[Orechem] Phone call Monday, July 13 noon Eastern US time

[Carl Lagoze]

Who can get this for Bill?
On Jul 13, 2009, at 10:02 AM, WILLIAM J BROUWER wrote:

> Thanks Peter, that makes things very clear for Mark/I
>
> If someone could get us access to the requisite document collection  
> to batch & properly test our codes,
> that's all we need
>
> cheers,
> bill
>
> On Mon, Jul 13, 2009 09:43 AM, Peter Murray-Rust <pm286 at cam.ac.uk>  
> wrote:
> I am not sure whether Alex and/or I can get out of the meeting at  
> 0900. I am in Alex's hands. My input:
>
> (a) ontologies. As we go through the computational workflow we are  
> building the basis of an ontology for compchem and for Gaussian.  
> This will be empirical at first but is designed to link into the  
> workflow and be compatible with ChemAxiom. We have a student on  
> another project who may be able to help systematize the material we  
> collect and test it out.
>
> (b) HT computation of the literature.
>
> The overall scheme is:
> 1. scrape the supplemental data from chemistry papers and expose the  
> PDFs as an Atom Feed.
> 2. ingest this feed and extract the molecules and spectra and expose  
> as SVG Atom feed
> 3. ingest SVGAtom and transform tp CMLAtom
> 4. ingest CMLAtom, compute properties and expose enhanced CMLAtom+
> 5. ingest CMLAtom+ and transform to RDFAtom (this step is tentative)
>
> (1). Currently Nick Day is doing this for supp data ACTION: Nick to  
> provide simple example of PDFAtom feed. (Later we expect similar  
> from Lee+P for fulltext)
>
> (2). Bill and Mark own this step. ACTION: (i) To test ingestion of  
> PDFAtom.  (ii) to produce example of SVGAtom output (iii) to  
> implement workflow
>
> (3) Cambridge. (i) test ingestion of SVGAtom (ii) build Lensfield  
> workflow (iii) provide CMLAtom feed
>
> (4)Marlon with help from Cambridge (i) ingest CMLAtom feed (ii)  
> install Lensfield for gaussian calculations (iii) create process for  
> submitting and retrieving jobs (iv) expose CMLAtom+
>
> (5) to be discussed.
>
> I think the most challenging step is 2
>
> If I am not there I may still have Skypechat or Googlechat active
>
> P.
>
>
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>
> On Fri, Jul 10, 2009 at 9:20 PM, Carl Lagoze <clagoze at gmail.com>  
> wrote:
> As previously announced we had a phone call scheduled for noon on  
> July 13 Eastern US time. Alex, can you please give us a conference  
> call number?
>
> Here is the agenda for the call:
>
> 1. Discussion of ontologies. Please review the information that has  
> been put up on the wiki. The writer of each wiki page should be  
> prepared to do a short presentation of what they have put up.
>
> 2. Discussion of Indiana work in cooperation with Cambridge and Penn  
> State. Marlon, can you please be prepared to present this.
>
> 3. Discussion what we should propose for a presentation at the  
> October Microsoft eScience conference in Pittsburgh. I am happy to  
> write up a proposal but I think the topic should be something that  
> we jointly develop.
>
> 4. Alternatives for our next face-to-face meeting. The obvious one  
> is in connection with the Pittsburgh conference, but we need to  
> discuss this. Previously we had spoken about something in the UK,  
> perhaps for December?
>
> Talk to you all day, have a great weekend.
>
> Carl
>
> PS. A number of you never answered the call scheduling doodle.  
> Please join the call if you can.
>
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>
>
> -- 
> 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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>

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