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Re: BioRDF Telcon

From: Kei Cheung <kei.cheung@yale.edu>
Date: Fri, 24 Jul 2009 12:18:19 -0400
To: Helen Parkinson <parkinson@ebi.ac.uk>
Cc: HCLS <public-semweb-lifesci@w3.org>, James Malone <malone@ebi.ac.uk>
Message-id: <4A69DECB.1040009@yale.edu>
Hi Helen,

Please see my response below.

Helen Parkinson wrote:

> 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

That's related to our current mciroarray  use case where we're exploring 
a few examples (experiements) that hopefully contains enough 
neuron-related annotation.

>>
>>>
>>> 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.


As part of the current biordf effort, we're in the process of coming up 
with questions that we can ask across neuroscience microarray experiments.

>
>>>
>>> 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 
>
>
The experiment: E-GEOD-4757 compares gene expression prolifes of layer 2 
stellate island neurons of the entorhinal cortex between normal and AD 
subjects

The experiment: E-GEOD-9770 compares gene expression profiles of Layer 
II stellate neurons (entorhinal cortex) and layer III cortical neurons 
(hippocampus CA1, middle temporal gyrus, posterior cingulate, superior 
frontal gyrus, primary visual cortex) for subjects with mild cognitive 
impairment.

These two experiments are also in the NIH microarray consortium. There 
is an overlap of neuron type, brain region, and phenotype (memory) 
between the two experiements. This may be a start ...

> 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)
>>>>>
>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>
>>
>
Received on Friday, 24 July 2009 16:19:06 GMT

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