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Re: BioRDF Telcon

From: Kei Cheung <kei.cheung@yale.edu>
Date: Tue, 21 Jul 2009 15:26:42 -0400
To: Helen Parkinson <parkinson@ebi.ac.uk>
Cc: HCLS <public-semweb-lifesci@w3.org>, James Malone <malone@ebi.ac.uk>
Message-id: <4A661672.20005@yale.edu>
Hi Helen,

Thanks for your interest in our microarray use case. It's good to have 
EBI get involved so that we can establish collaboration between the 
semantic web community and the microarray community.  Please see my 
response below.

Helen Parkinson wrote:
> Hi,
> 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.
I think it's the right thing to do both to enrich data annotation and to 
enhance data quality. This will help data integration a lot.
> 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 www.ebi.ac.uk/efo
Currently, we are exploring query federation in the neuroscience 
context. It'd be great if we can use the neuroscience use case(s) to 
help drive your ontology development for text mining and data 
visualization. In addition to the NIH neuroscience microarray 
consortium, it may be possible to collaborate with the Neuroscience 
Information Framework (NIF) to see if we can utilize some of its 
resources (e.g., neuron ontology).

> 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.
It fits well with what we're currently exploring in terms of gene list 
representation and linking genes and samples to existing ontologies. 
It'd be great if we can download or fetch RDF triples from EBI atlas.
> 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 think it's a great idea to do a themed atlas (e.g., neuro-atlas). I 
just played with gxa a little bit. It's nice! For example, I could find 
genes that are over-expressed in the hippocampus brain region across 
different experiments. However, when I tried to do the same thing for 
neurons, there are only a few neuron types that I can select. It'd be 
nice if we can have more neuron types, for instance.
> 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
We are also looking into the possibility of establishing collaboration 
with the scientific discourse task force based on the microarray use 
case. We're planning to have a microarray-related presentation and 
discussion on Aug. 31 (Monday, 11 am EDT/5 pm CET). Details will be 
announced later. It'd be great if you can join the BioRDF call to 
participate in the discussion.


> best regards
> Helen
> 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)
Received on Tuesday, 21 July 2009 19:27:30 UTC

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