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Re: BioRDF Telcon

From: mdmiller <mdmiller53@comcast.net>
Date: Fri, 4 Dec 2009 06:39:36 -0800
Message-ID: <409D2B6EF5224A81AC59A519C9B863CB@mmPC>
To: "Satya Sahoo" <sahoo.2@wright.edu>, "Helena Deus" <helenadeus@gmail.com>
Cc: "Kei Cheung" <kei.cheung@yale.edu>, "HCLS" <public-semweb-lifesci@w3.org>
hi satya,

my apologies, my strength is as a developer not a molecular biologist so an expert would be better.  but one interesting thing i did pick up is that there are often higher level analysis that are done simply to find out if there is some statistical interesting phenomena in the data which doesn't actual tell what that might be, it then takes further analysis.  i think an example of this is Anova.  these might not be recorded anywhere but the HLA that did help produce the actual gene list should be somewhere.

"2. BioSource: ontology term-http://mged.sourceforge.net/ontologies/MGEDOntology.owl#BioSource
   Examples: entorhinal cortex (EC control 1, EC_affected_4), hippocampus (HIP control 13), medial temporal gyrus (MTG control 11), posterior cingulate (PC control 1, PC control 4), primary visual cortex (VCX control 6), posterior cingulate cortex (PC_affected_7)"

so my follow-up email suggests treating these as individual instances of BioSource since in this context "entorhinal cortex (EC control 1, EC_affected_4)" doesn't refer to the abstract concept but the actual physical specimen removed from a body.

cheers,
michael
  ----- Original Message ----- 
  From: Satya Sahoo 
  To: mdmiller ; Helena Deus 
  Cc: Kei Cheung ; HCLS 
  Sent: Tuesday, December 01, 2009 12:36 PM
  Subject: Re: BioRDF Telcon


  Hi all,
  michael wrote:
  > what is usually missing from those documents, along with the final gene list, is how that gene list was obtained, what higher level analysis was used, that is generally only in the paper unfortunately.

  Could you list some specific terms that describe "how gene list was obtained" and "higher level of analysis"? - we can include these in the list of provenance terms I am compiling to describe the experiment context. An initial list of provenance terms from a MAGE-ML file [1] is located at [2].

  lena: I am trying to get edit rights for the wiki pages (I believe my username "SatyaSahoo" needs to be added to a list according to the new W3C wiki policy). I will send out an update and link once I get access.

  Best,
  satya

  Kno.e.sis center, WSU
  http://knoesis.wright.edu/researchers/satya

  [1] http://np2.ctrl.ucla.edu/np2/mage/mageml.jsp
  [2]  http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2?action=AttachFile&do=get&target=NeuroscienceMicroarrayConsortium_ProvenanceTerms.txt



  > On Tue, Nov 24, 2009 at 9:59 AM, mdmiller 
  <mdmiller53@comcast.net <mailto:mdmiller53@comcast.net> wrote:
   >
   >     hi all,
   >
   >     (from the minutes)
   >
   >     "Yolanda/Kei/Scott: semantic annotation/description 
  of workflow
   >     would enable the retrieval of data relevant to that 
  workflow (i.e..
   >     data that could be used to populate that workflow for 
  a different
   >     experimental scenario)"
   >
   >     what is typically in a MAGE-TAB/MAGE-ML document are 
  the protocols
   >     for how the source was processed into the extract 
  then how the
   >     hybridization, feature extraction, error and 
  normalization were
   >     performed.  these are interesting and different 
  protocols can
   >     cause differences at this level but it is pretty much 
  a known art
   >     and usually not of too much interest or variability.
   >
   >     what is usually missing from those documents, along 
  with the final
   >     gene list, is how that gene list was obtained, what 
  higher level
   >     analysis was used, that is generally only in the 
  paper unfortunately.
   >
   >     cheers,
   >     michael
   >     .
  > >     ----- Original Message ----- From: "Kei Cheung"
  > >
  > >     <kei.cheung@yale.edu <mailto:kei.cheung@yale.edu>>
  > >     To: "HCLS" <public-semweb-lifesci@w3.org
  > >
  > >     <mailto:public-semweb-lifesci@w3.org>>
  > >     Sent: Monday, November 23, 2009 1:27 PM
  > >     Subject: Re: BioRDF Telcon
  > >
  > >
  > >
  > >         Today's BioRDF minutes are available at the following:
  > >
  > >        
  >  http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2009/11-23_Conference_Call
  > >
  > >         Thanks to Rob for scribing.
  > >
  > >         Cheers,
  > >
  > >         -Kei
  > >
  > >         Kei Cheung wrote:
  > >
  > >             This is a reminder that the next BioRDF 
  > telcon call will
  > >             be held at 11 am EDT (5 pm CET) on Monday, 
  > November 23
  > >             (see details below).
  > >
  > >             Cheers,
  > >
  > >             -Kei
  > >
  > >             == Conference Details ==
  > >             * Date of Call: Monday November 23, 2009
  > >             * Time of Call: 11:00 am Eastern Time
  > >             * Dial-In #: +1.617.761.6200 (Cambridge, MA)
  > >             * Dial-In #: +33.4.89.06.34.99 (Nice, France)
  > >             * Dial-In #: +44.117.370.6152 (Bristol, UK)
  > >             * Participant Access Code: 4257 ("HCLS")
  > >
  > >             * IRC Channel: irc.w3.org 
  > <http://irc.w3.org> port 6665
  > >             channel #
  > >
Received on Friday, 4 December 2009 14:41:17 UTC

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