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Re: BioRDF Telcon

From: Helen Parkinson <parkinson@ebi.ac.uk>
Date: Tue, 21 Jul 2009 16:15:39 +0100
Message-ID: <4A65DB9B.7070301@ebi.ac.uk>
To: Kei Cheung <kei.cheung@yale.edu>
CC: HCLS <public-semweb-lifesci@w3.org>, James Malone <malone@ebi.ac.uk>

I've been lurking on this list for a while, and I see that there's some 
interest in microarray data from the last call minutes. I run the 
ArrayExpress database and we have some resources that may be of interest 
to this group:

1. We have text mined much of the Affymetrix GEO data, curated it and 
imported it into  ArrayExpress - there is now much better sample 
annotation than the native data in GEO. We also are running QC across 
all the data files so we know which should be excluded for future analyses.

2. We have developed an ontology for text mining and visualisation of 
the data - it's been tested by us and the Bioportal and gives the best 
coverage on public domain gene expression data of all tested ontologies 
- the next best is the NCI thesaurus. It's not very rich for 
neuroscience, but we could improve it if there's interest and use cases 

3. We have summary level data of genes x conditions for ~30,000 hybs 
worth of data in our gene expression atlas with p values indicating 
relative under/over-expression. We are planning to export these as 
triples as soon as we publish the atlas - these may be of interest. 
www.ebi.ac.uk/gxa - there's an API at present, but it will be improved 
in the next month or so.

4. If neuroscience data is of specific interest we could do a themed 
atlas release where we add datasets for a given community or project and 
make these available. These can be identified by ArrayExpress or GEO 
accession or pubmed and we can re-annotate the genes vs Uniprot/Ensembl, 
add GO terms, etc and curate the sample attributes and experimental 
variables. These pipelines are already in place as part of our 
production workflow.

I'd be very happy to collaborate, and for this group to use our data, we 
spend a lot of time adding semantic value to it, so please let me know 
if this is of interest

best regards


Kei Cheung wrote:
> The minutes for yesterday's BioRDF call are available at:
> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/Meetings/2009-07-20_Conference_Call 
> Thanks to Lena for scribing and Eric for retrieving the transcript 
> from the IRC log.
> Cheers,
> -Kei
> Kei Cheung wrote:
>> This is a reminder that the next BioRDF teleconf. will be held at 11 
>> am EDT (5 pm CET) on Monday, July 20 (see details below).
>> I created the following wiki page for discussing the microarray use 
>> case:
>> http://esw.w3.org/topic/HCLSIG_BioRDF_Subgroup/QueryFederation2
>> Cheers,
>> -Kei
>> == Conference Details ==
>> * Date of Call: Monday July 20, 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 port 6665 channel #hcls (see 
>> [http://www.w3.org/Project/IRC/ W3C IRC page] for details, or see 
>> [http://cgi.w3.org/member-bin/irc/irc.cgi Web IRC])
>> * Duration: ~1 hour
>> * Frequency: bi-weekly
>> * Convener: Kei Cheung
>> == Agenda ==
>> * Roll call and introduction (Kei)
>> * TCM data quick update (Jun, Kei)
>> * Query federation use case expanison (microarray) (All)

Helen Parkinson, PhD
ArrayExpress Production Coordinator,
Microarray Informatics Team, 

EBI 01223 494672
Skype: helen.parkinson.ebi
Received on Tuesday, 21 July 2009 17:17:20 UTC

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