[MOBY-l] revised service output...need some explanations though...

[Michael Jensen]

Thanks for your help Mark, and Ken! Here is the output of my service 
(extractGeneProteinNames) when 'We observed an increase in 
mitogen-activated protein kinase (MAPK) activity.' is the input (it 
extracts names of genes or proteins and scores them, along with 
acronyms):

<?xml version='1.0' encoding='UTF-8'?>
<moby:MOBY xmlns:moby='http://www.biomoby.org/moby' 
xmlns='http://www.biomoby.org/moby'>
     <moby:Response moby:authority='not_provided'>
         <Collection>
             <Scored_string namespace="" id="">
                     <String namespace="" id="" 
articleName="acronym">MAPK</String>
                     <Object namespace="Global_keyword" 
id="mitogen-activated protein kinase" articleName="string_component"/>
                     <Long namespace="" id="" 
articleName="score">0.90884572798250385</Long>
             </Scored_string>
             <Scored_string namespace="" id="">
                     <String namespace="" id="" articleName="acronym"/>
                     <Object namespace="Global_keyword" id="MAPK" 
articleName="string_component"/>
                     <Long namespace="" id="" 
articleName="score">1</Long>
             </Scored_string>
             <Scored_string namespace="" id="">
                     <String namespace="" id="" articleName="acronym"/>
                     <Object namespace="Global_keyword" 
id="mitogen-activated protein kinase" articleName="string_component"/>
                     <Long namespace="" id="" 
articleName="score">1</Long>
             </Scored_string>
             <Scored_string namespace="" id="">
                     <String namespace="" id="" articleName="acronym"/>
                     <Object namespace="Global_keyword" id="increase" 
articleName="string_component"/>
                     <Long namespace="" id="" 
articleName="score">0.06212914418525689</Long>
             </Scored_string>
             <Scored_string namespace="" id="">
                     <String namespace="" id="" articleName="acronym"/>
                     <Object namespace="Global_keyword" id="We" 
articleName="string_component"/>
                     <Long namespace="" id="" 
articleName="score">1.0000000000000237e-300</Long>
             </Scored_string>
         </Collection>
     </moby:Response>
</moby:MOBY>

I like Mark's idea of using a collection for this, rather than 
formatted text. I think something like MedLine abstracts are more fit 
for the formatted text option. I am trying to figure out a few things 
still. What do I need to put in for the Scored_string namespace 
attribute?

<Scored_string  namespace="$inputNS" id="$inputID">

Does that mean the user will be sending a namespace and I just pass 
that through? And if there is none then I leave it blank? Same 
questions with the id attribute.

My second question is about the Global_keyword. One of the problems I 
see is that the returned scored text isn't always just one word, like 
'MAPK' or 'increase', but will spell out an acronym and return that, as 
in 'mitogen-activated protein kinase'. From what I know, Global_keyword 
is designed to be only ONE word, so is there something else like 
Global_text or do I have to make that or what?

My third question is with this new Scored_string thing. Is it an 
object? I'm a little confused about that, but I think once I know what 
it is I can figure out how to register it. Do I have to do anything 
different because it is part of a collection or no?

THANKS everyone!

-Michael Jensen
mdjgf8 at mizzou.edu

(Mark, my email box was full I think so your email kept bouncing back. 
It is empty now. :)