Incorporating Commercial and Private Data into an - Open PHACTS

24 Pages·2013·1.75 MB·English

by  Alasdair Gray

Incorporating Commercial and Private
Data into an Open Linked Data Platform
for Drug Discovery
Carole Goble, Alasdair J G Gray, Lee Harland,
Karen Karapetyan, Antonis Loizou, Ivan Mikhailov,
Yrjänä Rankka, Stefan Senger, Valery Tkachenko,
Antony J Williams, and Egon L Willighagen

www.openphacts.org [email protected]
@open_phacts @gray_alasdair
Pre-competitive Informatics
Pharmaceutical companies are all accessing, processing,
storing & re-processing external research data
Repeat @
Downloads x
Literature Genbank Databases
each
Patents PubChem
company
Firewalled Databases
Data Integration Data Analysis
Lowering industry firewalls: pre-competitive informatics in drug discovery
Nature Reviews Drug Discovery (2009) 8, 701-708 doi:10.1038/nrd2944
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Open PHACTS objective
Apps
Interactive
responses
Open
Standards
Domain API
Provenance of
data
Drug Discovery Platform
Production
quality
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Drug Discovery Data
Pathways
Proteins
Interactions
Pharmacological
Genes
Activities
Transcripts
Clinical Drug
Applications
Biological
Drugs
Processes
Indications
Pathological Diseases
Processes Compounds
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Public Data
Pathways
Proteins
Interactions
Pharmacological
Genes
Activities
Transcripts
Clinical Drug
Applications
Biological
Drugs
Processes
Indications
Pathological Diseases
Processes Compounds
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Real Business Questions
Pathways
“Let me compare
Proteins
MW, logP and PSA
for known Interactions “What is thPeh armacological
oxidoreductase selectivity profile of
Genes
Activities
inhibitors” known p38 inhibitors?”
Transcripts
Clinical Drug
Applications
“Find me compounds
Biological
Drugs
that inhibit targets in
Processes
Indications
NFkB pathway assayed
in only functional assays
Pathological with a potency <1 μM” Diseases
Processes Compounds
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OPS Discovery Platform
Apps
Identity
“Adenosine Domain
Linked Data API
Resolution
receptor 2a”
(RDF/XML, TTL, JSON) Specific
Service
m
Services
r
o
f Identifier
t P12374 Semantic Workflow Engine
a Management
l EC2.43.4
P Service
CS4532

e
r Chemistry
o
Data Cache
Registration
C
Normalisatio
(Virtuoso Triple Store)
n & Q/C
Indexing
VoID
VoID VoID VoID VoID

Nanopub Nanopub Nanopub
Public
Ontologies Db Db Db Db
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Public Content Commercial
Annotations
Present Content: Public Data
Source Initial Records Triples Properties
ChEMBL 1,247,403 305,419,649 77
DrugBank 19,628 517,584 74
UniProt ? 533,394,147 82
ENZYME 6,187 73,838 2
ChEBI 40,575 40,575 2
GeneOntology 38,137 1,265,273 26
GOA ? 23,489,501 15
ChemSpider 1,194,437 161,336,857 26
ConceptWiki 2,828,966 3,739,884 1
WikiPathways 946 1,449,981 34
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Semantic Integration Methodology
1. Define use cases
2. Identify Data
– Create RDF
– VoID dataset descriptions
3. Create mappings
– between data set and known data sets
(instance level)
– index for text to URL conversion

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Semantic Integration Methodology
4. Ingest RDF into data cache
(i.e. triple store)
5. Define access paths to core concepts in data
6. Extend or create SPARQL queries for API calls
7. Publish API calls

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