0
Användningen av länkade data
principer och semantic web
standards i läkemedelsforskningen
Kerstin Forsberg (@kerfors on Tw...
About AstraZeneca
• Alongside our own R&D, we partner
with others, combining skills and
resources to broaden the potential...
Länkade Data i Läkemedelsforskningen
Två exempel på hur AstraZeneca arbetar med europeiska
forskningssamarbeten och intern...
Webben fyllde 25 år 12 mars
4 Kerstin Forsberg | Vinnova webbinar 18 mars 2013 AZIT | R&D Information
Web of (Linked) Data...
RDF (semantic web basen) fyllde 15 år 22 febr.
5 Kerstin Forsberg | Vinnova webbinar 18 mars 2013 AZIT | R&D Information
W...
The Project
The Innovative Medicines
Initiative
• EC funded public-private
partnership for
pharmaceutical research
• Focus...
Pre-competitive Informatics:
Pharma are all accessing, processing, storing & re-processing external research data
Literatu...
ChEMBL DrugBank
Gene
Ontology
Wikipathways
UniProt
ChemSpider
UMLS
ConceptWiki
ChEBI
TrialTrove
GVKBio
GeneGo
TR Integrity...
Number sum Nr of 1 Question
15 12 9 All oxidoreductase inhibitors active <100nM in both human and mouse
18 14 8
Given comp...
Nanopub
Db
VoID
Data Cache
(Virtuoso Triple Store)
Semantic Workflow Engine
Linked Data API (RDF/XML, TTL, JSON)
Domain
Sp...
Platform Explorer
Standards
Apps
API
“Provenance Everywhere”
Clinical data standards, today’s documentation
12 Kerstin Forsberg | Vinnova webbinarium 18 mars 2013 AZIT | R&D Informati...
Clinical data standards in the Semantic Web
Enable end-to-end interoperable data standards
for clinical research
13 Kersti...
Clinical data standards in the Semantic Web
Example: 14 RDF triples describing one variable (“AEACN”)
14 Kerstin Forsberg ...
• CDISC2RDF started Oct 2012 as a pre-
competitive project with AZ, Roche, W3C et al.
to show case Semantic Web standards ...
AstraZeneca’s view on “Semantics”
Enabling the hyperconnected enterprise
16 Kerstin Forsberg | Vinnova webbinarium 18 mars...
Acknowledgements
AZ’s Linked Data of Practice members:
Tom Plasterer (lead), Jim Morris, Courtland Yockey, Sorana
Popa, Ro...
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Lankade data Vinnova webbinarium

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Slides to be presented at a webinar arranged by Metasolution as part of a Vinnova project http://metasolutions.se/2014/03/webbinarium-med-kerstin-forsberg-om-lankade-data-i-lakemedelsforskningen/

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  • Mx/psa, how calculated who did it?Mash up. With your data too,- top layer join together but need them allcommerical
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  • Transcript of "Lankade data Vinnova webbinarium "

    1. 1. Användningen av länkade data principer och semantic web standards i läkemedelsforskningen Kerstin Forsberg (@kerfors on Twitter, SlideShare etc.) AZ IT | R&D Information Kompetensförstärkning kring länkade öppna data - dialog, webbinarier och vitbok Webbinarium arrangerat av 18 mars 2014
    2. 2. About AstraZeneca • Alongside our own R&D, we partner with others, combining skills and resources to broaden the potential for successful innovation. • We believe that only by working together with others who have a part of play in improving healthcare can real progress be made. • We work closely with others in the healthcare community, including physicians and those who pay for healthcare, to understand their challenges and how we can combine skills and resources to achieve a common goal: improved health. 2 Kerstin Forsberg | Vinnova webbinarium 18 mars 2013 AZIT | R&D Information
    3. 3. Länkade Data i Läkemedelsforskningen Två exempel på hur AstraZeneca arbetar med europeiska forskningssamarbeten och internationella standard organisationer för att göra kemidata och kliniska studie data enklare att använda med hjälp av nästa generations web teknik. 3 Kerstin Forsberg | Vinnova webbinarium 18 mars 2013 Set area descriptor | Sub level 1
    4. 4. Webben fyllde 25 år 12 mars 4 Kerstin Forsberg | Vinnova webbinar 18 mars 2013 AZIT | R&D Information Web of (Linked) Data Web of Documents An Intro To The Semantic Web: Why You Need To Know About It Sooner Than Later , by Samantha Wong Image Source: Frederic Martin
    5. 5. RDF (semantic web basen) fyllde 15 år 22 febr. 5 Kerstin Forsberg | Vinnova webbinar 18 mars 2013 AZIT | R&D Information Web of (Linked) Data Web of Documents subject predicat object Common Model (“Triples”) Resource Description Framework
    6. 6. The Project The Innovative Medicines Initiative • EC funded public-private partnership for pharmaceutical research • Focus on key problems – Efficacy, Safety, Education & Training, Knowledge Management The Open PHACTS Project • Create a semantic integration hub (“Open Pharmacological Space”)… • Delivering services to support on-going drug discovery programs in pharma and public domain • Not just another project; Leading academics in semantics, pharmacology and informatics, driven by solid industry business requirements • 23 academic partners, 8 pharmaceutical companies, 3 biotechs • Work split into clusters: • Tehnical Build • Scientific Drive • Community & Sustainability
    7. 7. Pre-competitive Informatics: Pharma are all accessing, processing, storing & re-processing external research data Literature PubChem Genbank Patents Databases Downloads Data Integration Data Analysis Firewalled Databases Repeat @ each company x Lowering industry firewalls: pre-competitive informatics in drug discovery Nature Reviews Drug Discovery (2009) 8, 701-708 doi:10.1038/nrd2944
    8. 8. ChEMBL DrugBank Gene Ontology Wikipathways UniProt ChemSpider UMLS ConceptWiki ChEBI TrialTrove GVKBio GeneGo TR Integrity “Find me compounds that inhibit targets in NFkB pathway assayed in only functional assays with a potency <1 μM” “What is the selectivity profile of known p38 inhibitors?” “Let me compare MW, logP and PSA for known oxidoreductase inhibitors”
    9. 9. Number sum Nr of 1 Question 15 12 9 All oxidoreductase inhibitors active <100nM in both human and mouse 18 14 8 Given compound X, what is its predicted secondary pharmacology? What are the on and off,target safety concerns for a compound? What is the evidence and how reliable is that evidence (journal impact factor, KOL) for findings associated with a compound? 24 13 8 Given a target find me all actives against that target. Find/predict polypharmacology of actives. Determine ADMET profile of actives. 32 13 8 For a given interaction profile, give me compounds similar to it. 37 13 8 The current Factor Xa lead series is characterised by substructure X. Retrieve all bioactivity data in serine protease assays for molecules that contain substructure X. 38 13 8 Retrieve all experimental and clinical data for a given list of compounds defined by their chemical structure (with options to match stereochemistry or not). 41 13 8 A project is considering Protein Kinase C Alpha (PRKCA) as a target. What are all the compounds known to modulate the target directly? What are the compounds that may modulate the target directly? i.e. return all cmpds active in assays where the resolution is at least at the level of the target family (i.e. PKC) both from structured assay databases and the literature. 44 13 8 Give me all active compounds on a given target with the relevant assay data 46 13 8 Give me the compound(s) which hit most specifically the multiple targets in a given pathway (disease) 59 14 8 Identify all known protein-protein interaction inhibitors Business Question Driven Approach http://www.sciencedirect.com/science/article/pii/S1359644613001542
    10. 10. Nanopub Db VoID Data Cache (Virtuoso Triple Store) Semantic Workflow Engine Linked Data API (RDF/XML, TTL, JSON) Domain Specific Services Identity Resolution Service Chemistry Registration Normalisation & Q/C Identifier Management Service Indexing CorePlatform P12374 EC2.43.4 CS4532 “Adenosine receptor 2a” VoID Db Nanopub Db VoID Db VoID Nanopub VoID Public Content Commercial Public Ontologies User Annotations Apps
    11. 11. Platform Explorer Standards Apps API “Provenance Everywhere”
    12. 12. Clinical data standards, today’s documentation 12 Kerstin Forsberg | Vinnova webbinarium 18 mars 2013 AZIT | R&D Information Human readable documentation in 200+ pages PDF:s, Excel:s (and some in XML).
    13. 13. Clinical data standards in the Semantic Web Enable end-to-end interoperable data standards for clinical research 13 Kerstin Forsberg | Vinnova webbinarium 18 mars 2013 AZIT | R&D Information
    14. 14. Clinical data standards in the Semantic Web Example: 14 RDF triples describing one variable (“AEACN”) 14 Kerstin Forsberg | Vinnova webbinarium 18 mars 2013 AZIT | R&D Information RDF triples describing one variable/data element and also linked to related standard parts
    15. 15. • CDISC2RDF started Oct 2012 as a pre- competitive project with AZ, Roche, W3C et al. to show case Semantic Web standards and Linked Data principles. • FDA meeting Nov 2012: Solutions for Study Data Exchange Standards Meeting – W3C Semantic Web presentation • June 2013 the Semantic Technology project, a FDA/PhUSE working group for Emerging Technologies, with 25+ repr. from FDA, CDISC, Pharma:s, CRO:s and software vendors. • Oct 2013 press release: Representing existing standards (SDTM, CDASH, SEND, ADaM) in RDF. Clinical standards in the Semantic Web Community building and knowledge sharing 15 Kerstin Forsberg | Vinnova webbinarium 18 mars 2013 AZIT | R&D Information CDISC Interchange Europe 2011 and 2012 presentations from Roche and AstraZeneca
    16. 16. AstraZeneca’s view on “Semantics” Enabling the hyperconnected enterprise 16 Kerstin Forsberg | Vinnova webbinarium 18 mars 2013 AZIT | R&D Information “We need to build a linked data architecture enabling us to ask questions and solve business problems across a heterogeneous information landscape extending beyond the traditional boundaries of the enterprise.” semanticsconnectsusall
    17. 17. Acknowledgements AZ’s Linked Data of Practice members: Tom Plasterer (lead), Jim Morris, Courtland Yockey, Sorana Popa, Rob Hernandez, Mike Westaway, Rajan Desai, Simon Rakov, Dana Crowley, Ian Dix, Johan Törnqvist Collaborators and Advisors: • Charlie Mead – IO Informatics • Dean Allemang – Working Ontologist • Frederik Malfait – IMOS consulting / Roche • Phil Ashworth – TopQuadrant 17 Kerstin Forsberg | Vinnova webbinarium 18 mars 2013 AZIT | R&D Information Thank you! Kerstin.l.forsberg@astrazeneca.com
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