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RE: HCLS Scientific Discourse Call Monday, May 2nd, 10 am EST - minutes

From: Michael Miller <Michael.Miller@systemsbiology.org>
Date: Wed, 4 May 2011 08:47:38 -0700
Message-ID: <b779c9e7127a7710738daea0f6e9ba03@mail.gmail.com>
To: "Waard, Anita de A (ELS-AMS)" <A.dewaard@elsevier.com>, "M. Scott Marshall" <mscottmarshall@gmail.com>
Cc: Alexander Garcia Castro <alexgarciac@gmail.com>, Jodi Schneider <jodi.schneider@deri.org>, barend mons <barend.mons@nbic.nl>, Tim Clark <tim_clark@harvard.edu>, HCLS IG <public-semweb-lifesci@w3.org>, Alberto Accomazzi <aaccomazzi@cfa.harvard.edu>, Sophia Ananiadou <Sophia.Ananiadou@manchester.ac.uk>, Philip Bourne <bourne@sdsc.edu>, Gully Burns <gully@usc.edu>, "Daniel, Ronald (ELS-SDG)" <R.Daniel@elsevier.com>, Rahul Dave <rahuldave@gmail.com>, Alf Eaton <A.Eaton@nature.com>, Matthew Gamble <matthew.gamble@gmail.com>, Yolanda Gil <gil@isi.edu>, Alyssa Goodman <agoodman@cfa.harvard.edu>, Paul Groth <pgroth@gmail.com>, Tudor Groza <tudor.groza@deri.org>, "Hays, Ellen (ELS-BUR)" <E.Hays@elsevier.com>, Maryann Martone <maryann@ncmir.ucsd.edu>, David R Newman <drn05r@ecs.soton.ac.uk>, "Scerri, Antony (ELS-CAM)" <A.scerri@elsevier.com>, Jack Park <jackpark@gmail.com>, Silvio Peroni <speroni@cs.unibo.it>, Steve Pettifer <steve.pettifer@manchester.ac.uk>, Philippe Rocca-Serra <proccaserra@googlemail.com>, Cartic Ramakrishnan <cartic@isi.edu>, RebholzSchuhmann <d.rebholz.schuhmann@gmail.com>, David Shotton <david.shotton@zoo.ox.ac.uk>, Kaitlin Thaney <k.thaney@digital-science.com>, Karin Verspoor <Karin.Verspoor@ucdenver.edu>, Lynette Hirschman <lynette@mitre.org>, Susanna-Assunta Sansone <sa.sansone@gmail.com>, Kees van Bochove <business@keesvanbochove.nl>, Katy Wolstencroft <katy@cs.man.ac.uk>, Jun Zhao <jun.zhao@zoo.ox.ac.uk>, Paul Groth <pgroth@few.vu.nl>, Marco Roos <M.Roos1@uva.nl>
hi all,

i did a quick search on the articles cited to find their associated data.
two of the articles (14 and 15) appear to be different takes on the same
data:

> [13] Dunckley T, Beach TG, et al.. (2006). Gene expression correlates
> of neurofibrillary tangles in Alzheimer's disease. Neurobiol
> Aging;27:1359-71. http://www.ncbi.nlm.nih.gov/pubmed/16242812
GEO: GSE4757 ArrayExpress: E-GEOD-4757

> [14] Liang WS, Dunckley T, et al.. (2007). Gene expression profiles in
> anatomically and functionally distinct regions of the normal aged human
> brain. Physiol Genomics 28: 311-22.
> http://www.ncbi.nlm.nih.gov/pubmed/18332434
GEO: GSE5281(same as below) ArrayExpress: N/A

> [15] Liang WS, Reiman EM, et al.. (2008). Alzheimer's disease is
> associated with reduced expression of energy metabolism genes in
> posterior cingulate neurons. Proc Natl Acad Sci U S A l2008;105: 4441-
> 6.
> http://www.ncbi.nlm.nih.gov/pubmed/17077275
GEO: GSE5281(same as above) ArrayExpress: N/A

cheers,
michael

> -----Original Message-----
> From: public-semweb-lifesci-request@w3.org [mailto:public-semweb-
> lifesci-request@w3.org] On Behalf Of Waard, Anita de A (ELS-AMS)
> Sent: Tuesday, May 03, 2011 1:46 PM
> To: M. Scott Marshall
> Cc: Alexander Garcia Castro; Jodi Schneider; barend mons; Tim Clark;
> HCLS IG; Alberto Accomazzi; Sophia Ananiadou; Philip Bourne; Gully
> Burns; Daniel, Ronald (ELS-SDG); Rahul Dave; Alf Eaton; Matthew Gamble;
> Yolanda Gil; Alyssa Goodman; Paul Groth; Tudor Groza; Hays, Ellen (ELS-
> BUR); Maryann Martone; David R Newman; Scerri, Antony (ELS-CAM); Jack
> Park; Silvio Peroni; Steve Pettifer; Philippe Rocca-Serra; Cartic
> Ramakrishnan; RebholzSchuhmann; David Shotton; Kaitlin Thaney; Karin
> Verspoor; Lynette Hirschman; Susanna-Assunta Sansone; Kees van Bochove;
> Katy Wolstencroft; Jun Zhao; Paul Groth; Marco Roos
> Subject: RE: HCLS Scientific Discourse Call Monday, May 2nd, 10 am EST
> - minutes
>
> Dear Scott, all:
>
> We had a most productive call yesterday, largely echoing your thoughts,
> below. Two points were covered: a discussion of the BioRDF
> demonstrator, and a proposal to make a joint demonstrator - see also
> http://www.w3.org/wiki/HCLSIG/SWANSIOC/Actions/RhetoricalStructure/meet
> ings/20110502.
>
> 1. BioRDF Demonstrator:
>
> BioRDF group: http://www.w3.org/wiki/HCLSIG_BioRDF_Subgroup)
> Demo: http://biordfmicroarray.googlecode.com/hg/sparql_endpoint.html)
> Annotated corpus with triples:
> http://biordfmicroarray.googlecode.com/hg/all3_genelists_provenance.ttl
>
> Corpus:
> [13] Dunckley T, Beach TG, et al.. (2006). Gene expression correlates
> of neurofibrillary tangles in Alzheimer's disease. Neurobiol
> Aging;27:1359-71. http://www.ncbi.nlm.nih.gov/pubmed/16242812
> [14] Liang WS, Dunckley T, et al.. (2007). Gene expression profiles in
> anatomically and functionally distinct regions of the normal aged human
> brain. Physiol Genomics 28: 311-22.
> http://www.ncbi.nlm.nih.gov/pubmed/18332434
> [15] Liang WS, Reiman EM, et al.. (2008). Alzheimer's disease is
> associated with reduced expression of energy metabolism genes in
> posterior cingulate neurons. Proc Natl Acad Sci U S A l2008;105: 4441-
> 6.
> http://www.ncbi.nlm.nih.gov/pubmed/17077275
>
> Need help to automate:
> 1) Institution provenance and PIs etc.
> 2) Experimental context: what platform (e.g. microarray experiments -
> what company etc); disease patients have; where in the brain samples
> were collected, how far along was the disease when the sample was
> collected.
> 3) From this: generate list of genes, need details of statistical
> methods, what was algorithm etc. and analysis provenance etc. and
> confidence in statistical results
>
> Current use case: cancer; previous use case: Alzheimers
>
> 2. BioRDF-Scientific Discourse Joint Demonstrator proposal
>
> The scientific discourse group (in particular: Jodi, Anita and Paolo)
> will mark up the corpus that the BioRDF group has worked on.
> We will mark up these documents with
> a) ORB
> b) Annotation Ontology
> within the Harvard Annotation Framework, and link the BioRDF triples to
> specific locations in the text.
>
> This serves three purposes:
> 1) It allows the Scientific Discourse group to test if ORB + AO is
> enough to mark a given location in the document. If so - that concludes
> the deliverables of the subtask; if not, we need and will define a
> 'medium-grained' ontology.
> 2) It provides the BioRDF group with more detailed, location-linked
> annotations to their test corpus 3) This can help them in their quest
> to automate the mining of these triples
>
> After this markup is done, the evaluations will be:
> 1) Is ORB + AO enough? Is the SciDisc/Rhetorical structure group done?
> 2) Can this be a useful start towards automating the knowledge the
> BioRDF group wants to automate?
>
> If anyone from either group is interested in participating in this
> exercise, please let us know.
>
>
> Best,
>
> - Anita.
>
> Anita de Waard
> Disruptive Technologies Director, Elsevier Labs
> http://elsatglabs.com/labs/anita/
> a.dewaard@elsevier.com
>
>
>
> -----Original Message-----
> From: M. Scott Marshall [mailto:mscottmarshall@gmail.com]
> Sent: Mon 5/2/2011 9:51
> To: Waard, Anita de A (ELS-AMS)
> Cc: Alexander Garcia Castro; Jodi Schneider; barend mons; Tim Clark;
> HCLS IG; Alberto Accomazzi; Sophia Ananiadou; Philip Bourne; Gully
> Burns; Daniel, Ronald (ELS-SDG); Rahul Dave; Alf Eaton; Matthew Gamble;
> Yolanda Gil; Alyssa Goodman; Paul Groth; Tudor Groza; Hays, Ellen (ELS-
> BUR); Maryann Martone; David R Newman; Scerri, Antony (ELS-CAM); Jack
> Park; Silvio Peroni; Steve Pettifer; Philippe Rocca-Serra; Cartic
> Ramakrishnan; RebholzSchuhmann; David Shotton; Kaitlin Thaney; Karin
> Verspoor; Lynette Hirschman; Susanna-Assunta Sansone; Kees van Bochove;
> Katy Wolstencroft; Jun Zhao; Paul Groth; Marco Roos
> Subject: Re: HCLS Scientific Discourse Call Monday, May 2nd, 10 am EST
> - the real invite
>
> Regrets - have a meeting during that time.
>
> Addressing overlap with other task forces: at last year's C-SHALS,
> Tim, Kei, and I noticed some overlap in the RDF representation of
> experiments and started teleconferences in which BioRDF and SciDisc
> (Sudeshna Das) could stay coordinated. We are continuing that work in
> the form of a W3C note about RDF for expression studies (i.e.
> microarrays but not necessarily excluding other forms of expression
> data). We are hoping to find common (stable) ground for the W3C note
> by comparing / contrasting a number of existing approaches. We have
> presented our approaches in BioRDF telcons and a 'Metadata Capture'
> meeting in the Netherlands organized by Kees van Bochove.
>
> About ways to further combine across the overlaps:
>
> I see a lot of potential to combine approaches from the task forces by
> putting together several common elements (that already exist to some
> extent):
>
> * representation of provenance for text-mined assertions
>
> * representation of microarray experiment results in RDF with
> provenance information about the RDF itself, in addition to experiment
> provenance and RDF representation of experiment metadata
>
> A) performing microarray analysis in a workflow
> B) performing text mining in a workflow
> C) linking microarray analysis results with literature (linking RDF
> output from A & B)
>
> The above (A - C) combines a microarray experiment with a
> computational experiment (in the form of a workflow in which the
> analysis is done), which makes it important to clearly delineate
> different types of provenance - that of the microarray experiment,
> that of the workflow, and that of the RDF production.
>
> Perhaps there's a way to use a medium granularity markup of the
> microarray study article to enhance the literature mining, or use it
> together with the results RDF somehow.
>
> BTW, if one considers a nanopublication as a sort of prescribed
> provenance for a particular type of data, then you could consider the
> gene list (or each gene on it) to be a nanopublication.
>
> Cheers,
> Scott
>
> P.S. I had the above combination of ideas in mind for my presentation
> to SciDisc. Sorry to blurt it out without being able to stick around
> to explain what I mean. Maybe at the next telcon.
>
> P.P.S. There is a EU project Workflow4ever that has some common
> interests in the above.
>
> --
> M. Scott Marshall, W3C HCLS IG co-chair, http://www.w3.org/blog/hcls
> http://staff.science.uva.nl/~marshall
>
> On Mon, May 2, 2011 at 2:41 PM, Waard, Anita de A (ELS-AMS)
> <A.dewaard@elsevier.com> wrote:
> > Apologies for my confusing mail this weekend: obviously I'm not quite
> ready to send real emails from my iPhone! The goal was to discuss our
> conclusions from the April 18th meeting, which I copied below, and look
> back on our use cases and the work from other HCLS subgroups.
> >
> > Please find an improved version below or at
> //www.w3.org/wiki/HCLSIG/SWANSIOC/Actions/RhetoricalStructure/meetings/
> 20110502.
> >
> > Best,
> >
> > - Anita.
> >
> > Anita de Waard
> > Disruptive Technologies Director, Elsevier Labs
> > http://elsatglabs.com/labs/anita/
> > a.dewaard@elsevier.com
> >
> >
> http://www.w3.org/wiki/HCLSIG/SWANSIOC/Actions/RhetoricalStructure/meet
> ings/20110502
> >
> > Please join the HCLS Scientific Discourse concall on Monday, May 2 10
> am EST, 3 pm BST, 7 am Pacific
> >
> > Agenda:
> >
> > 1) Timeframe and names for plans below
> > 2) How close are we to fulfilling our original use cases?
> (http://www.w3.org/wiki/HCLSIG/SWANSIOC/Actions/RhetoricalStructure/)
> > 3) Overlap with other HCLS subgroups (see
> http://www.w3.org/wiki/HCLSIG for a listing)
> > 4) Next steps.
> >
> > Conclusions meeting April 18:
> >
> > 1) Joint work on annotation a corpus of documents with links to
> workflow components and data. This will allow a concrete instantiation
> of the medium-grained ontology, and offer a discussion point for
> describing the experiment/paper link which we are approaching from many
> different sides. Alex Garcia will jumpstart this process by making a
> collection of full-text Elsevier documents available which he has
> annotated with RDF; after seeing these, we will select a subcorpus to
> mark up a) Data b) Experimental model c) Key discourse components from,
> and work to make a demonstrator.
> >
> > 2) A paper. Discussing our various models, and ways to integrate;
> include discussion re. overlap/difference between (explicit, personal)
> knowledge in discourse and (implicit, shared) knowledge that underlies
> experimental models. Could be possible outcome of demo.
> >
> > 3) A face-to-face meeting. Kees van Bochove has kindly agreed to
> organise this. Possible venues: ISMB in Vienna, ICBO in Buffalo, or a
> one-off workshop in the Netherlands. Topic: Experiment/discourse
> integration: models, examples, and next steps.
> >
> >
> > Dial-in & IRC Information
> >
> >    * Dial-In #: +1.617.761.6200 (Cambridge, MA)
> >    * Dial-In #: +33.4.26.46.79.03 (Paris, France)
> >    * Dial-In #: +44.203.318.0479 (London, UK)
> >    * Participant Access Code: 42572 ("HCLS2")
> >    * IRC Channel: irc.w3.org port 6665 channel #HCLS2 use IRC direct
> link or (see W3C IRC page for details, or see Web IRC)
> >    * Mibbit quick start: Click on mibbit for instant IRC access
> >    * Duration: 1hr
> > Elsevier B.V. Registered Office: Radarweg 29, 1043 NX Amsterdam, The
> Netherlands, Registration No. 33156677 (The Netherlands)
> >
> >
>
>
> Elsevier B.V. Registered Office: Radarweg 29, 1043 NX Amsterdam, The
> Netherlands, Registration No. 33156677 (The Netherlands)
>
>
Received on Wednesday, 4 May 2011 15:48:09 GMT

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