[MOBY-l] text-plain and text_plain

[Mark Wilkinson]

The last time this was discussed I believe that the conclusion was that we  
(whoever was interested in the particular node-conflict) would write to  
the host of the "offending" service and politely ask them to use the more  
accepted node.  It was not discussed beyond that, but it makes sense that  
it would then fall as the responsibility of the reporting person to  
de-register the unused nodes if/when the provider agrees (since it is in  
their interests to do so)

It may well be that many of those "offending" nodes are not being used - I  
may sit at Taverna for a couple of hours one day this week and do some  
pruning...  It's nice that the API prevents you from deregistering  
anything that is being used, so basically one just needs to sit there and  
"hit the delete button" until your fingers get tired :-)

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.  The Encyclopaedia helps  
(http://mobycentral.icapture.ubc.ca/cgi-bin/list.services.cgi), and that's  
what I generally use since that particular search functionality isn't in  
any of the other main registry clients (e.g. Dashboard).  Maybe we can  
convince Eddie or Martin to put the functionality in?  :-)

M



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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