I am online so skype if required.<br><br>The initial video has shown both Carl and OREChem and also PMR and Word2007...<br><br><br><br><div class="gmail_quote">On Mon, Jul 13, 2009 at 3:02 PM, WILLIAM J BROUWER <span dir="ltr"><<a href="mailto:wjb19@psu.edu">wjb19@psu.edu</a>></span> wrote:<br>
<blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div>Thanks Peter, that makes things very clear for Mark/I<br><br>If someone
could get us access to the requisite document collection to batch &
properly test our codes,<br>that's all we need
</div></blockquote><div><br>We'll set up a test harness for each step. I'll look to Nick to advise on the PDFAtom feed and that should set the scene for the others.<br><br>Talked to Alex at breakfast and he should have set the scene on this. I have suggested we have a working pipeline by mid-august so we should have the Atom feed formats formalised in the next week. <br>
<br>P.<br></div><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;"><div><br><br>cheers,<br>bill<div class="im"><br><br>On Mon, Jul 13, 2009 09:43 AM, <b>Peter
Murray-Rust <<a href="mailto:pm286@cam.ac.uk" target="_blank">pm286@cam.ac.uk</a>></b> wrote:<br></div><blockquote style="border-left: 1px solid rgb(0, 0, 0); padding-left: 3px; padding-right: 0px; margin-left: 3px; margin-right: 0px;">
<span><span><div class="im"><p>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:<br><br>(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.<br><br>(b) HT computation of the literature.<br><br>The overall scheme
is:<br>1. scrape the supplemental data from chemistry papers and expose the
PDFs as an Atom Feed. <br>2. ingest this feed and extract the molecules and
spectra and expose as SVG Atom feed<br>
3. ingest SVGAtom and transform tp CMLAtom<br>4. ingest CMLAtom, compute
properties and expose enhanced CMLAtom+<br>5. ingest CMLAtom+ and transform to
RDFAtom (this step is tentative)<br><br>(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)<br><br>(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<br><br>(3) Cambridge. (i) test
ingestion of SVGAtom (ii) build Lensfield workflow (iii) provide CMLAtom
feed<br><br>(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+ <br><br>(5) to be discussed.<br><br>I
think the most challenging step is 2<br><br>If I am not there I may still have
Skypechat or Googlechat
active<br><br>P.<br><br><br><br><br><br><br><br><br><br></p>
</div><div class="gmail_quote"><div class="im">On Fri, Jul 10, 2009 at 9:20 PM, Carl Lagoze <span dir=""><<a href="#122746ca666b0004_">clagoze@gmail.com</a>></span> wrote:<br></div><div><div></div><div class="h5"><blockquote class="gmail_quote" style="border-left: 1px solid rgb(204, 204, 204); margin: 0pt 0pt 0pt 0.8ex; padding-left: 1ex;">
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?<br><br>
Here is the agenda for the call:<br><br>
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.<br><br>
2. Discussion of Indiana work in cooperation with Cambridge and Penn State.
Marlon, can you please be prepared to present this.<br><br>
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.<br><br>
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?<br><br>
Talk to you all day, have a great weekend.<br><br>
Carl<br><br>
PS. A number of you never answered the call scheduling doodle. Please join the
call if you can.<br><br>
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</blockquote>
</div></div></div>
<br><br clear="all"><br><div class="im">-- <br>Peter Murray-Rust<br>Reader in Molecular Informatics<br>Unilever Centre, Dep. Of Chemistry<br>University of Cambridge<br>CB2 1EW, UK<br>+44-1223-763069<br></div></span></span>
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</div></pre></blockquote><br><br><br></div>
</blockquote></div><br><br clear="all"><br>-- <br>Peter Murray-Rust<br>Reader in Molecular Informatics<br>Unilever Centre, Dep. Of Chemistry<br>University of Cambridge<br>CB2 1EW, UK<br>+44-1223-763069<br>