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

Re: Action Items from call today

From: Jun Zhao <jun.zhao@zoo.ox.ac.uk>
Date: Sat, 31 Oct 2009 21:23:26 +0000
Message-ID: <4AECAACE.7070802@zoo.ox.ac.uk>
To: mdmiller <mdmiller53@comcast.net>
CC: Kei Cheung <kei.cheung@yale.edu>, Helen Parkinson <parkinson@ebi.ac.uk>, HCLS <public-semweb-lifesci@w3.org>, Tony Burdett <tburdett@ebi.ac.uk>
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 Saturday, 31 October 2009 21:24:03 UTC

This archive was generated by hypermail 2.3.1 : Wednesday, 7 January 2015 14:52:41 UTC