Re: BioRDF Telcon

hi kei,

> Just want to clarify that what I meant was that it might be beyond the 
> scope of our use case to accurately, comprehensively, and precisely define 
> what gene expression really  mean given the degree of complexity involved.

exactly, i believe we can trust the authors of the gene expression papers 
and the journals themselves for this

cheers,
michael

----- Original Message ----- 
From: "Kei Cheung" <kei.cheung@yale.edu>
To: "mdmiller" <mdmiller53@comcast.net>
Cc: "HCLS" <public-semweb-lifesci@w3.org>
Sent: Wednesday, May 26, 2010 7:23 AM
Subject: Re: BioRDF Telcon


> Hi Michael,
>
> mdmiller wrote:
>> hi kei,
>>
>>> What do we mean by differentially expressed genes? One definition is 
>>> that differentially  expressed  genes are genes with significantly 
>>> different expression in two samples/conditions/experimental 
>>> factors/dimensions (e.g., treated vs. untreated, disease vs, normal, 
>>> time point1 vs. time point 2) of microarray experiments.
>>
>> yes, this was my meaning.
>>
>> this is to differentiate between a gene that is always expressed under 
>> normal conditions because it is part of an essential pathway that is 
>> always running, that gene is only interesting if its expression level 
>> changes--similarly for a normally unexpressed gene.
>
> Thanks for confirming. A consensus definition (even it's broad) is 
> important to our gene list representation. There are a variety of methods 
> (e.g., statistical tests) that can be used to identify a list of 
> differentially expressed genes in two different groups. That's Scott's 
> point about the importance of capturing as part of the genelist context 
> what methods have been used for detecting differentially expressed genes. 
> I hope the use case can help convince the community the need/use of a 
> common vocabulary for describing such methods.
>>
>>> How to measure or infer gene expression (e.g., from mRNA) is a whole 
>>> complex question that may be beyond the scope of our use case.
>>
>> yes, which i think was scott's point in his reply.  in fact, for the 
>> BioRDF use case, initially at least, it is probably sufficient that the 
>> authors of the paper state that a gene is part of the significant gene 
>> list.
> Just want to clarify that what I meant was that it might be beyond the 
> scope of our use case to accurately, comprehensively, and precisely define 
> what gene expression really  mean given the degree of complexity involved.
>
> Cheers,
>
> -Kei
>>
>> cheers,
>> michael
>>
>>
>> ----- Original Message ----- From: "Kei Cheung" <kei.cheung@yale.edu>
>> To: "mdmiller" <mdmiller53@comcast.net>
>> Cc: "M. Scott Marshall" <marshall@science.uva.nl>; "HCLS" 
>> <public-semweb-lifesci@w3.org>
>> Sent: Tuesday, May 25, 2010 8:52 PM
>> Subject: Re: BioRDF Telcon
>>
>>
>>> Hi Michael et al,
>>>
>>> What do we mean by differentially expressed genes? One definition is 
>>> that differentially  expressed  genes are genes with significantly 
>>> different expression in two samples/conditions/experimental 
>>> factors/dimensions (e.g., treated vs. untreated, disease vs, normal, 
>>> time point1 vs. time point 2) of microarray experiments.
>>>
>>> How to measure or infer gene expression (e.g., from mRNA) is a whole 
>>> complex question that may be beyond the scope of our use case.
>>>
>>> Cheers,
>>>
>>> -Kei
>>>
>>> mdmiller wrote:
>>>
>>>> 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
>>>>>>>>>>>>
>>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>>
>>>>>>>>>>
>>>>>>>>>
>>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>>
>>>>>
>>>>
>>>>
>>>>
>>>
>>>
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>
>
>

Received on Wednesday, 26 May 2010 17:47:31 UTC