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

From: Jodi Schneider <jodi.schneider@deri.org>
Date: Sun, 8 May 2011 14:50:40 +0100
Cc: "Waard, Anita de A (ELS-AMS)" <A.dewaard@elsevier.com>, "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>
Message-Id: <39A6FD80-3271-44EC-8AF1-E57FD85A0419@deri.org>
To: Michael Miller <Michael.Miller@systemsbiology.org>
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)
>> 
>> 
Received on Sunday, 8 May 2011 13:50:52 GMT

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