Re: [Cuitools-users] --mesh option

[Bridget T. M. <bth...@cs...>]

Hi Ted,

I am not certain. I am going to redownload the package, do a clean install 
and try it again. Hopefully I will be able to recreate it.

Thanks!

Bridget

On Wed, 23 Jul 2008, Ted Pedersen wrote:

> 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
>