2011-12-02 Open PHACTS at STM Innovation

Health & Medicine Technology Education

A 5-minute flash session (timed 15 secs/slide) presented by Richard Kidd at the STM Innovation Seminar 2011.

In vivo Safety

Pipeline Patents

Literature SAR News

data integration
data integration
data integration
data integration
data integration
data integration
data integration
data integration
data integration
data integration

The Innovative Medicines Initiative
EC funded public-private partnership for
pharmaceutical research

Focus on key problems
Efficacy
Safety
Education & Training
Knowledge Management

Open PHACTS
an infrastructure project
Develop / apply a set of robust standards…
Implementing the standards in a semantic integration
platform (“Open Pharmacological Space”)…
Delivering services to support on-going drug discovery
programs in pharma and public domain
Mix ideal with the pragmatic. Build open that can
accommodate non-open components in the real
world.

23 partners
9 pharma
14 academic/SME/society
5 new partners in the process

Pharma bring...
Pre-competitive collaboration
Agreement on standards, approaches
Research questions drive development
Clear use cases
Drive and direction

Example research questions
Give all compounds with IC50 < xxx for target Y in species
W and Z plus assay data
What substructures are associated with readout X (target,
pathway, disease, …)
Give all experimental and clinical data for compound X
Give all targets for compound X or a compound with a
similarity > y%

73 questions identified across consortium

What does „Open‟ mean?
OPS Open - open access to all
OPS Consortia - data sets licensed just to the consortia
OPS Academia - fully open to academia
“My OPS”

Open Source
Open Access Infrastructure. GUI and back-end platform, online
or download both + data for local setup
Open Services: for example, RSC services
Open Data + Private Data: licensing fun for all the family
Commercial providers: abstract service interface to swap in
commercial and open source platforms

Sustainability and community
Data in and data out

Consortium (pharma) members
Public and commercial
databases
Publishers
Services built on OPS

Sustainability $

After 3 years?

Pharma customers
Public funders
Services built on top
Publishing data in

Focus and future
One area - pharmacology
“Production Level” software
Semantic pragmatics: everyday use
by scientists not informaticians Developers
(Builders)

An infrastructure that can be built
upon, to provide a stable foundation
for further pre-competitive informatics End users
collaboration (Drivers)

Nanopublications
Capturing scientific information in the Triple Store

Onwards and Upwards
Connection between developers and users
Architecture
Services: e.g. entity identification and resolution
and representing similarity, ORCID, DataCite
Models: RDF / Nanopublication model spec and
guidelines

Prototype
March 2012: Internal Prototype Delivery
September 2012: Release 1st Prototype

Why should you care?
Will be first real large scale semantic
data integration project – a pilot that
can be extended

Provides a single delivery format and
pipeline to your customers?

Find out more?

Email me

Apr/May 2012 - a workshop and intro
for publishers

also for data providers/vendors

Time’s Up!
About your speaker:
Name: Richard Kidd
Company: RSC
Tel: +44 1223 432344
Email: kiddr@rsc.org
Social Media: @open_phacts
slideshare.com/open_phacts
Lash-up: youtube.com/openphacts

This document summarizes a webinar on moving research informatics to the cloud. It introduces four panelists from Elsevier, Accenture, Merck, and Google who discuss their experiences with cloud computing. They cover challenges around data management, the benefits of a cloud-based approach for data sharing and scalability, and how a platform strategy enabled by cloud infrastructure can help transform research processes over multiple years. The panelists describe case studies of migrating applications and databases to the cloud and discuss how a cloud-based platform can drive productivity and cost savings.

Open PHACTS MIOSS may 2016

Open PHACTS provides a single access point for integrating multiple biomedical data resources. It has transitioned from an EU project to the Open PHACTS Foundation to sustain the platform long-term. Challenges included addressing licensing issues across different data sources and enabling maximum dissemination. Usage has grown to over 500 million queries. The Foundation is pursuing collaboration, grants, and industry partnerships to support ongoing development and new projects. It welcomes contributions to improve services and develop new data and workflows.

Pistoia Alliance US Conference 2015 - 1.1.2 Innovation in Pharma - Chris Waller

The document discusses innovation through platforms and modeling at the "edge." It describes how platforms can create and capture value by enabling new applications and business outcomes. Specifically, it outlines Merck's plans to develop a Scientific Modeling Platform to integrate data and predictive models across research, development, and medical domains. This platform would support collaborative modeling efforts and drive innovation by providing predictive insights earlier in the drug development process. Ultimately, the platform aims to transform drug discovery and development at Merck through increased use of analytics, data-driven decision making, and more successful projects.

Pistoia Alliance conference April 2016: Big Data: Eric Little

The document discusses moving from simply analyzing large amounts of data (Big Data) to performing more advanced analysis (Big Analysis) by combining semantic technologies with traditional data science methods. It proposes that Big Analysis allows for a new approach to analysis by using both logic-based semantic reasoning and statistics-based reasoning to provide deeper insights from complex data. The dawn of Big Analysis represents a natural evolution from Big Data to Big Content by integrating different technologies for more informed decision making.

Pistoia Alliance USA Conference 2016

Pharmacelera develops software and hardware solutions to accelerate drug discovery by finding better candidate molecules faster and in less time. Their technology includes a database of fragments and compounds with pre-computed descriptors, molecular simulation software that models interaction fields, and a computing platform with hardware accelerators. Pharmacelera has achieved strong growth since 2015 through international expansion and new technology releases. They are presenting at the President's Startup Challenge to gain recognition, mentorship, and advisory support to further accelerate their strategy and internationalization.

Collaboration - theory & Practice

Sean Ekins

The document discusses collaboration in biomedical research and drug discovery. It defines collaboration and open innovation, and describes how tools like the Collaborative Drug Discovery (CDD) platform can facilitate data sharing and modeling between researchers from different organizations. The document advocates for more precompetitive open data and greater industry-academia partnerships to accelerate drug development through mass collaboration enabled by new technologies.

Pistoia Alliance USA Conference 2016

The Pistoia Alliance HELM Project aims to set standards for exchanging biomolecular data by developing a representation language and toolkit to bridge existing gaps between tools for small molecules and sequences/biomolecules. The main goal is the HELM Ecosystem, which includes R&D organizations, software vendors, content providers and regulatory agencies. The supporting goal is to improve the "adoptability" of HELM by removing barriers to adoption such as addressing biomolecular ambiguity representation and improving the architecture. Next steps include exploring continuity mechanisms after the project finishes at the end of 2016 or early 2017.

Pistoia Alliance US Conference 2015 - 1.4.3 Startup finalists - Repositive

Repositive.io is building a data discovery platform and privacy-preserving query engine (PPQE) to enable efficient and trusted access to genomic data repositories while maintaining best practices and privacy. Their business model is a SaaS platform where basic access to public data and metadata is free, while premium services include private data collaboration, custom PPQE queries, and analytics. They plan to commercialize the platform with an initial team experienced in genomics from Illumina and other institutions.

The document summarizes a webinar presented by the Pharmaceutical User Software Exchange (PhUSE) on their framework for adopting cloud technology in the regulated life sciences industry. The webinar covered the benefits of cloud computing, issues that need to be addressed, an overview of the PhUSE framework, and examples of cloud supply chain models. Speakers from life sciences companies and cloud providers discussed key aspects of the framework and how it provides guidance for quality management system practices that enable scalable, agile, and automated use of cloud systems in a regulated environment.

2019-10-11 The value of FAIR data in health data networks - The Hyve - ELIXIR...

Healthcare Interoperability: Deceptively Difficult

Tim Benson

This document summarizes a presentation on healthcare interoperability. It discusses how interoperability is deceptively difficult to achieve due to technical, commercial, professional and political barriers. It recommends adopting Fast Healthcare Interoperability Resources (FHIR) and streamlining SNOMED CT as two proposals to help address issues with existing standards. Incentives are also needed to encourage interoperability and discourage data locking. The overall message is that while digital health holds promise, achieving true interoperability will require overcoming significant challenges.

Open Science FAIR 2021: FAIRsharing and the FAIR Cookbook

Healthcare Interoperability

Jarod Ferguson

ICIC 2014 New Product Presentations ChemAxon

ChemAxon provides a suite of informatics tools and applications to help scientists manage chemical data. They have developed these tools together with customers and partners. ChemAxon is considered the market leader in mainstream chemical structure handling tools. Their portfolio offers the broadest range of solutions and good value. ChemAxon's tools allow for extraction of chemistry information from text documents and enable curation and visualization of chemical data.

IC-SDV 2019: Competitive Intelligence: how to optimize the analysis of pipeli...

The document discusses two methods for optimizing data visualization for competitive intelligence analysis of pipeline and clinical trials data: 1) Using BizInt and VantagePoint solutions to combine pipeline, clinical trial, and other data sources and generate customizable reports and visualizations. 2) Developing an in-house tool called VALEM360 to provide a 360-degree view of pancreatic cancer competitive landscape data through multiple interactive visualization dashboards and a treatment decision tree. The VALEM360 tool demonstrated the potential of a data-driven approach but would benefit from improving data quality, automation of updates, and applying the methodology to other disease areas. Overall, data visualization is very useful for competitive intelligence analysis but requires expertise in topic areas,

FAIR resources, selected examples from ELIXIR-related projects

Business context of FAIR health data networks - The Hyve - MEDINFO Lyon 2019

MedInfo Lyon 2019: FAIR Health Data Sharing Initiatives in Europe: Opportunities and Challenges for international cooperation (Ulli Prokosch, Thomas Ganslandt, Ulrich Sax, Christian Lovis, Carlos Luis Parra Calderón, Peter Rijnbeek, Nigel Hughes, Wiro Niessen, Barend Mons, Kees Van Bochove) In the data-driven age of medical research many initiatives and projects focus on data linkage and functional integration as well as data reuse. Providing “FAIR data” is a common challenge for all of them. For this workshop leaders of six nation-wide and European initiatives/projects have joined in order to identify the major concepts, challenges and hurdles. This presentation was used to provide the business context of FAIR data in health data networks.

The Horizon 2020 Open Data Pilot - OpenAIRE webinar (Oct. 21 2014) by Sarah J...

OpenAIRE

ICIC 2014 Finding Answers in the Data – The Future Role of Text and Data Mini...

Vast amounts of new information and data are generated every day through scientific research. More and more of this data is stored in rapidly growing, but siloed databases, creating “Big Data” challenges. New technologies such as text and data mining make it possible to efficiently search and improve knowledge by applying analytics across these data sources. Research-intensive companies in the pharmaceutical and chemical industry are exploring the use of text and data mining (TDM) techniques to glean new insights from patents, clinical data, scientific literature, and other data sources. These insights are seen as critical to accelerating the process of drug and product discovery. As these researchers leverage TDM techniques, obtaining easy, centralized access to TDM-ready full-text content from multiple publishers becomes more and more important. What will be the future role of TDM in 2014 and beyond? What are the major TDM trends and what solutions are companies looking for to accelerate their R&D; efforts? Based on the experience gathered in a text and data mining pilot program successfully run by RightsDirect’s parent company Copyright Clearance Center (CCC) in 2013, RightsDirect’s General Manager Kim Zwollo will give an overview of current market needs, options and trends in Text and Data Mining. Using CCC’s TDM solution as an example, the presentation outlines critical success factors in technology and business models that need to be part of a comprehensive approach to text and data mining.

The FAIR Principles and FAIRsharing

Compound passport (BOS)

David Andrews

FAIR data and standards for a coordinated COVID-19 response

Enabling FAIR - what works?

The document discusses enabling FAIR (Findable, Accessible, Interoperable, Reusable) practices through both bottom-up and top-down approaches. It describes several EU and US biomedical data infrastructure programs and projects since 2014 that have taken bottom-up approaches through multi-institutional collaborations. It also discusses the FAIRsharing registry, a top-down approach that has been recommending standards, databases, and policies since 2011 to help researchers and improve data sharing policies of journals and funders. Lessons learned include the need to work both with technical and social aspects to define and measure success.

ICIC 2013 Conference Proceedings Krishna Molecular Connections

Alejandra Gonzalez-Beltran

Enriching Content with Semantic Tagging K. Krishna (Molecular Connections (India)) Jignesh Bhate (Molecular Connections, India) In spite of rapid transformation of publishing landscape brought about by digital technologies, content remains the focal point for publishers as well as consumers. Content deluge has increasingly made it challenging for consumers to discover and analyze relevant content. Approaches like semantic tagging provide an effective solution to this burgeoning problem. Semantic tagging facilitates enhanced knowledge discovery and management, automated categorization of content, improved web navigation, easier integration of new knowledge in existing content and better exchange of information across diverse services. In this talk, we will discuss about various content enrichment methodologies and share some insights from application of our in-house semantic tagging platform for enriching content of publishers.

Metadata for Interoperable Bioscience

Behind the FAIR brand: Thinkers, Doers and Dreamers

Behind the FAIR Brand: Thinkers, Doers and Dreamers discusses the development of FAIR (Findable, Accessible, Interoperable, Reusable) principles for digital assets. It outlines how FAIR was developed in 2014-2016 with researcher endorsement and describes ongoing work to implement FAIR through infrastructure programs, standards, policies and cultural changes to realize the benefits of better organized and accessible data. The talk highlights the collaborative effort still needed across many stakeholders to make digital resources FAIR.

Data quality supporting AI in Life Sciences webinar 10 dec 2018

EnablingFAIR - Open research data in the UK

CaseCase Study of hcltech.com study

HCL Technologies moved their website from ASP to Drupal in order to improve their online presence, user experience, and search functionality while reducing maintenance costs. They selected Drupal due to its abilities for content management, search engine optimization, and security through frequent updates as an open source platform. The transition faced challenges with content migration and performance optimization but provided benefits like enhanced content discovery, social sharing, and SEO friendliness. The project was successful and won an award with a small dedicated team.

Front end optimization

Front end optimization is important because 80% of end-user response time is spent on the front-end and front-end optimization can cut page load times by 25-50%. Page load times significantly impact user experience and business metrics. Tools like Yslow and Google PageSpeed can help identify optimization opportunities. Image optimization, minimizing HTTP requests by combining files, and reducing payload sizes are some techniques that should be applied from the start of a project. Progressive page loading, splitting components across domains, browser caching, and preloading components can further improve performance.

What's hot

Pistoia Alliance Debates: PhUSE Framework for the Adoption of Cloud Technolog...

2019-10-11 The value of FAIR data in health data networks - The Hyve - ELIXIR...

Healthcare Interoperability: Deceptively Difficult

Tim Benson

Open Science FAIR 2021: FAIRsharing and the FAIR Cookbook

Healthcare Interoperability

Jarod Ferguson

ICIC 2014 New Product Presentations ChemAxon

IC-SDV 2019: Competitive Intelligence: how to optimize the analysis of pipeli...

FAIR resources, selected examples from ELIXIR-related projects

Business context of FAIR health data networks - The Hyve - MEDINFO Lyon 2019

The Horizon 2020 Open Data Pilot - OpenAIRE webinar (Oct. 21 2014) by Sarah J...

OpenAIRE

ICIC 2014 Finding Answers in the Data – The Future Role of Text and Data Mini...

The FAIR Principles and FAIRsharing

Compound passport (BOS)

David Andrews

FAIR data and standards for a coordinated COVID-19 response

Enabling FAIR - what works?

ICIC 2013 Conference Proceedings Krishna Molecular Connections

Alejandra Gonzalez-Beltran

Metadata for Interoperable Bioscience

Behind the FAIR brand: Thinkers, Doers and Dreamers

Data quality supporting AI in Life Sciences webinar 10 dec 2018

EnablingFAIR - Open research data in the UK

What's hot (20)

Pistoia Alliance Debates: PhUSE Framework for the Adoption of Cloud Technolog...

2019-10-11 The value of FAIR data in health data networks - The Hyve - ELIXIR...

Healthcare Interoperability: Deceptively Difficult

Open Science FAIR 2021: FAIRsharing and the FAIR Cookbook

Healthcare Interoperability

ICIC 2014 New Product Presentations ChemAxon

IC-SDV 2019: Competitive Intelligence: how to optimize the analysis of pipeli...

FAIR resources, selected examples from ELIXIR-related projects

Business context of FAIR health data networks - The Hyve - MEDINFO Lyon 2019

The Horizon 2020 Open Data Pilot - OpenAIRE webinar (Oct. 21 2014) by Sarah J...

ICIC 2014 Finding Answers in the Data – The Future Role of Text and Data Mini...

The FAIR Principles and FAIRsharing

Compound passport (BOS)

FAIR data and standards for a coordinated COVID-19 response

Enabling FAIR - what works?

ICIC 2013 Conference Proceedings Krishna Molecular Connections

Metadata for Interoperable Bioscience

Behind the FAIR brand: Thinkers, Doers and Dreamers

Data quality supporting AI in Life Sciences webinar 10 dec 2018

EnablingFAIR - Open research data in the UK

Viewers also liked

CaseCase Study of hcltech.com study

Front end optimization

2011-10-11 Open PHACTS at BioIT World Europe

The document discusses the Innovative Medicines Initiative's Open PHACTS project, which aims to develop robust standards and apply them in a semantic integration platform ("Open Pharmacological Space") to integrate drug discovery data from various public and private sources. The project brings together partners from industry, academia, and non-profits to build an open infrastructure for linking drug discovery knowledge and supporting ongoing research. It outlines the technical approach, priorities, and initial progress on developing exemplar applications and a prototype "lash up" system.

Front-End Performance Optimizing

Michael Pehl

Front-end performance optimizing involves optimizing a website's HTML, CSS, JavaScript, and image files to achieve the fastest possible loading speed. This includes minimizing HTTP requests by combining files, compressing files, optimizing code by removing unused code and errors, leveraging browser caching, and parallelizing downloads across domains. The document outlines nine techniques for front-end optimization, such as optimizing file sizes, reducing download size through compression and caching, and minimizing HTTP requests through file combining and CSS sprites.

2015-04-28 Open PHACTS at Swedish Linked Data Network Meet-up

Front End Website Optimization

Gerard Sychay

UXify 2015 - Front-end Developers' Checklist for Better UX

Stoian Dipchikov

Good UX has always been one of the key factors for success in the contemporary web development and there fore has led to huge improvements in our industry in the last years. Nowadays the UX of a software product is not responsibility only of the UX Architects / Producers, but to each individual involved in the creation of an app or a website, including the Front-end developers. The talk presents a summarized list of DOs and DON’Ts, which Stoyan and his team believe should be respected by the Front-end developers if they want to build a useable web product, up to and above industry standards. There will be a lot of case studies and actual examples taken from Despark’s experience in the field.

Viewers also liked (7)

CaseCase Study of hcltech.com study

Front end optimization

2011-10-11 Open PHACTS at BioIT World Europe

Front-End Performance Optimizing

2015-04-28 Open PHACTS at Swedish Linked Data Network Meet-up

Front End Website Optimization

UXify 2015 - Front-end Developers' Checklist for Better UX

Similar to 2011-12-02 Open PHACTS at STM Innovation

Lankade data Vinnova webbinarium

Kerstin Forsberg

Open Insights Harvard DBMI - Personal Health Train - Kees van Bochove - The Hyve

In this talk, the Personal Health Train concept will be introduced, which enables running personalized medicine workflows as trains visiting data stations (e.g. hospital records, primary care records, clinical studies and registries, patient-held data from e.g. wearable sensors etc.) The Personal Health Train is a very powerful concept, which is however dependent on source medical data to be coded with appropriate metadata on consent, license, scope etc. of the data, and the data itself to be encoded using biomedical data standards, which is an ever growing field in biomedical informatics. In order to realize the Personal Health Train biomedical data will need to be FAIR, i.e. adopt the FAIR Guiding Principles. This talk will cover the emerging GO-FAIR international movement, and provide examples of how several European health data networks currently are adopting open standards based stacks, to enable routine health care data to be come accessible for research.

Precompetitive Collaborations

Chris Waller

This document discusses precompetitive collaborations in the pharmaceutical industry. It defines precompetitive as referring to standards, data, or processes that are common across an industry and provide no competitive advantage. The document outlines a precompetitive mission statement to foster collaborations between organizations to develop standards, identify partnerships, and transfer technology. It also describes current working groups focused on areas like biomarkers, clinical trial design, and data standards.

P4 c2011 slides ekins

Sean Ekins

Collaborative Drug Discovery provides three key services: 1. CDD Vault for securely storing private data. 2. CDD Collaborate for selectively sharing subsets of private data with collaborators. 3. CDD Public, containing over 3 million compounds for public searching and data analysis. The document outlines four collaborations using CDD to facilitate data and model sharing between academic and industry partners to further tuberculosis drug discovery. It argues that greater adoption of open data sharing and collaborative platforms could help address inefficiencies in the drug discovery process.

cBioPortal Webinar Slides (3/3)

This document discusses opportunities for using the open source cBioPortal platform in a commercial setting. It summarizes The Hyve's experiences supporting cBioPortal for the Center for Translational Molecular Medicine's TraIT project. The Hyve provides professional support for open source bioinformatics software like cBioPortal through software development, data services, consultancy, and hosting. For translation projects, The Hyve employs a phased approach including definition, pilot, implementation, and evaluation phases to implement cBioPortal and demonstrate its capabilities for data integration and analysis.

Let's work towards a #SaferWorldbyDesign - Knowledge-integrated Toxicology an...

Barry Hardy

Let's work towards a #SaferWorldbyDesign - Knowledge-integrated Toxicology and Safety Assessment, Barry Hardy, OpenTox Asia 2019, Hyderabad, India. To make a good decision we need to bring both expertise and relevant information together to form the basis for a structured well-informed discussion leading to best judgement based on available evidence and opinions formed on it. Such a knowledge integration is required in many areas of toxicology and safety assessment based on scientific knowledge generated by a growing number of alternative testing research methods and initiatives. Integration may include evidence from in vitro or in silico methods, biology or chemistry, science and engineering, human health or environment-oriented, and requires both effective organisation of knowledge and communications to reach common understandings. The requirements, context and format for applications may vary e.g., asking and answering scientific questions, carrying out a risk assessment on products, or performing a regulatory decision or submission. All applications however require a sound reproducible scientific basis and the use of good practices in characterising experiments, organising data and describing concepts in our ontology and knowledge framework. There is a growing opportunity to develop knowledge integration based on combining emerging concepts and frameworks e.g., OpenTox for data integration and resource interoperability, adverse outcome pathways for mapping data to events, evidence-based methods including systematic review applied to weight of evidence and read across methods for combining evidence from chemical or biological mechanistic categories. We also need community frameworks to bring different disciplines together for fruitful interactions and discussions. In this seminar we will review recent developments related to integrated testing and assessment including applications to chemicals, cosmetic ingredients and nanotechnology and including 3Rs goals of reducing and replacing animal testing.

Tag.bio aws public jun 08 2021

Sanjay Padhi, Ph.D

The document introduces Tag.bio as a low-code analytics application platform built from interconnected data products in a data mesh architecture. It consists of data, algorithms, and analysis apps contributed by different groups - data engineers, data scientists, and domain experts. The platform can integrate various data sources and enable collaboration between groups. It then provides demos of the Tag.bio developer studio and data portal. Key capabilities discussed include integration with AWS services like AI/ML and HealthLake, as well as security features like confidential computing. Example use cases presented are for clinical trials, healthcare, life sciences, and universities.

2015-02-10 The Open PHACTS Discovery Platform: Semantic Data Integration for ...

US Environmental Protection Agency (EPA), Center for Computational Toxicology and Exposure

Opening up pharmacological space, the OPEN PHACTs api

Chris Evelo

The document provides an overview of the Open PHACTS project, which aims to create an open pharmacological space (OPS) through semantic integration of public drug discovery resources. It discusses the challenges of accessing and integrating scientific data across organizational boundaries. Open PHACTS builds a service layer and applications to allow standardized access and analysis of data from various public sources. It is a collaborative project involving academic and industry partners seeking to make pre-competitive drug discovery data more accessible and useful through semantic integration and common standards.

Building on a FAIRly Strong Foundation to Connect Academic Research to Transl...

Jack DiGiovanna

Making data and analytics FAIR has transformative potential within organizations to build on existing knowledge. FAIR resources also democratize access to information and tools in underserved communities. Global standards and analysis platforms provide strong foundational elements. However, FAIRness across time and different sectors of the biomedical workforce presents challenges. Here we summarize how platforms make data and analysis FAIR today and what we see as key areas of future focus. BioIT 2024 invited talk.

Acs collaborative computational technologies for biomedical research an enabl...

Sean Ekins

This document discusses enabling more open and collaborative approaches to drug discovery through computational technologies. It argues that pre-competitive data sharing could help integrate historical knowledge and deliver high value. Open drug discovery may be a better approach than the traditional closed model. Tools and open interfaces could facilitate more open collaboration between different sectors involved in biomedical research. Mobile apps may help scientists access and share data more easily. Crowdsourcing approaches could engage more contributors to knowledge bases.

HPCC Systems Engineering Summit Presentation - Collaborative Research with FA...

HPCC Systems

Presenters: Borko Furht, Department of Electrical & Computer Engineering and Computer Science, FAU In 2009, Florida Atlantic University (FAU) received a grant from the National Science Foundation (NSF) to create the site of the Center for Advanced Knowledge Enablement (CAKE) as an Industry/University Cooperative Research Center (I/UCRC) that provides a framework for interaction between university faculty and industry in the areas of information technology, communication, and computing. LexisNexis is currently one of the CAKE industry members. In this session, we will talk about the significance of the membership, joint accomplishments, contributions back to the HPCC Systems community, as well as sharing experiences on including a Data Intensive Computing program in the FAU curriculum. NOTE: This is one of 3 presentations for this session and is the 2nd one shown in the accompanying YouTube video.

IHE / RSNA Image Sharing Project - IHE Colombia Workshop (12/2014) Module 5a

IHE Brasil

This document provides an overview of IHE (Integrating the Healthcare Enterprise), including: - IHE is an international initiative that provides frameworks for standards-based interoperability between healthcare systems. - It involves participation from various professional organizations and vendors to address real-world clinical needs. - IHE defines integration profiles that specify how multiple standards can be coordinated to address specific use cases. Products are tested and can publish integration statements about supported profiles.

A Reference Architecture for Digitalization in the Pharmaceutical Industry

Capgemini

Collaborative Computational Technologies for Biomedical Research: An Enabler ...

The current paradigm in the pharmaceutical industry is that products can only be created and developed by massive collaborative teams. Each company has to build their own costly R&D platforms and IT infrastructure. Other research industries realized decades ago that they had to share data and methods because of cost. The pharmaceutical industry has been slow to realize this. Expanding beyond our recent book (Collaborative Computational Technologies for Biomedical Research) in which a growing number of technologies, consortia, precompetitive initiatives and complex collaboration networks are described, we suggest a more open drug discovery is being enabled by collaborative computational technologies. Academia however, is not training the next generation of scientists to practice open science or even collaborate, this represents challenges and opportunities. We will describe our observations and make recommendations that impact everyone from technology developers to granting agencies. This may enable future discoveries to be made outside traditional institutions.

Stratergies for the intergration of information (IPI_ConfEX)

Ben Gardner

The document discusses approaches to integrating internal and external data across pharmaceutical research. It describes utilizing a data warehousing strategy through a Research Information Factory (RIF) to create a single global repository for research data. However, integrating external data from various sources poses additional challenges. Tools like PharmaMatrix provide a pre-indexed mine of scientific literature linking drug targets to indications, but result sets can be large. The document suggests that Web 2.0 technologies like wikis, blogs and tagging could help turn integrated information into knowledge by enabling collaboration and sharing. Industry-wide data standards and common ontologies would also help facilitate external data integration.

Semantics and linked data at astra zeneca

Kerstin Forsberg

1. The document summarizes Kerstin Forsberg's presentation on semantics and linked data at AstraZeneca R&D. It discusses (1) an internal competitive intelligence tool called CI360, (2) public pre-competitive projects like Open PHACTS and standards bodies, (3) AstraZeneca's Linked Data Community of Practice, and (4) ongoing work on study identifiers and APIs. 2. It provides an overview of Kerstin Forsberg's background and goal of improving the utility of clinical trial data through semantic interoperability. It also outlines some of AstraZeneca's collaborations and contributions to linked data initiatives. 3. The presentation highlights AstraZeneca

The Pistoia Alliance Biology Domain Strategy April 2011

Software Sustainability Institute

Neil Chue Hong

The Software Sustainability Institute (SSI) provides services to help research groups sustain their software over the long term. It collaborates with groups in various fields to improve key software through advice, training, and partnerships. Case studies describe projects in fields like fusion energy, climate modeling, geospatial data, and computational chemistry. The SSI aims to promote best practices and change perceptions so software is recognized as a valuable long-term asset, not just for initial research. Sustaining software requires support for both technical aspects and community engagement over decades.

Using Healthcare Data for Research @ The Hyve - Campus Party 2016

In this presentation, Kees van Bochove, founder & CEO of The Hyve, a services company in biomedical open source software, presents a number of different types of healthcare data. As an example, he also provides details of a project in which The Hyve participates and which uses that kind of data. Covered are: translational medicine data using tranSMART and cBioPortal, population health data using OMOP and OHDSI, and personal health data processing using open mHealth Shimmer and Apache Kafka.

Similar to 2011-12-02 Open PHACTS at STM Innovation (20)

Lankade data Vinnova webbinarium

Open Insights Harvard DBMI - Personal Health Train - Kees van Bochove - The Hyve

Precompetitive Collaborations

P4 c2011 slides ekins

cBioPortal Webinar Slides (3/3)

Let's work towards a #SaferWorldbyDesign - Knowledge-integrated Toxicology an...

Tag.bio aws public jun 08 2021

2015-02-10 The Open PHACTS Discovery Platform: Semantic Data Integration for ...

Opening up pharmacological space, the OPEN PHACTs api

Building on a FAIRly Strong Foundation to Connect Academic Research to Transl...

Acs collaborative computational technologies for biomedical research an enabl...

HPCC Systems Engineering Summit Presentation - Collaborative Research with FA...

IHE / RSNA Image Sharing Project - IHE Colombia Workshop (12/2014) Module 5a

A Reference Architecture for Digitalization in the Pharmaceutical Industry

Collaborative Computational Technologies for Biomedical Research: An Enabler ...

Stratergies for the intergration of information (IPI_ConfEX)

Semantics and linked data at astra zeneca

The Pistoia Alliance Biology Domain Strategy April 2011

Software Sustainability Institute

Using Healthcare Data for Research @ The Hyve - Campus Party 2016

More from open_phacts

Open PHACTS April 2017 Science webinar Workflow tools

This webinar discusses workflow tools to support life science research. It includes presentations on the Common Workflow Language (CWL) by Michael Crusoe and uses of Knime and Pipeline Pilot workflows with Open PHACTS examples. There will also be a panel discussion on the future of workflows for life science research with speakers from Eli Lilly, Janssen, and others. Example CWL workflows are shown to demonstrate portable life science workflows.

Open PHACTS Webinar Series - Chemistry Platform

Open PHACTS webinar June 2016 - Data2Discovery

Open PHACTS Webinar: Computational Protocols for In Silico Target Validation

Patent annotations: From SureChEMBL to Open PHACTS

2013-12-04 Experimental data guided docking allows to elucidate the molecular...

2015-05-19 Open PHACTS Drug Discovery Workflow Workshop - KNIME

2015-05-19 Open PHACTS Drug Discovery Workflow Workshop - The API

2014-03-20 Open PHACTS - A Data Platform for Drug Discovery

A data platform is proposed for drug discovery that would lower industry firewalls and enable pre-competitive data integration, analysis, and reuse across pharmaceutical companies. The platform would integrate external research data from literature, databases, and other sources on compounds, targets, pathways, and diseases. It would provide data integration and analysis tools through a firewalled database system and applications. The goal is to advance drug discovery by allowing multiple companies to access and build upon the same large foundation of pre-competitive research data.

2012-10-08 Practical Semantics In The Pharmaceutical Industry - The Open PHAC...

2013 Open PHACTS Architecture Poster

2013 Open PHACTS Scientific Questions Poster

This document discusses scientific competency questions that were collected by the Open PHACTS consortium to guide the development of the Open PHACTS integrated pharmacological data platform. 83 questions were provided by consortium members and prioritized, with the top 20 questions clustered into two groups related to compound-target and compound-target-disease/pathway interactions. Analyzing the questions revealed that compound, target, pathway and disease data needs to be associated to answer them. This informed the selection of public databases and drove the requirements for linking data sources in Open PHACTS.

2013 Open PHACTS Exemplars Poster

This document introduces several exemplar applications that were developed to showcase the capabilities of the Open PHACTS platform API. The exemplars include ChemBio Navigator, which allows browsing chemical and biological data for drug discovery applications; Polypharmacology Browser tools like GARField and PharmaTrek that enable exploration of compound-target interactions; and the Target Dossier, which compiles target-related information for decision support in target selection and validation. These exemplars demonstrate how diverse data integrated through the Open PHACTS platform can address relevant problems in drug development and biomedical research.

2011-11-28 Open PHACTS at RSC CICAG

2011-11-07 Open PHACTS Poster