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Re: BioRDF Telcon

From: mdmiller <mdmiller53@comcast.net>
Date: Wed, 2 Dec 2009 08:11:41 -0800
Message-ID: <ED2CC08223514A6CA9A4AAD41527B568@mmPC>
To: "Jim McCusker" <james.mccusker@yale.edu>, "Helena Deus" <helenadeus@gmail.com>
Cc: "Kei Cheung" <kei.cheung@yale.edu>, "HCLS" <public-semweb-lifesci@w3.org>
hi jim and lena,

great progress!  this will be a nice tool.

a couple of comments.

1) i think ProtocolApplication is based seen as an individual instance of 
the Protocol class.  quite often there are arguments whether ontologies 
should have individuals or be simply classes.  to me, that doesn't apply 
here where real world objects are being connected to ontologies.  the 
BioSource is realized as the  'Source Name' column in MAGE-TAB and those 
entries represent real people in studies, mice or rats in non-clinical 
studies, etc., and the characteristics values like age represent real 
individual instances of age.  in the same way, the values in the Protocol 
REF column of MAGE-TAB are real wet-lab or analysis individual instances of 
protocols, called protocol applications in MAGE-OM.

failure to make this distinction, to me, has obscured how much value 
ontologies can have in the real world.  too often i see ontologies seen in 
and of themselves, which has its own value certainly, but not for the use 
cases i have dealing with real biological data.

2) the usefulness, for this use case, of the information between the 'Source 
Name' and its characteristics and the 'Derived Array Data Matrix File' or 
'Derived Array Data File' has limited usefulness, error correction and 
normalization can make some difference but if the provider of the MAGE-TAB 
is trusted, all that is pretty routine these days.  the above combined with 
experimental factors and experiment design info is probably 95% to 99.9% the 
worthwhile information from the MAGE-TAB.  if one notices a difference in 
the final gene set between two experiments that look the same, only then it 
might be worthwhile going into more detail.

and has been noted the MAGE-TAB information needs to be supplemented with 
the information on the final gene set, its expression values, and the 
higher-level level analysis that was used, that is buried in the paper 

3) i'm not sure if there was a desire to capture the raw data in the RDF. 
that will be, for affymetrix, a million to six million probes in the CEL 
file, even the processed data in the CHP file would have 20,000 to 60,000 
probe sets.  i'm not sure if that is the best way to represent that.


Michael Miller

----- Original Message ----- 
From: "Jim McCusker" <james.mccusker@yale.edu>
To: "Helena Deus" <helenadeus@gmail.com>
Cc: "Kei Cheung" <kei.cheung@yale.edu>; "mdmiller" <mdmiller53@comcast.net>; 
"HCLS" <public-semweb-lifesci@w3.org>
Sent: Monday, November 30, 2009 8:19 AM
Subject: Re: BioRDF Telcon

I'm following a similar strategy, but have been folowing the MGED
ontology where possible. I've finished aligning the IDF portion, and
have started on SDRF. MGED ontology is missing a property and class
for what is often termed as ProtocolApplication, which usually serves
as an edge between derived from and derived nodes, while linking to
the protocol used for the derivation. I am planning on creating this
link in a MAGE extensions ontology, but would like to vet the
structure here:

ProtocolApplication is a class.

New properties:


And then ProtocolApplication would have the restrictions:

has_protocol some Protocol

I don't put, domains, etc. on the derived properties to allow use in
directly describing derivations if people so choose. There is no
superclass for all nodes that can be derived or derived from, so I'm
not bothering with restrictions for those, although I could add a
union restriction to it.

If this structure us acceptable to people, I can publish the ontology
for general use pretty quickly, and let us work from the same data
structure. I would appreciate any feedback.


On Monday, November 30, 2009, Helena Deus <helenadeus@gmail.com> wrote:
> @Kei,
> When you said data structure, did you mean the RDF structure
> For now, all I have is the java object returned by parser. I've been using 
> Limpopo, which creates an object that I can then parse to RDF uing Jena. 
> The challenge, though, has been coming up with the predicates to formalize 
> the relationships between the various elements. I'm using the XML 
> structures fir IDF/SDRF etc. at http://magetab-om.sourceforge.net to 
> automatically generate the structure that will contain the data. My plan 
> is to then create the RDF triples that use the attributes described in 
> those documents and populate them with the data from the MAGE-TAB java 
> object created by Limpopo.
> Right now all I have is a very raw RDF/XML document describing the 
> relationships in the IDF structure: 
> http://magetab2rdf.googlecode.com/svn/trunk/magetabpredicates.rdf
> The triples for that had to be encoded manually using Jena by reading the 
> model.
> @Satya and Jun
> I would very much like to be involved in that effort, do you already have 
> a URL that I can look at?
> ThanksLena
> On Tue, Nov 24, 2009 at 2:19 PM, Kei Cheung <kei.cheung@yale.edu> wrote:
> Hi Lena et al,
> When you said data structure, did you mean the RDF structure. If so, is a 
> pointer to the structure that we can look at?
> As discussed during yesterday's call, Jun and Satya will help create a 
> wiki page for listing some of the requirements for provenance/workflow in 
> the context of gene lists, perhaps we should also use it to help 
> coordinate some of the future activities (people also brought up Taverna 
> during the call yesterday). Please coordinate with Satya and Jun.
> Cheers,
> -Kei
> Helena Deus wrote:
> Hi all,
> I apologize for missing the call yesterday! It seems you had a pretty 
> interesting discussion! :-)
> If I understand Michael's statement, parsing the MAGE-TAB/MAGE-ML into RDF 
> would result in obtaining only the raw and processed data files but not 
> the mechanism used to process it nor the resulting gene list. That's also 
> what I concluded after looking at the data structure created by Tony 
> Burdett's Limpopo parser. However, having the raw data as linked data is 
> already a great start! Kei, should I be looking into Taverna in order to 
> reprocessed the raw files with a traceable analysis workflow?
> Thanks!
> Lena
> 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 #: + (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 #

Jim McCusker
Programmer Analyst
Krauthammer Lab, Pathology Informatics
Yale School of Medicine
james.mccusker@yale.edu | (203) 785-6330

PhD Student
Tetherless World Constellation
Rensselaer Polytechnic Institute
Received on Wednesday, 2 December 2009 16:12:42 UTC

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