The Pistoia SESL Project aims to pilot a biomedical knowledge brokering service through a collaboration between Pistoia Alliance members. The project will develop a minimal configuration to test a brokering service for assertions about type 2 diabetes pulled from structured databases and literature. It will involve building vocabularies, extracting data from sources like UniProt and ArrayExpress, developing a query interface, and documenting standards. The goal is to evaluate the technical feasibility of a "push model" for disseminating biomedical knowledge and inform recommendations for further work.
Developing Knowledge Brokering Standards for Biological Text and Data Integra...Ian Harrow
The Pistoia Alliance SESL Project aims to develop standards for biomedical knowledge brokering through a vehicle brokering pilot.
The pilot will develop an assertion database for type 2 diabetes combining data from structured sources and literature. It will establish APIs and a demonstrator interface. The goals are to streamline non-competitive workflows, engage stakeholders, and assess moving to a production "push model" of content delivery.
Assuming technical success, the project seeks input on opportunities for integrating literature into biomedical infrastructure, who benefits most from a push content model, how publication may be impacted, and challenges in further engaging publishers.
Emerging Life Sciences Collaboration on Common Service SpecificationPistoia Alliance
Presentation by Pistoia Alliance reps Ian Harrow (Pfizer) and Nick Lynch (AstraZeneca) at the International Conference on Trends for Scientific Information Professionals, October 2010.
The Pistoia Alliance Information Ecosystem WorkshopPistoia Alliance
Michael Braxenthaler, president of the Pistoia Alliance, introduces the concept of the information ecosystem in life science research and discusses the role the Pistoia Alliance can play within this ecosystem. The workshop occurred in October 2011.
Enabling Enterprise Collaboration with SharePoint 2010InnoTech
Applied Materials is a global company that produces equipment for semiconductor, display, and solar industries. It has over 14,600 employees worldwide and invested over $1 billion annually in R&D. The company implemented SharePoint 2010 to enable collaboration across its global operations. It started with standard out-of-the-box SharePoint sites and custom sites, and established governance and support structures. Over two years, it expanded usage to include an employee portal, business-specific sites, and mobile access, establishing SharePoint as its collaboration platform.
The document discusses a presentation given by AARNet to the CAUDIT Spring Meeting. The agenda includes an overview of AARNet's strategy and customer focus, services available on the network, and future service development. AARNet aims to deliver a high-performance network while adding value through collaboration, content delivery, and mobility applications and services. Customers have expressed interest in these types of services to better utilize the core network. AARNet considers factors like customer benefit, cost reduction, existing infrastructure use, and support longevity when prioritizing new service development.
Developing Public Support For Utility Infrastructure.071309Christopher Kenny
STAR Group uses a structured stakeholder involvement process to help utilities build public support for infrastructure projects. Their approach includes convening leadership teams and search conferences to identify solutions, as well as establishing working groups to ensure meaningful public engagement. Client testimonials and case studies demonstrate that STAR Group's methods achieve regulatory approval while minimizing controversy and costs.
Learn about the Open Data Center Alliance Workgroups, Usage Models and Roadmap Structure from the perspective of the Alliance Technical Coordination Committee. This presentation was used in the Nov. 18, 2010 Alliance Webcast delivered by Howard Grodin, VP of Strategic Programs, Terrermark; Alliance Technical Coordination Committee Member, and Ravi Subranamiam, Intel Corporation; Alliance Technical Advisor.
For more information about the Open Data Center Alliance, visit www.opendatacenteralliance.org. You will also find the Webcast recording that accompanies this presentation there.
This document provides an overview of service-oriented architecture (SOA) implementation and case studies. It discusses the SOA delivery lifecycle including analysis, design, development, testing, deployment, administration and acquisition of skills. It then presents several case studies including implementations in travel insurance, telecommunications and healthcare. The healthcare case studies focus on implementations in the UK National Health Service including a large integration project linking hospitals and clinics.
Developing Knowledge Brokering Standards for Biological Text and Data Integra...Ian Harrow
The Pistoia Alliance SESL Project aims to develop standards for biomedical knowledge brokering through a vehicle brokering pilot.
The pilot will develop an assertion database for type 2 diabetes combining data from structured sources and literature. It will establish APIs and a demonstrator interface. The goals are to streamline non-competitive workflows, engage stakeholders, and assess moving to a production "push model" of content delivery.
Assuming technical success, the project seeks input on opportunities for integrating literature into biomedical infrastructure, who benefits most from a push content model, how publication may be impacted, and challenges in further engaging publishers.
Emerging Life Sciences Collaboration on Common Service SpecificationPistoia Alliance
Presentation by Pistoia Alliance reps Ian Harrow (Pfizer) and Nick Lynch (AstraZeneca) at the International Conference on Trends for Scientific Information Professionals, October 2010.
The Pistoia Alliance Information Ecosystem WorkshopPistoia Alliance
Michael Braxenthaler, president of the Pistoia Alliance, introduces the concept of the information ecosystem in life science research and discusses the role the Pistoia Alliance can play within this ecosystem. The workshop occurred in October 2011.
Enabling Enterprise Collaboration with SharePoint 2010InnoTech
Applied Materials is a global company that produces equipment for semiconductor, display, and solar industries. It has over 14,600 employees worldwide and invested over $1 billion annually in R&D. The company implemented SharePoint 2010 to enable collaboration across its global operations. It started with standard out-of-the-box SharePoint sites and custom sites, and established governance and support structures. Over two years, it expanded usage to include an employee portal, business-specific sites, and mobile access, establishing SharePoint as its collaboration platform.
The document discusses a presentation given by AARNet to the CAUDIT Spring Meeting. The agenda includes an overview of AARNet's strategy and customer focus, services available on the network, and future service development. AARNet aims to deliver a high-performance network while adding value through collaboration, content delivery, and mobility applications and services. Customers have expressed interest in these types of services to better utilize the core network. AARNet considers factors like customer benefit, cost reduction, existing infrastructure use, and support longevity when prioritizing new service development.
Developing Public Support For Utility Infrastructure.071309Christopher Kenny
STAR Group uses a structured stakeholder involvement process to help utilities build public support for infrastructure projects. Their approach includes convening leadership teams and search conferences to identify solutions, as well as establishing working groups to ensure meaningful public engagement. Client testimonials and case studies demonstrate that STAR Group's methods achieve regulatory approval while minimizing controversy and costs.
Learn about the Open Data Center Alliance Workgroups, Usage Models and Roadmap Structure from the perspective of the Alliance Technical Coordination Committee. This presentation was used in the Nov. 18, 2010 Alliance Webcast delivered by Howard Grodin, VP of Strategic Programs, Terrermark; Alliance Technical Coordination Committee Member, and Ravi Subranamiam, Intel Corporation; Alliance Technical Advisor.
For more information about the Open Data Center Alliance, visit www.opendatacenteralliance.org. You will also find the Webcast recording that accompanies this presentation there.
This document provides an overview of service-oriented architecture (SOA) implementation and case studies. It discusses the SOA delivery lifecycle including analysis, design, development, testing, deployment, administration and acquisition of skills. It then presents several case studies including implementations in travel insurance, telecommunications and healthcare. The healthcare case studies focus on implementations in the UK National Health Service including a large integration project linking hospitals and clinics.
Pistoia Alliance: Emerging Life Sciences Collaboration on Common Service Spec...Ian Harrow
The Pistoia Alliance provides a collaborative environment for life sciences organizations to work on pre-competitive projects. This document discusses four current Pistoia Alliance projects: the SESL pilot project aims to develop a framework for biomedical knowledge brokering; the Vocabulary Standards Initiative seeks to standardize representations of drug targets; the Sequence Services project plans to provide hosted sequence analysis tools; and the ELN project works to define standards for querying electronic lab notebook data across vendors.
The document discusses the role of a knowledge broker at York University. Specifically:
1) The knowledge broker helps facilitate the flow of research knowledge between academics and non-academic audiences through developing strategies for knowledge mobilization, nurturing relationships between researchers and research users, and assisting with grant proposals and administration.
2) Setting the context of York University's history in knowledge mobilization and strategic research plan emphasizing collaborative research and community partnerships.
3) Lessons learned include the importance of planning, phased implementation, and working within the norms of the organization.
Knowledge Mobilization: Building Two Way Roads Steven Zuiker
Knowledge mobilization agendas support accessible, actionable, and practical efforts to impact learning and teaching. Arizona schools, libraries, museums, parks, and after-school programs among many other organizations remain the targets of impact. Yet, the fact that they remain embedded in a larger civic ecology implicates wide-ranging stakeholders in the work of public scholarship and the attendant events, networks, and products through which knowledge is mobilized. This symposium enlists separate surveys of educational researchers and educational practitioners as well as in-depth interviews with a subset of respondents from each survey in order to characterize knowledge mobilization. Separate presentations develop profiles of opportunities and challenges that knowledge mobilization presents to education organizations in Arizona and in relation to other profiles of education organizations elsewhere in North America. These profiles communicate that knowledge mobilization is neither a singular process nor a uniform approach. The range and variation of tactics and emerging strategies underscores that knowledge mobilization reflects the diversity within and between organizations operating in the civic ecologies that public scholarship seeks to impact. Finally, the symposium enlists the idea of building two-way roads as a metaphor for exploring the implications of these profiles.
Pistoia Alliance SESL pilot Bio IT World Hanover 12 Oct 2011Ian Harrow
Towards a brokering framework for knowledge-based services: learning from the Pistoia Alliance SESL pilot
Ian Harrow PhD for the Pistoia Alliance
This presentation describes a pilot project to determine the feasibility of biomedical knowledge brokering. It shows query across multiple disparate data sources through a brokering demonstrator built from RDF triple store technology. The learning from this pilot is contributing to larger scale projects such as the Innovative Medicines Initiative, OpenPFACTs.
1) The document discusses the opportunity for technology to improve organizational efficiency and transition economies into a "smart and clean world."
2) It argues that aggregate efficiency has stalled at around 22% for 30 years due to limitations of the Second Industrial Revolution, but that digitizing transport, energy, and communication through technologies like blockchain can help manage resources and increase efficiency.
3) Technologies like precision agriculture, cloud computing, robotics, and autonomous vehicles may allow for "dematerialization" and do more with fewer physical resources through effects like reduced waste and need for transportation/logistics infrastructure.
The Pistoia Alliance: Update on Strategy and ProgressPistoia Alliance
Ramesh Durvasula, Pistoia Alliance board member, discusses the Pistoia Alliance mission and recaps activities in 2011-12, with particular emphasis on the successful completion of the Sequence Squeeze Competition and Sequence Services Phase 2. The presentation was delivered at BioITWorld in Boston in April 2012.
Pistoia presentation bio it-worldexpo 21april2010Nick Lynch
The document summarizes the origins and operations of the Pistoia Alliance, a non-profit organization formed to facilitate pre-competitive collaboration in the life sciences industry. The Pistoia Alliance was formed in Pistoia, Italy by GSK, AZ, Pfizer and Novartis to address common challenges with data interchange. Its mission is to standardize data exchange to reduce costs. Current projects include developing standards for semantic enrichment of literature, sequence data services, and electronic lab notebook queries. The organization has over 30 members and operates working groups to develop open standards through a governance process.
A breakout discussion led by David Klatte at the Pistoia Alliance Information Ecosystem Workshop proposed a number of potential projects. The workshop was held in October 2011.
This document provides an overview of standards and standardization. It discusses why standards are important, how the standardization process works, and examples of organizations that develop standards like ISO, W3C, NISO, IETF, and Library of Congress. It also summarizes some specific standards around identifiers, records management, country codes, formats, and taxonomy-related standards. The presentation aims to educate about leveraging content semantically through the use of standards.
Towards a brokering framework for knowledge-based services: Learning from the...Pistoia Alliance
Ian Harrow, co-leader of the Pistoia Alliance SESL pilot, describes the vision for the SESL pilot, the outcomes, and the project's future. The presentation at the 2011 BioITWorld Conference and Expo included a link to the SESL public demonstrator.
This chapter discusses a new perspective on how free and open source software (FOSS) can drive development by encouraging greater participation. It analyzes this new "FOSS4D advocacy" approach through the lenses of international development, ICT4D, and technology. The research methodology considers how FOSS enables a more participatory development model with new actors like individuals, businesses, and grassroots organizations collaborating across borders. The chapter contributes to the book by presenting a wider view of FOSS4D that incorporates dimensions beyond traditional economic and technical advantages, and proposes this participatory approach as a new perspective for future FOSS4D strategies and projects.
Bioindustry Park Silvano Fumero and bioPmedmet3project
The Bioindustry Park Silvano Fumero is a 22,000 square meter science park specialized in healthcare located in Italy. It houses labs, office spaces, and a conference center for companies. The park also provides consultancy services and manages bioPmed, a cluster of over 250 healthcare companies. BioPmed takes a "converging technologies" approach, bringing together different fields like ICT, mechatronics, and materials to find innovative medical solutions. The Bioprotech project aims to improve research capacities at the Centre of Biotechnology of Sfax in Tunisia around bioprocesses and biotech applications, and better integrate it with the European Research Area through collaboration with partners from Italy, France, and Germany.
Open Data Center Alliance
Intel Developer Forum 2011 lecture session with:
Anna Claiborne
ODCA WG Chair, ODCA & Product Manager Security Services, Terremark
Ravi Subramaniam
Lead Technical Facilitator, ODCA & Principal Engineer, Intel
Open Data Center Alliance (ODCA) Overview
Overview:
Why Should You Care? (How can you participate?)
1st Release Introduction
Usage Topics Discussion
Ecosystem Opportunities and Engagement
An attempt to capture the many ways you could describe the role of community management, including roles, responsibilities, competencies. Main focus on internal communities but I guess can be used for community management in general.
Also a short explanation what management should do when dealing with an internal community, and how you should reward active community employees.
This document outlines a research strategy to study goat value chain development models in order to generate evidence and lessons learned. It will take a participatory action research approach using innovation platforms and producer hubs to test interventions, monitor changes, and conduct focused studies. Key questions focus on how these models impact practices, market access, and benefits for actors. A hybrid monitoring and evaluation approach using outcome mapping and indicators will track behavioral changes and value chain performance over time.
This document provides guidelines for partnership agreements regarding intellectual property rights (IPR). It discusses the importance of partnership management for cooperation between technology transfer offices and industry partners. The guidelines aim to facilitate negotiations by addressing IPR issues like ownership of patents, improvements to background IP, and publication of research results. While case-by-case analysis is still needed, having principles around IPR established in the guidelines can simplify the partnership agreement process.
RDAP13 Mark Parsons: The Research Data Alliance: Making Data WorkASIS&T
Mark Parsons, Rensselaer Polytechnic Institute
Mark A. Parsons and Francine Berman: "The Research Data Alliance: Making Data Work"
Panel: Global scientific data infrastructure
Research Data Access & Preservation Summit 2013
Baltimore, MD April 4, 2013 #rdap13
Civil Service Live 2012 - using the G-Cloud to Herd CatsKahootz
The document provides an overview of a presentation on using cloud collaboration tools to facilitate teamwork and information sharing across government agencies. Some key points:
1) Case studies are presented of different government organizations that have successfully used online collaboration tools for purposes like stakeholder engagement, project management, and information sharing within and across agencies.
2) Benefits discussed include lower costs, improved communication and participation, and the ability to quickly set up workspaces for different teams and audiences.
3) The presentation explores how procurement of cloud-based collaboration services through the new G-Cloud framework could help government organizations be more agile and innovative by making it easier to set up and share workspaces and solutions.
Pistoia Alliance: Emerging Life Sciences Collaboration on Common Service Spec...Ian Harrow
The Pistoia Alliance provides a collaborative environment for life sciences organizations to work on pre-competitive projects. This document discusses four current Pistoia Alliance projects: the SESL pilot project aims to develop a framework for biomedical knowledge brokering; the Vocabulary Standards Initiative seeks to standardize representations of drug targets; the Sequence Services project plans to provide hosted sequence analysis tools; and the ELN project works to define standards for querying electronic lab notebook data across vendors.
The document discusses the role of a knowledge broker at York University. Specifically:
1) The knowledge broker helps facilitate the flow of research knowledge between academics and non-academic audiences through developing strategies for knowledge mobilization, nurturing relationships between researchers and research users, and assisting with grant proposals and administration.
2) Setting the context of York University's history in knowledge mobilization and strategic research plan emphasizing collaborative research and community partnerships.
3) Lessons learned include the importance of planning, phased implementation, and working within the norms of the organization.
Knowledge Mobilization: Building Two Way Roads Steven Zuiker
Knowledge mobilization agendas support accessible, actionable, and practical efforts to impact learning and teaching. Arizona schools, libraries, museums, parks, and after-school programs among many other organizations remain the targets of impact. Yet, the fact that they remain embedded in a larger civic ecology implicates wide-ranging stakeholders in the work of public scholarship and the attendant events, networks, and products through which knowledge is mobilized. This symposium enlists separate surveys of educational researchers and educational practitioners as well as in-depth interviews with a subset of respondents from each survey in order to characterize knowledge mobilization. Separate presentations develop profiles of opportunities and challenges that knowledge mobilization presents to education organizations in Arizona and in relation to other profiles of education organizations elsewhere in North America. These profiles communicate that knowledge mobilization is neither a singular process nor a uniform approach. The range and variation of tactics and emerging strategies underscores that knowledge mobilization reflects the diversity within and between organizations operating in the civic ecologies that public scholarship seeks to impact. Finally, the symposium enlists the idea of building two-way roads as a metaphor for exploring the implications of these profiles.
Pistoia Alliance SESL pilot Bio IT World Hanover 12 Oct 2011Ian Harrow
Towards a brokering framework for knowledge-based services: learning from the Pistoia Alliance SESL pilot
Ian Harrow PhD for the Pistoia Alliance
This presentation describes a pilot project to determine the feasibility of biomedical knowledge brokering. It shows query across multiple disparate data sources through a brokering demonstrator built from RDF triple store technology. The learning from this pilot is contributing to larger scale projects such as the Innovative Medicines Initiative, OpenPFACTs.
1) The document discusses the opportunity for technology to improve organizational efficiency and transition economies into a "smart and clean world."
2) It argues that aggregate efficiency has stalled at around 22% for 30 years due to limitations of the Second Industrial Revolution, but that digitizing transport, energy, and communication through technologies like blockchain can help manage resources and increase efficiency.
3) Technologies like precision agriculture, cloud computing, robotics, and autonomous vehicles may allow for "dematerialization" and do more with fewer physical resources through effects like reduced waste and need for transportation/logistics infrastructure.
The Pistoia Alliance: Update on Strategy and ProgressPistoia Alliance
Ramesh Durvasula, Pistoia Alliance board member, discusses the Pistoia Alliance mission and recaps activities in 2011-12, with particular emphasis on the successful completion of the Sequence Squeeze Competition and Sequence Services Phase 2. The presentation was delivered at BioITWorld in Boston in April 2012.
Pistoia presentation bio it-worldexpo 21april2010Nick Lynch
The document summarizes the origins and operations of the Pistoia Alliance, a non-profit organization formed to facilitate pre-competitive collaboration in the life sciences industry. The Pistoia Alliance was formed in Pistoia, Italy by GSK, AZ, Pfizer and Novartis to address common challenges with data interchange. Its mission is to standardize data exchange to reduce costs. Current projects include developing standards for semantic enrichment of literature, sequence data services, and electronic lab notebook queries. The organization has over 30 members and operates working groups to develop open standards through a governance process.
A breakout discussion led by David Klatte at the Pistoia Alliance Information Ecosystem Workshop proposed a number of potential projects. The workshop was held in October 2011.
This document provides an overview of standards and standardization. It discusses why standards are important, how the standardization process works, and examples of organizations that develop standards like ISO, W3C, NISO, IETF, and Library of Congress. It also summarizes some specific standards around identifiers, records management, country codes, formats, and taxonomy-related standards. The presentation aims to educate about leveraging content semantically through the use of standards.
Towards a brokering framework for knowledge-based services: Learning from the...Pistoia Alliance
Ian Harrow, co-leader of the Pistoia Alliance SESL pilot, describes the vision for the SESL pilot, the outcomes, and the project's future. The presentation at the 2011 BioITWorld Conference and Expo included a link to the SESL public demonstrator.
This chapter discusses a new perspective on how free and open source software (FOSS) can drive development by encouraging greater participation. It analyzes this new "FOSS4D advocacy" approach through the lenses of international development, ICT4D, and technology. The research methodology considers how FOSS enables a more participatory development model with new actors like individuals, businesses, and grassroots organizations collaborating across borders. The chapter contributes to the book by presenting a wider view of FOSS4D that incorporates dimensions beyond traditional economic and technical advantages, and proposes this participatory approach as a new perspective for future FOSS4D strategies and projects.
Bioindustry Park Silvano Fumero and bioPmedmet3project
The Bioindustry Park Silvano Fumero is a 22,000 square meter science park specialized in healthcare located in Italy. It houses labs, office spaces, and a conference center for companies. The park also provides consultancy services and manages bioPmed, a cluster of over 250 healthcare companies. BioPmed takes a "converging technologies" approach, bringing together different fields like ICT, mechatronics, and materials to find innovative medical solutions. The Bioprotech project aims to improve research capacities at the Centre of Biotechnology of Sfax in Tunisia around bioprocesses and biotech applications, and better integrate it with the European Research Area through collaboration with partners from Italy, France, and Germany.
Open Data Center Alliance
Intel Developer Forum 2011 lecture session with:
Anna Claiborne
ODCA WG Chair, ODCA & Product Manager Security Services, Terremark
Ravi Subramaniam
Lead Technical Facilitator, ODCA & Principal Engineer, Intel
Open Data Center Alliance (ODCA) Overview
Overview:
Why Should You Care? (How can you participate?)
1st Release Introduction
Usage Topics Discussion
Ecosystem Opportunities and Engagement
An attempt to capture the many ways you could describe the role of community management, including roles, responsibilities, competencies. Main focus on internal communities but I guess can be used for community management in general.
Also a short explanation what management should do when dealing with an internal community, and how you should reward active community employees.
This document outlines a research strategy to study goat value chain development models in order to generate evidence and lessons learned. It will take a participatory action research approach using innovation platforms and producer hubs to test interventions, monitor changes, and conduct focused studies. Key questions focus on how these models impact practices, market access, and benefits for actors. A hybrid monitoring and evaluation approach using outcome mapping and indicators will track behavioral changes and value chain performance over time.
This document provides guidelines for partnership agreements regarding intellectual property rights (IPR). It discusses the importance of partnership management for cooperation between technology transfer offices and industry partners. The guidelines aim to facilitate negotiations by addressing IPR issues like ownership of patents, improvements to background IP, and publication of research results. While case-by-case analysis is still needed, having principles around IPR established in the guidelines can simplify the partnership agreement process.
RDAP13 Mark Parsons: The Research Data Alliance: Making Data WorkASIS&T
Mark Parsons, Rensselaer Polytechnic Institute
Mark A. Parsons and Francine Berman: "The Research Data Alliance: Making Data Work"
Panel: Global scientific data infrastructure
Research Data Access & Preservation Summit 2013
Baltimore, MD April 4, 2013 #rdap13
Civil Service Live 2012 - using the G-Cloud to Herd CatsKahootz
The document provides an overview of a presentation on using cloud collaboration tools to facilitate teamwork and information sharing across government agencies. Some key points:
1) Case studies are presented of different government organizations that have successfully used online collaboration tools for purposes like stakeholder engagement, project management, and information sharing within and across agencies.
2) Benefits discussed include lower costs, improved communication and participation, and the ability to quickly set up workspaces for different teams and audiences.
3) The presentation explores how procurement of cloud-based collaboration services through the new G-Cloud framework could help government organizations be more agile and innovative by making it easier to set up and share workspaces and solutions.
The International Society of Service Innovation Professionals (ISSIP) aims to promote service innovations through linking service innovators globally. ISSIP will support existing professional associations in their conferences and publications. ISSIP will have Special Interest Groups, chapters, and ambassadors to help professionals work together better across disciplines, sectors, and regions. ISSIP's mission is to promote service innovations for an interconnected world through the stories of service innovators.
The document provides an overview and roadmap for establishing a Virtual Knowledge Commons (VKC) at the Council for Scientific and Industrial Research (CSIR) in South Africa. It outlines the project in four phases from April 2010 to March 2011. The first phase involves defining objectives and scope. The second phase develops a roadmap for implementation in consultation with stakeholders. Phase three implements the roadmap, and phase four establishes practices and assesses the VKC based on the roadmap. The goal is to extend knowledge sharing and collaboration beyond the physical Knowledge Commons into a virtual space, amplifying connections between people and information across the organization.
Evolving the enterprise - IT legacy to SOACapgemini
This document presents information about evolving legacy enterprise IT systems to a service-oriented architecture (SOA). It describes the L2SOA project overview, team, drivers for legacy modernization like high costs and lack of agility. It outlines an approach combining TOGAF with SOA principles. Key principles discussed include well-defined service contracts, granular services, and security standards. The document also covers organizational processes needed like managed transformation programs, skills development, and risk analysis.
Presentation to the IEA DSM ExCo of changes to our draft workplan after input from 50+ experts. All proposed changes were accepted in Norway, May 2012.
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Title: Sense of Smell
Presenter: Dr. Faiza, Assistant Professor of Physiology
Qualifications:
MBBS (Best Graduate, AIMC Lahore)
FCPS Physiology
ICMT, CHPE, DHPE (STMU)
MPH (GC University, Faisalabad)
MBA (Virtual University of Pakistan)
Learning Objectives:
Describe the primary categories of smells and the concept of odor blindness.
Explain the structure and location of the olfactory membrane and mucosa, including the types and roles of cells involved in olfaction.
Describe the pathway and mechanisms of olfactory signal transmission from the olfactory receptors to the brain.
Illustrate the biochemical cascade triggered by odorant binding to olfactory receptors, including the role of G-proteins and second messengers in generating an action potential.
Identify different types of olfactory disorders such as anosmia, hyposmia, hyperosmia, and dysosmia, including their potential causes.
Key Topics:
Olfactory Genes:
3% of the human genome accounts for olfactory genes.
400 genes for odorant receptors.
Olfactory Membrane:
Located in the superior part of the nasal cavity.
Medially: Folds downward along the superior septum.
Laterally: Folds over the superior turbinate and upper surface of the middle turbinate.
Total surface area: 5-10 square centimeters.
Olfactory Mucosa:
Olfactory Cells: Bipolar nerve cells derived from the CNS (100 million), with 4-25 olfactory cilia per cell.
Sustentacular Cells: Produce mucus and maintain ionic and molecular environment.
Basal Cells: Replace worn-out olfactory cells with an average lifespan of 1-2 months.
Bowman’s Gland: Secretes mucus.
Stimulation of Olfactory Cells:
Odorant dissolves in mucus and attaches to receptors on olfactory cilia.
Involves a cascade effect through G-proteins and second messengers, leading to depolarization and action potential generation in the olfactory nerve.
Quality of a Good Odorant:
Small (3-20 Carbon atoms), volatile, water-soluble, and lipid-soluble.
Facilitated by odorant-binding proteins in mucus.
Membrane Potential and Action Potential:
Resting membrane potential: -55mV.
Action potential frequency in the olfactory nerve increases with odorant strength.
Adaptation Towards the Sense of Smell:
Rapid adaptation within the first second, with further slow adaptation.
Psychological adaptation greater than receptor adaptation, involving feedback inhibition from the central nervous system.
Primary Sensations of Smell:
Camphoraceous, Musky, Floral, Pepperminty, Ethereal, Pungent, Putrid.
Odor Detection Threshold:
Examples: Hydrogen sulfide (0.0005 ppm), Methyl-mercaptan (0.002 ppm).
Some toxic substances are odorless at lethal concentrations.
Characteristics of Smell:
Odor blindness for single substances due to lack of appropriate receptor protein.
Behavioral and emotional influences of smell.
Transmission of Olfactory Signals:
From olfactory cells to glomeruli in the olfactory bulb, involving lateral inhibition.
Primitive, less old, and new olfactory systems with different path
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Pistoia Alliance: SESL Pilot for a Biomedical Brokering Service
1. The Pistoia SESL
Project
An Emerging Vehicle for SESL Pilot
Pistoia Alliance Collaboration:
TheBiomedical Brokering Service
for a Pistoia Alliance
Ian Harrow, Wendy Filsell, Dietrich Rebholz Schuhmann
8th PharmaTech IT Congress http://pistoiaalliance.org
16th Sept 2010
2. Presentation Outline
• Pistoia Background
• SESL: Biomedical Knowledge Brokering
• The Knowledge Service Framework
• The Pilot
• Minimal configuration to test a brokering service
• SESL user interface Mock Up
• Project Timelines
• Summary
• Acknowledgements
3. Pistoia Background – How it all started
2007 2008 2009 2010 Now
Informal Met in Create Pistoia as Not Official 7 / 10 top Pharma as members
meeting Pistoia for profit company Launch 33 members
Stanhope Gate Domains Established
Pistoia
Lhasa Curzon
Informal Collaborations Collaboration/project meeting
Pistoia Description History
The primary purpose of the Pistoia Alliance is to
Initial Meeting with GSK, AZ,
streamline non-competitive elements of the life Pfizer and Novartis – outlined
science workflow by the specification of common similar challenges and
standards, business terms, relationships and frustrations in the Informatics
sector of Discovery
processes
Pistoia Goals The advent of Web Services and Web 2.0 allow for
decoupling of proprietary data from technology
• to allow this framework to encompass/support
most pre-competitive work between the Publicly available structural and biological DBs allow
organisations for a non-IP related analysis and as a scientific test
suite.
• to support life science workflow prior to
submission Sponsorship from R&D IS heads within Life Science
• to work with other Standards organisations industry
4. Pistoia Domains
Pistoia Domains group areas of interest, scope and deliver projects
Pistoia Domain – high level collection
Pistoia Groups – as of Working Groups with common themes
External
Groups
defined in byelaws Domain Allows governance across outside of
Steering a domain using Working
Pistoia
Board of Groups Group chairs and
Technical Committee reps
Directors Could:
• join Pistoia
Working The main project delivery • influence Pistoia
Working mechanism in Pistoia. All
Officers Groups members
Groups standards will be • influence through
(Operational delivered by WGs other standards
Team) groups and activities
Provide expertise for WGs • Collaborate on
and running Pistoia standards’ feasibility
Technical Pistoia Define: studies
•Requirements • Collaborate through
Committee Members •Technical Standards non-Pistoia
•Service Standards Standards initiatives
5. Pistoia Domains
Pistoia Domains focus on business workflows /supply chains
Enabling Knowledge and Information Services
Vocabulary
Visualisation
Application Integration
Workflow
Others Biology Chemistry Translational
Data Data Data
Services Services Services
6. SESL: Biomedical Knowledge Brokering
• Challenge:
– No single system for retrieving gene to disease relationships contained in
both published & biological database content
– Need a ‘push model’ for biomedical knowledge access: the current model
requires the consumer to search 1000’s of content sources
• Opportunity: Pilot Project with key stakeholders
– Pilot a ‘push model’ for biomedical knowledge brokering
– Engage multiple consumers, content providers and a single, public group to
develop the necessary infrastructure to explore the standards required for
the model to work in production
• History:
– May 2008: Common Disease Knowledge Environment (CDKE) IMI call drafted
– Sep 2008: postponed call publication
– Jan 2009: x-pharma meeting in London on how to progress CDKE
– Apr 2009: CDKE presented at SESL workshop
– Oct 2009: SESL Pilot meeting (funders)
– Jan 2010: Pilot launch
7. The Knowledge Service Framework
Multiple
Consumers
‘Consumer’
Disease Dossier Knowledge
Firewall Applications
Service Layer Std Public Common
Open Assertion & Meta Data Mgmt Vocabularies Service
Stds Transform / Translate Business Broker
Integrator Rules
Supplier
Firewall Content
Suppliers
Db 2
Effort required
Db 4 to fit DBs to
Corpus 1 service layer
Db 3 Corpus 5
7
8. A Production Service vision...
Consumer
Side Exemplar
Disease Dossier Application
License
Service Layer Std Public Service Layer Std Public Service Layer Std Public Service Layer Std Public
Vocabularies Vocabularies Vocabularies Vocabularies
Assertion & Meta Data Mgmt Assertion & Meta Data Mgmt Assertion & Meta Data Mgmt Assertion & Meta Data Mgmt
Transform / Translate Business Transform / Translate Business Transform / Translate Business Transform / Translate Business
Rules Rules Rules Rules
Integrator Integrator Integrator Integrator
Broker Org #1 Broker Org #2 Broker Org #3 Internal Broker
License
Corpus 1 Db 3 Corpus 5 Db 7 Corpus 9 Db 11 Corpus 13 Db 15
Corpus 4 Corpus 8 Corpus 12 Corpus 16
Db 2 Db 6 Db 10 Db 14
Supplier
Side
10. The Pilot
• Deliverables:
– Publication of standards & recommendations for service implementation
– Pilot implementation of service for a single disease (assertions from pre-defined
document sets & databases)
– Establish ways of working pre-competitively across industry/vendor/academia
– Dialogue and assessment of cost / value, with key content suppliers in moving to
such a push model for content (viability of moving to production)
• Status:
– AZ, Pfizer, GSK, Roche, Unilever, EBI, NPG, OUP, Elsevier & RSC
– 12 month project, £200K direct funding (+ PM & Architecture support)
– Contract between Pistoia & EBI signed 20th January 2010 for 1 year
• Scope:
– Development of an assertion database in combination with a user interface and
associated web services for one disease/indication/phenotype of broad interest:
Type II Diabetes
– Assertional content derived from 3 structured data sources and limited Journal
content (co-occurrence & statistical derivation from full text)
– Assertional evidence for filtering and drill down to primary data.
– Limited vocabulary development for area of focus: Type II Diabetes
11. Minimal configuration to test a
Brokering Service
Interface
User Interface Layer
at consumer org’n
Condition:
Service Layer
Assertion & Meta Data Mgmt
Std Public
Vocabularies
Service Layer
Assertion & Meta Data Mgmt
Std Public
Vocabularies Brokering service
Identical structure.
Different content
Transform / Translate Query Transform / Translate Query Layer
templates templates
which can overlap. Triple store 1 Triple store 2
at EBI
Broker #1 Broker #2
Primary source
Elsevier RSC Layer
corpus corpus NPG
corpus
OUP
corpus
at provider org’n
EBI Swissprot EBI Ensembl EBI Array EBI Swissprot
database gene Express database
database
12. SESL user interface mock-up: Query
Gene: abc
Relationship: Any
Disease: Diabetes
Constraint: Species: Any
Tissue: Any
13. SESL user interface mock-up: Results
Gene R’ship Disease Species Evidence
1 abc1 Co-occurs Diabetes Mus Paper UID:1234
2 abc1 Up-Reg Diabetes Homo ArrayExpress: XXX
3 abc2 Co-occurs Diabetes Homo Paper UID:1344
4 abc13 Co-occurs Diabetes Mus Paper UID:1314
5 abc7 Mutation Diabetes Rattus OMIMI: XXX
6 abc1 Co-occurs Diabetes Mus Paper UID:45643
7 abc1 Co-occurs Diabetes Homo Paper UID:2143
8 abc1 Co-occurs Diabetes Mus Paper UID:1204
14. Diabetes genes in SESL prototype
Primary data sources SESL project
Gene symbols UNIPROT Involvement in OMIM in ArrayExpress Atlas? SESL? SESL co-occurence SESL OMIM SESL Arrayexpress
diabetes type 2? diabetes? in Full Text diabetes? Atlas?
literature?
ABCC8 Y - NIDDM Y Y Y Y Y N
ADIPOQ Y - NIDDM Y Y Y Y N N
ALMS1 Y - NIDDM N Y Y Y N N
BLK Y - MODY11 Y Y Y Y N N
CAPN10 Y - NIDDM Y Y Y Y Y N
CEL Y - MODY8 Y Y Y Y Y N
ENPP1 Y - NIDDM Y Y Y Y Y N
GCK Y - MODY2 Y Y Y Y Y N
HNF1A Y - MODY3 Y Y Y Y Y N
HNF1B Y - MODY5 Y Y Y Y Y N
HNF4A Y - MODY1 Y Y Y Y Y N
INPPL1 Y - NIDDM N Y N
INS Y - MODY10 Y Y Y Y N N
IRS1 Y - NIDDM Y Y Y Y N N
KCNJ11 Y - NIDDM Y Y N
KLF11 Y - MODY7 Y Y Y Y Y N
LIPC Y - NIDDM Y Y Y Y Y N
MAPK8IP1 Y - NIDDM Y Y Y Y Y N
MCF2L2 Y - NIDDM N Y N
NEUROD1 Y - MODY6 Y N Y Y Y N
PAX4 Y - MODY9 Y Y Y Y Y N
PDX1 Y - MODY4 Y Y Y Y N N
PPARG Y - NIDDM Y Y Y Y Y N
PPP1R3A Y - NIDDM Y Y Y Y N Y
SLC30A8 Y - NIDDM Y Y Y N Y N
TCF7L2 Y - NIDDM Y Y Y Y Y N
UCP1 Y - NIDDM N Y Y Y N N
WFS1 Y - NIDDM Y Y Y Y Y N
15. Timelines: Development Phase
Task/Deliverable Phase Type Jan-10 Feb-10 Mar-10 Apr-10 May-10 Jun-10 Jul-10 Aug-10 Sep-10 Oct-10 Nov-10 Dec-10 Jan-11 Feb-11
Month 0 Month 1 Month 2 Month 3 Month 4 Month 5 Month 6 Month 7 Month 8 Month 9 Month 10 Month 11 Month 12
Finalised Technical Specification Deliverable
^
document (Month 4) 1
Build vocabularies within scope Development Task 2
RDF data export from UniProt Development Task 3
and Ensembl
RDF data export of Array Express Development Task 4
Extract literature assertions for Development Task 6
T2DB from publishers’ content
Develop RDF triple store schema Development Task 7
and demonstrator
Develop query definitions Development Task 8
Establish API services for remote Development Task 9
access
Develop simple user interface for Development Task 10
demonstrator (based on mock-
up)
Write documentation that Development Task 11
defines the standard framework
Access to early prototype Deliverable
demonstrator and report
(Month 7 & 8)
2&3 ^^
Final prototype demonstrator, Deliverable
recommendations post-pilot, 4&5
^ ^^
report (Month 11 & 12) and
public launch
16. Timelines:
Testing and Communication Phase
Task/Deliverable Phase Type Jan-10 Feb-10 Mar-10 Apr-10 May-10 Jun-10 Jul-10 Aug-10 Sep-10 Oct-10 Nov-10 Dec-10 Jan-11 Feb-11
Month 0 Month 1 Month 2 Month 3 Month 4 Month 5 Month 6 Month 7 Month 8 Month 9 Month 10 Month 11 Month 12
Tests of the demonstrator (full Testing and Task 12
private and limited public communication
instance)
Deploy publc demonstrator Testing and Task 13
communication
Write publication for standard Testing and Task 14
definition communication
Develop recommendations for Testing and Task 15
post-pilot project communication
Final prototype demonstrator, Deliverable
recommendations post-pilot 4&5 ^ ^
and report (Month 11 & 12)
Public release of limited Deliverable
demonstrator (Month 13) 6 ^
17. Summary of Accomplishments
• Significant progress to towards realising
the technical goal of knowledge brokering
– Can a push model work? A hyperstandard?
• A unique consortium from three cultures:
industry, publishers and academia
– Working together – sharing costs and risks
• Business opportunities and concerns
– For data providers and consumers?
18. Acknowledgements
Industry Publishers EMBL-EBI
Mike Westaway Claire Bird – OUP Christoph Grabmueller
Ian Stott Richard O’Bierne – OUP Silvestras Kavaliauskas
Peter Woollard Jabe Wilson – Elsevier Roderigo Lopez
Nigel Wilkinson Bradley Allen – Elsevier Dominic Clark
Catherine Marshall Colin Batchelor – RSC Jo McEntyre
Ian Dix Richard Kidd – RSC Janet Thornton
Nick Lynch David Hoole – NPG Cath Brooksbank
Michael Braxenthaler Alf Eaton - NGP
Ashley George