When are two entries about a small molecule in different datasets the same? If they have the same drug name, chemical structure, or some other criteria? The choice depends upon the application to which the data will be put. However, existing Linked Data approaches provide a single global view over the data with no way of varying the notion of equivalence to be applied. In this paper, we present an approach to enable applications to choose the equivalence criteria to apply between datasets. Thus, supporting multiple dynamic views over the Linked Data. For chemical data, we show that multiple sets of links can be automatically generated according to different equivalence criteria and published with semantic descriptions capturing their context and interpretation. This approach has been applied within a large scale public-private data integration platform for drug discovery. To cater for different use cases, the platform allows the application of different lenses which vary the equivalence rules to be applied based on the context and interpretation of the links.

1. Scientific lenses to support
multiple views over linked
Chemistry data
Alasdair J G Gray
A.J.G.Gray@hw.ac.uk
alasdairjggray.co.uk
@gray_alasdair
Open PHACTS
pmu@openphacts.org
openphacts.org
@open_phacts

2. Multiple Identities
GB:29384
P12047
X31045
21 October 2014 Scientific Lenses – A. J. G. Gray 1

3. Gleevec®: Imatinib Mesylate
Imatinib
Imatinib MesylateMesylate
YLMAHDNUQAMNNX-UHFFFAOYSA-N
ChemSpider Drugbank PubChem
21 October 2014 Scientific Lenses – A. J. G. Gray 2

4. Gleevec®: Imatinib Mesylate
Imatinib
Are these records the same?
It depends upon your task!
Imatinib MesylateMesylate
YLMAHDNUQAMNNX-UHFFFAOYSA-N
ChemSpider Drugbank PubChem
21 October 2014 Scientific Lenses – A. J. G. Gray 3

5. Example Use Cases
I need to perform an
analysis, give me details
of the active compound
in Gleevec.
Which targets are
known to interact
with Gleevec?
21 October 2014 Scientific Lenses – A. J. G. Gray 4

6. Structure Lens
I need to perform an analysis, give me
Strict Relaxed
Analysing Browsing
skos:exactMatch
(InChI)
Scientific Lenses – A. J. G. Gray 5
21 October 2014
details of the active compound in
Gleevec.

7. Name Lens
Which targets are known to interact
Strict Relaxed
Analysing Browsing
skos:closeMatch
(Drug Name)
skos:exactMatch
(InChI)
skos:closeMatch
(Drug Name)
Scientific Lenses – A. J. G. Gray 6
21 October 2014
with Gleevec?

8. What is a Scientific Lens?
A lens defines a conceptual view over the data
 Specifies operational equivalence conditions
Consists of:
 Identifier (URI)
 Title
(dct:title)
 Description
(dct:description)
 Documentation link
(dcat:landingPage)
 Creator
(pav:createdBy)
 Timestamp
(pav:createdOn)
 Equivalence rules
(bdb:linksetJustification)
16 October 2014 Scientific Lenses – A. J. G. Gray 7

9. Lens Effects: Ibuprofen
Ibuprofen consists of two equally active stereoisomers.
• Stereoisomers not always represented in data
Users wish to retrieve information for any stereoisomer.
CHEMBL427526
CHEMBL521
CHEMBL175
21 October 2014 Scientific Lenses – A. J. G. Gray 8

10. Default Lens
Ibuprofen consists of two equally active stereoisomers.
• Stereoisomers not always represented in data
Users wish to retrieve information for any stereoisomer.
21 October 2014 Scientific Lenses – A. J. G. Gray 9

11. Stereoisomer Lens
Ibuprofen consists of two equally active stereoisomers.
• Stereoisomers not always represented in data
Users wish to retrieve information for any stereoisomer.
21 October 2014 Scientific Lenses – A. J. G. Gray 10

12. Mapping Generation
✔
ops:OPS437281
has_stereoundefined_parent
[ci:CHEMINF_000456]
ops:OPS380297
is_stereoisomer_of
[ci:CHEMINF_000461]
ops:OPS380292
Other relationships
• has part
• is tautomer of
• uncharged counterpart
• isotope
…
21 October 2014 Scientific Lenses – A. J. G. Gray 11

13. Explorer Screenshot
21 October 2014 Scientific Lenses – A. J. G. Gray 12

14. Explorer Screenshot
21 October 2014 Scientific Lenses – A. J. G. Gray 13

15. OPS Discovery Platform
Linked Data API (RDF/XML, TTL, JSON)
Semantic Workflow Engine
VoID
Nanopub
Db
Data Cache
(Virtuoso Triple Store)
Domain
Specific
Services
Identity
Resolution
Service
Chemistry
Registration
Normalisation
& Q/C
Identifier
Management
Service
Indexing
Core Platform
“Adenosine
receptor 2a”
P12374
EC2.43.4
CS4532
VoID
Db
VoID
Nanopub
Db
VoID
Db
VoID
Nanopub
Public Content Commercial
Public Ontologies
User
Annotations
Apps
21 October 2014 Scientific Lenses – A. J. G. Gray 14

16. Lenses: Under the hood
GRAPH <http://rdf.chemspider.com> {
cw:979b545d-f9a9 cheminf:logd ?logd .
?iri cheminf:logd ?logd .
FILTER (?iri = cw:979b545d-f9a9 ||
?iri = cs:2157 ||
?iri = chembl:1280 ||
?iri = db:db00945 )
}
GRAPH <http://…
Q, L1 Q’
Query
Expander
Service
Identity
Mapping
Service
(BridgeDB)
Mappings
Profiles
cw:979b545d-f9a9, L1
[cw:979b545d-f9a9,
cs:2157,
chembl:1280,
db:db00945]
• IMS call adds overhead
• Call time below human perception [1]
• Can also be achieved through UNION
[1] C. Y. A. Brenninkmeijer, C. Goble, A. J. G. Gray, P. Groth, A.
Loizou, and S. Pettifer, “Including Co-referent URIs in a SPARQL
Query,” COLD2013, http://ceur-ws.org/Vol-1034/
21 October 2014 Scientific Lenses – A. J. G. Gray 15

17. API Hits
April 2013 – March 2014: 15.8m
April 2014 – Sept 2014: 14m
Total: 29.8 million
21 October 2014 Scientific Lenses – A. J. G. Gray 16

18. Conclusions
 Scientific data is complex and messy
 Requires flexibility in linking
 Equivalence depends upon context
 Lenses provide support for operational
equivalence
 Chemical structures support automatic
computing of links with justification
21 October 2014 Scientific Lenses – A. J. G. Gray 17

19. Co-authors
Royal Society of Chemistry
 Colin Batchelor
 Karen Karapetyan
 Jon Steele
 Valery Tkachenko
 Antony Williams
University of Manchester
 Christian Brenninkmeijer
 Ian Dunlop
 Carole Goble
 Steve Pettifer
 Robert Stevens
Swiss Institute for Bioinformatics
 Christine Chichester
European Bioinformatics Institute
 Mark Davies
 Anna Gaulton
 John Overington
University of Vienna
 Daniela Digles
Maastricht University
 Chris Evelo
 Andra Waagmeester
 Egon Willighagen
VU University of Amsterdam
 Paul Groth
 Antonis Loizou
Connected Discovery
 Lee Harland
21 October 2014 Scientific Lenses – A. J. G. Gray 18

20. Questions
Alasdair J G Gray
A.J.G.Gray@hw.ac.uk
alasdairjggray.co.uk
@gray_alasdair
Open PHACTS
pmu@openphacts.org
openphacts.org
@open_phacts
Demo at stall 33 this evening!
21 October 2014 Scientific Lenses – A. J. G. Gray 19

21. Open PHACTS Data
Source Initial Records Triples Properties
ChEMBL 1,481,473 304,360,749 77
DrugBank 19,628 517,584 74
UniProt 564,246 405,473,138 82
ENZYME 6,187 73,838 2
ChEBI 40,575 1,673,863 2
GeneOntology 38,137 2,447,682 26
GOA 661,232 1,765,622,393 15
ChemSpider 1,361,568 215,193,441 23
ConceptWiki 2,828,966 4,291,131 1
WikiPathways 946 1,949,074 34
21 October 2014 Scientific Lenses – A. J. G. Gray 20

22. App Ecosystem An “App Store”?
Explorer Explorer2 ChemBioNavigator Target Dossier Pharmatrek Helium
MOE Collector Cytophacts Utopia Garfield SciBite
KNIME Mol. Data Sheets PipelinePilot scinav.it Taverna
http://www.openphactsfoundation.org/apps.html
21 October 2014 Scientific Lenses – A. J. G. Gray 21

23. Discovery Platform
Apps
Method
Calls
Domain API
Drug Discovery Platform
Interactive
responses
Production quality
integration platform
21 October 2014 Scientific Lenses – A. J. G. Gray 22

24. Linked Data API
Drug
Target Pathway
Disease (1.4)
https://dev.openphacts.org/
21 October 2014 Scientific Lenses – A. J. G. Gray 23