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RE: Reminder: BioRDF telcon on Monday at 11AM EDT (4PM UK, 5PM CET)

From: Michael Miller <Michael.Miller@systemsbiology.org>
Date: Mon, 11 Jul 2011 07:51:33 -0700
Message-ID: <d6bb775836a55b23976d8ea1b84041ac@mail.gmail.com>
To: Helena Deus <helenadeus@gmail.com>, "M. Scott Marshall" <mscottmarshall@gmail.com>, HCLS <public-semweb-lifesci@w3.org>
hi all,

my regrets, i'm under deadline pressure for the project i'm currently
working on and am attending a course on the TPP tools for mass spec this

" b) (NCBI gene id vs Ensembl gene id)"

this is an issue that goes beyond just gene expression.  the common sequence
databases (to which these two belong) cross reference each other in well
known ways--i'm not sure how this is reflected in the RDF representations
but suspect it is there.  the less well known (like affymetrix gene
expression array designs) also tend to reference into at least one well



*From:* public-semweb-lifesci-request@w3.org [mailto:
public-semweb-lifesci-request@w3.org] *On Behalf Of *Helena Deus
*Sent:* Monday, July 11, 2011 3:50 AM
*To:* M. Scott Marshall; HCLS
*Subject:* Re: Reminder: BioRDF telcon on Monday at 11AM EDT (4PM UK, 5PM

Dear all,

Today's BioRDF call with focus on aligning multiple genelist representations
(and their experimental context) derived from microarray experimental
results to improve integration of linked data represented using different

There are several things that need to be aligned before such integration is

1) Classes and properties; 2) Different URI used for identifying genes,
diseases, anatomical part, etc ; 3) Methods to transform the data when
statement values are not of the same datatype

We are currently dealing with three different represetantions of similar

a. RDF representation of genelists from the gene experession atlas

SPARQL endpoint at http://www.open-biomed.org.uk/sparql/endpoint/gxa

b. RDF representation of Provenance of Microarray Experiments by the bioRDF

SPARQL endpoint at

c. RDF representation of microarrays and the raw .CEL files derived from
those experiments

SPARQL endpoint at http://bloodprogram.hsci.harvard.edu/sparql

To answer the same competency questions from each of the endpoints, the
syntax of the SPARQL queries are necessarily different.

As an example for 1), consider the question "list all experiments".

in a) the question should be formulated as "?experiment
rdf:type               <http://www.ebi.ac.uk/efo/EFO_0004033> . "

in b) the question should be formulated as "?experiment        rdf:type
. "

in c) the quesion should be formulate as "?experiment        rdf:type
   <http://mged.sourceforge.net/ontologies/MGEDontology.php#BioAssay> ."

To solve and align these three we have prepared a table with the equivalent
classes and properties between the three representations (

For an  example of 2), we will have to link different gene identifiers in a)
and b) (NCBI gene id vs Ensembl gene id) and for an example of 3) data
transformation will be required before the datasets can be integrated since
in a. differential expression is encoded as "UP" or "DOWN" whereas in b.
differential expression encoded as fold change values (e.g. foldChange>0 <=>

We would be delighted if those of you who are interested in such matters
could join the call today with the purpose of helping us solve these
integration issues in microarray result representation.



On Mon, Jul 11, 2011 at 8:05 AM, M. Scott Marshall <mscottmarshall@gmail.com>

Here is the reminder for today's BioRDF call:

Conference Details

Date of Call: Monday, July 11, 2011
Time of Call: 11:00 am Eastern Time, 4 pm UK, 5 pm CET
Dial-In #: +1.617.761.6200 (Cambridge, MA)
[Note: limited access to European dial in numbers below]
Dial-In #: + (Nice, France)
Dial-In #: +44.203.318.0479 (Bristol, UK)
Participant Access Code: 4257 ("HCLS")
IRC Channel: irc.w3.org port 6665 channel #HCLS (see W3C IRC page for
details, or see Web IRC), Quick Start: Use
http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls for
IRC access.
Duration: ~1 hour
Convener: Helena Deus
Scribe: TBD


Discuss JBI article - Helena
Microarray, Expression RDF, Progress on the W3C note - All
Feedback to the new Gene Expression Atlas SPARQL endpoint - All

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

Helena F. Deus

Post-Doctoral Researcher at DERI/NUIG

Received on Monday, 11 July 2011 14:52:14 UTC

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