[Bioc-devel] biocViews preprocessing term

[Florian Hahne]

Sure, I can do that. Just need to figure out if there is an easy way  
to parse through the whole repository, I hope that Patrick can help  
with that. However, I still don't see how one would specify a term  
like flow cytometry -> preprocessing in the DESCRIPTION file. Or do yo  
mean unique node names by syntactic atoms? So far, only the leaf node  
seems to be used to assign a package to a category.
Florian


On 03.09.2008, at 03:42, Vincent Carey 525-2265 wrote:

> Thanks for carrying on this thread, Patrick,
> looks like I got distracted.
>
> Now I see how the vocabulary is maintained.
> biocViews/inst/dot has a nice human-readable rendering
> of the vocabulary in biocViewsVocab.dot
>
> Each node reference in the dot is a topic, and any
> node in that dot file can be used as a biocViews
> field value in the package.
>
> Florian, would you like to make the changes to
> biocViews/inst/dot that reflect your desired vocabulary
> modifications, rebuild the vocabulary using biocViews/updateVocab.sh,
> and then commit the modified biocViews package (with a bump to the
> version tag in DESCRIPTION)?  It would be nice to have some
> mechanism of testing that the build system will survive such
> a change (perhaps testing some validity conditions on the new
> graph, such as 1 connected component, all nodes are syntactic
> atoms, checking the correspondence between biocViews fields
> present in the repository and the nodes in the graph).
>
> I will do the changes mentioned in Florian's e-mail and commit
> if people want to funnel this through me ...
>
> ---
> Vince Carey, PhD
> Assoc. Prof Med (Biostatistics)
> Harvard Medical School
> Channing Laboratory - ph 6175252265 fa 6177311541
> 181 Longwood Ave Boston MA 02115 USA
> stvjc at channing.harvard.edu
>
> On Wed, 3 Sep 2008, Patrick Aboyoun wrote:
>
>> On the second point, the build system uses the ontology in  
>> biocViews and
>> will adapt accordingly when biocViews is changed. Any vocabulary term
>> that is not recognized by biocViews will be ignored and an internal
>> build warning will be issued. Periodically I check the ignored  
>> terms to
>> see if this is due to misspellings (which I correct), but in some
>> situations packages include categories that don't exist. If changes  
>> are
>> made to the ontology, package authors can modify their biocViews
>> DESCRIPTION field prior to changes being made to biocViews without  
>> any
>> adverse build outcome.
>>
>>
>> Patrick
>>
>>
>>
>> Vincent Carey 525-2265 wrote:
>>> yes in specific, and although you did not ask it does
>>> appear that we need some renovation of the biocViews
>>> vocabulary.
>>>
>>> alas i am not really clear on how modifications to the
>>> vocabulary impact the build system.  i will take a look
>>> at this and make a proposal momentarily.
>>>
>>> ---
>>> Vince Carey, PhD
>>> Assoc. Prof Med (Biostatistics)
>>> Harvard Medical School
>>> Channing Laboratory - ph 6175252265 fa 6177311541
>>> 181 Longwood Ave Boston MA 02115 USA
>>> stvjc at channing.harvard.edu
>>>
>>> On Tue, 2 Sep 2008, Florian Hahne wrote:
>>>
>>>
>>>> Hi Vince,
>>>> the cellHTS and cellHTS2 package provide (mostly) preprocessing
>>>> functionality for cell-based assays, and assigning the biocViews  
>>>> term
>>>> "Preprocessing" seems to be reasonable. However, in the ontology  
>>>> this is
>>>> defined as "Microarray -> Preprocessing;", and that's not really  
>>>> what we
>>>> want. Shouldn't there be a general "Preprocessing" term  
>>>> independent of
>>>> micro arrays. I guess this will also become interesting for many  
>>>> of the
>>>> other emerging new technologies like deep sequencing. With the  
>>>> current
>>>> design, it seems this is not possible, since terms have to be
>>>> unambiguous. Is there any reasonable way of dealing with this  
>>>> problem
>>>> other than adding a new term like "General Preprocessing"? And  
>>>> wouldn't
>>>> it be useful to allow for terms like "Technology -> FlowCytometry
>>>> ->Preprocessing;"
>>>>
>>>> Florian
>>>>
>>>> --
>>>> Florian Hahne, PhD
>>>> Computational Biology Program
>>>> Division of Public Health Sciences
>>>> Fred Hutchinson Cancer Research Center
>>>> 1100 Fairview Ave. N, M2-B876
>>>> PO Box 19024
>>>> Seattle, Washington 98109-1024
>>>> 206-667-3148
>>>> fhahne at fhcrc.org
>>>>
>>>>
>>>>
>>>
>>> _______________________________________________
>>> Bioc-devel at stat.math.ethz.ch mailing list
>>> https://stat.ethz.ch/mailman/listinfo/bioc-devel
>>>
>>
>>
>>
>>
>>
>>
>
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