Re: [Cuitools-users] --mesh option

[Ted P. <tpederse@d.umn.edu>]

Hi Bridget,

Thanks for this script - I ran it and it seems to give me back a fair
number of results...so I seem to be able to access PubMed ok...

marimba(4): perl get-mesh.pl 9337195
         9337195 : *Birth Weight,Blood Glucose/metabolism,Blood
Pressure,Brachial Artery/anatomy &
histology/*physiology/ultrasonography,Cardiovascular
Diseases/*epidemiology,Child,Cholesterol,
LDL/blood,England,Female,Humans,Lipids/blood,Muscle, Smooth,
Vascular/anatomy &
histology/physiology/ultrasonography,Parity,Pregnancy,Regional Blood
Flow,Risk Factors,Socioeconomic Factors,Tobacco Smoke
Pollution,*Vasodilation

What could I check next?

Thanks,
Ted

On Wed, Jul 23, 2008 at 2:17 PM, Bridget Thomson McInnes
<bth...@cs...> wrote:
> Hi Ted
>
> I attached a test script to check. It is called : get-msh.pl
>
> Here is an example run:
>
> bthomson@caesar (~) % perl get-msh.pl 9337195
> 9337195 : *Birth Weight,Blood Glucose/metabolism,Blood Pressure,Brachial
> Artery/anatomy & histology/*physiology/ultrasonography,Cardiovascular
> Diseases/*epidemiology,Child,Cholesterol,
> LDL/blood,England,Female,Humans,Lipids/blood,Muscle, Smooth,
> Vascular/anatomy &
> histology/physiology/ultrasonography,Parity,Pregnancy,Regional Blood
> Flow,Risk Factors,Socioeconomic Factors,Tobacco Smoke
> Pollution,*Vasodilation
>
>
> This is the same result that I get on my computer at school and here at
> work.
>
> Thanks!
>
> Bridget
>
>
> On Wed, 23 Jul 2008, Ted Pedersen wrote:
>
>> Hi Bridget,
>>
>> TDP.mm is just a copy of McInnesPC07.dir.mm from the Demos directory.
>> Did you mean
>> that, or the actual output?
>>
>> I do have an internet connection so I don't think that's the problem.
>> How would I know if
>> PubMed cut me off?
>>
>> Thanks!
>> Ted
>>
>> On Wed, Jul 23, 2008 at 12:40 PM, Bridget Thomson McInnes
>> <bth...@cs...> wrote:
>> > Hi Ted,
>> >
>> > I am not certain why this is happening. I don't have this problem. The
>> > mesh terms are obtained using the PubMed API. I can see two potential
>> > problems:
>> >        1. No internet connection
>> >                - which I will put in the documentation!
>> >
>> >        2. Do you think PubMed cut you off? They have done that to me
>> >                before. They just start rejecting my queries if they
>> >                think I have been using it to much. I have not quite
>> >                determined what to much is yet. I will write a
>> >                check in the program to make certain that something
>> >                is coming back and if not error out.
>> >
>> > Otherwise I can't think of what it is. It isn't like using the UMLSKS API
>> > where the ip address needs to be registered. I have only tested this
>> > inside NLM - my connection at the apartment goes in and out so I haven't
>> > been able to test this on my laptop.
>> >
>> > Could you send me your TDP.mm file?
>> >
>> > Thanks!
>> >
>> > Bridget
>> >
>> >
>> > On Wed, 23 Jul 2008, Ted Pedersen wrote:
>> >
>> >> Hi Bridget,
>> >>
>> >> When using the Mesh option (--mesh) by itself, I seem to never get any
>> >> features...
>> >>
>> >> My arff files all look something like this...
>> >>
>> >> @RELATION pressure
>> >> @ATTRIBUTE Sense {M1,M2,M3,None}
>> >> @DATA
>> >> M1 % 97403834
>> >> M1 % 98281278
>> >> M1 % 98124304
>> >>
>> >> And so I end up getting a majority classifier...
>> >>
>> >> Is there something I am supposed to be doing to get the mesh features?
>> >> I am just running like this...
>> >>
>> >> supervised-disambiguate.pl TDP.mm --mesh
>> >>
>> >> where TDP.mm is a directory with all the NLM-WSD data in .mm format
>> >> (one file per word). All the files
>> >> seem to be getting processed, and no errors are shown, but the results
>> >> are pretty much just a majority
>> >> classifier (due to lack of features...)
>> >>
>> >> Any idea on this?
>> >>
>> >> Thanks!
>> >> Ted
>> >>
>> >> --
>> >> Ted Pedersen
>> >> http://www.d.umn.edu/~tpederse
>> >>
>> >
>>
>>
>>
>> --
>> Ted Pedersen
>> http://www.d.umn.edu/~tpederse
>>



-- 
Ted Pedersen
http://www.d.umn.edu/~tpederse