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Re: BioRDF Telcon

From: mdmiller <mdmiller53@comcast.net>
Date: Tue, 25 May 2010 10:55:48 -0700
Message-ID: <1ADF865F8A3E4FF18ABC5AA0F278B31B@mmPC>
To: "M. Scott Marshall" <marshall@science.uva.nl>
Cc: "HCLS" <public-semweb-lifesci@w3.org>
hi scott,

i think you, jim and lena are doing a great job moving the technical aspect 
of this work forward.  i'm looking forward to seeing the end results.

cheers,
michael

----- Original Message ----- 
From: "M. Scott Marshall" <marshall@science.uva.nl>
To: "mdmiller" <mdmiller53@comcast.net>
Cc: "Kei Cheung" <kei.cheung@yale.edu>; "HCLS" 
<public-semweb-lifesci@w3.org>
Sent: Tuesday, May 25, 2010 10:21 AM
Subject: Re: BioRDF Telcon


> Hi Michael,
>
> Thanks for the clarification. I also explained those concepts during
> the BioRDF teleconference but it is difficult for the scribe to
> capture such details accurately from a phone conversation. Just
> knowing that a gene has changed (either up or down) already gives us
> something to work with. Since we started with the microarray use case,
> we have aimed to focus on the list of differentially expressed genes
> as our entry point into related molecular information, phenotypes,
> pathways, diseases, etc.
>
> In addition to the gene list and experimental factors, there is some
> data provenance information that characterizes the origins of the gene
> list, such as the type of significant analysis or technique that was
> performed (ANOVA, LIMMA, ..) and p-value cutoff for the list discussed
> in the associated article(s), software packages used (specific R
> package from BioConductor, GeneSpring, NextBio, ..). It would be handy
> if there was a common vocabulary for this type of information (URI's
> for statistical techniques and software packages). I think that some
> related resources have been described by myGrid/myExperiment. However,
> lacking a complete vocabulary, it is still possible to make use of the
> gene list without such a fine grained description of its provenance.
>
> Cheers,
> Scott
>
> On Tue, May 25, 2010 at 9:35 AM, mdmiller <mdmiller53@comcast.net> wrote:
>> hi all,
>>
>> sorry i ended up not being able to make the call.
>>
>> "P value
>> The probability (ranging from zero to one) that the results observed in a
>> study could have occurred by chance if the null hypothesis was true. A P
>> value of ? 0.05 is often used as a threshold to indicate statistical
>> significance." (1)
>>
>> the exact meaning of p-value depends on what is being measured.
>>
>> also, sometimes it isn't so important that a gene is up or down regulated
>> but whether its expression changes from up or down regulated over the
>> experimental factors, e.g. if you increase the dose of the drug do the
>> target genes go from non-expressed to up regulated.
>>
>> cheers,
>> michael
>>
>> 1)
>> http://www.ncbi.nlm.nih.gov/bookshelf/br.fcgi?book=antiepi&part=appendixes.app2
>>
>> ----- Original Message ----- From: "Kei Cheung" <kei.cheung@yale.edu>
>> To: "HCLS" <public-semweb-lifesci@w3.org>
>> Sent: Monday, May 24, 2010 11:40 AM
>> Subject: Re: BioRDF Telcon
>>
>>
>>> Today's minutes are available at:
>>>
>>>
>>> http://esw.w3.org/HCLSIG_BioRDF_Subgroup/Meetings/2010/05-24_Conference_Call
>>>
>>> Thanks to Matthias for scribing.
>>>
>>> Cheers,
>>>
>>> -Kei
>>>
>>> mdmiller wrote:
>>>>
>>>> hi kei,
>>>>
>>>> look forward to joining the call,
>>>> michael
>>>>
>>>> ----- Original Message ----- From: "Kei Cheung" <kei.cheung@yale.edu>
>>>> To: "mdmiller" <mdmiller53@comcast.net>; "HCLS"
>>>> <public-semweb-lifesci@w3.org>
>>>> Sent: Saturday, May 22, 2010 12:10 PM
>>>> Subject: Re: BioRDF Telcon
>>>>
>>>>
>>>>> Hi Michael,
>>>>>
>>>>> Yes, May 24 was what I meant. It was a typo.
>>>>>
>>>>> Thanks,
>>>>>
>>>>> -Kei
>>>>>
>>>>> mdmiller wrote:
>>>>>
>>>>>> hi kei,
>>>>>>
>>>>>> do you mean monday (may 24)?
>>>>>>
>>>>>> cheers,
>>>>>> michael
>>>>>>
>>>>>> ----- Original Message ----- From: "Kei Cheung" <kei.cheung@yale.edu>
>>>>>> To: "JunZhao" <jun.zhao@zoo.ox.ac.uk>
>>>>>> Cc: <public-semweb-lifesci@w3.org>
>>>>>> Sent: Friday, May 21, 2010 2:28 PM
>>>>>> Subject: Re: BioRDF Telcon
>>>>>>
>>>>>>
>>>>>>> Since there were only Jun and Scott who attended the last BioRDF 
>>>>>>> call
>>>>>>> (I was not able to attend due to some emergency meetings), we 
>>>>>>> decided to
>>>>>>> have the next BioRDF call on the coming Monday (May 21) at 11 am 
>>>>>>> (EDT). The
>>>>>>> agenda will be the same (see below).
>>>>>>>
>>>>>>> Cheers,
>>>>>>>
>>>>>>> -Kei
>>>>>>>
>>>>>>> JunZhao wrote:
>>>>>>>
>>>>>>>> This is a reminder that the next BioRDF telcon call will be held at
>>>>>>>> 11
>>>>>>>> am EDT (4 pm CET) on Monday, May 17 (see details below).
>>>>>>>>
>>>>>>>> Cheers,
>>>>>>>>
>>>>>>>> -Jun
>>>>>>>>
>>>>>>>>
>>>>>>>> == Conference Details ==
>>>>>>>> * Date of Call: Monday, May 17, 2010
>>>>>>>> * Time of Call: 11:00 am Eastern Time (4 pm CET)
>>>>>>>> * 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 W3C IRC page
>>>>>>>> for
>>>>>>>> details, or see Web IRC), Quick Start: Use
>>>>>>>> http://www.mibbit.com/chat/?server=irc.w3.org:6665&channel=%23hcls
>>>>>>>> for
>>>>>>>> IRC access.
>>>>>>>> * Duration: ~1 hour
>>>>>>>> * Frequency: bi-weekly
>>>>>>>> * Convener: Jun
>>>>>>>> * Scribe: to-be-determined
>>>>>>>>
>>>>>>>> ==Agenda==
>>>>>>>> * Introduction
>>>>>>>> * Gene list RDF representation
>>>>>>>> * iPhone demo
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>>
>>>
>>
>>
>>
>>
> 
Received on Tuesday, 25 May 2010 17:56:43 GMT

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