[Go] Muscle Biology Content Meeting Publication

[Alexander Diehl]

Jen and Erika,

Starting with Midori's revision, I made some changes of my own, 
indicated by the track changes.  I removed a number of superfluous 
commas and added some too, converting all series to the "Oxford comma," 
since about half were and half were not using it.  I also changed a few 
words to eliminate repetitive use of some words in particular paragraphs 
and made a few other changes as well.

One idea to address Chris' comment regarding adding an example of 
concrete improvement would be to take the set of muscle genes (from the 
172 you identified) that overlap with the Reference Genome genes and ask 
Mary Dolan to graph their annotations before and after the muscle 
biology changes to the ontologies were implemented.  You don't even have 
to mention that these are Reference Genome genes (or just provide a URL 
reference to the RGG project page), but since they are, they should have 
a good bit of annotation already.  Even if this annotation is not to new 
terms introduced in this revision, it should (hopefully) illustrate the 
improved structure of the ontology.  You could prune off not muscle 
biology annotation to simplify the graphs as well.

Thanks,

Alex



Chris Mungall wrote:
> hmm, seem to have lost my edits.. ah well
>
>   
>> Our revised ontology structure should facilitate the interpretation  
>> of high-throughput experiments (e.g. gene expression microarrays)  
>> in the area of muscle science and muscular disease. Such studies  
>> yield a very large number of data points and this makes it a  
>> challenge to determine which genes specifically contribute to a  
>> disease phenotype [17]. However the use of GO ontologies and  
>> annotations within GO-related statistical analysis tools [18]  
>> should greatly simplify this analysis .
>>     
>
>
> So I think this is very true, but what would make this highly  
> compelling would be some examples. Perhaps:
>
> * A reference genome gene that is muscle related, graphs before and  
> after the ontology change
> * Some actual high throughput experimental results, enriched, before  
> and after
>
> Of course changes will only be reflected in the upper level grouping  
> of results, as people may not have time to annotate to the newer more  
> specific terms
>
> I can help with this, given a gene list.
>
> On Mar 19, 2008, at 7:34 AM, Midori Harris wrote:
>
>   
>> Hi,
>>
>> The manuscript looks well organized and summarizes the changes  
>> nicely. I've made some comments and suggestions in the attached  
>> version.
>>
>> m
>>
>> On Fri, 14 Mar 2008, Jennifer Deegan (nee Clark) wrote:
>>
>>     
>>> Hi,
>>>
>>> Erika Feltrin and I have written a paper about the Muscle Biology
>>> Content Meeting, to be sent to BMC Medical Genomics.
>>> We would really appreciate any comments on the manuscript:
>>> http://www.ebi.ac.uk/~jdeegan/stored/musclepaper/ 
>>> muscle_paper_ver_1.doc
>>>
>>> We are also offering a small prize for anyone who can come up with a
>>> suitably cheezy title, including a bad pun on the word 'GO'.
>>>
>>> Thanks,
>>>
>>> Jen
>>>
>>>
>>> <muscle_paper_ver_1a.doc>
>>>       
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>>     
>
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-- 
Alexander Diehl, Ph.D.
Senior Scientific Curator
Mouse Genome Informatics
The Jackson Laboratory
600 Main Street
Bar Harbor, ME  04609

email:  adiehl at informatics.jax.org
work:  +1 (207) 288-6427
fax:  +1 (207) 288-6131

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