an architecture for an open science molecular compound database
DESCRIPTION
The past few years has seen a tremendous leap forward in public compound databases. Both PubChem and ChemSpider have made a clear message: chemical sciences can only move forward if we can search existing chemistry. However, the exact Open nature of “public” database is not always crystal clear. PubChem is mostly public domain but contains proprietary content too, while ChemSpider is mostly proprietary but has Open Data content. Neither are clear in how the Open Data parts of these databases can be used, modified, and redistributed, the three corner stones of Open Science. We will demo, based on previous work on http://rdf.openmolecules.net/, an architecture where semantic web technologies, the InChI, and Open Source cheminformatics tools are used to create a Panton Principles-compliant compound database to aid the next-generation public databases. Standards proposed in the Open PHACTS community will be use to specify links between this new resource and other databases, and to provide compound properties. All this input will be available with provenance on the origin of that data, as separate downloadable files, and using ontologies to provide explicit meaning. Using ontologies like ChEBI and CHEMINF, applications in the areas of metabolomics and toxicology will be presented.TRANSCRIPT
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Department of Bioinformatics - BiGCaT 1
An architecture for anOpen Sciencemolecular compound database
Egon Willighagen, @egonwillighagenDept. of Bioinformatics - BiGCaT - Maastricht University
orcid.org/0000-0001-7542-0286
ACS New Orleans, 9 April 2013, #ACSNola
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Department of Bioinformatics - BiGCaT 2
This session: Public Databases ...
• Public: what's that?– free access?– redistribute?–Modify?
• BTW, what is “Open Access” ???
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Department of Bioinformatics - BiGCaT 3
This session: Serving the community...
• Service–What do people want?–Do they know what is possible?
• Community–Who are they? Personas!→–Usability must include learnability
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Department of Bioinformatics - BiGCaT 4
Personas
• Not every scientist is alike• You cannot and must not target one
user• Instead, target at least 2 different
users, particularly:–The hacker doing all the actual
bioinformatics in the lab–The professor who has too little time to
understand things outside his narrow field
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Department of Bioinformatics - BiGCaT 5
Reason #1: Bioclipse decision support
Spjuth, O. et al. JCIM 2011 51(8):1840-1847.
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Department of Bioinformatics - BiGCaT 6
Data #1: Linked Open Drug Data
M. Samwald, et al, Linked open drug data for pharmaceutical research and development, 2011, JChemInf.
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Department of Bioinformatics - BiGCaT 7
Data^2: Linked Open Data
Linking Open Data cloud diagram, by Richard Cyganiak and Anja Jentzsch. http://lod-cloud.net/ Sept 2011, CC-BY-SA.
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Department of Bioinformatics - BiGCaT 8
Linked Open Data in the Life Sciences
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Department of Bioinformatics - BiGCaT 9
WikiPathways
Pico, AR et al. PLoS biology 6.7 (2008): e184.
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Department of Bioinformatics - BiGCaT 10
PathVisio: Pathway Analysis
Van Iersel, M. et al. BMC Bioinfo. 2008 9(1):399.
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Department of Bioinformatics - BiGCaT 11
Reason #2: Publishing
• Journals will increasingly require data deposition–e.g. BioMed Central:
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Department of Bioinformatics - BiGCaT 12
Needs
• We must propagate rights–whether open or not!
• We must make things explicit–e.g. by using semantics–e.g. by using the InChI
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Department of Bioinformatics - BiGCaT 13
Tool #1: licensing
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Department of Bioinformatics - BiGCaT 14
Open Data #1: crystallography
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Department of Bioinformatics - BiGCaT 15
Open Data #2: Open Notebook Science
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Department of Bioinformatics - BiGCaT 16
Open Data #3: CrystalEye
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Department of Bioinformatics - BiGCaT 17
Licensing Open not Required→
• But not providing info is a killer–no, not really because
no scientist seems to care
–yes, because how will a machine do? Think scalability and massive data integration efforts
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Department of Bioinformatics - BiGCaT 18
Why does explicit licensing matter?
Because when there is a fire, you want immediate access to the fire hose. You do not want to wait for permission from the mayor.
Because when you like to validate your scientific results, you want immediate access to related data. You do not want to wait for permission from that professor who is on a conference tour for the next 4 weeks. You must have an immediate answer, whatever it is.
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Department of Bioinformatics - BiGCaT 19
Tool #2: Semantic Web to the rescue
• Allows provenance–provide where data came from– tells us our rights
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Department of Bioinformatics - BiGCaT 20
App #1: Spidering the semantic web
Spjuth, O et al. JChemInf 2013 5:14.
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Department of Bioinformatics - BiGCaT 21
App #2: Making a web
http://rdf.openmolecules.net/
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Department of Bioinformatics - BiGCaT 22
App #3: Open PHACTS Explorer
http://www.openphacts.org/ → room 349, 2:20pm
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Department of Bioinformatics - BiGCaT 23
How #1: RDF Graphs
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Department of Bioinformatics - BiGCaT 24
How #1: RDF Graphs
PREFIX cheminf: <http://semanticscience.org/resource/>
SELECT ?graph ?p ?o WHERE { GRAPH ?graph { ?mol cheminf:CHEMINF_000200 [ a cheminf:CHEMINF_000059 ; cheminf:SIO_000300 "$inchikey" ] ; ?p ?o . }}
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Department of Bioinformatics - BiGCaT 25
NanoPub.org
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Department of Bioinformatics - BiGCaT 26
Graph output
orcid.org/0000-0001-7542-0286
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Department of Bioinformatics - BiGCaT 27
Is that it?!? Just an architecture??
Yes, but a simple and flexible one. Keep an eye out on my blog. This will happen in the next few months:
1. Aggregate all CCZero/PDDL data around chemical properties
1.Open Notebook Science (solubility, melting point)
2.ChemPedia
3.Crystallography (COD, CrystalEye)
4....
2. Calculate molecular properties with the CDK (and release as CCZero)
3. Host on http://linkedchemistry.info/chembox
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Department of Bioinformatics - BiGCaT 28
CHEMINF ontology
orcid.org/0000-0001-7542-0286
Hastings, J. et al. PLoS ONE 2011 6(10):e25513.
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Department of Bioinformatics - BiGCaT 29
Architecture
Triple Store(e.g. Virtuoso)
Web server(HTML / RDF)
• Graphs• Explicit license
info• InChI/FixedH
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/FixedH ?!?!
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Department of Bioinformatics - BiGCaT 31
Conclusions & Outlook
• We must propagate rights–whether open or not!
• We must make things explicit–e.g. by using semantics–e.g. by using the InChI with FixedH
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Department of Bioinformatics - BiGCaT 32
More information
• @egonwillighagen• http://chem-bla-ics.blogspot.com/• http://egonw.github.com/
• http://orcid.org/0000-0001-7542-0286