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Re: HCLS Scientific Discourse Call Monday, 11 April 2011 10 am EST, 3 PM BST: talk by Jodi Schneider

From: M. Scott Marshall <mscottmarshall@gmail.com>
Date: Mon, 2 May 2011 15:10:37 +0200
Message-ID: <BANLkTikedXBgg_c9PaaZF0WcYmaBPk7DiQ@mail.gmail.com>
To: Jodi Schneider <jodi.schneider@deri.org>
Cc: Helena Deus <helenadeus@gmail.com>, "Anita de A (ELS-AMS) Waard" <A.dewaard@elsevier.com>, Kees van Bochove <business@keesvanbochove.nl>, HCLS <public-semweb-lifesci@w3.org>
Hi Jodi,

Did you get all the material that you need from Lena? In principle,
you can go to the the PubMed articles that we used and choose one.

The Pubmed links for the following can be found at (first three):

The data was used to create the demo RDF at a SPARQL endpoint. Diagram
and explanation here:

and to write the paper at:

[13] Dunckley T, Beach TG, et al.. (2006). Gene expression correlates of
neurofibrillary tangles in Alzheimer's disease. Neurobiol Aging;27:

[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.

[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.

As far as what kind of markup Kees is planning, I am not sure that I
understand the question. Do you mean for the Generic Study Capture
Framework (GSCF)? CC'ing Kees.


M. Scott Marshall, W3C HCLS IG co-chair, http://www.w3.org/blog/hcls

On Wed, Apr 20, 2011 at 1:25 PM, Jodi Schneider <jodi.schneider@deri.org> wrote:
> Hi Scott,
> From Lena & my discussion yesterday, it sounds like the BioRDF task has just what the middle-grained ontology task needs at the moment:
> - a corpus that has already undergone significant scientific analysis
> - which gets at the goal of generating hypotheses
> - and which needs further analysis of rhetorical structure in order to get there.
> I'd like to get the corpus and markup, as well as to understand what rhetorical analysis seems to be needed at this point.
> In other thoughts--publishing RDF nanopublications from the ConceptWiki is a good idea. I also remember that from the Beyond the PDF meeting in January, we discussed that we'd use whatever came out of the meeting to markup/publish/etc our publications this year; I'm also not sure what's come of that... What kind of markup is Kees planning?
> On 19 Apr 2011, at 22:39, M. Scott Marshall wrote:
>> Hi Lena, Jodi,
>> Curious what came out of your conversation. I spoke to Kees van
>> Bochove and Barend Mons today. Kees told me a little about the demo
>> ambitions - markup an entire article - sounds ambitious. I curious if
>> anyone remembers my suggestion back in December to take assertions
>> from the ConceptWiki, create nanopublications, then publish them in
>> RDF.
>> I was stuck in a 'wireless free zone' at a Dutch Bioinformatics
>> Conference - well, Ewan Birney (EMBL) was giving his keynote around
>> that time.
> No worries -- I wasn't expecting you, just keeping you in the loop!
> -Jodi
>> Cheers,
>> Scott
>> On Tue, Apr 19, 2011 at 1:26 PM, Jodi Schneider <jodi.schneider@deri.org> wrote:
>>> Great, let's talk around 5! :) -Jodi
>>> On 19 Apr 2011, at 12:16, Helena Deus wrote:
>>>> Hi Jodi,
>>>> I regret missing your talk, it seems †that you are †doing some work closely
>>>> related to mine, in particular the part about describing experiments,
>>>> something that we are also struggling with at the BioRDF weekly calls :-)
>>>> We are currently taking a bottom up approach of going from a list to genes
>>>> reported in a microarray experiment paper up to the description about the
>>>> experiment. We are trying to expand on the work that we started here -
>>>> http://people.csail.mit.edu/pcm/tempISWC/workshops/SWPM2010/InvitedPaper_6.p
>>>> df, demo here -
>>>> http://biordfmicroarray.googlecode.com/hg/sparql_endpoint.html;
>>>> A bit of background: lists of genes are commonly generated from microarray
>>>> experiments designed to understand a certain disease. A list of 100 genes
>>>> cannot be used to generate hypothesis because it simply is too big. Having
>>>> that list of genes as RDF would be great to help decrease the list of genes
>>>> to a "workable" number by linking those genes to available information about
>>>> genetic pathways, known genetic diseases, etc.
>>>> But a critical factor in reusing such lists of genes is the provenance or
>>>> contextual information , usually the description of the experiments
>>>> themselves, which we often have to painfully assemble from the
>>>> publications... For example, we want the information about the list of genes
>>>> to be reliable by cross comparing multiple experiments of the same type
>>>> (e.g. same disease, same organism, same organ where samples were collected).
>>>> Also, it is very important to represent the statistical information about
>>>> the generation of the list of genes, which we also must collect from the
>>>> paper.
>>>> Would you have time to talk a bit this afternoon?
>>>> ( Adding Scott to the conversation as he is probably paying attention to
>>>> both sides already anyway :-) )
>>>> Cheers,
>>>> Lena
>>>> -----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: 17 April 2011 21:57
>>>> To: Alexander Garcia Castro; Jodi Schneider
>>>> Cc: barend mons; M. Scott Marshall; 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
>>>> Subject: RE: HCLS Scientific Discourse Call Monday, 11 April 2011 10 am EST,
>>>> 3 PM BST: talk by Jodi Schneider
>>>> Dear all,
>>>> Jodi's talk last week seemed to spur on a great amount of discussion, and
>>>> this week, as we don't have a speaker, I would like to spend our time about
>>>> the issues Jodi's talk brought up. These include:
>>>> - Alex's points below - links between the paper and workflow and
>>>> experimental ontologies;
>>>> - The connection (and if there is one) between
>>>> nanopublications/triples/research highlights (will explain on the call) and
>>>> medium-grained structure
>>>> - Uses for medium-grained structure mark up: what would be a good set of use
>>>> cases? Can we find some concrete projects to work on?
>>>> - An issue that has been discussed on a few calls now which we can also
>>>> discuss is the difference between data, author's intent, persuasive
>>>> structure and nanopublication-type summaries.
>>>> - A point that Joanne raised: can we plan a meeting to discuss this stuff in
>>>> person?
>>>> I am sure much more will come up, once we start talking. Feel free to send
>>>> around more questions before the call, so we have a list of them to consider
>>>> before we start.
>>>> Thanks, and look forward to talking to you tomorrow,
>>>> Best,
>>>> - Anita.
>>>> Anita de Waard
>>>> Disruptive Technologies Director, Elsevier Labs
>>>> http://elsatglabs.com/labs/anita/ a.dewaard@elsevier.com
>>>> -----Original Message-----
>>>> From: public-semweb-lifesci-request@w3.org on behalf of Alexander Garcia
>>>> Castro
>>>> Sent: Mon 4/11/2011 11:25
>>>> To: Jodi Schneider
>>>> Cc:...
>>>> Hi Jodi, nice talk.
>>>> As a general question, shouldn't the description of †experiments be
>>>> something to be described by domain specific ontologies? Also, there are
>>>> repositories for experiments, e.g †Array express for microarrays; there are
>>>> also minimal standards for reporting several experimental procedures,
>>>> shouldn't the sections in the document make use of, pointing to, these
>>>> resources? if ORB and other document related ontologies go into describing
>>>> experimental information I am afraid it may be difficult to maintain and not
>>>> very practical to implement.
>>>> fine-graining ORB should, in my opinion, make use of other ontologies for
>>>> addressing domain specific issues. for instance, if a researcher wants to go
>>>> deeper into materials and methods most likely the information that will
>>>> allow him/her to "replicate" the experiment will be living somewhere else in
>>>> the web; also, most likely there will be an ontology for specific
>>>> experimental procedures, measures, etc involved.
>>>> Once the structure of the document is solved it is easy to use resources
>>>> such as bio2rdf to resolve it against existing resources in the web. if not,
>>>> then authors can easily point to these external resources -AO can easily
>>>> deal with such a use case. my point is, experimental information is highly
>>>> domain specific and there are now ontologies (OBI) and repositories for
>>>> experimental information as well as efforts for standardizing minimal
>>>> amounts of information (http://www.mibbi.org/index.php/Main_Page) for
>>>> reporting specific experimental procedures, shouldn't the fine grained
>>>> structure of ORB †seek to make use of these resources?
>>>> On Mon, Apr 11, 2011 at 8:09 AM, Jodi Schneider
>>>> <jodi.schneider@deri.org>wrote:
>>>>> Looking forward to talking with you in about an hour.
>>>>> Here are slides for discussion -- about the overall goal of bridging
>>>>> between ORB and the fine-grained ontology with a middle-grained ontology.
>>>>> The other two PDFs show
>>>>> (1) the relationship between ORB and Anita's middle-grained ontology
>>>>> and
>>>>> (2) a first attempt to bridge between DExI (top-level) and Anita's
>>>>> middle-grained ontology.
>>>>> -Jodi
>>>>> On 10 Apr 2011, at 19:38, Waard, Anita de A (ELS-AMS) wrote:
>>>>>> Dear all,
>>>>>> Monday's scientific discourse call will focus on an update of the
>>>>> medium-grained ontology alignment by Jodi Schneider: see agenda and
>>>>> call details below, or at
>>>>> http://www.w3.org/wiki/HCLSIG/SWANSIOC/Actions/RhetoricalStructure/mee
>>>>> tings/20110411
>>>>>> Kind regards,
>>>>>> Anita
>>>>>> Anita de Waard
>>>>>> Disruptive Technologies Director, Elsevier Labs
>>>>>> http://elsatglabs.com/labs/anita/ a.dewaard@elsevier.com
>>>>>> Meeting April 11, 2011, 10 am EST, 3 pm BST, 4 pm CET [edit] Agenda:
>>>>>> † * Jodi Schneider: 'Medium-grained ontology and alignment'
>>>>>> † * Status of ontology development
>>>>>> † * AOB
>>>>>> [edit] Dial-in & IRC Information
>>>>>> † * Dial-In #: +1.617.761.6200 (Cambridge, MA)
>>>>>> † * Dial-In #: + (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)
>>>> --
>>>> Alexander Garcia
>>>> http://www.alexandergarcia.name/
>>>> http://www.usefilm.com/photographer/75943.html
>>>> http://www.linkedin.com/in/alexgarciac
>>>> Postal address:
>>>> Alexander Garcia, Tel.: +49 421 218 64211 Universitšt Bremen
>>>> Enrique-Schmidt-Str. 5
>>>> D-28359 Bremen
>>>> Elsevier B.V. Registered Office: Radarweg 29, 1043 NX Amsterdam, The
>>>> Netherlands, Registration No. 33156677 (The Netherlands)
>> --
>> M. Scott Marshall, W3C HCLS IG co-chair, http://www.w3.org/blog/hcls
>> http://staff.science.uva.nl/~marshall
Received on Monday, 2 May 2011 13:11:05 UTC

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