cheers,
michael
Michael Miller
mdmille...@comcast.net
----- Original Message ----- From: "Jim McCusker"
<james.mccus...@yale.edu>
To: "Helena Deus" <helenad...@gmail.com>
Cc: "Kei Cheung" <kei.che...@yale.edu>; "mdmiller"
<mdmille...@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:
has_derivation_source
has_derivative
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.
Jim
On Monday, November 30, 2009, Helena Deus <helenad...@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.che...@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 <mdmille...@comcast.net
<mailto:mdmille...@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.che...@yale.edu <mailto:kei.che...@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 #
