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.
Jena based implementation of a iso 11179 meta data registryA. Anil Sinaci
The ISO/IEC 11179 family of specifications introduces a standard model for meta-data registries to increase the interoperability of applications with the use of common data elements. Jena based implementation of a standard meta-data registry, brings semantic processing and reasoning capabilities on top of the common data elements and their consumer applications.
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.
Jena based implementation of a iso 11179 meta data registryA. Anil Sinaci
The ISO/IEC 11179 family of specifications introduces a standard model for meta-data registries to increase the interoperability of applications with the use of common data elements. Jena based implementation of a standard meta-data registry, brings semantic processing and reasoning capabilities on top of the common data elements and their consumer applications.
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.
The Pistoia Alliance: Strategy, Progress, MomentumPistoia Alliance
Pistoia Alliance Board Member Ramesh Durvasula of BMS provides an overview of the Pistoia Alliance and project status at the BioITWorld Expo in Boston on April 13, 2011.
Notes taken to support breakout discussion of possible business models necessary to support the information ecosystem in life science R&D during the Pistoia Alliance Information Ecosystem Workshop in October 2011.
Richard Bolton (GSK and Pistoia's ELN query services workstream coordinator) discusses the Alliance's chemistry strategy, which includes ELN query standards, hosted ELN, and chemistry externalization faciliation
David Klatte (Pfizer) presented on this potential new working group during the "Dragons' Den" portion of the Pistoia Alliance Conference in Boston, MA, on April 24, 2012.
The Pistoia Alliance Conference in April 2011 included a series of 10-minute "lightning talks" from vendors about what they think pharma will look like in 2020. This presentation was delivered by Rajiv Sabharwal of Infosys.
Presentation delivered at the annual general meeting of Pistoia members. Describes the results of board member elections, the state of the Alliance's project portfolio, progress over the past year, and insights from new member Constellation Technologies about why they joined the Alliance.
The Pistoia Alliance Biology Domain Strategy April 2011Pistoia Alliance
Michael Braxenthaler (Roche and external liaison officer for Pistoia) describes the Pistoia Alliance biology domain strategy at the first Pistoia Alliance Conference in April 2011.
Resource Description Framework Approach to Data Publication and FederationPistoia Alliance
Bob Stanley, CEO, IO Informatics, explains the utility to RDF as a standard way of defining and redefining data that could have utility in managing life science information.
The Pistoia Alliance Conference in April 2011 included a series of 10-minute "lightning talks" from vendors about what they think pharma will look like in 2020. This presentation was delivered by Richard Resnick of GenomeQuest (and yes, this 41 slide talk was over in just 8 minutes!)
Alex Drijver (ChemAxon) provides an overview of this potential Pistoia Alliance working group during the "Dragons' Den" session at the Pistoia Alliance Conference in Boston, MA, on April 24, 2012.
The Pistoia Alliance Conference in April 2011 included a series of 10-minute "lightning talks" from vendors about what they think pharma will look like in 2020. This presentation was delivered by Kevin Lustig of Assay Depot.
Presentation by Simon Thornber, lead of the Pistoia Alliance sequence services working group, about the RFP issued for the second phase of the project.
Collaborative Drug Discovery -- Life Science Collaboration & Virtualization: ...Pistoia Alliance
The Pistoia Alliance Conference in April 2011 included a series of 10-minute "lightning talks" from vendors about what they think pharma will look like in 2020. This presentation was delivered by Sean Ekins of Collaborative Drug Discovery.
Nick Lynch, president of the Pistoia Alliance, delivered this presentation summarizing the mission of the Alliance, its current deliverables and progress, and its strategy for the next several years.
Enterprise Integration of Disruptive TechnologiesDataWorks Summit
This talk will detail the HSBC Big Data journey to date walking through the genesis of the Big Data initiative which was triggered by continual challenges in delivering data driven products. The global scale, diversity and legacy of an organization like HSBC presents challenges for Hadoop adoption not typically faced by younger companies. Big Data technologies are by their very nature disruptive to the established Enterprise IT environment. Hadoop and the peripheral toolsets in the big data ecosystem do not fit comfortably into an Enterprise Data Centre, IT Operational processes and can even prove disruptive to current organization structures. Alasdair will focus on the steps that HSBC has taken to mitigate concerns about Hadoop and raise awareness of the game changing benefits a successful adoption of the technology will bring. HSBC have taken an innovative approach to proving out the value of the technology engaging developers with a brakes off opportunity to use the platform and by placing Hadoop in a competitive scenario with traditional technologies. The Hadoop journey in HSBC was initiated in Scotland, blessed in London and proved out in China.
A set of slides that summarize how MarkLogic is being used in the healthcare industry including case studies on M*Modal and Informatics Corporation of America
The Pistoia Alliance: Strategy, Progress, MomentumPistoia Alliance
Pistoia Alliance Board Member Ramesh Durvasula of BMS provides an overview of the Pistoia Alliance and project status at the BioITWorld Expo in Boston on April 13, 2011.
Notes taken to support breakout discussion of possible business models necessary to support the information ecosystem in life science R&D during the Pistoia Alliance Information Ecosystem Workshop in October 2011.
Richard Bolton (GSK and Pistoia's ELN query services workstream coordinator) discusses the Alliance's chemistry strategy, which includes ELN query standards, hosted ELN, and chemistry externalization faciliation
David Klatte (Pfizer) presented on this potential new working group during the "Dragons' Den" portion of the Pistoia Alliance Conference in Boston, MA, on April 24, 2012.
The Pistoia Alliance Conference in April 2011 included a series of 10-minute "lightning talks" from vendors about what they think pharma will look like in 2020. This presentation was delivered by Rajiv Sabharwal of Infosys.
Presentation delivered at the annual general meeting of Pistoia members. Describes the results of board member elections, the state of the Alliance's project portfolio, progress over the past year, and insights from new member Constellation Technologies about why they joined the Alliance.
The Pistoia Alliance Biology Domain Strategy April 2011Pistoia Alliance
Michael Braxenthaler (Roche and external liaison officer for Pistoia) describes the Pistoia Alliance biology domain strategy at the first Pistoia Alliance Conference in April 2011.
Resource Description Framework Approach to Data Publication and FederationPistoia Alliance
Bob Stanley, CEO, IO Informatics, explains the utility to RDF as a standard way of defining and redefining data that could have utility in managing life science information.
The Pistoia Alliance Conference in April 2011 included a series of 10-minute "lightning talks" from vendors about what they think pharma will look like in 2020. This presentation was delivered by Richard Resnick of GenomeQuest (and yes, this 41 slide talk was over in just 8 minutes!)
Alex Drijver (ChemAxon) provides an overview of this potential Pistoia Alliance working group during the "Dragons' Den" session at the Pistoia Alliance Conference in Boston, MA, on April 24, 2012.
The Pistoia Alliance Conference in April 2011 included a series of 10-minute "lightning talks" from vendors about what they think pharma will look like in 2020. This presentation was delivered by Kevin Lustig of Assay Depot.
Presentation by Simon Thornber, lead of the Pistoia Alliance sequence services working group, about the RFP issued for the second phase of the project.
Collaborative Drug Discovery -- Life Science Collaboration & Virtualization: ...Pistoia Alliance
The Pistoia Alliance Conference in April 2011 included a series of 10-minute "lightning talks" from vendors about what they think pharma will look like in 2020. This presentation was delivered by Sean Ekins of Collaborative Drug Discovery.
Nick Lynch, president of the Pistoia Alliance, delivered this presentation summarizing the mission of the Alliance, its current deliverables and progress, and its strategy for the next several years.
Enterprise Integration of Disruptive TechnologiesDataWorks Summit
This talk will detail the HSBC Big Data journey to date walking through the genesis of the Big Data initiative which was triggered by continual challenges in delivering data driven products. The global scale, diversity and legacy of an organization like HSBC presents challenges for Hadoop adoption not typically faced by younger companies. Big Data technologies are by their very nature disruptive to the established Enterprise IT environment. Hadoop and the peripheral toolsets in the big data ecosystem do not fit comfortably into an Enterprise Data Centre, IT Operational processes and can even prove disruptive to current organization structures. Alasdair will focus on the steps that HSBC has taken to mitigate concerns about Hadoop and raise awareness of the game changing benefits a successful adoption of the technology will bring. HSBC have taken an innovative approach to proving out the value of the technology engaging developers with a brakes off opportunity to use the platform and by placing Hadoop in a competitive scenario with traditional technologies. The Hadoop journey in HSBC was initiated in Scotland, blessed in London and proved out in China.
A set of slides that summarize how MarkLogic is being used in the healthcare industry including case studies on M*Modal and Informatics Corporation of America
Reflections on knowledge management practice case studyRichard Vines
This presentation provides some early reflections of a KM start up project related to Victoria's agricultural sector (Australia) some 16 months after commencement. It also draws upon some work undertaken at the University of Melbourne on the topic of regulatory burden reduction
The Allotrope Foundation led discussion on building an open framework for laboratory data - recommending a holistic approach to build upon & promote industry standards & best practices by providing software that instantiates them.
Fairification experience clarifying the semantics of data matricesPistoia Alliance
This webinar presents the Statistics Ontology, STATO which is a semantic framework to support the creation of standardized analysis reports to help with review of results in the form of data matrices. STATO includes a hierarchy of classes and a vocabulary for annotating statistical methods used in life, natural and biomedical sciences investigations, text mining and statistical analyses.
Innovation applications of microphysiological systems (MPS) have been growing over the past decade, especially with respect to the use of complex human tissues for assessing safety of drug candidates – but broad industry adoption of MPS methods has not yet become a reality.
This webinar addresses some recent advances in MPS development and begins to explore the barriers to increased incorporation of MPS to improve drug safety assessment and to provide safer, more effective drugs into the clinical pipeline.
Federated Learning (FL) is a learning paradigm that enables collaborative learning without centralizing datasets. In this webinar, NVIDIA present the concept of FL and discuss how it can help overcome some of the barriers seen in the development of AI-based solutions for pharma, genomics and healthcare. Following the presentation, the panel debate on other elements that could drive the adoption of digital approaches more widely and help answer currently intractable science and business questions.
It seems that AI is also becoming a buzzword, like design thinking. Everyone is talking about AI or wants to have AI, and sees all the ideas and benefits – that’s fine, but how do you get started? But what’s different now? Three innovations have finally put AI on the fast track: Big Data, with the internet and sensors everywhere; massive computing power, especially through the Cloud; and the development of breakthrough algorithms, so computers can be trained to accomplish more sophisticated tasks on their own with deep learning. If you use new technology, you need to explore and know what’s possible. With design thinking, it aids to outline the steps and define the ways in which you’re going to create the solution. Starting with mapping the customer journey, defining who will be using that service enhanced with intelligent technology, or who will benefit and gain value from it. We discuss how these two worlds are coming together, and how you get started to transform your venture with Artificial Intelligence using Design Thinking.
Speaker: Claudio Mirti, Principal Solution Specialist – Data & AI, Microsoft
Themes and objectives:
To position FAIR as a key enabler to automate and accelerate R&D process workflows
FAIR Implementation within the context of a use case
Grounded in precise outcomes (e.g. faster and bigger science / more reuse of data to enhance value / increased ability to share data for collaboration and partnership)
To make data actionable through FAIR interoperability
Speakers:
Mathew Woodwark,Head of Data Infrastructure and Tools, Data Science & AI, AstraZeneca
Erik Schultes, International Science Coordinator, GO-FAIR
Georges Heiter, Founder & CEO, Databiology
Knowledge graphs ilaria maresi the hyve 23apr2020Pistoia Alliance
Data for drug discovery and healthcare is often trapped in silos which hampers effective interpretation and reuse. To remedy this, such data needs to be linked both internally and to external sources to make a FAIR data landscape which can power semantic models and knowledge graphs.
2020.04.07 automated molecular design and the bradshaw platform webinarPistoia Alliance
This presentation described how data-driven chemoinformatics methods may automate much of what has historically been done by a medicinal chemist. It explored what is reasonable to expect “AI” approaches might achieve, and what is best left with a human expert. The implications of automation for the human-machine interface were explored and illustrated with examples from Bradshaw, GSK’s experimental automated design environment.
This presentation reviewed the challenges in identifying, acquiring and utilizing research data in relation to an evolving data market. Strategic solutions were examined in which the FAIR principles play a key role in the future of data management.
Dr. Dennis Wang discusses possible ways to enable ML methods to be more powerful for discovery and to reduce ambiguity within translational medicine, allowing data-informed decision-making to deliver the next generation of diagnostics and therapeutics to patients quicker, at lowered costs, and at scale.
The talk by Dr. Dennis Wang was followed by a panel discussion with Mr. Albert Wang, M. Eng., Head, IT Business Partner, Translational Research & Technologies, Bristol-Myers Squibb.
With the explosion of interest in both enhanced knowledge management and open science, the past few years have seen considerable discussion about making scientific data “FAIR” — findable, accessible, interoperable, and reusable. The problem is that most scientific datasets are not FAIR. When left to their own devices, scientists do an absolutely terrible job creating the metadata that describe the experimental datasets that make their way in online repositories. The lack of standardization makes it extremely difficult for other investigators to locate relevant datasets, to re-analyse them, and to integrate those datasets with other data. The Center for Expanded Data Annotation and Retrieval (CEDAR) has the goal of enhancing the authoring of experimental metadata to make online datasets more useful to the scientific community. The CEDAR work bench for metadata management will be presented in this webinar. CEDAR illustrates the importance of semantic technology to driving open science. It also demonstrates a means for simplifying access to scientific data sets and enhancing the reuse of the data to drive new discoveries.
Open interoperability standards, tools and services at EMBL-EBIPistoia Alliance
In this webinar Dr Henriette Harmse from EMBL-EBI presents how they are using their ontology services at EMBL-EBI to scale up the annotation of data and deliver added value through ontologies and semantics to their users.
Fair webinar, Ted slater: progress towards commercial fair data products and ...Pistoia Alliance
Elsevier is a global information analytics business that helps institutions and professional’s
advance healthcare and open science to improve performance for the benefit of humanity.
In this webinar, we discuss how Elsevier is increasingly leveraging the FAIR Guiding Principles to improve its products and services to better serve the scientific community.
Application of recently developed FAIR metrics to the ELIXIR Core Data ResourcesPistoia Alliance
The FAIR (Findable, Accessible, Interoperable and Reusable) principles aim to maximize the discovery and reuse of digital resources. Using recently developed software and metrics to assess FAIRness and supported through an ELIXIR Implementation Study, Michel worked with a subset of ELIXIR Core Data Resources to apply these technologies. In this webinar, he will discuss their approach, findings, and lessons learned towards the understanding and promotion of the FAIR principles.
Implementing Blockchain applications in healthcarePistoia Alliance
Blockchain technology can revolutionise the way information is exchanged between parties by bringing an unprecedented level of security and trust to these transactions. The technology is finding its way into multiple use cases but we are yet to see full adoption and real-world business implementation in the Healthcare industry.
In this webinar we will explore the main challenges and considerations for the implementation of Blockchain technology in Healthcare use cases. This is the third webinar in our Blockchain Education series.
Building trust and accountability - the role User Experience design can play ...Pistoia Alliance
In this webinar our panel of UX specialists give a brief introduction to User Experience before presenting the design opportunities UX can bring to AI. We all know that AI has great potential but has some significant hurdles to overcome not least so the human aspect of trust and ethical considerations when designing in the life sciences.
In the late Fall and Winter of 2018, the Pistoia Alliance in cooperation with Elsevier and charitable organizations Cures within Reach and Mission: Cure ran a datathon aiming to find drugs suitable for treatment of childhood chronic pancreatitis, a rare disease that causes extreme suffering. The datathon resulted in identification of four candidate compounds in a short time frame of just under three months. In this webinar our speakers discuss the technologies that made this leap possible
PA webinar on benefits & costs of FAIR implementation in life sciences Pistoia Alliance
The slides from the Pistoia Alliance Debates Webinar where a panel of experts from technology support providers and the biopharma industry, who have been invited to share their views on the "Benefits and costs of FAIR Implementation for life science industry".
Creating novel drugs is an extraordinarily hard and complex problem.
One of the many challenges in drug design is the sheer size of the search space for novel chemical compounds. Scientists need to find molecules that are active toward a biological target or pathway and at the same time have acceptable ADMET properties.
There is now considerable research going on using various AI and ML approaches to tackle these challenges.
Our distinguished speakers, Drs. Alex Tropsha and Ola Engkvist, will discuss their recent work in Drug Design involving Deep Reinforcement Learning and Neural Networks, and will answer questions from the audience on the current state of the research in the field.
Speakers:
Prof Alex Tropsha, Professor at University of North Carolina at Chapel Hill, USA
Dr. Ola Engkvist, Associate Director at AstraZeneca R&D, Gothenburg, Sweden
State of ICS and IoT Cyber Threat Landscape Report 2024 previewPrayukth K V
The IoT and OT threat landscape report has been prepared by the Threat Research Team at Sectrio using data from Sectrio, cyber threat intelligence farming facilities spread across over 85 cities around the world. In addition, Sectrio also runs AI-based advanced threat and payload engagement facilities that serve as sinks to attract and engage sophisticated threat actors, and newer malware including new variants and latent threats that are at an earlier stage of development.
The latest edition of the OT/ICS and IoT security Threat Landscape Report 2024 also covers:
State of global ICS asset and network exposure
Sectoral targets and attacks as well as the cost of ransom
Global APT activity, AI usage, actor and tactic profiles, and implications
Rise in volumes of AI-powered cyberattacks
Major cyber events in 2024
Malware and malicious payload trends
Cyberattack types and targets
Vulnerability exploit attempts on CVEs
Attacks on counties – USA
Expansion of bot farms – how, where, and why
In-depth analysis of the cyber threat landscape across North America, South America, Europe, APAC, and the Middle East
Why are attacks on smart factories rising?
Cyber risk predictions
Axis of attacks – Europe
Systemic attacks in the Middle East
Download the full report from here:
https://sectrio.com/resources/ot-threat-landscape-reports/sectrio-releases-ot-ics-and-iot-security-threat-landscape-report-2024/
Elevating Tactical DDD Patterns Through Object CalisthenicsDorra BARTAGUIZ
After immersing yourself in the blue book and its red counterpart, attending DDD-focused conferences, and applying tactical patterns, you're left with a crucial question: How do I ensure my design is effective? Tactical patterns within Domain-Driven Design (DDD) serve as guiding principles for creating clear and manageable domain models. However, achieving success with these patterns requires additional guidance. Interestingly, we've observed that a set of constraints initially designed for training purposes remarkably aligns with effective pattern implementation, offering a more ‘mechanical’ approach. Let's explore together how Object Calisthenics can elevate the design of your tactical DDD patterns, offering concrete help for those venturing into DDD for the first time!
Securing your Kubernetes cluster_ a step-by-step guide to success !KatiaHIMEUR1
Today, after several years of existence, an extremely active community and an ultra-dynamic ecosystem, Kubernetes has established itself as the de facto standard in container orchestration. Thanks to a wide range of managed services, it has never been so easy to set up a ready-to-use Kubernetes cluster.
However, this ease of use means that the subject of security in Kubernetes is often left for later, or even neglected. This exposes companies to significant risks.
In this talk, I'll show you step-by-step how to secure your Kubernetes cluster for greater peace of mind and reliability.
Dev Dives: Train smarter, not harder – active learning and UiPath LLMs for do...UiPathCommunity
💥 Speed, accuracy, and scaling – discover the superpowers of GenAI in action with UiPath Document Understanding and Communications Mining™:
See how to accelerate model training and optimize model performance with active learning
Learn about the latest enhancements to out-of-the-box document processing – with little to no training required
Get an exclusive demo of the new family of UiPath LLMs – GenAI models specialized for processing different types of documents and messages
This is a hands-on session specifically designed for automation developers and AI enthusiasts seeking to enhance their knowledge in leveraging the latest intelligent document processing capabilities offered by UiPath.
Speakers:
👨🏫 Andras Palfi, Senior Product Manager, UiPath
👩🏫 Lenka Dulovicova, Product Program Manager, UiPath
Smart TV Buyer Insights Survey 2024 by 91mobiles.pdf91mobiles
91mobiles recently conducted a Smart TV Buyer Insights Survey in which we asked over 3,000 respondents about the TV they own, aspects they look at on a new TV, and their TV buying preferences.
Connector Corner: Automate dynamic content and events by pushing a buttonDianaGray10
Here is something new! In our next Connector Corner webinar, we will demonstrate how you can use a single workflow to:
Create a campaign using Mailchimp with merge tags/fields
Send an interactive Slack channel message (using buttons)
Have the message received by managers and peers along with a test email for review
But there’s more:
In a second workflow supporting the same use case, you’ll see:
Your campaign sent to target colleagues for approval
If the “Approve” button is clicked, a Jira/Zendesk ticket is created for the marketing design team
But—if the “Reject” button is pushed, colleagues will be alerted via Slack message
Join us to learn more about this new, human-in-the-loop capability, brought to you by Integration Service connectors.
And...
Speakers:
Akshay Agnihotri, Product Manager
Charlie Greenberg, Host
Builder.ai Founder Sachin Dev Duggal's Strategic Approach to Create an Innova...Ramesh Iyer
In today's fast-changing business world, Companies that adapt and embrace new ideas often need help to keep up with the competition. However, fostering a culture of innovation takes much work. It takes vision, leadership and willingness to take risks in the right proportion. Sachin Dev Duggal, co-founder of Builder.ai, has perfected the art of this balance, creating a company culture where creativity and growth are nurtured at each stage.
Kubernetes & AI - Beauty and the Beast !?! @KCD Istanbul 2024Tobias Schneck
As AI technology is pushing into IT I was wondering myself, as an “infrastructure container kubernetes guy”, how get this fancy AI technology get managed from an infrastructure operational view? Is it possible to apply our lovely cloud native principals as well? What benefit’s both technologies could bring to each other?
Let me take this questions and provide you a short journey through existing deployment models and use cases for AI software. On practical examples, we discuss what cloud/on-premise strategy we may need for applying it to our own infrastructure to get it to work from an enterprise perspective. I want to give an overview about infrastructure requirements and technologies, what could be beneficial or limiting your AI use cases in an enterprise environment. An interactive Demo will give you some insides, what approaches I got already working for real.
LF Energy Webinar: Electrical Grid Modelling and Simulation Through PowSyBl -...DanBrown980551
Do you want to learn how to model and simulate an electrical network from scratch in under an hour?
Then welcome to this PowSyBl workshop, hosted by Rte, the French Transmission System Operator (TSO)!
During the webinar, you will discover the PowSyBl ecosystem as well as handle and study an electrical network through an interactive Python notebook.
PowSyBl is an open source project hosted by LF Energy, which offers a comprehensive set of features for electrical grid modelling and simulation. Among other advanced features, PowSyBl provides:
- A fully editable and extendable library for grid component modelling;
- Visualization tools to display your network;
- Grid simulation tools, such as power flows, security analyses (with or without remedial actions) and sensitivity analyses;
The framework is mostly written in Java, with a Python binding so that Python developers can access PowSyBl functionalities as well.
What you will learn during the webinar:
- For beginners: discover PowSyBl's functionalities through a quick general presentation and the notebook, without needing any expert coding skills;
- For advanced developers: master the skills to efficiently apply PowSyBl functionalities to your real-world scenarios.
JMeter webinar - integration with InfluxDB and GrafanaRTTS
Watch this recorded webinar about real-time monitoring of application performance. See how to integrate Apache JMeter, the open-source leader in performance testing, with InfluxDB, the open-source time-series database, and Grafana, the open-source analytics and visualization application.
In this webinar, we will review the benefits of leveraging InfluxDB and Grafana when executing load tests and demonstrate how these tools are used to visualize performance metrics.
Length: 30 minutes
Session Overview
-------------------------------------------
During this webinar, we will cover the following topics while demonstrating the integrations of JMeter, InfluxDB and Grafana:
- What out-of-the-box solutions are available for real-time monitoring JMeter tests?
- What are the benefits of integrating InfluxDB and Grafana into the load testing stack?
- Which features are provided by Grafana?
- Demonstration of InfluxDB and Grafana using a practice web application
To view the webinar recording, go to:
https://www.rttsweb.com/jmeter-integration-webinar
JMeter webinar - integration with InfluxDB and Grafana
Towards a brokering framework for knowledge-based services: Learning from the Pistoia Alliance SESL pilot
1. Towards a brokering framework
for knowledge-based services:
Learning from the Pistoia Alliance
SESL pilot
Ian Harrow, PhD
Co-Leader of Pistoia Alliance SESL pilot (ex-Pfizer)
Founder, Director & Principal Consultant at Ian Harrow Consulting Ltd
Bio IT World, Hanover, October 2011
http://pistoiaalliance.org
2. Outline
• Industry Drivers
• Mission and Strategy of Pistoia
• Vision for the SESL pilot
• Minimal configuration to test a
brokering service
• Public demonstrator and standards
• Deliverables achieved by SESL pilot
• Learning and future direction
2
3. What is Core to your Business?
What is Critical?
Core?
Externalize
Focus
for 1990
Staff on
Best
Critical?
Innovation
Practices
2012
Reduce Externalize
Non-Value for Cost
Added Work Reduction
3
4. Why the Pistoia Alliance?
• Industry was at a cross roads Henry Chesbrough, UC Berlkey 2011
– Change in business models required
• We are all in this (mess) together (Life Science,
technology vendors, service IT, academia, etc.)
• Need industry applicable services and
standards
• Collect all the stakeholders together
– Agree on commonly-shared, pre-competitive use
cases
• Focus on delivery of proofs of concept to
stimulate and foster new business models
4
5. The Mission of the Pistoia Alliance
Lowering the barriers to innovation
by improving the interoperability of
R&D business processes
via pre-competitive collaborations
5
11. Domains of Action
Biology &
Translational Chemistry
Medicine
Scientific
Collaboration
11
12. The Focus of Each Domain
Big Data,
Supply Chain,
Analytics,
Tech Transfer
Semantics
Biology Chemistry
Vocabularies,
Use Cases,
Best Practices
Scientific Collaboration 12
13. Try this at your desk….
Which diseases are correlated to the gene, TCF7L2?
Gene/Protein Literature - Abstracts Literature – Full Text
Inherited diseases Gene expression
13
14. Try it again with Pistoia’s SESL….
Gene naming/synonyms
Gene Function
Literature statistics
Disease co-occurrences
Gene/protein interactions
…all in one report from one
search
HOW? A standard vocabulary,
data model, query language,
report structure, etc.
14
15. SESL Pilot project description
• Deliverables:
– Publication of standards and recommendations for brokering service
implementation
– Public demonstrator service for a single disease area
– Dialogue and assessment of potential business impact with key content
suppliers
• 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 and 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
• Participants and Cost:
– AZ, Pfizer, GSK, Roche, Unilever, EMBL-EBI, NPG, OUP, Elsevier & RSC
– Single contract between Pistoia Alliance & EMBL-EBI
– £200K cost (=2 x FTEs) – shared by industry
– 12 month project, January 2010 start
15
16. The Knowledge Service Framework
Multiple
Consumers
‘Consumer’
Disease Dossier Knowledge
Applications
Firewall
Service Layer Std Public
Common
Open Assertion & Meta Data Management Vocabularies
Service
Stand Transform /Translate (RDF triples) Business Broker
-ards Integrator/Aggregator (Triple store) Rules
Supplier
Firewall Content
Suppliers
Db 2
Db 4
Corpus 1
Db 3 Corpus 5
16
16
17. Minimal configuration to test the technical
feasibility of a Knowledge Broker Service
Interface
User Interface Layer
Service Layer Std Public Service Layer Std Public
Condition:
Brokering service
Vocabularies Vocabularies
Assertion & Meta Data Mgmt Assertion & Meta Data Mgmt
Identical structure.
Transform / Translate Query Transform / Translate Query
Different content
which can overlap Triple store 1
templates
Triple store 2
templates Layer
Broker #1 Broker #2
Primary source
Layer
RSC
UK-Pubmed NPG OUP
corpus
Central corpus corpus
EBI Uniprot corpus EBI Array EBI Uniprot
database Express database
Elsevier database
NCBI OMIM corpus
database 17
18. Simple Graphical User Interface to the
SESL public demonstrator
1. Single point of query through a simple GUI 2. Aggregated Results on a single web page
Full text detail
A. Gene query results summary
Title: Authors:
1) Co-occurrence Documents Citation
2) Uniprot names and annotation Co-occurrence of
3) OMIM disease names gene and disease
4) Array express disease and/or mentions in text
pancreas expression extracts
5) Uniprot GO terms
6) Uniprot Binary interactions
A. Gene Query
Show: and/or The results include links out to the primary sources
B. Disease Query Full text detail
B. Disease query results summary
Title: Authors:
1) Co-occurrence Documents Citation
2) OMIM disease names Co-occurrence of
3) Array express disease expression gene and disease
Filtered by:
1) Everything mentions in text
extracts
2) Consensus
3) Co-occurrence
4) OMIM
5) Array Express SESL public demonstrator:
http://www.pistoia-sesl.org
18
20. Gene discovery in SESL demonstrator
Pancreas T2D disease
1 gene
expression
in Array mention
Express db in OMIM db
3 1 Gene count
20 10 0
3
intersections from
4
the data sources in
the demonstrator
T2D disease T2D disease
genes in gene
Full Text 1 mention in
documents Uniprot db
20
21. Selected content loaded as RDF triples
Source Description # triples %
Expression data Array Express 182,840 0.5%
Experimental Factor Ontology from Array Express 49,026 0.1%
Disease vocabulary from UMLS 6,906,735 18.8%
Vocabulary from Disease Ontology 1,863,664 5.1%
Terms from Gene Ontology 495,595 1.3%
Human genes from Uniprot 12,552,239 34.1%
Meta data from Full Text documents 3,485,212 9.5%
Gene annotations from Full Text documents 2,373,584 6.5%
Disease annotations from Full Text documents 4,983,788 13.6%
GO annotations from Full Text documents 3,870,834 10.5%
Totals 36,763,517 100%
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22. Signposting: Standards used in SESL
Category Name Community
RDF W3C
SPARQL W3C
Triple Store Jena, Sesame,
Open Source
Virtuoso
leXML EBI & CALBC
EBI, NaCTeM, U of
Text Mining LexEBI/BioLexicon
Pisa
CALCBC EBI & CALBC
UniProt EBI, PIR, SBI, etc
Disease Ontology and UMLS OBO, NIH/NLM
Blending of
URIs ArrayExpress EBI existing
NCBI Taxonomy NCBI standards
Dublin Core W3C
N3 notation W3C
RDF Schema Co-occurrence of gene-
EBI
disease
PMC doc standard NCBI
Relation ontology OBO
Ontology URI server W3C
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23. The Deliverables of the SESL pilot
• A proof-of-concept to demonstrate feasibility and
clarify requirements
– http://www.pistoia-sesl.org
• A functional specification for query brokering,
result filtering, report generation
– Expect publication by end 2011
– http://www.pistoiaalliance.com/workinggroups/sesl.html
• Academia, Life Science Industry and Publishers
– Attained a better understanding of each other’s needs
– Demonstration of potential for a new business model
– Explore follow-on via Open Innovation consortia
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24. Learning and Future Direction
• Framework to maximise re-use of existing standards
– Minimise use of bespoke, hard-coded implementations
• Crucial features of a knowledge brokering service:-
– RDF triples for a scalable, meta index to broker across
primary sources (both databases and literature)
– Important to define business rules for query & extraction
– Recommend a registry of suitable data sources
• similar to web services registry
• What is next?
– Example, follow-on to the SESL pilot:-
– Open PHACTs consortium => www.openphacts.org
– 3 year IMI pre-competitive project (started early 2011)
– Data providers and Life Science industry working together 24
25. Acknowledgements
Industry EMBL-EBI Publishers
Wendy Filsell - Unilever Dietrich Rebholz Schuhmann Claire Bird – OUP
(SESL co-leader) (Technical Team Leader) Richard O’Bierne – OUP
Ian Stott - Unilever Christoph Grabmueller
Silvestras Kavaliauskas Colin Batchelor – RSC
Nigel Wilkinson - PFE Richard Kidd – RSC
Catherine Marshall - PFE Dominic Clark
Roderigo Lopez David Hoole – NPG
Peter Woollard - GSK Jo McEntyre – UK-PMC Alf Eaton – NGP
Ashley George - GSK Janet Thornton
Jabe Wilson – Elsevier
Mike Westaway - AZ Bradley Allen – Elsevier
Nick Lynch - AZ
Ian Dix - AZ
Michael Braxenthaler – Roche
John Wise – Pistoia Alliance
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