Asking the scientific literature to tell us about metabolism
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Transcript of Asking the scientific literature to tell us about metabolism
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Extraction of metabolism data from the literature
Peter Murray-Rust, Dept of Chemistry and TheContentMine
Lhasa, Leeds, UK, 2017-01-12
contentmine.org is supported by a grant to PMR as a
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Thousands of scientists have to type the literature.
Machines should be doing it!
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Special ThanksMolecular Informatics, CambridgePeter CorbettAndy HowlettDaniel LoweLezan HawizyMark Williamson
OSCAR (chemical entities),OPSIN (name 2 structure)ChemicalTagger (recipes)“OSIRIS” (graphical chemistry)
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What is “Content”?
http://www.plosone.org/article/fetchObject.action?uri=info:doi/10.1371/journal.pone.0111303&representation=PDF CC-BY
SECTIONS
MAPS
TABLES
CHEMISTRYTEXT
MATH
contentmine.org tackles these
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Example papers – what do you want? What can we find?
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Entity extraction
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Reaction Schemes
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Tables
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Tables
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Graphs
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Entities
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Plot
Plot
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Maths?
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Models?
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Semantics in Wikidata
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What’s the title?
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Some demos
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“… simulated by 21cmFAST is in principle independent”
“it is a feature of the 21cmFAST code, and is explained in §3.1.”
SciCodes[1]: Searching for software in arXiv[1]
[1] Proposal to LJ Arnold Foundation (Alice Allen ASCL and PMR)
Using the semi-numerical simulation, 21cmFAST,
[2] arxiv.org: the physics/maths/astronomy.. Preprint server
The language identifies the software!
arxIv has >500 mentions of “21cmFast”
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http://chemicaltagger.ch.cam.ac.uk/
• Typical
Typical chemical synthesis
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Automatic semantic markup of chemistry
Could be used for analytical, crystallization, etc.
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AMI https://bitbucket.org/petermr/xhtml2stm/wiki/Home
Example reaction scheme, taken from MDPI Metabolites 2012, 2, 100-133; page 8, CC-BY:
AMI reads the complete diagram, recognizes the paths and generates the molecules. Then she creates a stop-fram animation showing how the 12 reactions lead into each other
CLICK HERE FOR ANIMATION
(may be browser dependent)
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UNITS
TICKS
QUANTITYSCALE
TITLES
DATA!!2000+ points
VECTOR PDF
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Dumb PDF
CSV
SemanticSpectrum
2nd Derivative
Smoothing Gaussian Filter
Automaticextraction
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https://rawgit.com/ContentMine/amidemos/master/zika/full.dataTables.html
Search on publicly accessible papers on “Zika”
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C) What’s the problem with this spectrum?
Org. Lett., 2011, 13 (15), pp 4084–4087
Original thanks to ChemBark
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After AMI2 processing…..
… AMI2 has detected a square
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