hi all,
here is he link to Molecular Signatures Database (MSigDB):
[1]: http://www.broadinstitute.org/gsea/msigdb/
cheers,
michael
----- Original Message -----
From: "mdmiller" <mdmille...@comcast.net>
To: "Kei Cheung" <kei.che...@yale.edu>
Cc: "Jim McCusker" <james.mccus...@yale.edu>; "Helena Deus"
<helenad...@gmail.com>; "HCLS" <public-semweb-lifesci@w3.org>
Sent: Thursday, December 10, 2009 6:49 AM
Subject: Re: BioRDF Telcon
hi kei,
To me, ontologies can be used to facilitate integrated semantic queries
across experiments/datasets.
yes, and this is starting to become a reality. this effort, along with
other HCLS initiatives are helping to pave the way.
While some of the protocols are standardized, the data protocols for
obtaining things like gene lists vary a lot. One of my questions is that
can such data analysis protocols be somehow entered into mage-tab.
yes it can be, along with the gene list, but in practice this is not done
by the submitter. after the Derived Array Data representing the
normalized data, like CHP files, there can be one or more Protocol REF
columns describing the analysis to obtain the gene list followed by a
Derived Array Data Matrix File that is the gene list with its signature.
perhaps MIAME needs to be extended to state this. it's something i'll be
bringing up with the MGED board. it's just now that this has become
something of value to be machine readable. besides GeneSigDB, there is
another effort, MSiqDB [1], that is also curating gene lists. so the
community is beginning to see the value of this.
At least for now, I don't think we need to convert the huge primary data
files (e.g., CEL file) into RDF. For the time being, we are more focused
on the processed gene lists that may be associated with more biological
meanings.
perhaps its worthwhile considering using an ontology 'raw data' class for
raw data that contains a reference to the data file. one could then use
appropriate analysis tools to produce normalized data which could then
also be referenced by a 'normalized data' class.
cheers,
michael
----- Original Message -----
From: "Kei Cheung" <kei.che...@yale.edu>
To: "mdmiller" <mdmille...@comcast.net>
Cc: "Jim McCusker" <james.mccus...@yale.edu>; "Helena Deus"
<helenad...@gmail.com>; "HCLS" <public-semweb-lifesci@w3.org>
Sent: Monday, December 07, 2009 7:32 AM
Subject: Re: BioRDF Telcon
mdmiller wrote:
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.
It sounds like we need to look at how to map column names and entries to
classes, instances, and relationships appropriately.
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.
To me, ontologies can be used to facilitate integrated semantic queries
across experiments/datasets.
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 usually.
While some of the protocols are standardized, the data protocols for
obtaining things like gene lists vary a lot. One of my questions is that
can such data analysis protocols be somehow entered into mage-tab.
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.
At least for now, I don't think we need to convert the huge primary data
files (e.g., CEL file) into RDF. For the time being, we are more focused
on the processed gene lists that may be associated with more biological
meanings.
Cheers,
-Kei
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 #