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

[Peter Murray-Rust]

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.









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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