Transcript How can it work for tissue knowledge management?

How does it work?
How can it work for tissue knowledge management?
Christine Chichester
@isb-sib.ch
October 30-31, 2013
IMI Tissue Knowledge
Management Workshop, Brussels
The Challenge
Public Drug Discovery Data:
Pharma are accessing, processing, storing, and re-processing public data repeatedly
Literature Genbank
Patents PubChem
Data Integration
Databases
Data Analysis
Downloads
Firewalled Databases
Overview
The Open PHACTS project has many non-technical benefits
The Open PHACTS discovery platform has many technical benefits
Outline
– Ecosystem and technical overview
– Data sources, integration, and delivery
– Dynamic equality via scientific lenses
– Community engagement
Components of Open PHACTS
Platform
[email protected]
API
Standards
Apps
Platform Overview
Core Platform
Applications
Identity
Resolution
Service
Identifier
Management
Service
“Adenosine
receptor 2a”
Linked Data API (RDF/XML, TTL, JSON)
P12374
EC2.43.4
CS4532
Domain
Specific
Services
Semantic Workflow Engine
Chemistry
Registration
Normalisation
& Q/C
Data Cache
(Virtuoso Triple Store)
indexing
VoID
VoID
VoID
Nanopub
Public
Ontologies
Db
Db
Public Content
VoID
Nanopub
Db
VoID
Nanopub
Db
Commercial
User
Annotations
Data sources and direct mappings
ChEMBL
HMDB
CAS
DrugBank
ChemSpider
ChEBI
PubChem
cmpd
KEGG cmpds
Wikipedia
RGD
ENZYME
ChEMBL
Target Class
UniGene
Gene
Ontology
neXtProt
UniProt
MeSH
Ensembl
ConceptWiki
WormBase
FlyBase
SGD
MEROPS
DisGeNet
FDA adverse
Wikipathways
events
Clinical
trials.org
EntrezGene
PathwayOnto
ZFIN
MGI
PDB
RefSeq
InterPro
Using the Power of Open PHACTS, London, 22-23 April 2013
Accessing the platform:
Uses URI’s
Linked Data API
(RDF/XML, TTL, JSON)
API Interaction for data delivery
Resolve User Input
1. User enters textual string
2. Resolve to URI for a concept
Request Data about URI (other API calls)
1. Expand URI for equivalences in each dataset
2. Run SPARQL query with URIs
Can include filters and restrictions on data returned
3. Download data in TSV format, import into Excel
Data for ddmore use case
Map compound textual name to URI
Search for compound pharmacology and filter for specific targets
Search for expression data for targets
Expression data still in test environment
Flexible mappings
Strict
Relaxed
Analysing
Browsing
Identity
Resolution
Service
“Adenosine
receptor 2a”
Identifier
Management
Service
P12374
EC2.43.4
CS4532
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Scientific Lens
Gives different
views on data
depending on
granularity
requirements
Tuneable (same data, different questions)
Domain specific
User driven
Traceable
Different views on data
Dynamic equality : Strict
Dynamic equality : Relaxed
Scientific lens for tissue knowledge
Flexible mappings
Cell Types
Tissues
Molecular Pathways
Genotype-Phenotype
Expression
Cell Ontology
Foundational Model of Anatomy
Gross Anatomy
Sign, Symptoms,
Radiological findings
UBERON
Community: Associated Partners
Community building
Open Development: Open Source
Open API: no restrictions
Reuse standards
Respect data providers: provenance, feedback
Acknowledgements
Open PHACTS Project Partners
Pfizer Limited – Coordinator
Universität Wien – Managing entity
Technical University of Denmark
University of Hamburg, Center for Bioinformatics
BioSolveIT GmBH
Consorci Mar Parc de Salut de Barcelona
Leiden University Medical Centre
Royal Society of Chemistry
Vrije Universiteit Amsterdam
Spanish National Cancer Research Centre
University of Manchester
Maastricht University
Aqnowledge
University of Santiago de Compostela
Rheinische Friedrich-Wilhelms-Universität Bonn
AstraZeneca
GlaxoSmithKline
Esteve
www.openphacts.org
Novartis
Merck
H. Lundbeck A/S
Eli Lilly
Netherlands Bioinformatics Centre
Swiss Institute of Bioinformatics
ConnectedDiscovery
EMBL-European Bioinformatics Institute
Janssen
OpenLink
Provenance - nanopublication
Highly curated database
Give credit to the curators
Provenance at the record level
Extends existing RDF based
infrastructure
– Progressively add these features as
needed
Assertion
Provenance
Publication
Information
PTM
Nanopublication
Explorer
Workflows
PharmaTrek
Utopia
ChemBioNavigator
iPharm