Re: [Cuitools-users] --mesh option

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

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
>