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Re: HCLS Sci Discourse: no call tomorrow

From: Waard, Anita de A (ELS-AMS) <A.dewaard@elsevier.com>
Date: Sun, 8 May 2011 18:35:30 -0400
Message-ID: <874EE34C-FAAB-4B7B-87EC-7BF5A8EAE6B5@elsevier.com>
To: "Jodi Schneider" <jodi.schneider@deri.org>
Cc: "Michael Miller" <Michael.Miller@systemsbiology.org>, "M. Scott Marshall" <mscottmarshall@gmail.com>, "Alexander Garcia Castro" <alexgarciac@gmail.com>, "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>
Dear all, the next Sci Discourse call will be held Monday, May 16- details to follow. Best,

Anita de Waard


On May 8, 2011, at 9:50 AM, "Jodi Schneider" <jodi.schneider@deri.org> wrote:

> Thanks for this, Michael.
> 
> I've added it as context to our notes on these articles:
> http://www.w3.org/wiki/HCLSIG/SWANSIOC/Actions/RhetoricalStructure/meetings/20110502#1._BioRDF_Demonstrator:
> 
> Can you tell me where you searched for this data? I'm not very familiar with this domain.
> 
> -Jodi
> 
> On 4 May 2011, at 16:47, Michael Miller wrote:
> 
>> 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)
>>> 
>>> 
> 

Elsevier B.V. Registered Office: Radarweg 29, 1043 NX Amsterdam, The Netherlands, Registration No. 33156677 (The Netherlands)

Received on Sunday, 8 May 2011 22:42:07 GMT

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