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Re: BioRDF Telcon

From: M. Scott Marshall <marshall@science.uva.nl>
Date: Tue, 25 May 2010 10:21:09 -0700
Message-ID: <AANLkTinXuCD8gsh0pKjOYZx655R_NLtxYXYfvsEHH4AS@mail.gmail.com>
To: mdmiller <mdmiller53@comcast.net>
Cc: Kei Cheung <kei.cheung@yale.edu>, HCLS <public-semweb-lifesci@w3.org>
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 17:21:37 GMT

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