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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