How I failed to do Open Notebook Cheminformatics
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Transcript of How I failed to do Open Notebook Cheminformatics
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Department of Bioinformatics - BiGCaT 1
How I failed to do
Open Notebook Cheminformatics
Egon Willighagen (@egonwillighagen)14 July 2014, Jean-Claude Bradley Memorial Symposium
#jcbms
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Department of Bioinformatics - BiGCaT 2
Jean-Claude Bradley
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Department of Bioinformatics - BiGCaT 3
“Open Notebook Science”
First response: jealousy
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Department of Bioinformatics - BiGCaT 4
How I failed
• I did Open Science–Strong focus on reproducibility–Open Source, Open Data, Open Standards
(ODOSOS)
• I did share notes...• I wrote up the stories (in a blog)...
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Department of Bioinformatics - BiGCaT 5
Realization
• Scholars need notebooks–They need exact instructions– Just giving the outcome and tools is not
enough
• This applies to cheminformatics too
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Department of Bioinformatics - BiGCaT 6
First notes where during education
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Department of Bioinformatics - BiGCaT 7
ODOSOS
• Software:–The Chemistry Development Kit
• based on CompChem, Jmol and JchemPaint
–Bioclipse, Jmol, ...
• Data–Blue Obelisk Data Repository–RDF translations of knowledge bases
• Standards–eNanoMapper ...
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Department of Bioinformatics - BiGCaT 8
Scribbling...
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Department of Bioinformatics - BiGCaT 9
Scribbline...
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Department of Bioinformatics - BiGCaT 10
Scribbline...
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Department of Bioinformatics - BiGCaT 11
Why important?
• Going back to the original (raw data).• Pedagogical effect• Education (howto's)• Machines care about negative data• If we want to progress, we need to
understand not just global patterns, but the fine details too
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Department of Bioinformatics - BiGCaT 12
Why cheminformatics too?
• Where is the latest RDF of solubility data? Of the melting point data?
• The trust problem applies to algorithms as much as data
• What if...
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Department of Bioinformatics - BiGCaT 13
What I have in mind...
WikiPedia, CC-BY-SA, http://en.wikipedia.org/wiki/Curtin%E2%80%93Hammett_principle
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Department of Bioinformatics - BiGCaT 14
Possible ONS of cheminformatics
• Is this set of atom types covering ChEBI?
• Can we map this metabolomics data to pathways?
• How many CAS registry numbers can I resolve for this data set?
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Department of Bioinformatics - BiGCaT 15
Conclusion
Some patience is needed, but I will start Open Notebook Science.
(And I will push this concept with my Bart and Cristian too.)
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Department of Bioinformatics - BiGCaT 16
Benchmarking / metrics