Presentation held at second Amicus workshop, http://amicus.uvt.nl/amicus_ws2011.htm: "Storytelling in Fairytales and Science:
Narrative structure models of scientific communication and folktales"
Have ever asked yourself how long does it take for me to drive from home to the office? You might be able to say the approximate time for your trip, but more likely, you’ll ask yourself again the following questions: which way, what day of the week, and what modes of transportation do I take; because the answer depends on the conditions.
You might not realize that you have just applied an assessment activity, just by asking question or contemplating the duration of your trip from home to your office.
Presentation by Tito Sierra at Code4Lib 2007 in Athens, GA.
The Smart Subjects tool attempts to increase broader user discovery of relevant library resources by serendipitously recommending library subjects related to a user's search query. The prototype tool uses large locally created subject indexes consisting of rich topical keyword content harvested from local sources. An OpenSearch interface allows this recommendation service to be integrated flexibly and easily in a variety of web applications.
Presentation to the J. Craig Venter Institute, Dec. 2014Mark Wilkinson
This is largely a compilation of various other talks that I have posted here - a summary of the past 3+ years of work on SADI/SHARE. It includes the (now well-worn!!) slides about SHARE, as well as some of the more contemporary stuff about how we extended GALEN clinical classes with richer semantic descriptions, and then used them to do automated clinical phenotype analysis. Also includes the slide-deck related to automated Measurement Unit conversion (related to our work on semantically representing Framingham clinical risk assessment rules)
So... for anyone who regularly follows my uploads, there isn't much "new" in here, but at least it's all in one place now! :-)
Specimen-level mining: bringing knowledge back 'home' to the Natural History ...Ross Mounce
A talk given at the Geological Society of London, UK on 2016/03/09 as part of the Lyell meeting on Palaeoinformatics. http://www.geolsoc.org.uk/lyell16 #lyell16
Current advances to bridge the usability-expressivity gap in biomedical seman...Maulik Kamdar
I presented a talk at the Protege research meeting on the 'Current advances to bridge the usability-expressivity gap in biomedical semantic search (and visualizing linked data)' https://sites.google.com/site/protegeresearchmeeting/meeting-materials/current-advances-to-bridge-the-usability-expressivity-gap-in-semantic-search
The Seven Deadly Sins of BioinformaticsDuncan Hull
Keynote talk at Bioinformatics Open Source Conference (BOSC) Special Interest Group at the 15th Annual International Conference on Intelligent Systems for Molecular Biology (ISMB 2007) in Vienna, July 2007 by Carole Goble, University of Manchester.
Web-scale Discovery Tools and the Backgrounding of Government InformationChristopher Brown
Brown, Christopher. C. “Web-scale Discovery Tools and the Backgrounding of Government Information.” Presentation given at the Electronic Resources & Libraries Conference, 23 February 2015, Austin, TX.
Web-scale discovery tools have opened up new realms of discovery for libraries and their electronic resources. However, government information is being short-changed and backgrounded in these tools. Find out why this is happening, the diagnostic tests to show that this is so, and what we can do about it.
An overview of Text and Data Mining (ContentMining) including live demonstrations. The fundamentals: discover, scrape, normalize , facet/index, analyze, publish are exemplified using the recent Zika outbreak. Mining covers textual and non-textual content and examples of chemistry and phylogenetic tress are given.
Slides for a talk given by Norman Meuschke at the National Institute of Informatics Tokyo in June 2018.
The talk gives an overview of the research of the Information Science group and presents recent work of Norman on analyzing nontextual content features to improve the detection capabilities for academic plagiarism. Identifying academic plagiarism is an important task for educational and research institutions, publishers, and funding agencies. Current plagiarism detection systems reliably find instances of copied and moderately reworded text. However, reliably detecting instances of concealed plagiarism, such as strong paraphrases, translations, and the reuse of nontextual content and ideas, is an open research problem. Norman’s research focuses on analyzing nontextual features of academic documents, such as citations, images, and mathematical expressions, to complement the well-performing text-based detection methods. His goal is to devise a hybrid detection approach that analyzes textual and nontextual content features in academic documents to best possibly cover the wide range of plagiarism forms. More information on the Information Science research group and Norman can be found at: www.isg.uni.kn and www.meuschke.org
Overview of scientific discourse annotatoinAnita de Waard
Presentation held at second Amicus workshop, http://amicus.uvt.nl/amicus_ws2011.htm: "Storytelling in Fairytales and Science:
Narrative structure models of scientific communication and folktales"
Have ever asked yourself how long does it take for me to drive from home to the office? You might be able to say the approximate time for your trip, but more likely, you’ll ask yourself again the following questions: which way, what day of the week, and what modes of transportation do I take; because the answer depends on the conditions.
You might not realize that you have just applied an assessment activity, just by asking question or contemplating the duration of your trip from home to your office.
Presentation by Tito Sierra at Code4Lib 2007 in Athens, GA.
The Smart Subjects tool attempts to increase broader user discovery of relevant library resources by serendipitously recommending library subjects related to a user's search query. The prototype tool uses large locally created subject indexes consisting of rich topical keyword content harvested from local sources. An OpenSearch interface allows this recommendation service to be integrated flexibly and easily in a variety of web applications.
Presentation to the J. Craig Venter Institute, Dec. 2014Mark Wilkinson
This is largely a compilation of various other talks that I have posted here - a summary of the past 3+ years of work on SADI/SHARE. It includes the (now well-worn!!) slides about SHARE, as well as some of the more contemporary stuff about how we extended GALEN clinical classes with richer semantic descriptions, and then used them to do automated clinical phenotype analysis. Also includes the slide-deck related to automated Measurement Unit conversion (related to our work on semantically representing Framingham clinical risk assessment rules)
So... for anyone who regularly follows my uploads, there isn't much "new" in here, but at least it's all in one place now! :-)
Presentation given at NUI, Galway 2019-04-11 for Open Science Week.
An overview of Early Career Researchers, their innovation and contribution towards Open Infrastructure
ContentMining for France and Europe; Lessons from 2 years in UKpetermurrayrust
I have spend 2 years carrying out Content Mining (aka Text and Data Mining) in the UK under the 2014 "Hargreaves" exception. This talk was given in Paris, to ADBU , after France had passed the law of the numeric Republique. I illustrate what worked in what did not and why and offer ideas to France and Europe
Open access for researchers, policy makers and research managers - Short ver...Iryna Kuchma
Presented at Open Access: Maximising Research Impact, April 23 2009, New Bulgarian University Library, Sofia. Open access for researchers: enlarged audience, citation impact, tenure and promotion. Open access for policy makers and research managers:
new tools to manage a university’s image and impact. How to maximize the visibility of research publications, improve the impact and influence of the work, disseminate the results of the research, showcase the quality of the research in the Universities and research institutions, better measure and manage the research in the institution, collect and curate the digital outputs, generate new knowledge from existing findings, enable and encourage collaboration, bring savings to the higher education sector and better return on investment. What are the key functions for research libraries?
Recomendations for infrastructure and incentives for open science, presented to the Research Data Alliance 6th Plenary. Presenter: William Gunn, Director of Scholarly Communications for Mendeley.
Talk at the World Science Festival at Columbia, June 2, 2017: session on Big Data and Physics: http://www.worldsciencefestival.com/programs/big-data-future-physics/
Data Repositories: Recommendation, Certification and Models for Cost RecoveryAnita de Waard
Talk at NITRD Workshop "Measuring the Impact of Digital Repositories" February 28 – March 1, 2017 https://www.nitrd.gov/nitrdgroups/index.php?title=DigitalRepositories
A Strategic Approach: GenAI in EducationPeter Windle
Artificial Intelligence (AI) technologies such as Generative AI, Image Generators and Large Language Models have had a dramatic impact on teaching, learning and assessment over the past 18 months. The most immediate threat AI posed was to Academic Integrity with Higher Education Institutes (HEIs) focusing their efforts on combating the use of GenAI in assessment. Guidelines were developed for staff and students, policies put in place too. Innovative educators have forged paths in the use of Generative AI for teaching, learning and assessments leading to pockets of transformation springing up across HEIs, often with little or no top-down guidance, support or direction.
This Gasta posits a strategic approach to integrating AI into HEIs to prepare staff, students and the curriculum for an evolving world and workplace. We will highlight the advantages of working with these technologies beyond the realm of teaching, learning and assessment by considering prompt engineering skills, industry impact, curriculum changes, and the need for staff upskilling. In contrast, not engaging strategically with Generative AI poses risks, including falling behind peers, missed opportunities and failing to ensure our graduates remain employable. The rapid evolution of AI technologies necessitates a proactive and strategic approach if we are to remain relevant.
A workshop hosted by the South African Journal of Science aimed at postgraduate students and early career researchers with little or no experience in writing and publishing journal articles.
Executive Directors Chat Leveraging AI for Diversity, Equity, and InclusionTechSoup
Let’s explore the intersection of technology and equity in the final session of our DEI series. Discover how AI tools, like ChatGPT, can be used to support and enhance your nonprofit's DEI initiatives. Participants will gain insights into practical AI applications and get tips for leveraging technology to advance their DEI goals.
Operation “Blue Star” is the only event in the history of Independent India where the state went into war with its own people. Even after about 40 years it is not clear if it was culmination of states anger over people of the region, a political game of power or start of dictatorial chapter in the democratic setup.
The people of Punjab felt alienated from main stream due to denial of their just demands during a long democratic struggle since independence. As it happen all over the word, it led to militant struggle with great loss of lives of military, police and civilian personnel. Killing of Indira Gandhi and massacre of innocent Sikhs in Delhi and other India cities was also associated with this movement.
Unit 8 - Information and Communication Technology (Paper I).pdfThiyagu K
This slides describes the basic concepts of ICT, basics of Email, Emerging Technology and Digital Initiatives in Education. This presentations aligns with the UGC Paper I syllabus.
Introduction to AI for Nonprofits with Tapp NetworkTechSoup
Dive into the world of AI! Experts Jon Hill and Tareq Monaur will guide you through AI's role in enhancing nonprofit websites and basic marketing strategies, making it easy to understand and apply.
Read| The latest issue of The Challenger is here! We are thrilled to announce that our school paper has qualified for the NATIONAL SCHOOLS PRESS CONFERENCE (NSPC) 2024. Thank you for your unwavering support and trust. Dive into the stories that made us stand out!
2024.06.01 Introducing a competency framework for languag learning materials ...Sandy Millin
http://sandymillin.wordpress.com/iateflwebinar2024
Published classroom materials form the basis of syllabuses, drive teacher professional development, and have a potentially huge influence on learners, teachers and education systems. All teachers also create their own materials, whether a few sentences on a blackboard, a highly-structured fully-realised online course, or anything in between. Despite this, the knowledge and skills needed to create effective language learning materials are rarely part of teacher training, and are mostly learnt by trial and error.
Knowledge and skills frameworks, generally called competency frameworks, for ELT teachers, trainers and managers have existed for a few years now. However, until I created one for my MA dissertation, there wasn’t one drawing together what we need to know and do to be able to effectively produce language learning materials.
This webinar will introduce you to my framework, highlighting the key competencies I identified from my research. It will also show how anybody involved in language teaching (any language, not just English!), teacher training, managing schools or developing language learning materials can benefit from using the framework.
Biological screening of herbal drugs: Introduction and Need for
Phyto-Pharmacological Screening, New Strategies for evaluating
Natural Products, In vitro evaluation techniques for Antioxidants, Antimicrobial and Anticancer drugs. In vivo evaluation techniques
for Anti-inflammatory, Antiulcer, Anticancer, Wound healing, Antidiabetic, Hepatoprotective, Cardio protective, Diuretics and
Antifertility, Toxicity studies as per OECD guidelines
"Protectable subject matters, Protection in biotechnology, Protection of othe...
De Waard Carusi
1. Changing modes of scientific
discourse analysis,
changing perceptions of science
Annamaria Carusi
eResearch Centre, Oxford University
Anita de Waard
Disruptive Technologies, Elsevier Labs
Utrecht Institute of Linguistics, U Utrecht
8. ‘Fact Extraction’ (MEDIE) - is not enough!
Alteration of nm23, P53, and S100A4 expression may
contribute to the development of gastric
9. ‘Fact Extraction’ (MEDIE) - is not enough!
Alteration of nm23, P53, and S100A4 expression may
contribute to the development of gastric
Previous studies have implicated miR-34a as a tumor
suppressor gene whose transcription is activated by p53.
10. ‘Fact Extraction’ (MEDIE) - is not enough!
without some idea of the status of the
sentence, it cannot be interpreted!
Alteration of nm23, P53, and S100A4 expression may
contribute to the development of gastric
Previous studies have implicated miR-34a as a tumor
suppressor gene whose transcription is activated by p53.
11. Hypotheses, Evidence and Relationships:
- Goal: Align and expand existing efforts on detection and
analysis of Hypotheses, Evidence & Relationships
- Partners:
- Harvard/MGH: SWAN, ARF
- Open University: Cohere
- Oxford University: CiTO, eLearning/Rhetoric
- DERI: SALT, aTags
- University of Trento: LiquidPub
- Xerox Research: XIP hypothesis identifier
- U Tilburg: ML for Science
- Elsevier, UUtrecht: Discourse analysis of biology
12. Hypotheses, Evidence and Relationships:
- Goal: Align and expand existing efforts on detection and
analysis of Hypotheses, Evidence & Relationships
- Partners:
- Harvard/MGH: SWAN, ARF
- Open University: Cohere
- Oxford University: CiTO, eLearning/Rhetoric
- DERI: SALT, aTags
- University of Trento: LiquidPub
- Xerox Research: XIP hypothesis identifier
- U Tilburg: ML for Science
- Elsevier, UUtrecht: Discourse analysis of biology
13. Hypotheses, Evidence and Relationships:
- Goal: Align and expand existing efforts on detection and
analysis of Hypotheses, Evidence & Relationships
- Partners:
- Harvard/MGH: SWAN, ARF
- Open University: Cohere
- Oxford University: CiTO, eLearning/Rhetoric
- DERI: SALT, aTags
- University of Trento: LiquidPub
- Xerox Research: XIP hypothesis identifier
- U Tilburg: ML for Science
- Elsevier, UUtrecht: Discourse analysis of biology
14. Hypotheses, Evidence and Relationships:
- Goal: Align and expand existing efforts on detection and
analysis of Hypotheses, Evidence & Relationships
- Partners:
- Harvard/MGH: SWAN, ARF
- Open University: Cohere
- Oxford University: CiTO, eLearning/Rhetoric
- DERI: SALT, aTags
- University of Trento: LiquidPub
- Xerox Research: XIP hypothesis identifier
- U Tilburg: ML for Science
- Elsevier, UUtrecht: Discourse analysis of biology
15. Hypotheses, Evidence and Relationships:
- Goal: Align and expand existing efforts on detection and
analysis of Hypotheses, Evidence & Relationships
- Partners:
- Harvard/MGH: SWAN, ARF
- Open University: Cohere
- Oxford University: CiTO, eLearning/Rhetoric
- DERI: SALT, aTags
- University of Trento: LiquidPub
- Xerox Research: XIP hypothesis identifier
- U Tilburg: ML for Science
- Elsevier, UUtrecht: Discourse analysis of biology
16. Hypotheses, Evidence and Relationships:
- Goal: Align and expand existing efforts on detection and
analysis of Hypotheses, Evidence & Relationships
- Partners:
- Harvard/MGH: SWAN, ARF
- Open University: Cohere
- Oxford University: CiTO, eLearning/Rhetoric
- DERI: SALT, aTags
- University of Trento: LiquidPub
- Xerox Research: XIP hypothesis identifier
- U Tilburg: ML for Science
- Elsevier, UUtrecht: Discourse analysis of biology
17. Hypotheses, Evidence and Relationships:
- Goal: Align and expand existing efforts on detection and
analysis of Hypotheses, Evidence & Relationships
- Partners:
- Harvard/MGH: SWAN, ARF
Hypothesis 22: Intramembrenous Aβ dimer may be toxic.
- Derived from: POSTAT_CONTRIBUTION(This essay explores the possibility that a
Open University: Cohere
fraction of these Abeta peptides never leave the membrane lipid bilayer after they are
- generated, but instead exerteLearning/Rhetoric competing with and compromising
Oxford University: CiTO, their toxic effects by
the functions of intramembranous segments of membrane-bound proteins that serve
- many critical functions.
DERI: SALT, aTags
- University of Trento: LiquidPub
- Xerox Research: XIP hypothesis identifier
- U Tilburg: ML for Science
- Elsevier, UUtrecht: Discourse analysis of biology
18. Hypotheses, Evidence and Relationships:
- Goal: Align and expand existing efforts on detection and
analysis of Hypotheses, Evidence & Relationships
- Partners:
- Harvard/MGH: SWAN, ARF
Hypothesis 22: Intramembrenous Aβ dimer may be toxic.
- Derived from: POSTAT_CONTRIBUTION(This essay explores the possibility that a
Open University: Cohere
fraction of these Abeta peptides never leave the membrane lipid bilayer after they are
- generated, but instead exerteLearning/Rhetoric competing with and compromising
Oxford University: CiTO, their toxic effects by
the functions of intramembranous segments of membrane-bound proteins that serve
- many critical functions.
DERI: SALT, aTags
- University of Trento: LiquidPub
- Xerox Research: XIP hypothesis identifier
- U Tilburg: ML for Science
- Elsevier, UUtrecht: Discourse analysis of biology
22. HypER Activities: http://hyper.wik.is
Current activities:
✓Aligning discourse ontologies: joint task with W3C HCLSSig
✓Format for a rhetorical conference paper (SWAN+ SALT + abcde)
23. HypER Activities: http://hyper.wik.is
Current activities:
✓Aligning discourse ontologies: joint task with W3C HCLSSig
✓Format for a rhetorical conference paper (SWAN+ SALT + abcde)
‣Parser test of hypothesis identification tools on pharmacology
corpus
24. HypER Activities: http://hyper.wik.is
Current activities:
✓Aligning discourse ontologies: joint task with W3C HCLSSig
✓Format for a rhetorical conference paper (SWAN+ SALT + abcde)
‣Parser test of hypothesis identification tools on pharmacology
corpus
‣Aligning architectures to exchange hypotheses + evidence
25. HypER Activities: http://hyper.wik.is
Current activities:
✓Aligning discourse ontologies: joint task with W3C HCLSSig
✓Format for a rhetorical conference paper (SWAN+ SALT + abcde)
‣Parser test of hypothesis identification tools on pharmacology
corpus
‣Aligning architectures to exchange hypotheses + evidence
Further interests:
26. HypER Activities: http://hyper.wik.is
Current activities:
✓Aligning discourse ontologies: joint task with W3C HCLSSig
✓Format for a rhetorical conference paper (SWAN+ SALT + abcde)
‣Parser test of hypothesis identification tools on pharmacology
corpus
‣Aligning architectures to exchange hypotheses + evidence
Further interests:
-Better structure of evidence: MyExperiment, KeFeD, ...
27. HypER Activities: http://hyper.wik.is
Current activities:
✓Aligning discourse ontologies: joint task with W3C HCLSSig
✓Format for a rhetorical conference paper (SWAN+ SALT + abcde)
‣Parser test of hypothesis identification tools on pharmacology
corpus
‣Aligning architectures to exchange hypotheses + evidence
Further interests:
-Better structure of evidence: MyExperiment, KeFeD, ...
-Granularity of annotation/access: entity, hypothesis, discussion?
30. Pragmatic Discourse Analysis
- How can we better tell computers what our
papers are about?
- Science is written in text, as a story
31. Pragmatic Discourse Analysis
- How can we better tell computers what our
papers are about?
- Science is written in text, as a story
- Text is created by humans to persuade other
humans (peers, that claims are facts)
32. Pragmatic Discourse Analysis
- How can we better tell computers what our
papers are about?
- Science is written in text, as a story
- Text is created by humans to persuade other
humans (peers, that claims are facts)
- To tell the computer how we encode our
knowledge, we need to understand:
33. Pragmatic Discourse Analysis
- How can we better tell computers what our
papers are about?
- Science is written in text, as a story
- Text is created by humans to persuade other
humans (peers, that claims are facts)
- To tell the computer how we encode our
knowledge, we need to understand:
=> How do humans tell stories?
34. Pragmatic Discourse Analysis
- How can we better tell computers what our
papers are about?
- Science is written in text, as a story
- Text is created by humans to persuade other
humans (peers, that claims are facts)
- To tell the computer how we encode our
knowledge, we need to understand:
=> How do humans tell stories?
=> How can we explain what matters, how these
stories create knowledge in our heads?
35. 1st Try: Classical Rhetoric
APA Style
Aristotle Quintilian Cell
Guide
The introduction of a speech, where one announces the
Introducti subject and purpose of the discourse, and where one Introductio
prooimion exordium Introduction
on usually employs the persuasive appeal of ethos in order to n
establish credibility with the audience.
The second part of a classical oration, following the
introduction or exordium. The speaker here provides a
Statement narrative account of what has happened and generally Introductio
prothesis narratio Introduction
of Facts explains the nature of the case. Quintilian adds that the n
narratio is followed by the propositio, a kind of summary of
the issues or a statement of the charge.
Coming between the narratio and the partitio of a classical
propostiti oration, the propositio provides a brief summary of what
Summary Abstract Abstract
o one is about to speak on, or concisely puts forth the
charges or accusation.
Following the statement of facts, or narratio, comes the
partitio or divisio. In this section of the oration, the speaker
Division/ outlines what will follow, in accordance with what's been Table of
partitio Article Outline
outline stated as the status, or point at issue in the case. Quintilian Contents
suggests the partitio is blended with the propositio and
also assists memory.
Following the division / outline or partitio comes the main
confirmati Methods,
pistis Proof body of the speech where one offers logical arguments as Results
o Results
proof. The appeal to logos is emphasized here.
Following the the confirmatio or section on proof in a
Refutatio classical oration, comes the refutation. As the name
refutatio Discussion Discussion
36. 2nd Try: Story Grammar
The Story of Goldilocks and Story Grammar Paper The AXH Domain of Ataxin-1 Mediates
the Three Bears Neurodegeneration through Its Interaction with Gfi-1/
Senseless Proteins
Once upon a time Time Setting Background The mechanisms mediating SCA1 pathogenesis are still not fully
understood, but some general principles have emerged.
a little girl named Goldilocks Characters Objects of study the Drosophila Atx-1 homolog (dAtx-1) which lacks a polyQ tract,
She went for a walk in the forest. Location Experimental studied and compared in vivo effects and interactions to those of the
Pretty soon, she came upon a setup human protein
house.
She knocked and, when no one Goal Theme Research Gain insight into how Atx-1's function contributes to SCA1
answered, goal pathogenesis. How these interactions might contribute to the disease
process and how they might cause toxicity in only a subset of neurons in
SCA1 is not fully understood.
she walked right in. Attempt Hypothesis Atx-1 may play a role in the regulation of gene expression
At the table in the kitchen, there Name Episode 1 Name dAtX-1 and hAtx-1 Induce Similar Phenotypes When Overexpressed in
were three bowls of porridge. Files
Goldilocks was hungry. Subgoal Subgoal test the function of the AXH domain
She tasted the porridge from the Attempt Method overexpressed dAtx-1 in flies using the GAL4/UAS system (Brand and
first bowl. Perrimon, 1993) and compared its effects to those of hAtx-1.
This porridge is too hot! she Outcome Results Overexpression of dAtx-1 by Rhodopsin1(Rh1)-GAL4, which drives
exclaimed. expression in the differentiated R1-R6 photoreceptor cells (Mollereau et
al., 2000 and O'Tousa et al., 1985), results in neurodegeneration in the
eye, as does overexpression of hAtx-1[82Q]. Although at 2 days after
eclosion, overexpression of either Atx-1 does not show obvious
morphological changes in the photoreceptor cells
So, she tasted the porridge from Data (data not shown),
the second bowl.
This porridge is too cold, she said Outcome Results both genotypes show many large holes and loss of cell integrity at 28 day
39. 3rd Try: Discourse Segmentation
Goal: ‘one new thought per segment’:
Figure 4A shows that following RASV12 stimulation, p53 was
stabilized and activated, and its target gene, p21cip1, was
induced in all cases, indicating an intact p53 pathway in these
cells.
40. 3rd Try: Discourse Segmentation
Goal: ‘one new thought per segment’:
Figure 4A shows that following RASV12 stimulation, p53 was
stabilized and activated, and its target gene, p21cip1, was
induced in all cases, indicating an intact p53 pathway in these
cells.
a. Figure 4a shows that
b. following RASV12 stimulation
c. p53 was stabilized and activated
d. and the target gene, p21cip1, was induced in all cases,
e. indicating an intact p53 pathway in these cells.
41. 3rd Try: Discourse Segmentation
Goal: ‘one new thought per segment’:
Figure 4A shows that following RASV12 stimulation, p53 was
stabilized and activated, and its target gene, p21cip1, was
induced in all cases, indicating an intact p53 pathway in these
cells.
a. Figure 4a shows that Intratextual
b. following RASV12 stimulation Method
c. p53 was stabilized and activated Result
d. and the target gene, p21cip1, was induced in all cases, Result
e. indicating an intact p53 pathway in these cells. Implication
42. 3rd Try: Discourse Segmentation
Goal: ‘one new thought per segment’:
Figure 4A shows that following RASV12 stimulation, p53 was
stabilized and activated, and its target gene, p21cip1, was
induced in all cases, indicating an intact p53 pathway in these
cells.
a. Figure 4a shows that Intratextual
b. following RASV12 stimulation Method
c. p53 was stabilized and activated Result
d. and the target gene, p21cip1, was induced in all cases, Result
e. indicating an intact p53 pathway in these cells. Implication
43. Tense and Realm
Realm, Segment Type Linguistic Meaning Sample segment
timeline Tense Tense
Concept Fact Present Eternal Present The TGF-β pathway is a potent inhibitor of
epithelial cell proliferation
Problem Present Eternal Present Further complicating their discovery are the
multifaceted mechanisms by which tumor
suppressor genes are inactivated,
Hypothesis Present + Modal Hyp Present [Other genes] may be found altered in tumors.
Implication Present Present [T]he transcriptional repressor REST/NRSF
plays a previously unappreciated role in tumor
suppression.
Experiment Method (Passive) Past Event Past we inhibited TGF-β signal transduction by
alternative mechanisms
Result Past Event Past Expression of either cDNA conferred growth in
semisolid media
Argumentation Reg-Implication Present Event Present we provide evidence that, implying that
Reg-Hypothesis Present Event Present Therefore, it is probable that/This supports the
hypothesis that
Reg-Problem Present Event Present This suggests that
Goal To-infinitive Goal To further examine the role of endogenous TGF-
β signaling in restraining cell transformation
Other research Reg-Others Present perfect Finalised Past disruption of adherens junction components [...]
has been linked to cancer progression in a
variety of tissues (Cavallaro and Christofori,
2004).
Intertextual Present Perfect Finalised Past To date, these models of human cell
transformation have incorporated genes already
implicated in human tumorigenesis.
46. Facts in the Endogenous small RNAs (miRNAs) regulate I sing of golden-throned Hera whom Rhea
eternal gene expression by mechanisms conserved bare. Queen of the immortals is she, surpassing
present across metazoans. all in beauty: she is the sister and the wife of
loud-thundering Zeus, --the glorious one whom
all the blessed throughout high Olympus
reverence and honor.
Events in the Vehicle-treated animals spent equivalent Now the wooers turned to the dance and to
simple past time investigating a juvenile in the first and gladsome song, and made them merry, and
second sessions in experiments waited till evening should come; and as they
conducted in the NAC and the striatum: made merry dark evening came upon them.
T1 values were 122 ± 6 s and 114 ± 5 s.
Events with We also generated BJ/ET cells expressing And she took her mighty spear, tipped with
embedded the RASV12-ERTAM chimera gene, which is sharp bronze, heavy and huge and strong,
facts only active when tamoxifen is added (De wherewith she vanquishes the ranks of men-of
Vita et al, 2005). warriors, with whom she is wroth, she, the
daughter of the mighty sire.
Attribution miRNAs have emerged as important In this book I have had old stories written
in the regulators of development and control down, as I have heard them told by intelligent
present processes such as cell fate determination people, concerning chiefs who have held
perfect and cell death (Abrahante et al., 2003, dominion in the northern countries, and who
Brennecke et al., 2003, Chang et al., 2004, spoke the Danish tongue; and also concerning
Chen et al., 2004, Johnston and Hobert, some of their family branches, according to
2003, Lee et al., 1993, ... what has been told me.
Implications These results indicate that although Now it is said that ever since then
are hedged, miR-372&3 confer complete protection to whenever the camel sees a place where ashes
and in the oncogene-induced senescence in a manner have been scattered, he wants to get revenge
present similar to p53 inactivation, the cellular with his enemy the rat and stomps and rolls in
tense response to DNA damage remains intact the ashes hoping to get the rat
49. Pragmatic Research Article:
- Does this help us tell computers what our
papers are about?
- Might help identify hypotheses in papers
automatically, but...
50. Pragmatic Research Article:
- Does this help us tell computers what our
papers are about?
- Might help identify hypotheses in papers
automatically, but...
- Helps increase/jig self-reflection by scientists of
their communication
51. Pragmatic Research Article:
- Does this help us tell computers what our
papers are about?
- Might help identify hypotheses in papers
automatically, but...
- Helps increase/jig self-reflection by scientists of
their communication
- New ways of publishing:
52. Pragmatic Research Article:
- Does this help us tell computers what our
papers are about?
- Might help identify hypotheses in papers
automatically, but...
- Helps increase/jig self-reflection by scientists of
their communication
- New ways of publishing:
- what should we model/structure/annotate
53. Pragmatic Research Article:
- Does this help us tell computers what our
papers are about?
- Might help identify hypotheses in papers
automatically, but...
- Helps increase/jig self-reflection by scientists of
their communication
- New ways of publishing:
- what should we model/structure/annotate
- what should we leave alone?
54. Pragmatic Research Article:
- Does this help us tell computers what our
papers are about?
- Might help identify hypotheses in papers
automatically, but...
- Helps increase/jig self-reflection by scientists of
their communication
- New ways of publishing:
- what should we model/structure/annotate
- what should we leave alone?
- author/editor/publisher/user/aggregator - who, what,
why?
55. Pragmatic Research Article:
- Does this help us tell computers what our
papers are about?
- Might help identify hypotheses in papers
automatically, but...
- Helps increase/jig self-reflection by scientists of
their communication
- New ways of publishing:
- what should we model/structure/annotate
- what should we leave alone?
- author/editor/publisher/user/aggregator - who, what,
why?
- how can we improve science with these formats?
56. Discourse
- Social usage of language (or other symbolic
systems); discursive vs linguistic ‘rules’ or
regularities
- Intentions and epistemic commitments/
meaning
- Dialogism (Bakhtin)
- Utterances are always directed towards
receivers --- meanings of utterances
cannot be exhausted by intentions of
senders or by linguistic codes
- Intertextuality / heteroglossia
57. Rhetoric
- Rhetoric has a very long history
- It has always been pragmatic -- Aristotle was
giving guidelines on how to give a good speech,
how to persuade.
- Rich: both in terms of making very fine
distinctions and in terms of its understanding of
discourse in general
- And discourse of different genres or types:
- poetic
- narrative --- eg plot [… and then …]
- scientific [… and this shows that ….]
- And these can be interestingly intertwined ….
16
58. subject-matter
Logos
context
text
speaker/writer listener/reader
Ethos Pathos
17
59. Argument
- ‘Logos’ in the rhetorical scheme
- Intersubjectivity of argument
- Combination of elements which are on a
continuum from the formalisable (and
formalised: eg logical forms) and non-
formalisable
- Argument extraction and diagramming
(formalisation) often require re-writing first; and
this requires interpretation
60. The witness said that he had seen Fred in the
vicinity of the shop at the time the fire started.
But we know this witness has a grudge
against Fred, and he has been known to give
unreliable evidence in the past. So we
cannot rely on this person's statement.
Hence Fred must have been
somewhere else when the fire was
started.
61. Neither shows deductive invalidity of this argument
But this does:
p: the witness is reliable
q: Fred was in the vicinity of the shop at the time of the fire
If p, then q [If the witness isfire]
shop at the time of the reliable then Fred was in the vicinity of the
not p [the witness is unreliable]
therefore not q [Fred was not in the vicinity of the shop at the time of
the fire]
Fallacy of denying the antecedent
62. Scientific self-reflection (1)
- Open-ended, ‘gappy’ or relational nature of any
utterance or move in a discourse.
- Gap between intention and interpretation
- Examples:
- epistemic force
- ‘refute’ : as a relation
63. Figure 3 – Examples of possible relationships between Comment and other SWAN classes. (Ciccarese, Wu & Cla rk
2007
64. Self-reflection (2)
- Not liked by the scientists
- But neither warranted by argumentation theory
- Refutation (to disprove a hypothesis) is
not something that one can simply
intend or maintain on his/her own
- Matter of the wider discourse of
science
- For Karl Popper, it is also a matter of
logic
- But what if there is a clash between the two?
- Methodological question
65. Self-reflection (3)
- In a ‘normal’ discourse situation these implicit
understandings of how discourse works are the
scaffolding without which interpretation cannot
operate, or without which it shifts in status and the
acceptance it seems to demand from users.
- (Disruptive) technology pushes this background
scaffolding to the fore
- Impulse may be to hide it or blackbox it: looks like
subjectivity creep
- But the discourse representation need not be made
to look more ‘objective’ and context transcendent
than it in fact is -- no need to hide it but rather
ensure that it is evident and can be interacted with.