[MOBY-l] structuring output of a service...

[Michael Jensen]

I have created a service out of an XML-RPC service that gets genes and  
proteins from text (extractGeneProteinNames), and returns a score for  
its likelihood of the returned word being a gene or protein. There are  
two types of outputs, one with any acronyms (like MAPK), and another  
with just regular words (like mitogen-activated protein kinase, or  
other words, genes, proteins etc). Here is a sample text output:

------------------------------------------------------------------------ 
----------------------------------------
(INPUT: We observed an increase in mitogen-activated protein kinase  
(MAPK) activity.)

ACRONYM: MAPK
LONG FORM: mitogen-activated protein kinase
SCORE: 0.90884572798250385

NAME: MAPK
SCORE: 1

NAME: mitogen-activated protein kinase
SCORE: 1

NAME: increase
SCORE: 0.06212914418525689

NAME: We
SCORE: 1.0000000000000237e-300
------------------------------------------------------------------------ 
----------------------------------------

So with this I need to have the input as some object. I found a  
namespace called Global that this may fit in, but I am unsure. There is  
an object named text-plain also, but I don't know if that works or not  
either.

------------------------------------------------------------------------ 
----------------------------------------
<Object namespace='Global'>We observed an increase in mitogen-activated  
protein kinase (MAPK) activity.</Object>
------------------------------------------------------------------------ 
----------------------------------------

And then here is the possible output:

------------------------------------------------------------------------ 
----------------------------------------
<Scored_string namespace='global_keyword' id=''>
   <String namespace='' id='' articleName='Acronym'>MAPK</String>
   <String namespace='' id='' articleName='Long_form'>mitogen-activated  
protein kinase</String>
   <Float  namespace='' id=''  
articleName='Score'>0.90884572798250385</Float>
</Scored_string>

<Scored_string namespace='global_keyword' id=''>
   <String namespace='' id='' articleName='Name'>mitogen-activated  
protein kinase</String>
   <Float  namespace='' id='' articleName='Score'>1</Integer>
</Scored_string>

<Scored_string namespace='global_keyword' id=''>
   <String namespace='' id='' articleName='Name'>increase</String>
   <Float  namespace='' id=''  
articleName='Score'>0.06212914418525689</Integer>
</Scored_string>
------------------------------------------------------------------------ 
----------------------------------------

I am guessing there are other places where some kind of score is given  
on analysis of something, so I don't think it is far off creating a new  
object for this one. I don't know if global_keyword fits either, or  
what to do with that namespace attribute.

I am not well-versed in all of this, so any comments and suggestions  
are very welcome! Thanks to Ken Steube for helping me get even this  
far!!!

-Michael Jensen
michael at inblosam.com