[moby] [MOBY-dev] Re: Problems with Biomoby services in Taverna 1.2

[Rebecca Ernst]

Hi Mark!

I will have to spank you a lot for either the last email or the one you 
sent me in February where I asked you how to use collections (see mail 
below):


Well... the answer depends on what the generic case of your output will
look like.  the rule is that you have to register every output object
that your service produces; i.e. every immediate child tag of a mobyData
block.  Therefore, if you are going to consistently output exactly 3
Genbank/gi's, then you would register your service as outputting 3 X
Object(NCBI_gi).  If you are outputting an indeterminate number of
objects, then you register it as outputting 1 X Collection.  

Collections map nicely onto the rdf:Bag structure, if that helps you
interpret them.

M



On Wed, 2005-02-02 at 02:36, Rebecca Ernst wrote:

>> Hi Mark!
>> 
>> We have problems interpreting the BioMoby API for the output objects.
>> 
>> The thing is that we have a service that gets ONE input object and 
>> executes a freetext search over several databases. This service will 
>> eventually return more that one result.
>> We don't want to put the result into a collection object because the 
>> single objects don't build any entity.
>> We also can't give back more that one mobyData block because we only 
>> have one query ID and therefore only one queryID to give back.
>> 
>> The only solution we can think of is an object like this:
>> 
>> <?xml version="1.0" encoding="UTF-8"?>
>>        <moby:MOBY xmlns:moby="http://www.biomoby.org/moby">
>>           <moby:mobyContent>
>>               <moby:mobyData queryID='a1'>
>>                    <Simple articleName=''>
>>                       <Object namespace="Genbank/gi" id="163483"/>
>>                    </Simple>
>>                    <Simple articleName=''>
>>                       <Object namespace="Genbank/gi" id="163484"/>
>>                    </Simple>
>>                    <Simple articleName=''>
>>                       <Object namespace="Genbank/gi" id="163485"/>
>>                    </Simple>
>>               </moby:mobyData>
>>           </moby:mobyContent>
>>        </moby:MOBY>
>> 
>> 
>> 
>> would this be a legal object or do we have to use collection even if the 
>> objects don't build an entity ?
>> 
>> 
>> Cheers,
>> Rebecca
>  
>
-- Mark Wilkinson Assistant Professor (Bioinformatics) Dept. Medical 
Genetics, UBC, Canada


-----------------------------------------------------------------------------------------------------------






Mark Wilkinson wrote:

>On Thu, 2005-07-07 at 17:34 +0200, Heiko Schoof wrote:
>
>  
>
>>I myself am confused about the use of collections. Originally I had in 
>>my mind that Collections were a construct to allow objects that 
>>inherently belong together to be "bagged".
>>    
>>
>
>You are 100% correct here.
>
>
>  
>
>>The confusion starts with the output of services. My understanding was 
>>that ONLY a service that is guaranteed to output exactly one object for 
>>each query (e.g. an averaging service that outputs the average of a 
>>list of inputs) is registered as outputting a Simple, all others have 
>>to output collections
>>    
>>
>
>No.
>
>  
>
>> (as there must be exactly one mobyData matching 
>>the queryID of the input in the response,
>>    
>>
>
>Yes
>
>  
>
>> and a mobyData may contain 
>>multiple Simple elements only if wrapped by a Collection).
>>    
>>
>
>No.  A mobyData element can wrap any number of outputs, and/or
>combinations of simples, collections, and secondaries.
>
>
>
>  
>
>>In practice, the Collection tag has been used to indicate when more 
>>than one Simple occurs, with no "semantic" meaning. This imho is not 
>>necessary; when more than one Simple occurs, why not put more than one 
>>Simple? It's easy enough for everyone to figure that out. Then, 
>>Collection could be used to actually transfer meaning ;-)
>>    
>>
>
>I think a lot of people are using Collections incorrectly, yes.
>
>
>
>  
>
>>make things clearer, also to e.g. the Taverna developers: Getting back 
>>many Simple articles in response to a query very intuitively indicates 
>>to continue on with each one individually, whereas getting back a 
>>Collection indicates to put the whole thing as input into the next 
>>service, which is what they implemented. Makes perfect sense, as there 
>>can and will be services that consume Collections.
>>    
>>
>
>I don't think that Taverna handled collections correctly in the past,
>and it would be a shame if that identical functionality was added back
>in :-)  The functionality does need to go back into Taverna, but
>correctly this time.
>
>
>
>  
>
>>Maybe I've made myself clear, maybe not. Anyway, the Collection issue 
>>has led to quite some discussions between Rebecca, Dirk and myself, and 
>>we are all not happy with the way they are currently handled.
>>    
>>
>
>I don't know if you are happier with them now that I have pointed out
>where you are misinterpreting them...??
>
>I agree, however, that their usage by many service providers is not
>correct... but there's no way for MOBY Central to know that it isn't
>correct, so we can't throw an error on registration of these "wonky"
>services...
>
>M
>
>
>
>  
>

-- 
Rebecca Ernst
MIPS, Inst. for Bioinformatics
GSF Research Center for Environment and Health
Ingolstaedter Landstr. 1
85764 Neuherberg
fon: +49 89 3187 3583
email: Rebecca.Ernst at gsf.de