[MOBY] [MOBY-l] registering Scored_string object...

[Michael Jensen]

I will try a different name for the Scored_string. I questioned the 
same thing, because I did have the acronym element in there it isn't 
quite universal.

About the identification of the protein, it actually doesn't know 
anything about the identity of the protein/gene, but rather infers that 
within the context of the sentence that word/phrase has a probability 
of *score* to be a gene or a protein. It is an algorithm that is used 
from here:

http://bionlp.stanford.edu/

There is a publication in the works about it.

-Michael




On Mar 30, 2004, at 10:46 AM, Mark Wilkinson wrote:

> On Mon, 2004-03-29 at 12:39, Michael Jensen wrote:
>
>> Starting with Ken's object registration example script, I put the
>> following together. On the ISA and HASA I am assuming below the first
>> value is what the tag is, like String, Object, or Long, unless it is a
>> ISA, then it is just what type it is. Then I assume the second value 
>> is
>> what the articleName is, and can be blank if there is none.
>
> No need to assume - it's in the POD documentation:
>
>         Title     :    registerObject ; registerObjectClass
>         Usage     :    $REG = $MOBY->registerObject(%args)
>         Usage     :    $REG = $MOBY->registerObjectClass(%args)
>         Function  :    register a new type of MOBY Object
>         Returns   :    MOBY::Registration object
>         Args      :    objectType => "the name of the Object"
>                        description => "a human-readable description of
> the object"
>                        contactEmail => "your at email.address"
>                        authURI => "URI of the registrar of this object"
>                        Relationships => {
>                            relationshipType1 => [
>                                [Object1, articleName],
>                                [Object2, articleName]],
>                            relationshipType2 => [
>                                [Object1, articleName]]}
>
>
>> Is this correct? Will what I have below register the object for the 
>> XML
>> output above?
>
> I believe so, yes.  That should work just fine!
>
> I wonder if perhaps you could change the name from "Scored_String" to
> something a bit more proprietary?  "Inblosam_Scored_String", or
> something like that?  Only because it isn't a universally common
> data-type, and it has a component that might be unexpected (the acronym
> component) based on a human-readable name "Scored_String", so this 
> might
> confuse people.  At the end of the day, the name of an object is
> ~irrelevant, and we shouldn't interpret them, but of course, we all do
> :-)
>
>
>>      input        => [ ['', ["text-plain" => []]], ],
>>      output       => [ ['', [["Scored_string" => []]]], ],
>>      category     => "moby",
>>      serviceType  => "Retrieval",
>>    );
>
> that looks correct (by eye).
>
>> I am not sure the "text-plain" is right for the input either, but all 
>> I
>> expect is something like this.
>
> You could register your input as "String", since there doesn't seem to
> be any implicit limitation on the type/structure of String that you
> consume... but I think "text-plain" is probably a better choice if you
> want to weed-out most of the single-word inputs, which are more likely
> to be carried in String objects than in text-plain objects (we hope!)
>
>> Thanks for all your help with all of my questions!!
>
> Good luck with this!  It is really quite a cool service - I'm wondering
> if you might be able to add some value to this by outputting Xref's
> inside of your Scored_String object.  Since you obviously have some
> knowledge of the identity of the protein (since you found it!), you
> could perhaps Xref it's SwissProt, or gi number or something like that.
> This would allow us to take free-text, pass it to your service, and
> automatically retrieve e.g. the genbank record for all of the proteins
> described therein, since I have already written the services that do
> this kind of retrieval...
>
> M
>
> -- 
> Mark Wilkinson (mwilkinson at mrl.ubc.ca)
> University of British Columbia iCAPTURE Centre
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