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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This session: Public Databases ...

• Public: what's that?– free access?– redistribute?–Modify?

• BTW, what is “Open Access” ???

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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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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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Reason #1: Bioclipse decision support

Spjuth, O. et al. JCIM 2011 51(8):1840-1847.

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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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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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Linked Open Data in the Life Sciences

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WikiPathways

Pico, AR et al. PLoS biology 6.7 (2008): e184.

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PathVisio: Pathway Analysis

Van Iersel, M. et al. BMC Bioinfo. 2008 9(1):399.

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Reason #2: Publishing

• Journals will increasingly require data deposition–e.g. BioMed Central:

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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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Tool #1: licensing

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Open Data #1: crystallography

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Open Data #2: Open Notebook Science

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Open Data #3: CrystalEye

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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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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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Tool #2: Semantic Web to the rescue

• Allows provenance–provide where data came from– tells us our rights

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App #1: Spidering the semantic web

Spjuth, O et al. JChemInf 2013 5:14.

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App #2: Making a web

http://rdf.openmolecules.net/

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App #3: Open PHACTS Explorer

http://www.openphacts.org/ → room 349, 2:20pm

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How #1: RDF Graphs

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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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NanoPub.org

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Graph output

orcid.org/0000-0001-7542-0286

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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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CHEMINF ontology

orcid.org/0000-0001-7542-0286

Hastings, J. et al. PLoS ONE 2011 6(10):e25513.

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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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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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More information

• @egonwillighagen• http://chem-bla-ics.blogspot.com/• http://egonw.github.com/

• http://orcid.org/0000-0001-7542-0286