W3C home > Mailing lists > Public > public-semweb-lifesci@w3.org > November 2009

Re: Action Items from call today

From: Kei Cheung <kei.cheung@yale.edu>
Date: Sun, 01 Nov 2009 08:44:40 -0500
Message-ID: <4AED90C8.2090504@yale.edu>
To: Jun Zhao <jun.zhao@zoo.ox.ac.uk>
CC: mdmiller <mdmiller53@comcast.net>, Helen Parkinson <parkinson@ebi.ac.uk>, HCLS <public-semweb-lifesci@w3.org>, Tony Burdett <tburdett@ebi.ac.uk>
Hi Jun et al,

The following gene list:

http://public.tgen.org/tgen.org/supplementarydata/neurogenomics/supplementarydata/brain_regions/PCA1_0_98_correlation.xls

was gereated using the Principal components analysis (PCA). It is an 
annotated list of 102 genes showing at least a 0.98 correlation to PCA1 
(first principal component). This is part of the following paper:

http://www.ncbi.nlm.nih.gov/pubmed/17077275?dopt=Abstract

I'm airport t to the airport now ...

Cheers,

-Kei

Jun Zhao wrote:

> Hello Michael,
>
> Sorry I didn't see this email from you since I have been traveling.
>
> I am aware of the scovo vocabulary. Actually scovo is used in the voiD 
> [1] vocabulary to describe statistics about data and I am one member 
> of the voiD working group. Although scovo is a well-designed model to 
> serve its purpose, we have found that it is quite difficult to query 
> for datasets using this vocabulary. Hence, in the current voiD working 
> group, proposing an alternative model to describe statistics of 
> datasets has been a high priority. We are planning to release voiD2.0 
> including a new statistics model around Christmas. It would be nice if 
> I can gather more user requirements from you and people on this list.:)
>
> [1] http://rdfs.org/ns/void-guide
>
> Best,
>
> Jun
>
> mdmiller wrote:
>
>> hi all,
>>
>> on a different HCLS thread i saw this proposal from jeni tennison for 
>> specifying a generic dataset, it might be a useful way to encode a 
>> list of differentially expressed genes.  it looks like one could do 
>> this encoding on the fly, so that the data itself at the source could 
>> be in whatever format is natural.
>>
>> http://sw.joanneum.at/scovo/schema.html
>>
>> cheers,
>> michael
>>
>> Michael Miller
>> mdmiller53@comcast.net
>>
>> ----- Original Message ----- From: "Kei Cheung" <kei.cheung@yale.edu>
>> To: "Helen Parkinson" <parkinson@ebi.ac.uk>
>> Cc: "HCLS" <public-semweb-lifesci@w3.org>; "Tony Burdett" 
>> <tburdett@ebi.ac.uk>
>> Sent: Wednesday, October 14, 2009 7:03 PM
>> Subject: Re: Action Items from call today
>>
>>
>>> Thanks, Helen.
>>>
>>> To make it more concrete. I've been thinking about some example 
>>> queries that I hope can be answered by the RDF data once converted. 
>>> I wonder if the following example quereis can be answered:
>>>
>>> Retrieve a list of differentially expressed genes between different 
>>> brain regions (e.g., hippocampus and entorhinal cortex) for normally 
>>> aged human subjects.
>>>
>>> Retrieve a list of differentially expressed genes for the same brain 
>>> region of normal human subjects and AD patients.
>>>
>>> Using these lists of genes one can issue (federated) queries to 
>>> retrieve addtional information about the genes for various types of 
>>> analyses (e.g., GO term enrichment).
>>>
>>> Just a thought.
>>>
>>> Cheers,
>>>
>>> -Kei
>>>
>>>
>>>
>>> Helen Parkinson wrote:
>>>
>>>> Hi
>>>>
>>>> here are my action items from the call today
>>>>
>>>> 1. MAGE-TAB->RDF, Lena requested details.
>>>>
>>>> Code here: https://sourceforge.net/projects/limpopo/
>>>>
>>>> Java Parser for MAGE-TAB developed by EBI, used by several groups. 
>>>> Contact Tony Burdett tburdett@ebi.ac.uk for details. Tony estimates 
>>>> for a simple RDF dump a few days work. Lena if you are interested 
>>>> in working on this java code please contact Tony as he's already 
>>>> designed  with rdf export in mind
>>>>
>>>> 2. MAGE-TAB->MAGE-ML  - code from Junmin Liu at UPenn
>>>>
>>>> https://sourceforge.net/projects/tab2mage/files/  - see mage2tab
>>>> Pretty much all public MAGE-ML comes from AE and is available from 
>>>> Arrayexpress ftp dirs as mage-tab already. Exceptions are Rosetta's 
>>>> mage-ml importer, and non public data
>>>>
>>>>
>>>> 3. EBI experimental factor ontology (EFO) slides, attached
>>>> see also www.ebi.ac.uk/efo
>>>>
>>>> 4. Noted that an RDF dump of atlas data and triple store access 
>>>> will be useful, we'll announce when these are available
>>>>
>>>> thanks
>>>>
>>>> Helen
>>>>
>>>>
>>>>
>>>
>>>
>>
>>
>>
>>
>
>
Received on Sunday, 1 November 2009 13:45:16 GMT

This archive was generated by hypermail 2.3.1 : Tuesday, 26 March 2013 18:00:57 GMT