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Re: BioRDF Telcon

From: Helen Parkinson <parkinson@ebi.ac.uk>
Date: Wed, 22 Jul 2009 10:55:27 +0100
Message-ID: <4A66E20F.9040306@ebi.ac.uk>
To: Kei Cheung <kei.cheung@yale.edu>
CC: HCLS <public-semweb-lifesci@w3.org>, James Malone <malone@ebi.ac.uk>
Responses in line.


>>
>>
>> 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.
>>
> 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).
Re-use of the neuron ontology is possible, but it depends on whether 
there is available data to annotate either in ArrayExpress or GEO. If 
you can get me a list of experiments accessions or pubmed ids I can see 
if this is feasible
>
>>
>> 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.
We have a student starting work on this in a month, if you can produce 
concrete use cases for how you want to access these data we can do 
something.
>>
>> 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.

This is probably as we don't have data - here's a list of human 
experiments with the term neuron - if any of these are useful, then I 
can prioritise their curation and inclusion in an atlas release

 http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=neuron&species=Homo+sapiens&array=&exptype=&pagesize=25&sortby=releasedate&sortorder=descending

and brain

http://www.ebi.ac.uk/microarray-as/ae/browse.html?keywords=brain&species=Homo+sapiens&array=&exptype=&pagesize=25&sortby=releasedate&sortorder=descending

>>
>> 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.
>
> Cheers,
>
> -Kei
>>
>> 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 #: +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 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

EBI 01223 494672
Skype: helen.parkinson.ebi
Received on Wednesday, 22 July 2009 09:56:15 GMT

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