[Orechem] High-throughput semantic computation in OREChem

[Peter Murray-Rust]

This is to review the subprojects that the computational geeks in OREChem
have put together over the last few days. (a) is long term, (b) is immediate
(a) The general goal is to compute NMR spectra for all new published
compounds and compare them with spectra. This is a new approach "robot
refereeing of chemistry publications" and any differences suggest errors or
new chemistry. This is long term (months) and consists of the following (as
we have put on the wiki):
* PSU-Lee/Prasenjit retrieve chemistry-rich docs from publisher sites (ask
for forgiveness policy) and segment the papers into text+non-text (tables,
diagrams). This passes to:
* Mark - Soton extracts molecules and spectra out of this and converts them
to SVG. The short-term goal is to get this working by the end of next week
in a pragmatic form. (we do not mind if recall is poor as long as we get a
few SVGs as we need to develop the machine-learning and/or heuristics and
find out what unknown horrors we have to deal with.
Bitmaps are rejected at this stage
* PMR- cambridge develops heuristics to interpret (i) molecules (ii) spectra
(C13 and H1). These might later be crowdsourced. The output is CML molecules
and spectra. It is unlikely we have assignments
* PSU - Bill+Karl. Analyse spectra with peak-fitting.
* IU - Marlon. (independently) molecules are passed to IU in CML and put
into the NMREye workflow for computing peaks (below). IU run this
automatically and return results in CML

(b) To get IU up to speed we shall start immediately on simple molecules
from Pubchem. This involves just Cambridge and IU.
* The NMREye workflow has been developed and tested and should work on
simple organic compounds. It consists of the following:
  - convert PubchemXML2CML (already available in JUMBO)
  - convert CML to Gaussian input. We have an XSLT script, but could convert
this to Java in an hour.
  - in parallel - create RDF metadata for provenance to this point (as this
does not survive the Gaussian run)
  ... submit and run job ... (IU) ... and collect results
 - convert LOG file to CML (JUMBOMarker, effectively done)
 - convert CML to RDF (JUMBO). Add GaussianOWL dictionary in RDF

upload RDFs into reopository/tripleStore

In (b) we would expect to get 10,000 - 100,000 small molecules from Pubchem
of up to, say , 15 first row atoms. These already have 3D coordinates (I am
ignoring conformers at this stage). The process should be automatic. Jobs
take from 0.1 seconds to 1 day (probably) as they scale with N^4.

P.

I will try to send this to the Wiki


-- 
Peter Murray-Rust
Reader in Molecular Informatics
Unilever Centre, Dep. Of Chemistry
University of Cambridge
CB2 1EW, UK
+44-1223-763069
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