[MOBY-l] text-plain and text_plain

Wed Aug 22 06:12:17 UTC 2007

On 21-Aug-07, at 8:01 AM, Mark Wilkinson wrote:
> I think the problem is that some of the most obviously useful nodes  
> are
> hidden below non-obviously useful nodes (e.g. DNA Sequence is under
> VirtualSequence), so people don't know where to look to find things  
> that
> are already there.

In what sense do you mean 'hidden'? If you mean that in all of the  
existing interfaces, we use hierarchical tree widgets (like the Java  
JTree) to display hierarchies and thus obscure these more 'useful'  
types, then yes, they are certainly hidden.

However, it occurred to me if we were to look at the frequency with  
which each type is used in a service interface, we could display the  
type hierarchy as a treemap and adjust the size of each cell in the  
map to be relative to this frequency. This is just something I came  
up with while walking home with groceries; I'm sure there exist  
better visualizations and better metrics to assess type 'popularity'  
than what I've suggested here.

Even a radial tree, where node sizes are weighted by popularity,  
would probably be much more useful than your average hierarchical view.

Some handy refs on treemaps, for those who are interested:

http://www.cs.umd.edu/hcil/treemap-history/
http://en.wikipedia.org/wiki/Treemapping

-Mike

>
>
> On Tue, 21 Aug 2007 02:46:58 -0700, Pieter Neerincx
> <Pieter.Neerincx at wur.nl> wrote:
>
>> Hi,
>>
>> On 20-Aug-2007, at 10:48 PM, Mark Wilkinson wrote:
>>
>>> Ugh...  Appendicitis!
>>>
>>> At some point someone registered text_plain when text-plain already
>>> existed... after that, people discovered one or the other and  
>>> started
>>> building inheritence trees from both of them.
>>>
>>> As a community, we have agreed to use hyphens.  We are supporting  
>>> the
>>> underscores only until there are no longer any services that
>>> utilize those
>>> nodes or their children. At that point, we will prune that node off
>>> completely :-)
>>
>> Is there a deadline for saying by by to text_plain or is it possible
>> to make these depreciated nodes "read only" so people can not
>> register new services or make more complex objects based on them?
>> Otherwise I bet such depreciated nodes will be stuck in the ontology
>> forever.
>>
>> Cheers,
>>
>> Pi
>>
>>
>>> So... please use hyphens preferentially.
>>>
>>> M
>>>
>>>
>>>
>>>
>>>
>>> On Mon, 20 Aug 2007 13:22:01 -0700, Michael DiBernardo
>>> <mikedebo at gmail.com> wrote:
>>>
>>>> I am peeking curiously at the types "text_plain" and "text- 
>>>> plain" in
>>>> the Objects ontology. (One uses an underscore and the other uses a
>>>> dash, if you weren't able to see the difference straightaway).
>>>>
>>>> Roughly 130 types in the Objects ontology derive from text-plain,
>>>> while roughly 50 derive from text_plain. What is the reasoning  
>>>> behind
>>>> this division, if any? Is this just a common typo/formatting issue
>>>> that we haven't gotten around to dealing with yet? I would classify
>>>> this as a pretty substantial annoyance, since it appears to make  
>>>> many
>>>> compatible services appear incompatible with one another.
>>>>
>>>> Is there anything I might be able to do straightaway that could
>>>> contribute to fixing this, if it indeed needs fixing?
>>>>
>>>> -Mike
>>>> _______________________________________________
>>>> moby-l mailing list
>>>> moby-l at lists.open-bio.org
>>>> http://lists.open-bio.org/mailman/listinfo/moby-l
>>>
>>>
>>>
>>> --
>>> --
>>> Mark Wilkinson
>>> Assistant Professor, Dept. Medical Genetics
>>> University of British Columbia
>>> PI Bioinformatics
>>> iCAPTURE Centre, St. Paul's Hospital
>>> Tel:  604 682 2344 x62129
>>> Fax:  604 806 9274
>>>
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>>
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