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notes from our DRO discussion last week

From: Jodi Schneider <jodi.schneider@deri.org>
Date: Mon, 13 Dec 2010 02:56:59 +0000
To: Tim Clark <tim_clark@harvard.edu>, HCLS IG <public-semweb-lifesci@w3.org>, David Shotton <david.shotton@zoo.ox.ac.uk>, Paolo Ciccarese <paolo.ciccarese@gmail.com>, "M. Scott Scott Marshall" <mscottmarshall@gmail.com>, John Madden <john.madden@duke.edu>, Alberto Accomazzi <aaccomazzi@cfa.harvard.edu>, Sophia Ananiadou <Sophia.Ananiadou@manchester.ac.uk>, Gully Burns <gully@usc.edu>, "Ronald (ELS-SDG) Daniel" <R.Daniel@elsevier.com>, Rahul Dave <rahuldave@gmail.com>, Anita de Waard <A.dewaard@elsevier.com>, Alf Eaton <A.Eaton@nature.com>, Alyssa Goodman <agoodman@cfa.harvard.edu>, Paul Groth <pgroth@gmail.com>, Tudor Groza <tudor.groza@deri.org>, ellen hays <E.Hays@elsevier.com>, "Antony (ELS-CAM) Scerri" <A.scerri@elsevier.com>, Jack Park <jackpark@gmail.com>, Silvio Peroni <speroni@cs.unibo.it>, Philippe Rocca-Serra <proccaserra@googlemail.com>, Karin Verspoor <Karin.Verspoor@ucdenver.edu>, Lynette Hirschman <lynette@mitre.org>, Susanna-Assunta Sansone <sansone@ebi.ac.uk>, Jun Zhao <jun.zhao@zoo.ox.ac.uk>, "Joanne Luciano (gmail)" <jluciano@gmail.com>, Sudeshna Das <sudeshna_das@harvard.edu>, David R Newman <drn05r@ecs.soton.ac.uk>, Alexander Garcia Castro <alexgarciac@gmail.com>
Message-Id: <4E543353-E030-45C7-B3EC-0B0B205623DE@deri.org>
Here are my notes from last Tuesday's DRO (middle-grained rhetorical structure) discussion. I've put them on the wiki -- please feel free to add to or amend them:

Sudesna & I will talk about DEXI Tuesday -- the current version of DEXI is at

My regrets for our larger conference call--Monday I'm in a meeting and just found out that my talk will be during our conference call slot.


Notes from the DRO discussion 2010-12-07
Tim Clark, Silvio Peroni, Jodi Schneider, David Shotton, Anita de Waard. (Alexander Garcia Castro -- unfortunately with line trouble)
Anita gave a little history about the middle-grained ontology project, which we're calling DRO.

We then discussed ORB, which consists of 5 disjoint classes: Header Introduction Methods Discussion References Some discussion concerned its alignment with external ontologies and structure, which we passed on to Tim to convey (and has since been discussed on the email list).

We then discussed DeXI, which is subset of OBI+MyExperiment+SWAN, under development by Sudeshna Das and others. We've since learned that the current version is at http://swan-ontology.googlecode.com/svn/trunk/experiments.owl

Tim explained that they're starting with genomic lab experiments and observational population studies. Covers experimental hypotheses, design, factors (similar to DRO's objects of study), characteristics of the biomaterial. While it's still missing a few concepts from the computational side, it already gives the ability to take an experimental finding in a paper and map it to the things you could export from arrayExpress (a public repository for microarray gene expression data, "genBank for arrays").

We next discussed DoCO. David Shotton explained that its goal is to republish documents and metadata as open Linked Data, starting with documents in the NLM DTD, to support the Open Bibliographic Project. There was some skepticism regarding converting a DTD into RDF. Smaller publishers are interested in using this; larger publishers have little incentive to change DTDs and have established workflows around custom formats used for a great variety of structures (not just research articles but also books, etc).

	 Tim will ping Paolo about the ORB write-up for a W3C note
	 Anita will share Ron Daniel's email about aligning the ORB Header with OAI, PRISM, DC, ...
	 Tim to put Jodi in touch with Sudeshna Das regarding DeXI
	 Tim to take feedback about ORB to Paolo and Tudor (e.g. referencing Head and References externally, Tail, )
Received on Monday, 13 December 2010 02:57:36 UTC

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