[BioNLP] papers related to using NLP to improve concept identification?

Bob Futrelle bob.futrelle at gmail.com
Sat Nov 5 16:00:43 EDT 2011


One might think that the word "important" in your example is important.

Factual statements are often modulated by propositional attitudes that are
important to capture.
Not to mention bald negation.

If something is "thought to be" is it a fact?
Should it be ignored? What's the loss?  Should be included?  How?

 -  Bob

On Sat, Nov 5, 2011 at 3:46 PM, Ning Kang <emukang at gmail.com> wrote:

> Hi, Bob,
>
> Thank you for your quick reply. I know for a lot of concept identification
> systems, they search the document to find the word in UMLS, and based on
> the context of the word, they got the correct concept ids and semantic
> groups for the words exists in this document.
>
> For example, for the sentence of "*Merozoite Surface Protein 1 is
> expressed on the surface of malaria merozoites and is important for
> invasion of the malaria parasite into erythrocytes.*" A concept
> identification system will find the following concepts
>
> ------------------------------------------------------------------------------------
>
> *Annotation content*
>
> *Annotation startPosition*
>
> *Annotation endPosition*
>
> *Annotation concept id*
>
> *Annotation concept name*
>
> *Annotation semanticTypeString*
>
> Merozoite
>
> 0
>
> 9
>
> 444659
>
> Merozoites
>
> 204
>
> expressed
>
> 31
>
> 40
>
> 1171362
>
> protein expression
>
> 45
>
> expressed
>
> 31
>
> 40
>
> 1515670
>
> mRNA Expression
>
> 45
>
> malaria
>
> 59
>
> 66
>
> 24530
>
> Malaria
>
> 47
>
> merozoites
>
> 67
>
> 77
>
> 444659
>
> Merozoites
>
> 204
>
> invasion
>
> 99
>
> 107
>
> 1269955
>
> tumor cell invasion
>
> 33
>
> invasion
>
> 99
>
> 107
>
> 2699153
>
> Cell Invasion
>
> 46
>
> malaria
>
> 115
>
> 122
>
> 24530
>
> Malaria
>
> 47
>
> parasite
>
> 123
>
> 131
>
> 30498
>
> Parasites
>
> 204
>
> erythrocytes
>
> 137
>
> 149
>
> 14792
>
> Erythrocytes
>
> 25
>
> ------------------------------------------------------------------------------------
>
> I would like to know if NLP(pos, chunking) can help concept
> identification. If so, what's the performance improvement.
>
> Thanks.
>
> On Sat, Nov 5, 2011 at 8:25 PM, Bob Futrelle <bob.futrelle at gmail.com>wrote:
>
>> "concept" is a very broad term. What are you thinking of more
>> specifically?
>> A few examples would help.
>>
>> - Bob Futrelle
>>   BioNLP.org
>>
>> On Sat, Nov 5, 2011 at 3:08 PM, Ning Kang <emukang at gmail.com> wrote:
>>
>>> Hi,
>>>
>>> Does anyone know some papers related to using NLP to improve concept
>>> identification?
>>>
>>> For example, using POS or Chunking to improve the performance of concept
>>> identification systems, or the performance variation of some concept
>>> identification systems with/without using NLP as a pre-process model?
>>>
>>> Thank you very much.
>>>
>>> Ning Kang
>>>
>>> _______________________________________________
>>> BioNLP mailing list
>>> BioNLP at lists.ccs.neu.edu
>>> https://lists.ccs.neu.edu/bin/listinfo/bionlp
>>> The BioNLP website: http://www.bionlp.org
>>>
>>>
>>
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>>
>>
>
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