[Orechem] Re: Some new things to look at - please read completely

[Carl Lagoze]

Hi all:

The response to request for responses via the doodle link at http://www.doodle.com/a9w2r3u3xw8zah5d 
  has been quite underwhelming (zero)!  Can people please follow  
through on this so we can have a productive meeting in December.

Carl
On Oct 28, 2009, at 10:22 AM, Carl Lagoze wrote:

> Hi all,
>
> At our recent meeting in Pittsburgh is a few action items to be  
> completed by last Friday. I missed that deadline, my apologies, but  
> here they are.
>
> First, I have put two new pages up on the wiki accessible from the  
> front page. One is to list presentations relevant to the project and  
> the other to list papers. I have also created corresponding places  
> in our SVN repository for these items. This repository is located at http://services.nsdl.org/svn/oreChem/ 
>  and now contains three directories; meeting materials,  
> presentations, and papers. This repository should be read write  
> accessible by all of you. After storing your materials here you can  
> then link to them from the appropriate wiki pages. I have uploaded a  
> number of presentations and papers from recent meetings, workshops,  
> and conferences. For example, in the papers wiki page I have linked  
> to papers submitted to the recent Web science and Microsoft eScience  
> conferences, and a link to copies of the eChemistry workshop white  
> paper and upcoming nature chemistry article on that white paper.  
> Please note, that copies of papers stored on these internal project  
> pages are not public and should be distributed only with the members  
> of the project.
>
> Second, I had promised to do some design work on our information  
> transfer format. This work is now written up at http://services.nsdl.org/trac/oreChem/wiki/DocumentOntology#Atomizingdocumentontologyinstances 
> .   Briefly summarizing, I have put together an OAI ore-based atom  
> encoding for the document information that we extract from documents  
> and then pass along to subsequent partners. It is based on the  
> workflow that we discussed at our meeting whereby Penn State  
> analyzes a raw document, extracts bibliographic and other data,  
> encodes that as an OAI ORE aggregation and resource map and then  
> makes it available via atom to Southhampton who extracts additional  
> information and enhances the aggregation resource map, passes out on  
> to Cambridge, etc. Following the suggestion of Jim Downing, I  
> believe this all should be done using the atom feed paging and  
> archiving technique outlined in RFC 5005 (http://www.ietf.org/rfc/rfc5005.txt 
> ). This workflow is illustrated in slide 17 of the slides accessible  
> at ms escience 2009.pptx.
>
> It's critically important that we converge on this (or some other)  
> transfer format and resolve the few open issues that I list as soon  
> as possible. Therefore, I would like each group to assign one person  
> to look at the format, evaluate whether it is sensible and whether  
> it fulfills our needs, and determined whether they can implement it  
> so we can get experiments running as soon as possible (e.g. before  
> our December meeting). I have put up a doodle page at http://www.doodle.com/a9w2r3u3xw8zah5d 
>  to schedule a meeting amongst the people who will do this  
> evaluation, I will of course be on that phone call. Again, this  
> phone call is only for the individuals in each group will be doing  
> this evaluation and possibly the development of the code to  
> implement it.
>
> I'd like to emphasize again that it is very important that we move  
> forward with this and implement it as soon as possible so we can  
> move on from our data collection and extraction process to  
> application development upon the triples that we will store.
>
>  Finally, I'd like to remind you of our next all group meeting in  
> London on December 5 and sixth. I will be getting back to you in the  
> near future with logistics and will schedule a phone call a week or  
> two before that meeting amongst all of us.
>
> I still need to get the notes up from the previous meeting, but  
> considered this stuff first priority.
>
> Thanks, Carl

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