[Orechem] Re: High-throughput semantic computation in OREChem

[WILLIAM J BROUWER]

cool peter...

I would also add that there's some mileage in substructure & similarity search
on spectra. Han gave a great talk this morning, there is strong application of
his graph mining work to building up complicated spectra on the basis of
simpler (sub)spectra...

-bill 


On Fri, Jun 12, 2009 10:31 AM, Peter Murray-Rust <pm286 at cam.ac.uk> wrote:
>
>
>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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